bluuebunny/crossref_metadata_2025 huggingface dataset:
Basal forebrain cholinergic neurons are part of the threat memory engram
Authors: Rajebhosale Prithviraj , Ananth Mala , Crouse Richard , Jiang Li , Hernández Gretchen López- , Arty Christian , Wang Shaohua , Jone Alice , Zhong Chongbo , Desai Niraj S. , Li Yulong , Picciotto Marina R. , Role Lorna W. , Talmage David A.
Published: May 2021

Although the engagement of cholinergic signaling in threat memory is well established (Knox, 2016a), our finding that specific cholinergic neurons are requisite partners in a threat memory engram is likely to surprise many. Neurons of the basal forebrain nucleus basalis and substantia innominata (NBM/SIp) comprise the major source of cholinergic input to the basolateral amygdala (BLA), whose activation are required for both the acquisition and retrieval of cued threat memory and innate threat response behavior. The retrieval of threat memory by the presentation of the conditioning tone alone elicits acetylcholine (ACh) release in the BLA and the BLA-projecting cholinergic neurons manifest immediate early gene responses and display increased intrinsic excitability for 2-5 hours following the cue-elicited memory response to the conditioned stimulus. Silencing cue-associated engram-enrolled cholinergic neurons prevents the expression of the defensive response and the subset of cholinergic neurons activated by cue is distinct from those engaged by innate threat. Taken together we find that distinct populations of cholinergic neurons are recruited to signal distinct aversive stimuli via the BLA, demonstrating exquisite, functionally refined organization of specific types of memory within the cholinergic basal forebrain.
Hypermethylation and small RNA expression are associated with increased age in almond (Prunus dulcis[Mill.] D.A. Webb) accessions
Authors: D’Amico-Willman Katherine M. , Niederhuth Chad E. , Sovic Michael , Anderson Elizabeth S. , Gradziel Thomas M. , Fresnedo Ramírez Jonathan
Published: May 2021

The focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders.

To profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old) using sRNA-Seq followed by differential expression analysis.

Weighted chromosome-level methylation analysis reveals hypermethylation in 11-year old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old.

Almond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups.
Evidence for the equilibrium between monomers and dimers of the death domain of the p75 neurotrophin receptor
Authors: Li Zhen , Lin Zhi , Ibáñez Carlos F.
Published: May 2021

The p75 neurotrophin receptor (p75NTR) is an important mediator of synaptic depression and neuronal cell death, and its expression increases upon nerve injury and in neurodegenerative diseases. However, the molecular mechanisms leading to the activation of this receptor are still a matter of debate. The oligomerization properties of the death domain (DD) of p75NTRare critical for our understanding of the activation mechanisms of the receptor. In this paper, we present additional evidence supporting the existence of an equilibrium between monomeric and dimeric forms of the p75NTRDD in solution and in the absence of any other protein. Dynamic light scattering (DLS) measurements of native, untagged human p75NTRDD at room temperature yielded Rh=2.11 for this domain in 20mM phosphate buffer, corresponding to a molecular weight (MW) of approximately 19kDa, much closer to the theoretical MW of the homodimer (i.e. 21kDa) than the monomer. MWs deduced from the Rh of different control proteins used as standards were all congruent with their theoretical MWs. In addition, size-exclusion FPLC profiles of un-tagged human p75NTRDD in both HEPES and phosphate buffers revealed elution volumes corresponding to a MW of about 15kDa, which is intermediate between monomer and dimer, and indicative of dynamic monomer/dimer interconversion during the run. Together with our previous NMR studies, as well as biophysical data for other investigators, these results support the notion that the DD of p75NTRexists in equilibrium between monomers and dimers in solution, a notion that is in agreement with the oligomerization properties of all members of the DD superfamily.
Preventing disproportionate mortality in ICU overload situations: Empirical evidence from the first COVID-19 wave in Europe
Authors: Buijs Paul , Catena Rodolfo , Holweg Matthias , van der Vaart Taco
Published: May 2021

