DARIAH Beyond Europe

International audienceDARIAH, the digital humanities infrastructure with origins and an organisational home in Europe, is nearing the completion of its implementation phase. The significant investment from the European Commission and member countries has yielded a robust set of technical and social infrastructures, ranging from working groups, various registries, pedagogical materials, and software to support diverse approaches to digital humanities scholarship. While the funding and leadership of DARIAH to date has come from countries in, or contiguous with, Europe, the needs that drive its technical and social development are widely shared within the international digital humanities community beyond Europe. Scholars on every continent would benefit from well-supported technical tools and platforms, directories for facilitating access to information and resources, and support for working groups.The DARIAH Beyond Europe workshop series, organised and financed under the umbrella of the DESIR project (“DARIAH ERIC Sustainability Refined,” 2017–2019, funded by the European Union’s Horizon 2020 Research and Innovation Program), convened three meetings between September 2018 and March 2019 in the United States and Australia. These workshops served as fora for cross-cultural exchange, and introduced many non-European DH scholars to DARIAH; each of the workshops included a significant delegation from various DARIAH bodies, together with a larger number of local presenters and participants. The local contexts for these workshops were significantly different in their embodiment of research infrastructures: on the one hand, in the U.S., a private research university (Stanford) and the de facto national library (the Library of Congress), both in a country with a history of unsuccessful national-scale infrastructure efforts; and in Australia, a system which has invested substantially more in coordinated national research infrastructure in science and technology, but very little on a national scale in the humanities and arts. Europe is in many respects ahead of both host countries in terms of its research infrastructure ecosystem both at the national and pan-European levels.The Stanford workshop had four main topics of focus: corpus management; text and image analysis; geohumanities; and music, theatre, and sound studies. As the first of the workshops, the Stanford group also took the lead in proposing next steps toward exploring actionable “DARIAH beyond Europe” initiatives, including the beginnings of a blog shared among participants from all the workshops, extra-European use of DARIAH’s DH Course Registry, and non-European participation in DARIAH Working Groups.The overall theme of the Library of Congress workshop was “Collections as Data,” building on a number of U.S.-based initiatives exploring how to enhance researcher engagement with digital collections through computationally-driven research. In Washington, D.C., the knowledge exchange sessions focussed on digitised newspapers and text analysis, infrastructural challenges for public humanities, and the use of web-archives in DH research. As at Stanford, interconnecting with DARIAH Working Groups was of core interest to participants, and a new Working Group was proposed to explore global access and use of digitised historical newspapers. A further important outcome was the agreement to explore collaboration between the U.S.-based “Collections as Data” initiatives and the Heritage Data Reuse Charter in Europe. The third and final workshop in the series took place in March 2019 in Australia, hosted by the National Library of Australia in Canberra. Convened by the Australian Academy of the Humanities (AAH), together with the Australian Research Data Commons (ARDC) and DARIAH, this event was co-located with the Academy’s second annual Humanities, Arts and Culture Data Summit. The first day of the event, targeted at research leadership and policy makers, was intended to explore new horizons for data-driven humanities and arts research, digital cultural collections and research infrastructure. The two subsequent days focused on engaging with a wide variety of communities, including (digital) humanities researchers and cultural heritage professionals. Organised around a series of Knowledge Exchange Sessions, combined with research-led lightning talks, the participants spoke in detail about how big ideas can be implemented practically on the ground. This poster reflects on the key outcomes and future directions arising from these three workshops, and considers what it might look like for DARIAH to be adopted as a fundamental DH infrastructure in a complex variety of international, national, and regional contexts, with diverse funding models, resources, needs, and expectations. One major outcome of all workshops was the shared recognition that, in spite of extensive funding, planning, and goodwill, these workshops were not nearly global enough in their reach: most importantly they were not inclusive of the Global South. Our new DARIAH beyond Europe community has a strong shared commitment to address this gap

Comprehensive Identification of Host Modulators of HIV-1 Replication using Multiple Orthologous RNAi Reagents

SummaryRNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, we combined information from the existing HDF screens together with new screens performed with multiple orthologous RNAi reagents (MORR). In addition to being traditionally validated, the MORR screens and the historical HDF screens were quantitatively integrated by the adaptation of an established analysis program, RIGER, for the collective interpretation of each gene’s phenotypic significance. False positives were addressed by the removal of poorly expressed candidates through gene expression filtering, as well as with GESS, which identifies off-target effects. This workflow produced a quantitatively integrated network of genes that modulate HIV-1 replication. We further investigated the roles of GOLGI49, SEC13, and COG in HIV-1 replication. Collectively, the MORR-RIGER method minimized the caveats of RNAi screening and improved our understanding of HIV-1–host cell interactions

Atypical Social Modulation of Imitation in Autism Spectrum Conditions.

Appropriate modulation of imitation according to social context is important for successful social interaction. In the present study we subliminally primed high-functioning adults with ASC and age- and IQ-matched controls with either a pro- or non- social attitude. Following priming, an automatic imitation paradigm was used to acquire an index of imitation. Whereas imitation levels were higher for pro-socially primed relative to non-socially primed control participants, there was no difference between pro- and non- socially primed individuals with ASC. We conclude that high-functioning adults with ASC demonstrate atypical social modulation of imitation. Given the importance of imitation in social interaction we speculate that difficulties with the modulation of imitation may contribute to the social problems characteristic of ASC

Innate immune activation by inhaled lipopolysaccharide, independent of oxidative stress, exacerbates silica-induced pulmonary fibrosis in mice

Acute exacerbations of pulmonary fibrosis are characterized by rapid decrements in lung function. Environmental factors that may contribute to acute exacerbations remain poorly understood. We have previously demonstrated that exposure to inhaled lipopolysaccharide (LPS) induces expression of genes associated with fibrosis. To address whether exposure to LPS could exacerbate fibrosis, we exposed male C57BL/6 mice to crystalline silica, or vehicle, followed 28 days later by LPS or saline inhalation. We observed that mice receiving both silica and LPS had significantly more total inflammatory cells, more whole lung lavage MCP-1, MIP-2, KC and IL-1β, more evidence of oxidative stress and more total lung hydroxyproline than mice receiving either LPS alone, or silica alone. Blocking oxidative stress with N-acetylcysteine attenuated whole lung inflammation but had no effect on total lung hydroxyproline. These observations suggest that exposure to innate immune stimuli, such as LPS in the environment, may exacerbate stable pulmonary fibrosis via mechanisms that are independent of inflammation and oxidative stress. © 2012 Brass et al

Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage

Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1 095 000, 20 bp sequences representing 4371 different signatures were generated from T.parva schizonts. Reproducible signatures were identified within 73% of potentially detectable predicted genes and 83% had signatures in at least one MPSS cycle. A predicted leader peptide was detected on 405 expressed genes. The quantitative range of signatures was 4–52 256 transcripts per million (t.p.m.). Rare transcripts (<50 t.p.m.) were detected from 36% of genes. Sequence signatures approximated a lognormal distribution, as in microarray. Transcripts were widely distributed throughout the genome, although only 47% of 138 telomere-associated open reading frames exhibited signatures. Antisense signatures comprised 13.8% of the total, comparable with Plasmodium. Eighty five predicted genes with antisense signatures lacked a sense signature. Antisense transcripts were independently amplified from schizont cDNA and verified by sequencing. The MPSS transcripts per million for seven genes encoding schizont antigens recognized by bovine CD8 T cells varied 1000-fold. There was concordance between transcription and protein expression for heat shock proteins that were very highly expressed according to MPSS and proteomics. The data suggests a low level of baseline transcription from the majority of protein-coding genes

Scholarship Fundraising Gala Concert (November 4, 2013)

