bluuebunny/crossref_metadata_2025 huggingface dataset:
Forest condition in the Congo Basin for the assessment of ecosystem conservation status
Authors: Shapiro Aurélie , Grantham Hedley S. , Aguilar-Amuchastegui Naikoa , Murray Nicholas J. , Gond Valery , Bonfils Djoan , Rickenbach Olivia
Published: March 2020

Measuring forest degradation is important for understanding and designing measures to protect biodiversity and the capacity of forests to deliver ecosystem services. Conservation planning, particularly the prioritization of management interventions for forests, is often lacking spatial data on ecological condition, and it is often overlooked within decision-making processes. Existing methods for assessing forest degradation via proxies or binary measures (i.e. intact or not) cannot adequately consider the important variations of ecological condition. Direct methods to measure degradation (e.g. through remote sensing) require extensive training data, calibration and validation, and may be too sensitive to small-scale or short-term changes which may not be related to degradation. We developed a metric termed Forest Condition (FC) which aims to measure the degree of forest degradation, incorporating temporal history of forest change over a large spatial extent. We parameterized this metric based on estimated changes in above ground biomass in the context of forest fragmentation over time to estimate a continuous measure of forest degradation for Congo Basin countries. We estimate that just less than 70% of Congo Basin forests remain fully intact. FC was validated by direct remote sensing measurements from Landsat imagery for DRC. Results showed that FC was significantly positively correlated with forest canopy cover, gap area per hectare, and magnitude of temporal change in Normalized Burn Ratio. We tested the ability of FC to distinguish primary and secondary degradation and deforestation and found significant differences in gap area and spectral anomalies to validate our theoretical model. We used the IUCN Red List of Ecosystems criteria to demonstrate the value of applying forest degradation to assess the risk of ecosystem collapse. Based on this assessment, we found that without including FC in the assessment of biotic disruption, 12 ecosystems could not have a threat status assigned, and a further 9 ecosystems would have a lower threat status. Our overall assessment of ecosystems found approximately half of forest of Congo Basin ecosystem types which cover over 20% of all forest area are threatened including 4 ecosystems (<1% of total area) which are critically engendered. FC is a transferrable and scalable assessment to support forest monitoring, planning, and management.
Ape cultures do not require behaviour copying
Authors: Acerbi Alberto , Snyder William Daniel , Tennie Claudio
Published: March 2020

While culture is widespread in the animal kingdom, human culture has been claimed to be special due to being cumulative. It is currently debated which cognitive abilities support cumulative culture, but behavioural form copying is one of the main abilities proposed. One important source of contention is the presence or absence of behaviour copying in our closest living relatives, non-human great apes (apes) – especially given that their behaviour does not show clear signs of cumulation. Those who claim that apes copy behaviour often base this claim on the existence of stable ape cultures in the wild. We developed an individual-based model to test whether ape cultural patterns can emerge in absence of any behaviour copying, when only allowing for a well-supported alternative social learning mechanism, socially mediated reinnovation, where only the frequency of reinnovation is under social influence, but the form of the behaviour is not. Our model reflects wild ape life conditions, including physiological and behavioural needs, demographic and spatial features, and possible genetic and ecological variation between populations. Our results show that, under a wide range of values of parameters, we can reproduce the defining features of wild ape cultural patterns. Overall, our results show that ape cultures can emerge and stabilise without behaviour copying. Ape cultures do not show the signatures of behaviour copying abilities, lending support to the notion that behaviour copying is, among apes, unique in the human lineage. It therefore remains an open question when and why behaviour copying evolved in hominins.
TMS alters multivoxel patterns in the absence of overall activity changes
Authors: Rafiei Farshad , Safrin Martin , Wokke Martijn E. , Lau Hakwan , Rahnev Dobromir
Published: March 2020

Transcranial magnetic stimulation (TMS) has become one of the major tools for establishing the causal role of specific brain regions in perceptual, motor, and cognitive processes. Nevertheless, a persistent limitation of the technique is the lack of clarity regarding its precise effects on neural activity. Here, we examined the effects of TMS intensity and frequency on concurrently recorded blood-oxygen level-dependent (BOLD) signals at the site of stimulation. In two experiments, we delivered TMS to the dorsolateral prefrontal cortex in human subjects of both sexes. In Experiment 1, we delivered a series of pulses at high (100% of motor threshold) or low (50% of motor threshold) intensity, whereas in Experiment 2, we always used high intensity but delivered stimulation at four different frequencies (5, 8.33, 12.5, and 25 Hz). We found that the TMS intensity and frequency could be reliably decoded using multivariate analysis techniques even though TMS had no effect on overall BOLD activity at the site of stimulation in either experiment. These results provide important insight into the mechanisms through which TMS influences neural activity.