Avoiding overloading the healthcare system remains a central issue during the COVID-19 pandemic. The logic of preventing such overload situations is intuitive since the level and quality of critical care is a function of the available capacity to provide it. Where this capacity is no longer available due to a surge in admissions, patient outcomes will invariably deteriorate in the long run – ultimately leading to disproportionate mortality. In this paper, we study the three worst affected regions in Italy, the Netherlands, and Germany during the first COVID-19 wave in the spring of 2020. We report on quantitative analyses that show how mortality rises non-linearly as the proportion of COVID-19 patients in the ICU increases. We identify changes to the patient-staff ratio, increasing exhaustion and infection levels amongst staff, as well as equipment shortages, as likely causes driving this rise in mortality. We explore these findings further with interviews of key stakeholders in the respective healthcare systems. Our results demonstrate that the common approach of managing COVID-19 surges by stretching ICU capacity in hotspot regions may be detrimental to patient outcomes. Instead, we posit that transferring patients proactively out of developing hotspots to less affected regions, well before high ICU workload situations emerge, will improve overall patient outcomes.
Use of Induced Pluripotent Stem Cells to Build Isogenic Systems and Investigate Type 1 Diabetes
Authors: Armitage Lucas H. , Stimpson Scott E. , Santostefano Katherine E. , Sui Lina , Ogundare Similoluwa O. , Newby Brittney N. , Castro-Gutierrez Roberto , Huber Mollie K. , Taylor Jared P. , Sharma Prerana , Radichev Ilian , Perry Daniel J. , Fredette Natalie C. , Savinov Alexei , Wallet Mark A. , Terada Naohiro , Brusko Todd M. , Russ Holger A. , Chen Jing , Egli Dieter , Mathews Clayton. E
Published: May 2021

Type 1 diabetes is a disease that arises due to complex immunogenetic mechanisms. Key cell-cell interactions involved in the pathogenesis of T1D are activation of autoreactive T cells by dendritic cells (DC), migration of T cells across endothelial cells (EC) lining capillary walls into the islets of Langerhans, interaction of T cells with macrophages in the islets, and killing of β-cells by autoreactive CD8+T cells. Overall, pathogenic cell-cell interactions are likely regulated by the individual’s collection of genetic T1D-risk variants. To accurately model the role of genetics, it is essential to build systems to interrogate single candidate genes in isolation during the interactions of cells that are essential for disease development. However, obtaining single-donor matched cells relevant to T1D is a challenge. Sourcing these genetic variants from human induced pluripotent stem cells (iPSC) avoids this limitation. Herein, we have differentiated iPSC from one donor into DC, macrophages, EC, and β-cells. Additionally, we also engineered T cell avatars from the same donor to provide anin vitroplatform to study genetic influences on these critical cellular interactions. This proof of concept demonstrates the ability to derive an isogenic system from a single donor to study these relevant cell-cell interactions. Our system constitutes an interdisciplinary approach with a controlled environment that provides a proof-of-concept for future studies to determine the role of disease alleles (e.g.IFIH1, PTPN22, SH2B3, TYK2)in regulating cell-cell interactions and cell-specific contributions to the pathogenesis of T1D.
The representation of priors and decisions in parietal cortex
Authors: Marshall Tom R. , Ruesseler Maria , Hunt Laurence T. , O’Reilly Jill X.
Published: May 2021

Animals actively sample their environment through orienting actions such as saccadic eye movements. Saccadic targets are selected based both on sensory evidence immediately preceding the saccade, and a ‘salience map’ or prior built up over multiple saccades. In the primate cortex, the selection of each individual saccade depends on competition between target-selective cells that ramp up their firing rate to saccade release. However it is less clear how a cross-saccade prior might be represented, either in neural firing or through an activity-silent mechanism such as modification of synaptic weights on sensory inputs. Here we present evidence from magnetoencephalography for two distinct processes underlying the selection of the current saccade, and the representation of the prior, in human parietal cortex. While the classic ramping decision process for each saccade was reflected in neural firing rates (measured in the event related field), a prior built up over multiple saccades was represented via modulation of the gain on sensory inputs from the preferred target, as evidenced by rapid frequency tagging. A cascade of computations over time (initial representation of the prior, followed by evidence accumulation and then updating) provides a mechanism by which a salience map may be built up across saccades in parietal cortex. It also provides insight into why evidence accumulation signals are present in parietal cortex, when inactivation of the region has been shown not to affect performance on single-trial tasks.
Classification of non-coding variants with high pathogenic impact
Authors: Moyon Lambert , Berthelot Camille , Louis Alexandra , Nguyen Nga Thi Thuy , Crollius Hugues Roest
Published: May 2021

