bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic arms race between a plant and a fungal pathogen
Authors: Liu Y. , Mahdi L.K. , Porzel A. , Stark P. , Esposto D. , Scherr-Henning A. , Bathe U. , Acosta I.F. , Zuccaro A. , Balcke G.U. , Tissier A. 
Published: July 2023

AbstractIn this work, we uncover a metabolite interaction between barley and the fungal pathogenBipolaris sorokiniana(Bs), involving hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties.Bsinfection of barley roots elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the synthesis pathway in yeast produced several hordedanes, including one of the most advanced products 19-b-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of the cluster are unable to produce hordedanes but, unexpectedly, show reducedBscolonization. Accordingly, 19-OH-HTA enhances both germination and growth ofBs, while it inhibits other fungi, andBschemically modifies 19-OH-HTA. Thus, plant and pathogen molecular interactions extend beyond protein-protein recognition and the simple detoxification of plant antimicrobial metabolites.One-Sentence SummaryA fungal pathogen uses barley diterpenoid phytoalexins to facilitate root colonization.
Gradient-based implementation of linear model outperforms deep learning models
Authors: Hamidi Hamid , Wang Dinghao , Long Quan , Greenberg Matthew 
Published: July 2023

AbstractDeep learning has been widely considered more effective than traditional statistical models in modeling biological complex data such as single-cell omics. Here we show the devil is hidden in details: by adapting a modern gradient solver to a traditional linear mixed model, we showed that conventional models can outperform deep models in terms of both speed and accuracy. This work reveals the potential of re-implementing traditional models with modern solvers.
South Western Ghats: a niche of clove (Syzygium aromaticum(L.) Merr. & Perry) diversification
Authors: Sreekala G. S. , Avinash M. , Reddappa J. B. , Reshma P. , Nainu J. , Anargha T. , Aswani J. S. 
Published: July 2023

AbstractSurvey conducted at major clove (Syzygium aromaticum(L.) Merr. & Perry) growing regions of South Western Ghats of India in the states of Kerala and Tamil Nadu identified thirty accessions with superior yield and distinct characters. Clove accessions were characterized based on twenty one qualitative and twelve quantitative traits. Variation among fifteen qualitative characters were found and the predominant traits observed were elliptical canopy shape, semi-erect branching pattern, lanceolate leaf lamina with acuminate apex, mid bud forming season, combination of 1,2,3,4,5 flower bud per cluster, medium sized bud, elliptical fruit and seed shape. Dendrogram constructed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method grouped thirty accessions into 5 major clusters at genetic similarity of 73%. Acc.19 was identified as a unique accession. Twelve quantitative characters were subjected to principal component analysis where three component groups were extracted, which explained 70.85 per cent of total variance. The score plot generated from the principal component loading grouped the accessions into 18 clusters. Minimal data set of four characters viz., plant height, canopy spread (EW), number of inflorescence per square meter and mature bud length was generated. Observation on the qualitative and minimum data set helps to identify the ideotypes. The geographical location was not found to influence genetic diversity.HighlightClove genotypes in South Western Ghats were surveyed and diversity identifiedCombination of 1,2,3,4,5 flower bud per cluster was a unique character identified among cultivated cloveMinimal data set of clove developed using plant height (m), canopy spread (EW), number of inflorescence per m2and mature bud length (mm)Ideotype of clove developed
An interbacterial lipase toxin with an unprecedented reverse domain arrangement defines a new class of type VII secretion system effector
Authors: Garrett Stephen R. , Mietrach Nicole , Deme Justin , Bitzer Alina , Yang Yaping , Ulhuq Fatima R. , Kretschmer Dorothee , Heilbronner Simon , Smith Terry K. , Lea Susan M. , Palmer Tracy 
Published: July 2023

SummaryThe type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such asStaphylococcus aureusoften specify toxic anti-bacterial activity. Here we describe the first example of a new class of T7 substrate, TslA, that has an unexpected reverse domain organisation. TslA is widely found across Bacillota includingStaphylococcus,EnterococcusandListeria. We show that theS. aureusTslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the extraordinary feature of recognising a secretion signal present at either end of a substrate.
SNP-Slice Resolves Mixed Infections: Simultaneously Unveiling Strain Haplotypes and Linking Them to Hosts
Authors: Ju Nianqiao P. , Liu Jiawei , He Qixin 
Published: July 2023

