The end of the reading room? Simulating the impact of digitisation on the physical access of archival collections

Digitisation has become an essential part of archival and library strategies to enhance access to collections. As the digital content is increasing due to large-scale digitisation projects, it is expected that providing digital access to the analogue collections will eventually reduce the number of archival records accessed in the reading room. In this paper, we investigate this issue using two approaches: system dynamics and agent-based modelling. We first analyse real data in order to identify the dynamic hypothesis of the model. Then, a sensitivity analysis is conducted on two baseline models to identify scenarios that match the real dataset. Although the two approaches suceed to simulate the number of requests in the reading room, the experimental results show that a better fit is obtained in the agent-based model when not only the number of records that have been accessed and digitised is taken into account, but also the number of times that such records have been accessed before digitisation. The proposed model can be used to explore the impact of different digitisation strategies on the decrease in access requests in the archival and library reading rooms

Genome-wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors.

'Candidatus Liberibacter' species are insect-transmitted, phloem-limited α-Proteobacteria in the order of Rhizobiales. The citrus industry is facing significant challenges due to huanglongbing, associated with infection from 'Candidatus Liberibacter asiaticus' (Las). In order to gain greater insight into 'Ca. Liberibacter' biology and genetic diversity, we have performed genome sequencing and comparative analyses of diverse 'Ca. Liberibacter' species, including those that can infect citrus. Our phylogenetic analysis differentiates 'Ca. Liberibacter' species and Rhizobiales in separate clades and suggests stepwise evolution from a common ancestor splitting first into nonpathogenic Liberibacter crescens followed by diversification of pathogenic 'Ca. Liberibacter' species. Further analysis of Las genomes from different geographical locations revealed diversity among isolates from the United States. Our phylogenetic study also indicates multiple Las introduction events in California and spread of the pathogen from Florida to Texas. Texan Las isolates were closely related, while Florida and Asian isolates exhibited the most genetic variation. We have identified conserved Sec translocon (SEC)-dependent effectors likely involved in bacterial survival and virulence of Las and analysed their expression in their plant host (citrus) and insect vector (Diaphorina citri). Individual SEC-dependent effectors exhibited differential expression patterns between host and vector, indicating that Las uses its effector repertoire to differentially modulate diverse organisms. Collectively, this work provides insights into the evolution of 'Ca. Liberibacter' species, the introduction of Las in the United States and identifies promising Las targets for disease management

DYRK1A promotes dopaminergic neuron survival in the developing brain and in a mouse model of Parkinson's disease

In the brain, programmed cell death (PCD) serves to adjust the numbers of the different types of neurons during development, and its pathological reactivation in the adult leads to neurodegeneration. Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) is a pleiotropic kinase involved in neural proliferation and cell death, and its role during brain growth is evolutionarily conserved. Human DYRK1A lies in the Down syndrome critical region on chromosome 21, and heterozygous mutations in the gene cause microcephaly and neurological dysfunction. The mouse model for DYRK1A haploinsufficiency (the Dyrk1a +/− mouse) presents neuronal deficits in specific regions of the adult brain, including the substantia nigra (SN), although the mechanisms underlying these pathogenic effects remain unclear. Here we study the effect of DYRK1A copy number variation on dopaminergic cell homeostasis. We show that mesencephalic DA (mDA) neurons are generated in the embryo at normal rates in the Dyrk1a haploinsufficient model and in a model (the mBACtg Dyrk1a mouse) that carries three copies of Dyrk1a. We also show that the number of mDA cells diminishes in postnatal Dyrk1a +/− mice and increases in mBACtg Dyrk1a mice due to an abnormal activity of the mitochondrial caspase9 (Casp9)-dependent apoptotic pathway during the main wave of PCD that affects these neurons. In addition, we show that the cell death induced by 1-methyl-4-phenyl-1,2,3,6 tetrahydropyridine (MPTP), a toxin that activates Casp9-dependent apoptosis in mDA neurons, is attenuated in adult mBACtg Dyrk1a mice, leading to an increased survival of SN DA neurons 21 days after MPTP intoxication. Finally, we present data indicating that Dyrk1a phosphorylation of Casp9 at the Thr125 residue is the mechanism by which this kinase hinders both physiological and pathological PCD in mDA neurons. These data provide new insight into the mechanisms that control cell death in brain DA neurons and they show that deregulation of developmental apoptosis may contribute to the phenotype of patients with imbalanced DYRK1A gene dosage