Whole genome sequencing is increasingly used to diagnose medical conditions of genetic origin. While both coding and non-coding DNA variants contribute to a wide range of diseases, most patients who receive a WGS-based diagnosis today harbour a protein-coding mutation. Functional interpretation and prioritization of non-coding variants represents a persistent challenge, and disease-causing non-coding variants remain largely unidentified. Depending on the disease, WGS fails to identify a candidate variant in 20-80% of patients, severely limiting the usefulness of sequencing for personalised medicine. Here we present FINSURF, a machine-learning approach to predict the functional impact of non-coding variants in regulatory regions. FINSURF outperforms state-of-the-art methods, owing to control optimisation during training. In addition to ranking candidate variants, FINSURF also delivers diagnostic information on functional consequences of mutations. We applied FINSURF to a diverse set of 30 diseases with described causative non-coding mutations, and correctly identified the disease-causative non-coding variant within the ten top hits in 22 cases. FINSURF is implemented as an online server to as well as custom browser tracks, and provides a quick and efficient solution to prioritize candidate non-coding variants in realistic clinical settings.
Membrane permeabilization is mediated by distinct epitopes in mouse and human orthologs of the necroptosis effector, MLKL
Authors: Sethi Ashish , Horne Christopher R. , Fitzgibbon Cheree , Wilde Karyn , Davies Katherine A. , Garnish Sarah E. , Jacobsen Annette V. , Samson André L. , Hildebrand Joanne M. , Wardak Ahmad , Czabotar Peter E. , Petrie Emma J. , Gooley Paul R. , Murphy James M.
Published: May 2021

Necroptosis is a lytic programmed cell death pathway with origins in innate immunity that is frequently dysregulated in inflammatory diseases. The terminal effector of the pathway, MLKL, is licensed to kill following phosphorylation of its pseudokinase domain by the upstream regulator, RIPK3 kinase. Phosphorylation provokes the unleashing of MLKL’s N-terminal four-helix bundle (4HB or HeLo) domain, which binds and permeabilizes the plasma membrane to cause cell death. The precise mechanism by which the 4HB domain permeabilizes membranes, and how the mechanism differs between species, remains unclear. Here, we identify the membrane binding epitope of mouse MLKL using NMR spectroscopy. Using liposome permeabilization and cell death assays, we validate K69 in the α3 helix, W108 in the α4 helix, and R137/Q138 in the first brace helix as crucial residues for necroptotic signaling. This epitope differs from the phospholipid binding site reported for human MLKL, which comprises basic residues primarily located in the α1 and α2 helices. In further contrast to human and plant MLKL orthologs, in which the α3-α4 loop forms a helix, this loop is unstructured in mouse MLKL in solution. Together, these findings illustrate the versatility of the 4HB domain fold, whose lytic function can be mediated by distinct epitopes in different orthologs.
Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations
Authors: Hu Haixiao , Campbell Malachy T. , Yeats Trevor H. , Zheng Xuying , Runcie Daniel E. , Covarrubias-Pazaran Giovanny , Broeckling Corey , Yao Linxing , Caffe-Treml Melanie , Gutiérrez Lucía , Smith Kevin P. , Tanaka James , Hoekenga Owen A. , Sorrells Mark E. , Gore Michael A. , Jannink Jean-Luc
Published: May 2021

Multi-omics prediction has been shown to be superior to genomic prediction with genome-wide DNA-based genetic markers (G) for predicting phenotypes. However, most of the existing studies were based on historical datasets from one environment; therefore, they were unable to evaluate the efficiency of multi-omics prediction in multi-environment trials and distantly-related populations. To fill those gaps, we designed a systematic experiment to collect omics data and evaluate 17 traits in two oat breeding populations planted in single and multiple environments. In the single-environment trial, transcriptomic BLUP (T), metabolomic BLUP (M), G+T, G+M and G+T+M models showed greater prediction accuracy than GBLUP for 5, 10, 11, 17 and 17 traits, respectively, and metabolites generally performed better than transcripts when combined with SNPs. In the multi-environment trial, multi-trait models with omics data outperformed both counterpart multi-trait GBLUP models and single-environment omics models, and the highest prediction accuracy was achieved when modeling genetic covariance as an unstructured covariance model. We also demonstrated that omics data can be used to prioritize loci from one population with omics data to improve genomic prediction in a distantly-related population using a two-kernel linear model that accommodated both likely casual loci with large-effect and loci that explain little or no phenotypic variance. We propose that the two-kernel linear model is superior to most genomic prediction models that assume each variant is equally likely to affect the trait and can be used to improve prediction accuracy for any trait with prior knowledge of genetic architecture.
Repeated administration of 2-hydroxypropyl-β-cyclodextrin (HPβCD) attenuates the chronic inflammatory response to experimental stroke
Authors: Becktel Danielle A. , Zbesko Jacob C. , Frye Jennifer B. , Chung Amanda G. , Hayes Megan , Calderon Kylie , Grover Jeffrey W. , Li Anna , Garcia Frankie G. , Tavera-Garcia Marco A. , Schnellmann Rick G. , Wu Hsin-Jung Joyce , Nguyen Thuy-Vi V. , Doyle Kristian P.
Published: May 2021