Significance

Transcranial magnetic stimulation (TMS) is a promising tool for the treatment of a number of neuropsychiatric disorders. However, its effectiveness is still impeded by an incomplete understanding of its neural effects. One fundamental unresolved issue is whether TMS leads to local changes in overall neural activity in the absence of a task. Here we performed two experiments where TMS was delivered inside an MRI scanner while brain activity was continuously monitored. We found converging evidence for the notion that TMS affects the pattern of local activity changes but does not lead to an overall increase in activity. These results help clarify the mechanisms of how TMS affects local neural activity.
Maximizing Quantitative Phosphoproteomics of Kinase Signaling Expands the Mec1 and Tel1 Networks
Authors: Faca Vitor Marcel , Sanford Ethan , Tieu Jennifer , Marshall Shannon , Comstock William , Smolka Marcus
Published: March 2020

Global phosphoproteome analysis is crucial for comprehensive and unbiased investigation of kinase-mediated signaling. However, since each phosphopeptide represents a unique entity for defining identity, site-localization, and quantitative changes, phosphoproteomics often suffers from lack of redundancy and statistical power for generating high confidence datasets. Here we developed a phosphoproteomic approach in which data consistency among experiments using reciprocal stable isotope labeling defines a central filtering rule for achieving reliability in phosphopeptide identification and quantitation. We find that most experimental error or biological variation in phosphopeptide quantitation does not revert in quantitation once light and heavy media are swapped between two experimental conditions. Exclusion of non-reverting data-points from the dataset not only reduces quantitation error and variation, but also drastically reduces false positive identifications. Application of our approach in combination with extensive fractionation of phosphopeptides by HILIC identifies new substrates of the Mec1 and Tel1 kinases, expanding our understanding of the DNA damage signaling network regulated by these kinases. Overall, the proposed quantitative phosphoproteomic approach should be generally applicable for investigating kinase signaling networks with high confidence and depth.
Conservation and discreteness of the atromentin gene cluster in fungi
Authors: Tauber James P. , Hintze John
Published: March 2020

The atromentin synthetase gene cluster is responsible for catalyzing the precursor pigment atromentin, which is further catalyzed into hundreds of different pigments that span different taxa in the Basidiomycota and is a distinguished feature of Boletales. Previous work identified co-transcription of the two essential clustered atromentin genes (the atromentin synthetase (NPS) and the aminotransferase) by inducible pigment conditions and also conserved genetic elements in the promoter regions (motifs). For this work, we found that theNPSand its promoter motif appeared to follow the same evolutionary path as the mushrooms’. TheNPSappears to predate Boletales and originate in Agaricomycetes, and with convergent/parallel evolution that allowed ascomycetes to produce atromentin. Additionally, a consensus of the intron-exon gene structure for basidiomycetous, atromentin-catalyzingNPSswas identified whereby a significant deviation occurred in the paraphyletic group, Paxillaceae. This gene structure was not present inNPSsin Aspergilli. Lastly, we found a putative TATA box adjacent to the palindromic motif ofNPS, indicating (co-)transcriptional control by a TATA(-like) binding transcription factor. Combined with previous decades’ worth of research, our results support that not only can atromentin derivatives be used for chemo-taxonomy, but also atromentin’s genetic basis. Future work using the putative promoter motif will provide new insight into which (co-)transcription factor may be responsible for the transcriptional control of atromentin synthetases.
Age-dependent selection on MHC class 2 variation in a free-living ruminant
Authors: Huang Wei , Dicks Kara L , Hadfield Jarrod D , Johnston Susan E , Ballingall Keith T , Pemberton Josephine M
Published: March 2020

Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection (PMS) is believed to be the main force maintaining diversity at MHC class I and II genes, but it has proven hard to demonstrate the exact PMS regime that is acting in natural populations. Demonstrating contemporary selection on MHC alleles is not trivial, and previous work has been constrained by limited genetic tools, low sample sizes and short time scales and has sometimes involved anticonservative statistical approaches. Here, we use appropriate statistical approaches to examine associations between MHC variation and several fitness measurements including total fitness (lifetime breeding success) and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored over their lifetimes between 1989 and 2012. We found haplotypes C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was positively associated with haplotype divergence. Of the eight MHC haplotypes (A-H), haplotypes C and F were associated with decreased adult male breeding success and decreased adult female life span respectively. Consistent with the increased male total fitness, haplotype D, which is the rarest, has increased in frequency throughout the study period. Our results suggest that contemporary balancing selection is acting on MHC class II genes in Soay sheep and that different selection mechanisms are acting between juveniles and adults.
First report of ‘CandidatusLiberibacter asiaticus’ affecting sour orange in urban areas of Mayabeque, Cuba
Authors: Pérez-López Edel , Dumonceaux Tim J.
Published: March 2020