Fanfare pour precede La Péri / Paul Dukas BSU Brass Choir Ballade in g minor, Op. 23, No. 1 / Frédéric Chopin Alex Heinrich, piano Mon cœur s\u27ouvre à ta voix / Charles-Camille Saint-Saëns from Samson and Delilah, Op. 47 Diane Card, alto Arrival of the Queen of Sheba / George Frederic Handel from Solomon BSU Flute Choir Night Bird / Karen Tanaka Chelsea Fisk, Alto Saxophone Dark Eyes (Les yeux noirs) / Trad. Jazz Manouche Project, Vlad Milenkovic, dir. Deh, vieni, non tardar / Wolfgang Amadeus Mozart from “Le Nozze di Figaro” Mary Sanker, soprano Sonata No. 1 / Bohuslav Martinů Allegro Moderato Jennifer Drake, flute Sunburst / Andrew York James Davidson, guitar Salmo 150 / Ernani Aguiar A Lover and his Lass / Matthew Harris from Shakespeare Songs, Book III BSU Chamber Singers, Dr. Steven Young, dir. World Street Jam / trad. Khakatay, Dr. Salil Sachdev, dir. Attitude Dance / Stephen Kupka and Emilio Castillo arr. Mark Taylor BSU Jazz Band, Dr. Donald Running, dirhttps://vc.bridgew.edu/student_concerts/1046/thumbnail.jp

IFITM3 Inhibits Influenza A Virus Infection by Preventing Cytosolic Entry

To replicate, viruses must gain access to the host cell's resources. Interferon (IFN) regulates the actions of a large complement of interferon effector genes (IEGs) that prevent viral replication. The interferon inducible transmembrane protein family members, IFITM1, 2 and 3, are IEGs required for inhibition of influenza A virus, dengue virus, and West Nile virus replication in vitro. Here we report that IFN prevents emergence of viral genomes from the endosomal pathway, and that IFITM3 is both necessary and sufficient for this function. Notably, viral pseudoparticles were inhibited from transferring their contents into the host cell cytosol by IFN, and IFITM3 was required and sufficient for this action. We further demonstrate that IFN expands Rab7 and LAMP1-containing structures, and that IFITM3 overexpression is sufficient for this phenotype. Moreover, IFITM3 partially resides in late endosomal and lysosomal structures, placing it in the path of invading viruses. Collectively our data are consistent with the prediction that viruses that fuse in the late endosomes or lysosomes are vulnerable to IFITM3's actions, while viruses that enter at the cell surface or in the early endosomes may avoid inhibition. Multiple viruses enter host cells through the late endocytic pathway, and many of these invaders are attenuated by IFN. Therefore these findings are likely to have significance for the intrinsic immune system's neutralization of a diverse array of threats

Genetic Variants in Nuclear-Encoded Mitochondrial Genes Influence AIDS Progression

Background: The human mitochondrial genome includes only 13 coding genes while nuclear-encoded genes account for 99% of proteins responsible for mitochondrial morphology, redox regulation, and energetics. Mitochondrial pathogenesis occurs in HIV patients and genetically, mitochondrial DNA haplogroups with presumed functional differences have been associated with differential AIDS progression. Methodology/Principal Findings: Here we explore whether single nucleotide polymorphisms (SNPs) within 904 of the estimated 1,500 genes that specify nuclear-encoded mitochondrial proteins (NEMPs) influence AIDS progression among HIV-1 infected patients. We examined NEMPs for association with the rate of AIDS progression using genotypes generated by an Affymetrix 6.0 genotyping array of 1,455 European American patients from five US AIDS cohorts. Successfully genotyped SNPs gave 50% or better haplotype coverage for 679 of known NEMP genes. With a Bonferroni adjustment for the number of genes and tests examined, multiple SNPs within two NEMP genes showed significant association with AIDS progression: acyl-CoA synthetase medium-chain family member 4 (ACSM4) on chromosome 12 and peroxisomal D3,D2-enoyl- CoA isomerase (PECI) on chromosome 6. Conclusions: Our previous studies on mitochondrial DNA showed that European haplogroups with presumed functional differences were associated with AIDS progression and HAART mediated adverse events. The modest influences of nuclearencoded mitochondrial genes found in the current study add support to the idea that mitochondrial function plays a role in AIDS pathogenesis