Globally, more than 67 million people are living with the effects of ischemic stroke. Importantly, many stroke survivors develop a chronic inflammatory response that may contribute to cognitive impairment, a common and debilitating sequela of stroke that is insufficiently studied and currently untreatable. 2-hydroxypropyl-β-cyclodextrin (HPβCD) is an FDA-approved cyclic oligosaccharide that can solubilize and entrap lipophilic substances. The goal of the present study was to determine whether the repeated administration of HPβCD curtails the chronic inflammatory response to stroke by reducing lipid accumulation within stroke infarcts in a distal middle cerebral artery occlusion mouse model of stroke. To achieve this goal, we subcutaneously injected young adult and aged male mice with vehicle or HPβCD three times per week, with treatment beginning one week after stroke. We evaluated mice at 7 weeks following stroke using immunostaining, RNA sequencing, lipidomics, and behavioral analyses. Chronic stroke infarct and peri-infarct regions of HPβCD-treated mice were characterized by an upregulation of genes involved in lipid metabolism and a downregulation of genes involved in innate and adaptive immunity, reactive astrogliosis, and chemotaxis. Correspondingly, HPβCD reduced the accumulation of lipid droplets, T lymphocytes, B lymphocytes, and plasma cells in stroke infarcts. Repeated administration of HPβCD also preserved NeuN immunoreactivity in the striatum and thalamus and c-Fos immunoreactivity in hippocampal regions. Additionally, HPβCD improved recovery through the protection of hippocampal-dependent spatial working memory and reduction of impulsivity. These results indicate that systemic HPβCD treatment following stroke attenuates chronic inflammation and secondary neurodegeneration and prevents post-stroke cognitive decline.

Significance Statement

Dementia is a common and debilitating sequela of stroke. Currently, there are no available treatments for post-stroke dementia. Our study shows that lipid metabolism is disrupted in chronic stroke infarcts, which causes an accumulation of uncleared lipid debris and correlates with a chronic inflammatory response. To our knowledge, these substantial changes in lipid homeostasis have not been previously recognized or investigated in the context of ischemic stroke. We also provide a proof of principle that solubilizing and entrapping lipophilic substances using HPβCD could be an effective strategy for treating chronic inflammation after stroke and other CNS injuries. We propose that using HPβCD for the prevention of post-stroke dementia could improve recovery and increase long-term quality of life in stroke sufferers.
Chicoric acid prevents neurodegeneration via microbiota-gut-brain axis in a mouse Parkinson’s disease model
Authors: Wang Ning , Pan Xin-Yue , Zhu Hong-Kang , Guo Ya-Hui , Qian He
Published: May 2021

It is determined that microbiota-gut-brain axis is involved in the pathogenesis of Parkinson’s Disease (PD) and may be the potential target for developing the therapeutic treatments for PD. Chicoric acid (CA) is a kind of natural polyphenolic acid compounds which are recognized as promising agents against neurodegenerative disease. Here, we investigated the influence of CA on microbiota-gut-brain axis in 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP) mice. The results demonstrated that oral pretreatments of CA significantly prevented the MPTP-indued motor disorders, death of nigrostriatal dopaminergic neurons and reduction in striatal neurotrophins. Sequencing results of 16S rRNA indicated the microbial dysbiosis occurred in MPTP mice, whereas CA exerted a remarkable impact on microbial diversity and microbiota compositions, as well as SCFAs production. Besides, CA pretreatment alleviated gliosis-mediated neuroinflammation and gut inflammation by suppressing TLR4/MyD88/NF-κB signaling cascade, along with preventing the colonic hyperpermeability. To conclude, CA prevented MPTP-induced neuroinflammation and neuronal degenerative processes through signaling multiple pathways of microbiota-gut-brain axis.
Meiosis-Specific Cohesin Complexes Display Distinct and Essential Roles in Mitotic ESC Chromosomes
Authors: Choi Eui-Hwan , Koh Young Eun , Yoon Seobin , Hahn Yoonsoo , Kim Keun P.
Published: May 2021