AbstractMulti-strain infection is a common yet under-investigated phenomenon of many pathogens. Currently, biologists analyzing SNP information have to discard mixed infection samples, because existing downstream analyses require monogenomic inputs. Such a protocol impedes our understanding of the underlying genetic diversity, co-infection patterns, and genomic relatedness of pathogens. A reliable tool to learn and resolve the SNP haplotypes from polygenomic data is an urgent need in molecular epidemiology. In this work, we develop a slice sampling Markov Chain Monte Carlo algorithm, named SNP-Slice, to learn not only the SNP haplotypes of all strains in the populations but also which strains infect which hosts. Our method reconstructs SNP haplotypes and individual heterozygosities accurately without reference panels and outperforms the state of art methods at estimating the multiplicity of infections and allele frequencies. Thus, SNP-Slice introduces a novel approach to address polygenomic data and opens a new avenue for resolving complex infection patterns in molecular surveillance. We illustrate the performance of SNP-Slice on empirical malaria and HIV datasets and provide recommendations for the practical use of the method.
Community structure of heritable viruses in aDrosophila-parasitoids complex
Authors: Varaldi Julien , Lepetit David , Burlet Nelly , Faber Camille , Baretje Bérénice , Allemand Rolland 
Published: July 2023

AbstractThe diversity and phenotypic impacts related to the presence of heritable bacteria in insects have been extensively studied in the last decades. On the contrary, heritable viruses have been overlooked for several reasons, including technical ones. This is regrettable because of the size of this gap knowledge and because case study indicate that viruses may have profound impact on the functionning of individuals and communities. Additionally, the factors that may shape viral communities are poorly known, except in some very specific viral-insect systems. Here we analyze the community structure of heritable viruses in a multi-hosts-multi-parasitoids community. Drosophilidae and their larval and pupal parasitoids were sampled in two locations, two years and two seasons. After two lab generations, putative DNA and RNA viruses were purified and sequenced. Our analysis revealed the presence of 53 viruses (including 37 new viruses), the great majority of which were RNA viruses. The "species" factor was by far the most significant one, explaining more than 50% of the variance in viral structure. Additionally, parasitoids had a higher number of heritable viruses compared to their hosts, suggesting that this lifestyle favours the association with viruses. Finally, our community-level survey challenged previous interpretation concerning the host range of some previously described viruses.
Wide-field Intensity Fluctuation Imaging
Authors: Fang Qingwei , Tomar Alankrit , Dunn Andrew K. 
Published: July 2023

AbstractThe temporal intensity fluctuations contain important information about the light source and light-medium interaction and are typically characterized by the intensity autocorrelation function,g2(τ). The measurement ofg2(τ) is a central topic in many optical sensing applications, ranging from stellar intensity interferometer in astrophysics, to fluorescence correlation spectroscopy in biomedical sciences and blood flow measurement with dynamic light scattering. Currently,g2(τ) at a single point is readily accessible through high-frequency sampling of the intensity signal. However, two-dimensional widefield measurement ofg2(τ) is still limited by camera frame rates. We propose and demonstrate a 2-pulse within-exposure modulation approach to break through the camera frame rate limit and obtain the quasig2(τ) map in wide field with cameras of only ordinary frame rates.HighlightsThe quasi intensity autocorrelation function can be measured at almost arbitrary time lagsCameras of ordinary frame rates are sufficient for the measurementIllumination within the camera exposure is modulated by an acoustic optical modulator using two short pulses
Topoisomerase IIα C-terminal Domain Mutations and Catalytic Function
Authors: Musselman Jessica R. , England Daniel C. , Fielding Lauren A. , Durham Clay T. , Baxter Emma , Jiang Xiaohua , Lisic Edward C. , Deweese Joseph E. 
Published: July 2023

AbstractTopoisomerase IIα is a nuclear enzyme needed for dealing with topological entanglements in the DNA arising from replication and transcription. The N-terminal region and core of the protein are utilized in the catalytic cycle of the enzyme, which generates a transient double-stranded break in one segment of DNA and passes another segment through the break. The C-terminal domain is a large, intrinsically disordered region that appears to be involved in regulating the function of the enzyme both in terms of substrate selection and the level of activity of the enzyme. In a previous study, we explored eleven targeted mutations to the C-terminal domain. This present study explores six of these mutants to determine whether there are any defects in closure of the N-terminal clamp and whether an experimental compound known as a Cu(II)-thiosemicarbazone affects DNA cleavage with the mutants. Based upon our results, the mutants are able to close the N-terminal clamp, but some of the mutants that displayed the least clamp closing activity also had the lowest catalytic activity. Further, Cu-APY-ETSC did impact the ability of the enzymes to cleave DNA to similar levels as seen with the WT enzyme. These results lay the groundwork for additional analyses of the C-terminal domain and indicate the C-terminal domain regions tested did not influence the action of Cu-APY-ETSC except at the level of coordination between the two active sites.
Global decoupling of cell differentiation from cell division in early embryo development
Authors: Kukreja Kalki , Patel Nikit , Megason Sean G , Klein Allon M 
Published: July 2023