‘CandidatusLiberibacter asiaticus’ (CLas) is an unculturable, Gram-negative, phloem restricted plant pathogenic bacterium associated with a very serious disease of citrus worldwide known as Citrus Huanglongbing (HLB). CLas is widely spread in the Americas. In Cuba, CLas has been associated with HLB symptoms and has seriously affected the Cuban citrus industry. In this short communication we discuss the identification of CLas-infected sour orange in urban areas of Mayabeque Province in Cuba, an area previously unexplored for the presence of HLB, and a host widely cultivated in gardens and yards along Cuba. We used for the first time the bacteria molecular barcode chaperonin-60 universal target (cpn60UT) to identify and to detect CLas in HLB-symptomatic host plants.
Evaluation of theEscherichia colipopulation in the intestinal microbiota of rattus wistar submitted to secondhand smoke and supplemented with prebiotics
Authors: Silva Bruna Rafaela dos Santos , Perez Paula Marioto , Bremer Neto Hermann , Keller Rogeria
Published: March 2020

Many chronic conditions, including smoking, have been shown to be associated with modifications in the gut microbiota and to remedy the effects of these changes, functional foods such as prebiotics have shown beneficial effects. The aim of this work was to evaluate changes in the bacterial population ofEscherichia coliin the intestinal microbiota of rats submitted to passive smoke and to the supplementation of prebiotics incorporated into the basal diet. The animals were divided into: Control Group (CG) = basal diet; Smoking Control Group (GCT) = basal diet with exposure to smoking; Prebiotic Group (GP) = basal diet incorporated with 1g of Immunowall® per kg of diet; Prebiotic Tobacco Group (GPT) = basal diet incorporated with 1g of ImmunowallTM per kg of diet with exposure to smoking. The animals were exposed to the smoke twice a day for 180 days. The obtained data were analyzed through the nonparametric Kruklla-Wallis test. Bacterial populations were amplified by real-time PCR. The results of this study revealed a significant decrease (p = 0.04 and p = 0.01) inEscherichia colipopulation in the group of animals supplemented with prebiotics in the intestinal microbiota of rats exposed and not exposed to cigarette smoke reinforcing the modulating effect of potential pathogens on the intestinal microbiota by functional foods.
Updated population viability analysis, population trends and PBRs for Hector’s and Maui dolphin
Authors: Slooten Elisabeth , Dawson Stephen Michael
Published: March 2020

EXECUTIVE SUMMARY

Updated population viability analyses, incorporating the latest abundance and bycatch data indicate that:

The estimated population decline for Maui dolphin is 2% per year

There is a 68% probability that the population is continuing to decline

After 30 years (6 more surveys) statistical power of detecting this rate of decline would be < 15%

Only very large declines (37%) and recovery (45%) would be detectable with 80% statistical power after 30 years (6 more surveys)

The level of conservation threat for Hector’s dolphin remains high despite a recent, larger population estimate off the east coast of the South Island

Increased overlap between dolphins and fisheries, due to more extensive offshore distribution of dolphins off the South Island east coast, more than offsets the apparently higher population size

The Hector’s dolphin population has declined 70% over the last 3 generations, exceeding the 50% threshold for Endangered

Population declines are predicted to continue under current protection levels

The results of this research are consistent with:

◯ NOAA proposal to list Hector’s and Maui dolphins under the US Endangered Species Act

◯ IWC recommendation to ban gillnets and trawling throughout Maui dolphin habitat

◯ IUCN recommendation to ban gillnets and trawling throughout Hector’s and Maui dolphin habitat
Pinpointing of cysteine oxidation sites in vivo by high-resolution proteomics reveals mechanism of redox-dependent inhibition of STING
Authors: Cuervo Natalia Zamorano , Fortin Audray , Caron Elise , Chartier Stéfany , Grandvaux Nathalie
Published: March 2020

Protein function is regulated by post-translational modifications, among which reversible oxidation of Cys (Cys ox-PTM) emerged as a key regulatory mechanism of cellular responses. The redox regulation of virus-host interactions is well documented, but in most cases, proteins subjected to Cys ox-PTM remain unknown. The identification of Cys ox-PTM sites in vivo is essential to underpin our understanding of the mechanisms of the redox regulation. In this study, we present a proteome-wide identification of reversible Cys ox-PTM sites in vivo during stimulation by oxidants using a maleimide-based bioswitch method coupled to mass spectrometry. We identified 2720 unique Cys ox-PTM sites encompassing 1473 proteins with distinct abundance, location and functions. Label-free quantification (LFQ)-based analysis revealed the enrichment of ox-PTM in numerous pathways, many relevant to virus-host interaction. Here, we focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway induced upon detection of cytosolic DNA. We provide the first in vivo demonstration of reversible oxidation of Cys148and Cys206of STING. Molecular analyses led us to establish a new model in which Cys148oxidation is constitutive, while Cys206oxidation is inducible by oxidative stress or by the natural ligand 2’3’-cGAMP. We show that oxidation of Cys206has an inhibitory function to prevent STING hyperactivation through the constraint of a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This provides new ground for the design of therapies targeting STING relevant to autoinflammatory disorders, immunotherapies and vaccines.