Cohesin is a chromosome-associated SMC kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. Through high-resolution 3D-structured illumination microscopy and functional analyses, we report multiple biological processes associated with the meiosis-specific cohesin components, REC8 and STAG3, and the distinct loss of function of meiotic cohesin during the cell cycle of embryonic stem cells (ESCs). First, we show that REC8 is translocated into the nucleus in a STAG3-dependent manner. REC8/STAG3-containing cohesin regulates chromosome topological properties and specifically maintains centromeric cohesion. Second, REC8 and mitotic cohesin RAD21 are located at adjacent sites but predominantly at nonoverlapping sites on ESC chromosomes, implying that REC8 can function independent of RAD21 in ESCs. Third, knockdown of REC8-cohesin not only leads to higher rates of premature centromere separation and stalled replication forks, which can cause proliferation and developmental defects, but also enhances compaction of the chromosome structure by hyperloading of retinoblastoma protein condensin complexes from prophase onward. We propose that the delicate balance between mitotic and meiotic cohesins may regulate ESC- specific chromosomal organization and mitotic program.
Functional characterisation of banana (Musaspp.) 2-oxoglutarate-dependent dioxygenases involved in flavonoid biosynthesis
Authors: Busche Mareike , Acatay Christopher , Martens Stefan , Weisshaar Bernd , Stracke Ralf
Published: May 2021

Bananas (Musa) are non-grass, monocotyledonous, perennial plants that are well-known for their edible fruits. Their cultivation provides food security and employment opportunities in many countries. Banana fruits contain high levels of minerals and phytochemicals, including flavonoids, which are beneficial for human nutrition. To broaden the knowledge on flavonoid biosynthesis in this major crop plant, we aimed to identify and functionally characterise selected structural genes encoding 2-oxoglutarate-dependent dioxygenases, involved in the formation of the flavonoid aglycon.

Musacandidates genes predicted to encode flavanone 3-hydroxylase (F3H), flavonol synthase (FLS) and anthocyanidin synthase (ANS) were assayed. Enzymatic functionalities of the recombinant proteins were confirmedin vivousing bioconversion assays. Moreover, transgenic analyses in correspondingArabidopsis thalianamutants showed thatMusaF3H, MusaFLSandMusaANSwere able to complement the respective loss-of-function phenotypes, thus verifying functionality of the enzymesin planta.

Knowledge gained from this work provides a new aspect for further research towards genetic engineering of flavonoid biosynthesis in banana fruits to increase their antioxidant activity and nutritional value.
Open issues for protein function assignment inHaloferax volcaniiand other halophilic archaea
Authors: Pfeiffer Friedhelm , Dyall-Smith Mike
Published: May 2021

Background

Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases the enzymes cannot be isofunctional. Here, we examine a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeonHaloferax volcanii.

Results

Annotated proteins ofHfx. volcaniiwere identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We list 50 of those cases, each with detailed background information so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Material.

Conclusions

Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet unexpected functions.
Correction of amblyopia in cats and mice after the critical period
Authors: Fong Ming-fai , Duffy Kevin R. , Leet Madison P. , Candler Christian T. , Bear Mark F.
Published: May 2021

Monocular deprivation early in development causes amblyopia, a severe visual impairment. Prognosis is poor if therapy is initiated after an early critical period. However, clinical observations have shown that recovery from amblyopia can occur later in life when the non-deprived (fellow) eye is removed. The traditional interpretation of this finding is that vision is improved by relieving interocular suppression in primary visual cortex. However, an alternative explanation is that elimination of activity in the fellow eye establishes conditions in visual cortex that enable the weak connections from the amblyopic eye to gain strength. Here we show in cats and mice that temporary inactivation of the fellow eye is sufficient to promote a full and enduring recovery from amblyopia at ages when conventional treatments fail. Thus, connections serving the amblyopic eye are capable of substantial plasticity beyond the critical period, and this potential is unleashed by reversibly silencing the fellow eye.
TheArabidopsis thalianaPeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource
Authors: van Wijk Klaas J. , Leppert Tami , Sun Qi , Boguraev Sascha S. , Sun Zhi , Mendoza Luis , Deutsch Eric W.
Published: May 2021

We developed a new resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis proteome, such as the significance of protein splice forms, post-translational modifications (PTMs), or simply obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) analyses collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical and biological metadata. Nearly 40 million out of ∼143 million MSMS spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17858 uniquely identified proteins (only isoform per gene) at the highest confidence level (FDR 0.0004; 2 non-nested peptides ≥ 9 aa each), assigned canonical proteins, and 3543 lower confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified, generated from pseudogenes, alternative start, stops and/or splice variants and sORFs; these features should be considered for updates to the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. This new PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS data.