AbstractAs tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. In the absence of cell division, differentiation slows down in some cell types, and cells exhibit global stress responses. While differentiation is robust to blocking cell division, the proportions of cells across cell states are not. This work simplifies our understanding of the role of cell division in development and showcases the utility of combining embryo-wide perturbations with single-cell RNA sequencing to uncover the role of common biological processes across multiple tissues.
Mining threats in high-level biodiversity conservation policies
Authors: Torres Aurora , zu Ermgassen Sophus O.S.E. , Navarro Laetitia M. , Ferri-Yanez Francisco , Teixeira Fernanda Z. , Wittkopp Constanze , Rosa Isabel M.D. , Liu Jianguo 
Published: July 2023

ABSTRACTAmid a global infrastructure boom, there is increasing recognition of the ecological impacts of the extraction and consumption of construction minerals, mainly as concrete. Recent research highlights the significant and expanding threat these minerals pose to global biodiversity. To what extent is this pressure acknowledged in biodiversity conservation policy? We investigate how high-level national and international biodiversity conservation policies, including the 2011-2020 and post-2020 biodiversity strategies, the national biodiversity strategies and action plans, and the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, address mining threats with a special focus on construction minerals. We find that mining appears rarely in national targets, but more frequently in national strategies with greater coverage of aggregates mining than limestone mining, yet it is dealt with superficially in most countries. We then outline an 8-point strategy to reduce the biodiversity impacts of construction minerals, which comprises actions such as targeting, reporting, and monitoring systems, the evidence-base around mining impacts on biodiversity, and the behavior of financial agents and businesses. Implementing these measures can pave the way for a more sustainable approach to construction mineral use and safeguard biodiversity.
Mapping forests with different levels of naturalness using machine learning and landscape data mining
Authors: Bubnicki Jakub W. , Angelstam Per , Mikusiński Grzegorz , Svensson Johan , Jonsson Bengt Gunnar 
Published: July 2023

AbstractTo conserve biodiversity, it is imperative to maintain and restore sufficient amounts of functional habitat networks. Hence, locating remaining forests with natural structures and processes over landscapes and large regions is a key task. We integrated machine learning (Random Forest) and open landscape data to scan all forest landscapes in Sweden with a 1 ha spatial resolution with respect to the relative likelihood of hosting High Conservation Value Forests (HCVF). Using independent spatial stand-and plot-level validation data we confirmed that our predictions (ROC AUC in the range of 0.89 - 0.90) correctly represent forests with different levels of naturalness, from deteriorated to those with high and associated biodiversity conservation values. Given ambitious national and international conservation objectives, and increasingly intensive forestry, our model and the resulting wall-to-wall mapping fills an urgent gap for assessing fulfilment of evidence-based conservation targets, spatial planning, and designing forest landscape restoration.
An individual-based simulation framework exploring the ecology and mechanistic underpinnings of larval crowding in laboratory populations ofDrosophila
Authors: Venkitachalam Srikant , Joshi Amitabh 
Published: July 2023

AbstractThe study of larval competition in laboratory populations ofDrosophila, implemented via the crowding of larval cultures, has contributed greatly to the understanding of the ecology of competition, the evolution of larval competitive ability, and formed the basis of rigorous testing of the theory of density-dependent selection. Earlier studies led to the view that the outcomes of larval competition, and resulting evolutionary consequences of crowding-adaptation, could largely be understood by varying the starting density of individuals in a crowded culture. However, recent studies have shown that the results of adaptation to larval crowding may not be well predicted by the total larval density (i.e., total starting individuals/total volume of food). Cultures raised at the same total density but at different egg number and food volume combinations were shown to have different underlying density-specific fitness functions, and crowding-adaptation in each of these cultures was attained through different evolutionary trajectories as well. A recent study showed that cultures with not just the same density, but the same egg and food volume combination, achieved through food columns of differing diameter and height, could also differ greatly in fitness-related trait outcomes. In that study, the density of larvae in the feeding band (volume of food close to the surface in contact with air, to which larval feeding is largely restricted) was a very important factor in predicting the outcomes of larval competition. Given these recent findings, it is important to understand the overall role of feeding band density, and how it influences density-specific fitness functions in different kinds of crowded cultures. As the older models of larval competition are now insufficient to capture current empirical data, we constructed an individual-based simulation framework informed in part by these more recent findings, in order to better understand the evolutionary ecology and mechanistic underpinnings of larval competition, and predict robust experiments for expanding our understanding of the process of larval competition inDrosophila.
Ceramic absorbed with calcium bicarbonate mesoscopic crystals partially inactivate scrapie prions
Authors: Iwamaru Yoshifumi , Furusaki Koichi , Sugiura Katsuaki , Haritani Makoto , Onodera Takashi 
Published: July 2023