Brief summary of the main results

The function of proteins is regulated by post-translational modifications, among which reversible oxidation of Cys recently emerged as a key component. Comprehension of redox regulation of cellular responses requires identification of specific oxidation sites in vivo. Using a bioswitch method to specifically label Cys subjected to reversible oxidation coupled to mass spectrometry, we identified thousands of novel oxidation sites. Many are relevant to virus-host interaction pathways. Here, we focused on the oxidation of STING, an adaptor critical for activating the innate immune type I interferon pathway engaged upon cytosolic DNA sensing. Molecular studies led us to establish a new model in which STING Cys148is oxidized at basal levels, while Cys206oxidation is induced by oxidative stress and ligand binding. We show that oxidation of Cys206has an inhibitory function to prevent STING hyperactivation. This study provides ground for novel research avenues aimed at designing therapeutics that target this pathway.
An ectosymbiosis-based mechanism of eukaryogenesis
Authors: Wong Tze-Fei , Chan Chung-Kwon , Long Xi , Xue Hong
Published: March 2020

The mechanisms proposed for eukaryogenesis are divisible into mitochondria-early and mitochondria-late ones, where the mitochondriate-eukaryotes (MTEs) were evolutionary precursors or products of the amitochondriate-eukaryotes (AMIs) respectively. Analysis of prokaryote-to-eukaryote gene transfers in eukaryogenesis showed two tranches of high-intensity transfers from prokaryotes to eukaryotes mediated by endosymbioses that gave rise to mitochondria and chloroplasts, and hundreds of medium-intensity transfers which included the transfer of hydrogenase and pyruvate: ferredoxin oxidoreductase genes from theThermoanaerobacter-Hungateiclostridium-Sporanaerobactergroup to the AMIs. Since 94.5% of these medium-intensity transfers generated more than 100 inter-proteome similarity hits between each donor-recipient pair, they were not readily explicable by horizontal gene transfers (HGTs) or endosymbioses, pointing instead to the participation of a large number of ectosymbiotic transfers. The euryarchaeonAciduliprofundum boonei(Abo) and the gammaproteobacteriumEscherichia coli(Eco) were the foremost contributors of archaeal and bacterial genes for the eukaryotic DNA-apparatus respectively, and the Abo/Eco ratios for the prokaryote-derived genes in eukaryotes decreased from Microsporidia to other AMIs, and even more so in the MTEs. These findings supported an ectosymbiosis-based mechanism of eukaryogenesis with Abo as the Archaeal Parent of Eukarya, and Microsporidia as the eukaryotes phylogenetically closest to the Last Eukaryotic Common Ancestor (LECA).
A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms
Authors: Long Lexin , Wang Ruojun , Chiang Ho Yin , Li Yong-Xin , Chen Feng , Qian Pei-Yuan
Published: March 2020

Biofilms are surface-attached multicellular communities that create many problems in human health and various industries. Given the prominence of biofilms in biofouling and infectious diseases, antibiofilm control approaches are highly sought after. In the present study, we identified elasnin as a potent antibiofilm agent through a bioassay-guided approach. Elasnin specifically inhibited the biofilm formation of bacterial mono-species and eradicated the mature biofilm of Gram-positive bacteria at concentrations below 2.5 μg/mL with a low toxic effect on cells and a low resistance risk. Confocal observations illustrated that elasnin decreased cell aggregations and destroyed the biofilm matrix. Furthermore, elasnin-based antibiofilm coatings were prepared and inhibited the formation of multi-species biofilms and the attachment of large biofouling organisms in the field test. These findings suggest that elasnin is a promising antibiofilm agent for future applications in biofilm control.

Importance

Due to the increased diversity of biofilm-associated infections and the failure of conventional antimicrobial treatment, new and effective biofilm-specific pharmacologic strategies are urgently needed. Elasnin is a new antibiofilm natural product produced by Streptomyces with high efficiency and low toxicity. Elasnin effectively destroyed the biofilm matrix of Gram-positive bacteria, thus making them more susceptible to antibiotics. Unlike currently deployed antibiotic vancomycin, which exclusively targets essential life processes and kills the pathogen, elasnin did not exhibit bactericidal effect and thus held great potential in delaying resistance. With high yield, elasnin-based coatings were easily prepared with low expenditures and exhibited favorable performance in field test. Collectively, the antibiofilm properties of elasnin, combined with the low cost of supply and the low risk of resistance, could provide the basis for the development of a novel antibiofilm agent that could help fight to antibiotics resistance.
Data Visualization for Surgical Informed Consent to Communicate Personalized Risks and Patient Preferences
Authors: Gisladottir Undina , Nakikj Drashko , Jhunjhunwala Rashi , Brat Gabriel , Gehlenborg Nils
Published: March 2020

STRUCTURED ABSTRACT

Objective

Identify key elements of an effective visualization method for communicating personalized surgical risks to patients.

Background

Currently, there is no consensus on which risks should be communicated during the informed consent process and how. Furthermore, patient preferences are often not considered during the consent process. These inefficiencies can lead to non-beneficial outcomes and raise the potential for legal implications. To address the limitations of the informed consent process, we propose a visual consent tool (VCT) that incorporates patient preferences and communicates personalized risks to patients using data visualization.

