| 1. |
- McGillivray, Barbara, et al.
(författare)
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The challenges and prospects of the intersection of humanities and data science: A White Paper from The Alan Turing Institute
- 2020
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Ingår i: White paper.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Since their beginnings, the digital humanities have engaged in an energetic debate about their scope, defining features, and relationship to the wider humanities, and have established themselves as a community of practice (Schreibman et al., 2004; Terras, 2010; Terras, 2013; Terras et al., 2013; Gold and Klein, 2016; The Digital Humanities Manifesto 2.0). The computational focus has characterised the field from its initial explorations (Hockey, 2004; Vanhoutte, 2013; Nyhan and Flinn, 2016) and the shift from the label ‘Humanities Computing’ to ‘Digital Humanities’ was a catalyst for change. In the history of the field, recurring cycles and productive tensions have arisen from the interfolding of computational methodologies and approaches with hermeneutic and critical modes of analysis (see McCarty, 2005; Rockwell and Sinclair, 2016; Jones, 2016). This document postulates that we are currently witnessing another one of these junctures, one that is calling for a critical involvement with data science. In many ways, we are seeing earlier methods blending into, or being extended by data science. Digitisation workflows are being augmented with automatic information extraction, data analysis, automated transcription of handwritten documents, and visualisation of transcribed content. Techniques developed for history, literary studies, and linguistics are being scaled towards larger datasets and more complex problems raising the bar of interpretability and questioning the validity of data collection and analysis methods. On the other hand, the field of data science has recently started to engage with non-STEM (Science, Technology, Engineering, and Mathematics) disciplines, by offering new data-driven modelling frameworks for addressing long-standing research questions (Kitchin, 2014; Lazer et al., 2009) and proposing so-called ‘human-centred approaches’ to data science, focussed on the interpretability of machine learning models and a more active role for human input in algorithms (See Chen et al., 2016). Moreover, in the current historical context we are witnessing an increased awareness of the questions of diversity and inclusion in research and academia, and we are seeing the creation of a strong movement aimed at addressing such issues globally. We believe that this paper can play a role in reinforcing a positive message in this respect.
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| 2. |
- Cabral, Rita A., et al.
(författare)
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Anomalous sulphur isotopes in plume lavas reveal deep mantle storage of Archaean crust
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 496:7446, s. 490-494
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Tidskriftsartikel (refereegranskat)abstract
- Basaltic lavas erupted at some oceanic intraplate hotspot volcanoes are thought to sample ancient subducted crustal materials(1,2). However, the residence time of these subducted materials in the mantle is uncertain and model-dependent(3), and compelling evidence for their return to the surface in regions of mantle upwelling beneath hotspots is lacking. Here we report anomalous sulphur isotope signatures indicating mass-independent fractionation (MIF) in olivine-hosted sulphides from 20-million-year-old ocean island basalts from Mangaia, Cook Islands (Polynesia), which have been suggested to sample recycled oceanic crust(3,4). Terrestrial MIF sulphur isotope signatures (in which the amount of fractionation does not scale in proportion with the difference in the masses of the isotopes) were generated exclusively through atmospheric photochemical reactions until about 2.45 billion years ago(5-7). Therefore, the discovery of MIF sulphur in these young plume lavas suggests that sulphur-probably derived from hydrothermally altered oceanic crust-was subducted into the mantle before 2.45 billion years ago and recycled into the mantle source of Mangaia lavas. These new data provide evidence for ancient materials, with negative Delta S-33 values, in the mantle source for Mangaia lavas. Our data also complement evidence for recycling of the sulphur content of ancient sedimentary materials to the subcontinental lithospheric mantle that has been identified in diamond-hosted sulphide inclusions(8,9). This Archaean age for recycled oceanic crust also provides key constraints on the length of time that subducted crustal material can survive in the mantle, and on the timescales of mantle convection from subduction to upwelling beneath hotspots.
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| 3. |
- Birse, Kenzie D., et al.