Data mining in collections: from epidemiology to demography

Random collection surveys can be a rich source of data on the material state of a collection. However, random surveys do not necessarily provide data on the causes of degradation of collection items, which is useful in terms of resource allocation. For this, the reliability theory provides us with the required concepts. Using appropriate survey methods and statistical methods of data analysis, the so obtained observational ‘epidemiology’ data has revealed risk factors that can lead to such degradation. We identified patterns in the observed data that corroborated experimental research findings and enabled us to carry out ‘demographic’ modelling of the dynamics of future change in the surveyed collection for the case study of the Amsterdam City Archives. The study shows how, using appropriate methods of collection surveying, empirical and modelling studies of real collections can be successfully integrated, leading to useful evidence supporting collection care decision making

Diagrams of equal area coverage: a new method to assess dust deposition in indoor heritage environments

Particulate matter can cause a loss of value of in indoor heritage, and for this reason it is frequently monitored. The process of deposition is well-described by theoretical models that relate deposition rates with environmental variables. However, we find that the inputs and outputs of models are not directly relevant to preventive conservation. While heritage managers are concerned about area coverage by particulates, the existing models use deposition velocities as the main variable. We propose an improved graphical representation of predictions of deposition, that takes inputs that can be modified as part of preventive conservation plans (concentration and air movement) and an output that can be related to risk assessment and cleaning schedules (time to visible area coverage). By comparing the predictions with experimental data, we show that this approach is useful for small particles of outdoor origin. We also find that further research is needed to make numerical predictions relevant for cases where deposition involves coarse dust and is caused by visitor movement

Sampling and distribution pattern of Trioza erytreae Del Guercio, 1918 (Hemiptera: Triozidae) in citrus orchard

Developing efficient sampling protocols is essential to monitor crop pests. One vector of the citrus disease HLB, the African citrus psyllid Trioza erytreae Del Guercio, 1918 (Hemiptera: Triozidae), currently threatens the lemon industry throughout the Mediterranean region. In this work, a pool of sampling methods devoted to monitoring the population of T. erytreae was compared, its spatial distribution in the orchard was assessed, and the minimum sampling effort for the best sampling method was estimated. Three lemon orchards in North-western Portugal were sampled for one year using two types of yellow sticky traps (standard yellow and fluorescent Saturn yellow), B-vac sampling and sweep net sampling. The method that best performed, in terms of cost-efficiency, was the yellow sticky traps. The two colours of the sticky traps tested did not yield a significantly different number of catches. The spatial distribution throughout the orchards was found to be aggregated towards the borders. A minimum of three sticky traps per hectare was found to be enough to estimate the population at 90% accuracy for the mean during the outbreak. These results should help to monitor and anticipate outbreaks that may even colonize neighbour orchards. Studies on the local dispersion patterns of T. erytreae throughout the orchard are mandatory to further refine and optimize efficient monitoring protocols.The authors are grateful to the Foundation for Science and Technology (FCT, Portugal), for financial support through national funds FCT/MCTES to CIMO (UIDB/00690/2020) and to the project PRE-HLB-Preventing HLB epidemics for ensuring citrus survival in Europe (H2020-SFS-2018-2 Topic SFS-05-2018-2019-2020, proj. No. 817526).info:eu-repo/semantics/publishedVersio

An effector from the Huanglongbing-associated pathogen targets citrus proteases

The citrus industry is facing an unprecedented challenge from Huanglongbing (HLB). All cultivars can be affected by the HLB-associated bacterium ‘Candidatus Liberibacter asiaticus’ (CLas) and there is no known resistance. Insight into HLB pathogenesis is urgently needed in order to develop effective management strategies. Here, we use Sec-delivered effector 1 (SDE1), which is conserved in all CLas isolates, as a molecular probe to understand CLas virulence. We show that SDE1 directly interacts with citrus papain-like cysteine proteases (PLCPs) and inhibits protease activity. PLCPs are defense-inducible and exhibit increased protein accumulation in CLas-infected trees, suggesting a role in citrus defense responses. We analyzed PLCP activity in field samples, revealing specific members that increase in abundance but remain unchanged in activity during infection. SDE1-expressing transgenic citrus also exhibit reduced PLCP activity. These data demonstrate that SDE1 inhibits citrus PLCPs, which are immune-related proteases that enhance defense responses in plants