Methods

To understand how patients perceive risk visualizations and their role in the informed consent discussion, we gathered feedback on visualizations by conducting semi-structured interviews during postoperative visits. Thematic analysis was performed to identify major themes. Iterative evaluation and consolidation of the major themes were performed with domain experts.

Results

A total of 20 patients were interviewed for this study with a median age of 59 (sd = 14). The thematic analysis revealed factors that influence the perception of risk, of risk visualizations, and the usefulness of the proposed VCT. We found that patients preferred VCT over the current methods and had different preferences for risk visualization. Further, our findings suggest that surgical concerns of patients were not in line with existing risk calculators.

Conclusion

We were able to identify key elements that influence effective risk communication in the perioperative setting. We found that patient preference is variable and should influence choices for risk presentation and visualization.
The effects of containment measures in the Italian outbreak of COVID-19
Authors: Supino M. , d’Onofrio A. , Luongo F. , Occhipinti G. , Co A. Dal
Published: March 2020

Background

The COVID-19 pandemic is spreading worldwide. Italy emerged early on as the country with the largest outbreak outside Asia. The outbreak in Northern Italy demonstrates that it is fundamental to contain the virus’ spread at a very early stage of diffusion. At later stages, no containment measure, even if strict, can prevent the saturation of the hospitals and of the intensive care units in any country.

Methods and Results

Here we show that it is possible to predict when the intensive care units will saturate, within a few days from the first cases of COVID-19 intensive care patients. Using early counts of intensive care patients, we predict the saturation for Lombardy, Italy.

Conclusions

Governments should use the Italian outbreak as a precedent and implement appropriate containment measures to prevent the saturation of their intensive care units and protect their population, also, and above all, in anticipation of a possible second rapid spread of infections.
Pathophysiological subtypes of Alzheimer’s disease based on cerebrospinal fluid proteomics
Authors: Tijms Betty M. , Gobom Johan , Reus Lianne , Jansen Iris , Hong Shengjun , Dobricic Valerija , Kilpert Fabian , Kate Mara ten , Barkhof Frederik , Tsolaki Magda , Verhey Frans RJ , Popp Julius , Alvarez Pablo Martinez-Lage , Vandenberghe Rik , Lleó Alberto , Molinuevo José Luís , Engelborghs Sebastiaan , Bertram Lars , Lovestone Simon , Streffer Johannes , Vos Stephanie , Bos Isabelle ,   ADNI, Blennow Kaj , Scheltens Philip , Teunissen Charlotte E. , Zetterberg Henrik , Visser Pieter Jelle
Published: March 2020

Alzheimer’s disease (AD) is biologically heterogeneous, and detailed understanding of the processes involved in patients is critical for development of treatments. Cerebrospinal fluid (CSF) contains hundreds of proteins, with concentrations reflecting ongoing (patho)physiological processes. This provides the opportunity to study many biological processes at the same time in patients. We studied whether AD biological subtypes can be detected in cerebrospinal fluid (CSF) proteomics using the dual clustering technique non-negative matrix factorization. In two independent cohorts (EMIF-AD MBD and ADNI) we found that 705 (77% of 913 tested) proteins differed between AD (defined as having abnormal amyloid, n=425) and controls (defined as having normal CSF amyloid and tau and intact cognition, n=127). Using these proteins for data-driven clustering, we identified within each cohorts three robust pathophysiological AD subtypes showing 1) hyperplasticity and increased BACE1 levels; 2) innate immune activation; and 3) blood-brain barrier dysfunction with low BACE1 levels. In both cohorts, the majority of individuals was labelled as having subtype 1 (80, 36% in EMIF-AD MBD; 117, 59% in ADNI), 71 (32%) in EMIF-AD MBD and 41 (21%) in ADNI were labelled as subtype 2, 72 (32%) in EMIF-AD MBD and 39 (20%) individuals in ADNI were labelled as subtype 3. Genetic analyses showed that all subtypes had an excess of genetic risk for AD (all p>0.01). Additional pathological comparisons that were available for a subset in ADNI only further showed that subtypes showed similar severity of AD pathology, and did not differ in the frequencies of co-pathologies, providing further support that these differences truly reflect AD heterogeneity. Compared to controls all non-demented AD individuals had increased risk to show clinical progression, and compared to subtype 1, subtype 2 showed faster progression to after correcting for age, sex, level of education and tau levels (HR (95%CI) subtype 2 vs 1 = 2.5 (1.2, 5.1), p = 0.01), and subtype 3 at trend level (HR (95%CI) = 2.1 (1.0, 4.4)). Together, these results demonstrate the value of CSF proteomics to study biological heterogeneity in AD patients, and suggest that subtypes may require tailored therapy.
On the assessment of more reliable COVID-19 infected number: the italian case
Authors: Tradigo Giuseppe , Guzzi Pietro Hiram , Veltri Pierangelo
Published: March 2020

COVID-19 (SARS-CoV-2) is the most recent pandemic disease the world is currently managing. It started in China at the end of 2019, and it is diffusing throughout Italy, one of the most affected countries, and it is currently spreading through European countries and USA. Patients affected by COVID-19 are identified employing medical swabs applied mainly to (i) citizens with COVID-19 symptoms such as flu or high temperature, or (ii) citizens that had contacts with COVID-19 patients. A percentage of COVID-19 affected patients needs hospitalisation, whereas a portion needs to be treated in Intensive Care Units (ICUs).