(författare)
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Genital Injury Signatures and Microbiome Alterations Associated With Depot Medroxyprogesterone Acetate Usage and Intravaginal Drying Practices
- 2017
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Ingår i: Journal of Infectious Diseases. - : Oxford University Press. - 0022-1899 .- 1537-6613. ; 215:4, s. 590-598
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Tidskriftsartikel (refereegranskat)abstract
- Background. Increasing evidence suggests depot medroxyprogesterone acetate (DMPA) and intravaginal practices may be associated with human immunodeficiency virus (HIV-1) infection risk; however, the mechanisms are not fully understood. This study evaluated the effect of DMPA and intravaginal practices on the genital proteome and microbiome to gain mechanistic insights. Methods. Cervicovaginal secretions from 86 Kenyan women, including self-reported DMPA users (n = 23), nonhormonal contraceptive users (n = 63), and women who practice vaginal drying (n = 46), were analyzed using tandem-mass spectrometry. Results. We identified 473 human and 486 bacterial proteins from 18 different genera. Depot medroxyprogesterone acetate use associated with increased hemoglobin and immune activation (HBD, HBB, IL36G), and decreased epithelial repair proteins (TFF3, F11R). Vaginal drying associated with increased hemoglobin and decreased phagocytosis factors (AZU1, MYH9, PLAUR). Injury signatures were exacerbated in DMPA users who also practiced vaginal drying. More diverse (H index: 0.71 vs 0.45; P =.009) bacterial communities containing Gardnerella vaginalis associated with vaginal drying, whereas DMPA showed no significant association with community composition or diversity. Conclusions. These findings provide new insights into the impact of DMPA and vaginal drying on mucosal barriers. Future investigations are needed to confirm their relationship with HIV risk in women.
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| 4. |
- Häggmark, Anna, 1985-, et al.
(författare)
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A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection
- 2019
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Ingår i: Molecular & Cellular Proteomics. - : AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC. - 1535-9476 .- 1535-9484. ; 18:3, s. 461-476
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Tidskriftsartikel (refereegranskat)abstract
- Women at high risk of HIV infection, including sex workers and those with active genital inflammation, have molecular signatures of immune activation and epithelial barrier remodeling in samples of their genital mucosa. These alterations in the local immunological milieu are likely to impact HIV susceptibility. We here analyze host genital protein signatures in HIV uninfected women, with high frequency of condom use, living in HIV-serodiscordant relationships. Cervicovaginal secretions from women living in HIV-serodiscordant relationships (n = 62) were collected at three time points over 12 months. Women living in HIV-negative seroconcordant relationships (controls, n = 25) were sampled at one time point. All study subjects were examined for demographic parameters associated with susceptibility to HIV infection. The cervicovaginal samples were analyzed using a high-throughput bead-based affinity assay. Proteins involved in epithelial barrier function and inflammation were increased in HIV-serodiscordant women. By combining several methods of analysis, a total of five proteins (CAPG, KLK10, SPRR3, elafin/PI3, CSTB) were consistently associated with this study group. Proteins analyzed using the affinity set-up were further validated by label-free tandem mass spectrometry in a partially overlapping cohort with concordant results. Women living in HIV-serodiscordant relationships thus had elevated levels of proteins involved in epithelial barrier function and inflammation despite low prevalence of sexually transmitted infections and a high frequency of safe sex practices. The identified proteins are important markers to follow during assessment of mucosal HIV susceptibility factors and a high-throughput bead-based affinity set-up could be a suitable method for such evaluation.
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| 5. |
- Lorand, Jean-Pierre, et al.
(författare)
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The sulfur budget and sulfur isotopic composition of Martian regolith breccia NWA 7533
- 2020
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Ingår i: Meteoritics and Planetary Science. - : John Wiley & Sons, Ltd. - 1086-9379 .- 1945-5100. ; 55:9, s. 2097-2116
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Tidskriftsartikel (refereegranskat)abstract
- The sulfur isotope budget of Martian regolith breccia (NWA 7533) has been addressed from conventional fluorination bulk rock analyses and ion microprobe in situ analyses. The bulk rock analyses yield 865 ± 50 ppm S in agreement with LA-ICP-MS analyses. These new data support previous estimates of 80% S loss resulting from terrestrial weathering of NWA 7533 pyrite. Pyrite is by far the major S host. Apatite and Fe oxyhydroxides are negligible S carriers, as are the few tiny igneous pyrrhotite-pentlandite sulfide grains included in lithic clasts so far identified. A small nonzero delta-33S (-0.029 ± 0.010) signal is clearly resolved at the 2σ level in the bulk rock analyses, coupled with negative CDT-normalized δ34S (-2.54 ± 0.10 permil) and near-zero delta-36S (0.002 ± 0.09 permil). In situ analyses also yield negative delta-33S values (-0.05 to -0.30 permil) with only a few positive delta-33S up to +0.38 permil. The slight discrepancy compared to the bulk rock results is attributed to a possible sampling bias. The occurrence of mass-independent fractionation (MIF) supports a model of NWA 7533 pyrite formation from surface sulfur that experienced photochemical reaction(s). The driving force that recycled crustal S in NWA 7533 lithologies - magmatic intrusions or impact-induced heat - is presently unclear. However, in situ analyses also gave negative δ34S values (+1 to -5.8 permil). Such negative values in the hydrothermal setting of NWA 7533 are reflective of hydrothermal sulfides precipitated from H2S/HS- aqueous fluid produced via open-system thermochemical reduction of sulfates at high temperatures (>300 °C).
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