One sentence summary

A new web resource providing the global community with mass spectrometry-based Arabidopsis proteome information and its spectral, technical and biological metadata integrated with TAIR and JBrowse
Synaptic control of temporal processing in theDrosophilaolfactory system
Authors: Fox David , Nagel Katherine I.
Published: May 2021

Temporal filtering of sensory stimuli is a key neural computation, but the way such filters are implemented within the brain is unclear. One potential mechanism for implementing temporal filters is short-term synaptic plasticity, which is governed in part by the expression of pre-synaptic proteins that position synaptic vesicles at different distances to calcium channels. Here we leveraged theDrosophilaolfactory system to directly test the hypothesis that short-term synaptic plasticity shapes temporal filtering of sensory stimuli. We used optogenetic activation to drive olfactory receptor neuron (ORN) activity with high temporal precision and knocked down the presynaptic priming factor unc13A specifically in ORNs. We found that this manipulation specifically decreases and delays transmission of high frequencies, leading to poorer encoding of distant plume filaments. We replicate this effect using a previously-developed model of transmission at this synapse, which features two components with different depression kinetics. Finally, we show that upwind running, a key component of odor source localization, is preferentially driven by high-frequency stimulus fluctuations, and this response is reduced by unc13A knock-down in ORNs. Our work links the extraction of particular temporal features of a sensory stimulus to the expression of particular presynaptic molecules.
Integration, coincidence detection and resonance in networks of spiking neurons expressing gamma oscillations and asynchronous states
Authors: Susin Eduarda , Destexhe Alain
Published: May 2021

Gamma oscillations are widely seen in the awake and sleeping cerebral cortex, but the exact role of these oscillations is still debated. Here, we used biophysical models to examine how gamma oscillations may participate to the processing of afferent stimuli. We constructed conductance-based network models of gamma oscillations, based on different cell types found in cerebral cortex. The models were adjusted to extracellular unit recordings in humans, where gamma oscillations always coexist with the asynchronous firing mode. We considered three different mechanisms to generate gamma, first a mechanism based on the interaction between pyramidal neurons and interneurons (PING), second a mechanism in which gamma is generated in interneuron networks (ING) and third, a mechanism which relies on gamma oscillations generated by pacemakerchatteringneurons (CHING). We find that all three mechanisms generate features consistent with human recordings, but that the ING mechanism is most consistent with the firing rate change inside Gamma bursts seen in the human data. We next evaluated the responsiveness and resonant properties of these networks, contrasting gamma oscillations with the asynchronous mode. We find that for both slowly-varying stimuli and precisely-timed stimuli, the responsiveness is generally lower during Gamma compared to asynchronous states, while resonant properties are similar around the Gamma band. We could not find conditions where Gamma oscillations were more responsive. We therefore predict that asynchronous states provide the highest responsiveness to external stimuli, while Gamma oscillations tend to overall diminish responsiveness.

Author summary

In the awake and attentive brain, the activity of neurons is typically asynchronous and irregular. It also occasionally displays oscillations in the Gamma frequency range (30-90 Hz), which are believed to be involved in information processing. Here, we use computational models to investigate how brain circuits generate oscillations in a manner consistent with microelectrode recordings in humans. We then study how these networks respond to external input, comparing asynchronous and oscillatory states. This is tested according to several paradigms, anintegrative mode, where slowly varying inputs are progressively integrated, acoincidence detection mode, where brief inputs are processed according to the phase of the oscillations, and aresonance modewhere the network is probed with oscillatory inputs. Surprisingly, we find that in all cases, the presence of Gamma oscillations tends to diminish the responsiveness to external inputs, and we found no paradigm by which Gamma oscillations would favor information flow compared to asynchronous states. We discuss possible implications of this responsiveness decrease on information processing and propose new directions for further exploration.
Potential role ofAphidius erviin protecting greenhouse bell pepper cultures fromMyzus persicaeaphids in India
Authors: Farhat Ambika , Dharmadhrt Ramila
Published: May 2021

Many aphids such asMyzus persicaeare major agricultural pest against which sustainable solutions must be developed. In the present study, we evaluated the role ofAphidius ervi (Hymenoptera: Braconidae), an aphid parasitoid, to controlM. persicaein bell pepper cultures in greenhouses. Parasitoids were released at one occasion in a greenhouse and M. persicae infested plants were followed before and after parasitoid introduction. We evaluated aphid numbers and parasitism rates at two different controlled temperatures (22°C and 25°C), and we measured diapause levels in released parasitoids.Aphidius ervishowed parasitism rates of 10.9±1.2% and 9.1±1.6%, at 21 and 25°C, respectively. The strain of parasitoids we used was not entering diapause under any temperature condition. Therefore, we suggest thatA. ervican be further investigated as a protection in greenhouse environments in India. More releases may be necessary to achieve a good protection.
Mathematical modeling of the production of magnetic nanoparticles through counter-flow non-premixed combustion for biomedical applications
Authors: Akbari Shahin , Hasanvand Nima , Sadeghi Sadegh , Bidabadi Mehdi , Xiong Qingang
Published: May 2021

Purpose

The widespread usage of magnetic nanoparticles (MNPs) requires their efficient synthesis during combustion process. This study aims to present a mathematical model for the oxidation of MNPs in a counter-flow non-premixed combustion system to produce MNPs, where the key sub-processes during the oxidation reaction are involved.