Nevertheless, it is a matter of current intuition that COVID-19 infected citizens are more than those detected, and sometime the infection is detected too late. Thus there are many efforts in both tracking people activities as well as diffusing low cost reliable COVID-19 tests for early detection.

Starting from mortality rates of diseases caused by viruses in the same family (e.g. MERS, SARS, H1N1), we study the relations between the number of COVID-19 infections and the number of deaths, through Italian regions. We thus assess several infections being higher than the ones currently measured. We thus focus on the characterisation of the pandemic diffusion by estimating the infected number of patients versus the number of death. We use such an estimated number of infections, to foresee the effects of restriction actions adopted by governments to constrain virus diffusion. We finally think that our model can support the healthcare system to react when COVID-19 is increasing.
A Simple Mathematical Model for Estimating the Inflection Points of COVID-19 Outbreaks
Authors: Ma Zhanshan Sam
Published: March 2020

Background

Exponential-like infection growths leading to peaks (which could be the inflection points or turning points) are usually the hallmarks of infectious disease outbreaks including coronaviruses. To predict the inflection points, i.e., inflection time (Tmax) & maximal infection number (Imax) of the novel coronavirus (COVID-19), we adopted a trial and error strategy and explored a series of approaches from simple logistic modeling (that has an asymptomatic line) to sophisticated tipping point detection techniques for detecting phase transitions but failed to obtain satisfactory results.

Method

Inspired by its success in diversity-time relationship (DTR), we apply the PLEC (power law with exponential cutoff) model for detecting the inflection points of COVID-19 outbreaks. The model was previously used to extend the classic species-time relationship (STR) for general DTR (Ma 2018), and it has two “secondary” parameters (computed from its 3 parameters including power law scaling parameter w, taper-off parameter d to overwhelm virtually exponential growth ultimately, and a parameter c related to initial infections): one that was originally used for estimating the potential or ‘dark’ biodiversity is proposed to estimate the maximal infection number (Imax) and another is proposed to determine the corresponding inflection time point (Tmax).

Results

We successfully estimated the inflection points [Imax, Tmax] for most provinces (≈85%) in China with error rates <5% in both Imax and Tmax. We also discussed the constraints and limitations of the proposed approach, including (i) sensitive to disruptive jumps, (ii) requiring sufficiently long datasets, and (iii) limited to unimodal outbreaks.
Non-Parametric Analysis of Inter-Individual Relations Using an Attention-Based Neural Network
Authors: Morita Takashi , Toyoda Aru , Aisu Seitaro , Kaneko Akihisa , Suda-Hashimoto Naoko , Adachi Ikuma , Matsuda Ikki , Koda Hiroki
Published: March 2020

Social network analysis, which has been widely adopted in animal studies over the past decade, enables the revelation of global characteristic patterns of animal social systems from pairwise inter-individual relations. Animal social networks are typically drawn based on geometric proximity and/or frequency of social behaviors (e.g., grooming), but the appropriate metric for inter-individual relationship is not clear, especially when prior knowledge on the species/data is limited.

In this study, researchers explored a non-parametric analysis of inter-individual relations using a neural network with the attention mechanism, which plays a central role in natural language processing. The high interpretability of the attention mechanism and flexibility of the entire neural network allow for automatic detection of inter-individual relations included in the raw data, without requiring prior knowledge/assumptions about what modes/types of relations are included in the data. For these case studies, three-dimensional location data collected from simulated agents and real Japanese macaques were analyzed.

The proposed method successfully recovered the latent relations behind the simulated data and discovered female-oriented relations in the real data, which are in accordance with previous generalizations about the macaque social structure.

The proposed method does not exploit any behavioral patterns that are particular to Japanese macaques, and researchers can use it for location data of other animals. The exibility of the neural network would also allow for its application to a wide variety of data with interacting components, such as vocal communication.
Iron acquisition system ofSphingobiumsp. strain SYK-6, a degrader of lignin-derived aromatic compounds
Authors: Fujita Masaya , Sakumoto Taichi , Tanatani Kenta , Yu Hong Yang , Mori Kosuke , Kamimura Naofumi , Masai Eiji
Published: March 2020

Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics,Sphingobiumsp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, andtonB2(SLG_34550), one of the sixtonBcomprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. AlthoughfeoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds.
panRGP: a pangenome-based method to predict genomic islands and explore their diversity
Authors: Bazin Adelme , Gautreau Guillaume , Médigue Claudine , Vallenet David , Calteau Alexandra
Published: March 2020

Motivation

Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of Genome Plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to Genomic Islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date no methods are available to identify GIs using hundreds of genomes to explore their diversity.