AbstractPrion diseases are fatal neurodegenerative disorders affecting both humans and animals. The causative agent, prion, is extremely resistant to common disinfection procedures. Thus, effective prion inactivation strategies using relatively safe and less corrosive disinfectants are required. A solution containing CAC‐717, mesoscopic crystals of calcium bicarbonate, exerts both antimicrobial and virucidal activities without apparent harmful effects. This study demonstrated that combined treatment with CAC‐717 absorbed on ceramic (CAC‐717 ceramic) and sodium dodecyl sulfate (SDS) substantially reduced the protein misfolding cyclic amplification (PMCA) seeding activity of Chandler strain scrapie mouse‐brain homogenates (ScBH). Additionally, bioassays demonstrated that ScBH‐inoculated mice treated with CAC‐717 ceramic in combination with sodium dodecyl sulfate (SDS) did not develop disease. Furthermore, this combination effectively inactivated PMCA seeding activity on ScBH‐coated stainless‐steel wires below the detection limit. Overall, the findings suggest that combined treatment with CAC‐717 ceramic and SDS represents a promising and less damaging approach for prion inactivation.
Citizens with Felony Convictions in the Jury Box: A Peer‐Judgment Argument
Authors: Poama Andrei , McGinnis Briana 
Published: July 2023

AbstractCurrently, almost all polities that allow for jury trials deprive people with felony convictions of their right to serve as jurors on criminal trials. Against these exclusionary practices, we contend that there are epistemic and political reasons to enable (and not merely allow) convicted felony defendants to serve as jurors. These reasons are derived from the ideal of peer judgment, which we take to be deeply ingrained in and relevant for ensuring fair jury‐judgment practices. In this article, we construct an account of peer judgment understood as equal subjection to coercive law, spell out the epistemic dimension of this account, and use it to argue that there are stronger reasons for having people with felony convictions serve as jurors, as compared to average, noncriminalized citizens. Our peer‐judgment argument is meant to both weaken and outweigh current justifications for excluding people with felony convictions from jury service.
Dose–response relationship between alcohol consumption and workplace absenteeism in Australia
Authors: Marzan Melvin Barrientos , Callinan Sarah , Livingston Michael , Jiang Heng 
Published: July 2023

AbstractIntroductionWorkplace absenteeism is a burden in Australia. The estimated productivity losses due to alcohol were around $4.0 billion in 2017, with absenteeism driving 90% of these costs. We aim to determine the dose–response relationship between average daily alcohol consumption and heavy episodic drinking (HED) frequency and workplace absenteeism amongst Australian workers.MethodsWe used the 2019 National Drug Strategy Household Survey of Australian employed workers aged ≥20 years to 69 years old. Respondents' average daily alcohol consumption was categorised into four: abstainers, light to moderate (1–20 g of alcohol/day), risky (>20–40 g of alcohol/day) and high‐risk (>40 g of alcohol/day). HED was classified into four frequency measures (never, less than monthly, monthly, weekly). The outcome variables came from dichotomised measures of: (i) absence due to alcohol consumption; and (ii) broader sickness absence–absence due to illness or injury in the previous 3 months.ResultsRisky (adjusted odds ratio 4.74 [95% CI 2.93–7.64]) and high‐risk drinking (adjusted odds ratio 6.61 [95% CI 4.10–10.68]) were linked to increased odds of alcohol‐related absence. Higher HED frequency was significantly associated with alcohol‐related and broader sickness absenteeism. No significant associations exist between regular alcohol consumption and broader sickness absence in fully adjusted models.Discussion and ConclusionsFindings suggest that only HED is linked to broader sickness absence. However, there is a strong dose–response association between alcohol consumption and alcohol‐related absences for both consumption measures amongst Australian workers. Population‐level policies that reduce alcohol consumption to moderate level and less frequent HED might address workplace absenteeism.
The impact of transportation capacity in pre‐positioning humanitarian supplies
Authors: Rothkopf Alexander , Acimovic Jason , Goentzel Jarrod 
Published: July 2023

ABSTRACTHumanitarian action saves lives by delivering supplies following a disaster. To effectively prepare, large humanitarian organizations solve optimization models to allocate inventory minimizing expected time‐to‐respond. However, these organizations also rely on transportation carriers to deliver this inventory, a feature often omitted from such models. Part of the reason is that capacity data on third‐party carriers are scant. Nevertheless, there is value in humanitarian organizations asking themselves the following: how should such data be incorporated into a model; how important is it to incorporate transportation capacities; where is it worth increasing transportation capacity? Building on previous inventory optimization models, we partner with the United States Federal Emergency Management Agency (FEMA) to answer these questions by incorporating transportation market capacity. Using public and proprietary data sets, we first approximate the trucking capacity near FEMA's warehouses. We develop intuitive metrics that guide practitioners to make decisions, understand trade‐offs in complex networks, and negotiate contracts. We show that when optimizing inventory, ignoring trucking capacity can lead to up to 18% higher response times. In discussions with FEMA, our research has guided strategic inventory deployment and has been a catalyst in a new initiative for transportation contracting.