Design/methodology/approach

To accurately describe structure of flame and determine distributions of temperature and mass fractions of both reactants and products, equations of energy and mass conservations were solved based on the prevailing assumptions that three regions, i.e. preheating, reaction and oxidizer zones exist.

Findings

The numerical simulation was first validated against experimental data and characteristics of the combustion process are discussed. Eventually, the influences of crucial parameters such as reactant Lewis numbers, strain rate ratio, particle size, inert gas and thermophoretic force on structure of flame and combustion behavior were examined. The results show that maximum flame temperature can achieve 2,205 K. Replacing nitrogen with argon and helium as carrier gases can increase flame temperature by about 27% and 34%, respectively. Additionally, maximum absolute thermophoretic force was found at approximately 9.6 × 10–8 N.

Originality/value

To the best of authors’ knowledge, this is the first time to numerically model the preparation of MNPs in a counter-flow non-premixed combustion configuration, which can guide large-scale experimental work in a more effective way.
“Waste not, want not”: fostering frugality amongst Muslim tourists in the Malaysian hotel industry
Authors: Bt Mohamed Sadom Nur Zulaikha , Quoquab Farzana , Mohammad Jihad
Published: May 2021

Purpose

The prevailing overconsumption issue in the hotel industry is attributable mainly to the irresponsible consumption behaviour of hotel guests. In parallel with Islamic principles, which advocate abstinence from excess consumption and frugality, the “waste not, want not” notion can be considered as one of the effective solutions to this problem. However, little is known about the factors that drive frugality amongst Muslim tourists. In addressing this gap, this study aims to predict the effect of environmental advertising and green attitude on frugality in the context of the Malaysian hotel industry. The study also tests the mediating role of the green attitude between environmental advertising and frugality. Furthermore, it examines the role of price consciousness as a moderator of the green attitude-frugality link.

Design/methodology/approach

The stimulus-organism-response theory was used to develop the conceptual framework of this study. A cross-sectional method was used to collect 222 usable questionnaires from Muslim tourists in Malaysia. The hypothesised relationships were tested using the structural equation modelling, partial least squares approach.

Findings

The study found support for the direct effect of environmental advertising and green attitude on frugality. It also confirmed the mediating effect of the green attitude in the environmental advertising-frugality link. However, price consciousness did not moderate the relationship.

Practical implications

The findings of the study provide valuable insight for hoteliers in developing a green strategy that will foster frugality amongst Muslim hotel guests. It will also help them develop better strategies for the frugal segment, especially for the Muslim community.

Originality/value

The study is amongst the pioneers in investigating frugality in the tourism industry. It is also the first to introduce price consciousness as a moderator of the relationship between the green attitude and frugality. Furthermore, its examination of frugality amongst Muslim hotel guests is a new contribution to the literature.
The impact of blacklists on external deposits: one size does not fit all
Authors: Jonsson Michael , Pettersson Jan , Larson Christian Nils , Artzi Nir
Published: May 2021

Purpose

This study aims to measure the impact of the Non-Cooperative Countries and Territories, Organization for Economic Cooperation and Development and US PATRIOT Act Section 311 blacklists on external deposits from blacklisted jurisdictions into BIS reporting countries in 1996–2008, a period when anti-money laundering-related actions were consistently less stringent than post-2010, to see whether they had an effect even absent the threat of sizable financial fines.

Design/methodology/approach

The study uses descriptive statistics and bivariate and multivariate regressions to analyze the probable impact from blacklists on non-bank external deposits. The country sample is divided into offshore financial centers (OFCs) and non-OFCs and includes 158 non-listed countries. The impact of the blacklists is tested both jointly and individually for the respective blacklists.

Findings

The authors find mixed impact from jurisdictions being blacklisted on the growth rate of stocks of deposits into BIS reporting countries. Effects are often zero, negative in several cases and positive in some cases. This is consistent with the “stigma effect” and the “stigma paradox” in the literature. An overall impact from blacklisting is difficult to discern. Different blacklists had different effects, and the same blacklist impacted countries differently, illustrating the importance of disaggregating the analysis by individual countries.

Research limitations/implications

Interpretation of these data is limited by the absence of comparable data on non-resident deposits in blacklisted jurisdictions.