Results

We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on Metagenome Assembled Genomes (MAGs) by redefining the borders of theleuXtRNA hotspot, a well studied spot of insertion inEscherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies.

Availability

The methods presented in the current work are available through the following software:https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available athttps://github.com/axbazin/panrgp_supdata.

Contact

vallenet@genoscope.cns.frandacalteau@genoscope.cns.fr

Supplementary information

None.
Action enhances predicted touch
Authors: Thomas Emily R. , Yon Daniel , de Lange Floris P. , Press Clare
Published: March 2020

It is widely believed that predicted tactile action outcomes are perceptually attenuated. The present experiments determined whether predictive mechanisms always generate attenuation, or instead can enhance perception – as typically observed in sensory cognition domains outside of action. We manipulated probabilistic expectations in a paradigm often used to demonstrate tactile attenuation. Participants produced actions and subsequently rated the intensity of forces on a passive finger. Experiment 1 confirmed previous findings that action outcomes are perceived less intensely than passive stimulation, but demonstrated more intense perception when active finger stimulation was removed. Experiments 2 and 3 manipulated prediction explicitly and found that expected touch during action is perceivedmoreintensely than unexpected touch. Computational modelling suggested that expectations increase the gain afforded to expected tactile signals. These findings challenge a central tenet of prominent motor control theories and demonstrate that sensorimotor predictions do not exhibit a qualitatively distinct influence on tactile perception.

Statement of Relevance

Perception of expected action outcomes is thought to be attenuated. Such a mechanism may be adaptive because surprising inputs are more useful - e.g., signalling the need to take new courses of action - and is thought to explain why we cannot tickle ourselves and unusual aspects of action and awareness in clinical populations. However, theories outside of action purport that predicted events are perceptually facilitated, allowing us to generate largely accurate representations of our noisy sensory world. We do not know whether action predictions really alter perception differently from other predictions because different manipulations have been performed. Here we perform similar manipulations and demonstrate that action predictions can enhance, rather than attenuate, touch. We thereby demonstrate that action predictions may not have a qualitatively distinct influence on perception, such that we must re-examine theories concerning how predictions influence perception across domains and clinical theories based upon their assumptions.
Localized inhibition in theDrosophilamushroom body
Authors: Amin Hoger , Suárez-Grimalt Raquel , Vrontou Eleftheria , Lin Andrew C.
Published: March 2020

Many neurons show compartmentalized activity, in which activity does not spread readily across the cell, allowing input and output to occur locally. However, the functional implications of compartmentalized activity for the wider neural circuit are often unclear. We addressed this problem in theDrosophilamushroom body, whose principal neurons, Kenyon cells, receive feedback inhibition from a large, non-spiking interneuron called APL. We used local stimulation and volumetric calcium imaging to show that APL inhibits Kenyon cells in both their dendrites and axons, and that both activity in APL and APL’s inhibitory effect on Kenyon cells are spatially localized, allowing APL to differentially inhibit different mushroom body compartments. Applying these results to theDrosophilahemibrain connectome predicts that individual Kenyon cells inhibit themselves via APL more strongly than they inhibit other individual Kenyon cells. These findings reveal how cellular physiology and detailed network anatomy can combine to influence circuit function.
SPEARS: Standard Performance Evaluation of Ancestral Reconstruction through Simulation
Authors: Manching H. , Wisser R. J.
Published: March 2020

Motivation

Ancestral haplotype maps provide useful information about genomic variation and biological processes. Reconstructing the descendent haplotype structure of homologous chromosomes, particularly for large numbers of individuals, can help with characterizing the recombination landscape, elucidating genotype-to-phenotype relationships, improving genomic predictions and more. Inferring haplotype maps from sparse genotype data is an efficient approach to whole-genome haplotyping, but this is a non-trivial problem. A standardized approach is needed to validate whether haplotype reconstruction software, conceived population designs and existing data for a given population provides accurate haplotype information for further inference.

Results

We introduce SPEARS, a pipeline for whole simulation-based appraisal of genome-wide ancestral haplotype inference. The pipeline generates virtual genotypes (truth data) with real-world missing data structure. It then proceeds to mimic analysis in practice, capturing sources of error due to imputation and reconstruction of ancestral haplotypes. Standard metrics allow researchers to assess which features of haplotype structure or regions of the genome are sufficiently accurate for analysis and reporting. Haplotype maps for 1,000 outcross progeny from a multi-parent population of maize is used to demonstrate SPEARS.

Availability

https://github.com/maizeatlas/spears
Loss ofdmrt1restores female fates in the absence ofcyp19a1abut notrbpms2
Authors: Romano Shannon , Kaufman Odelya H. , Marlow Florence L.
Published: March 2020

Sex determination and differentiation is a complex process regulated by multiple factors, including factors from the germline or surrounding somatic tissue. In zebrafish, sex-determination begins with establishment of a bipotential gonad that undergoes sex-specific differentiation and maintenance to form the functional adult gonad. However, the relationships among these factors are not fully understood. Here we identify potential Rbpms2 targets and apply genetic epistasis experiments to decipher the genetic hierarchy of regulators of sex-specific differentiation. We provide evidence that the critical female factor,rbpms2is epistatic to the male factordmrt1in terms of adult sex. Moreover, Rbpms2’s role in promoting female fates extends beyond repression of Dmrt1, as Rbpms2 is essential for female differentiation even in the absence of Dmrt1. In contrast, female fates can be restored in mutants lackingcyp19a1ain the absence ofdmrt1.Taken together this work indicates that Cyp19a1a-mediated suppression of Dmrt1 is key to establish a bipotential gonad and initiate female fate acquisition, possibly by promotingrbpms2. Then, after female fate specification, Cyp19a1a regulates subsequent oocyte maturation and sustains female fates independent of Dmrt1 repression.

Author Summary

We show thatcyp19a1a-mediated suppression ofdmrt1establishes a bipotential gonad and female fate acquisition, possibly throughrbpms2which is required for female fates, even in the absence of Dmrt1.
Immortalised hippocampal astrocytes from 3xTG-AD mice fail to support BBB integrityin vitro: Role of extracellular vesicles in glial-endothelial communication
Authors: Kriaučiūnaitė Karolina , Kaušylė Aida , Pajarskienė Justina , Tunaitis Virginijus , Lim Dmitry , Verkhratsky Alexei , Pivoriūnas Augustas
Published: March 2020

Impairments of the blood brain barrier (BBB) and vascular dysfunction contribute to Alzheimer’s disease (AD) from the earliest stages. However, the effects of AD-affected astrocytes on the BBB remain largely unexplored. In the present study we created an in vitro BBB using human immortalised endothelial cells in combination with immortalised astroglial cell lines from the hippocampus of 3xTG-AD and wild-type mice (3Tg-iAstro and WT-iAstro, respectively). We found that co-culturing endothelial monolayers with WT-iAstro up-regulates expression of endothelial tight junction proteins (claudin-5, occludin, ZO-1) and increases the trans-endothelial electrical resistance (TEER). In contrast, co-culturing with 3Tg-iAstro does not affect expression of tight junction proteins and does not change the TEER of endothelial monolayers. The same in vitro model has been used to evaluate the effects of extracellular vesicles (EVs) derived from the WT-iAstro and 3Tg-iAstro. The EVs derived from WT-iAstro increased TEER and up-regulated expression of tight junction proteins, whereas EVs from 3Tg-iAstro were ineffective. In conclusion, we show for the first time that immortalised hippocampal astrocytes from 3xTG-AD mice exhibit impaired capacity to support BBB integrity in vitro through paracrine mechanisms and may represent an important factor underlying vascular abnormalities during development of AD.
Sugar feeding patterns of New YorkAedes albopictusmosquitoes are affected by environmental dryness, flowers, and host seeking
Authors: Fikrig Kara , Peck Sonile , Deckerman Peter , Dang Sharon , Fleur Kimberly St , Goldsmith Henry , Qu Sophia , Rosenthal Hannah , Harrington Laura C.
Published: March 2020

Background

Sugar feeding is an important behavior which may determine vector potential of mosquitoes. Sugar meals can reduce blood feeding frequency, enhance survival, and decrease fecundity, as well as provide energetic reserves to fuel energy intensive behaviors such as mating and host seeking. Sugar feeding behavior also can be harnessed for vector control (e.g. attractive toxic sugar baits). Few studies have addressed sugar feeding ofAedes albopictus, a vector of arboviruses of public health importance, including dengue and Zika viruses. To address this knowledge gap, we assessed sugar feeding patterns ofAe. albopictusfor the first time in its invasive northeastern USA range.

Methodology/ Principal Findings

Using the cold anthrone fructose assay with robust sample sizes, we demonstrated that a large percentage of both male (49.6%) and female (41.8%)Ae. albopictusfed on plant or homopteran derived sugar sources within 24 hrs of capture. Our results suggest that sugar feeding behavior increases when environmental conditions are dry and may vary by behavioral status (host seeking vs. resting). Furthermore, mosquitoes collected on properties with flowers (>3 blooms) had higher fructose concentrations compared to those collected from properties with few to no flowers (0-3).

Conclusions/Significance

Our results provide the first evidence ofAe. albopictussugar feeding behavior in the Northeastern US and reveal relatively high rates of sugar feeding. These results suggest the potential success for regional deployment of toxic sugar baits. In addition, we demonstrate the impact of several environmental and mosquito parameters (environmental dryness, presence of flowers, host seeking status, and sex) on sugar feeding. Placing sugar feeding behavior in the context of these environmental and mosquito parameters provides further insight into spatiotemporal dynamics of feeding behavior forAe. albopictus, and in turn, provides information for evidence-based control decisions.