Practical implications

The impact of a blacklist depends in part on the structure of the listed jurisdictions’ economies, implying that country-specific sanctions may be more effective than blacklists.

Originality/value

This is one of the very few papers to date to rigorously test the impact of blacklists on external deposits.
Anxiety, isolation and diminishing resources: the impact of COVID-19 pandemic on residential care home facilities for older people in south-east Nigeria
Authors: Ekoh Prince Chiagozie
Published: May 2021

Purpose

Institutionalized older adults in care homes and long-care facilities have been identified as being at greater risk of COVID-19 related morbidity and mortality. Thus, this paper aims to explore the impact of COVID-19 on care homes in south-east Nigeria given the recent increasing popularity of care homes in Nigeria.

Design/methodology/approach

The study adopted qualitative research method, and data was collected from 10 older residents and 5 caregivers using interviews from two care homes, while ensuring the safety of the researcher and participants. The collected data was analyzed using thematic analysis.

Findings

Findings revealed that the physical health impact of the COVID-19 pandemic is not a major problem in the homes. However, fear and anxiety, social disconnection and economic hardship were the major problems identified by the older residents and caregivers in the homes.

Originality/value

The popularity of care homes in Nigeria is growing as family structures continue to change. However, previous studies which have revealed devastating effect of COVID-19 on institutionalized older adults have been from the global north. This is the first study designed to bridge the gap in literature and contribute to knowledge on this topic from Nigeria and Sub-Saharan Africa.
Australian rural community aged care services: Precarity and capacity
Authors: Savy Pauline , Hodgkin Suzanne
Published: May 2021

In Australia, the precarity of the aged care sector has been well documented over several decades. During this time, policy reforms have ultimately landed care, and the business of providing it, within a market model. Following recent evidence produced by the Royal Commission into Aged Care and Safety and the COVID‐19 Senate Committee, this model and the sector's incapacity to consistently deliver appropriate care has been the subject of intense public scrutiny and debate. The many COVID‐19‐related deaths of aged care residents have added to demands for urgent action to redress the sector's weaknesses, particularly those relating to workforce adequacy. This paper presents findings from a recent mixed methods study of community aged care provision by five providers who operate across a large rural part of regional Victoria. It utilises data to illustrate the impact of rural location on care provision, and significantly, on local capacity to maintain an appropriately skilled workforce. Demographic factors and funding shortfalls for consumers with multiple, complex care needs underscore the need for strategic planning to ensure workforce adequacy into the future. Encouragingly, our data showcase the many capacities of community aged services in this rural area and the opportunity to develop effective strategies relative to the recruitment and retention of direct care workers and the design of best practice models for meeting complex care needs.
Haley v Haley: Family Law Arbitration and the New Frontier of Private Ordering
Authors: Heenan Anna
Published: May 2021

Haley v Haley is required reading for anyone interested in family law dispute resolution or issues of access to justice. The case concerns family arbitration and, importantly, changes the test for challenging arbitral awards, making it easier to do so. This is connected to concerns about making arbitration more appealing in the family law context, which has implications for family law dispute resolution more broadly. Whilst separating couples have always been encouraged to settle outside of the court process, connected to an idea of private ordering, Haley marks a new frontier. Until now private ordering was also intended to ensure substantively better outcomes. This is no longer the case, and the attempt to divert more cases to arbitration in this judgment may compound existing issues of access to justice.
Primary and secondary effects of social origins on educational attainment: New findings for England
Authors: Bukodi Erzsébet , Goldthorpe John H. , Zhao Yizhang
Published: May 2021

We aim to bring together two current strands of research into inequalities in individuals’ educational attainment that are associated with their social origins: that concerned with the “primary” and “secondary” effects of social origins in creating inequalities, and that concerned with the relation between these inequalities and different components of social origins, taken to represent different forms of parental resources. Our main findings are the following. The secondary effects of social origins—their effects via the educational choices that young people make given their prior academic performance—are clearly operative across five key educational transitions within the English educational system. More specifically, we estimate that 35% of the total effect of social origins is secondary in the earliest transition that we consider, and from 15% to 20% in the subsequent four. Furthermore, mediation analyses reveal that secondary effects are most strongly associated with parental education and then, to a lesser degree with parental status, while little association exists with parental class and none at all with parental income. Primary effects are also at all transitions most strongly associated with parental education and status but in this case both parental class and parental income do retain some importance. We suggest an explanation for our empirical findings as resulting largely from the concern of highly educated, professional parents, and their children to avoid the occurrence of downward intergenerational mobility, especially in terms of education and status.