Provenance Record Research Articles

Spatial distributions of strontium isotope ratios in human hair and tap water from South Korea

Natural variations of 87Sr/86Sr ratios in biological samples, such as human hair, provide a biological record of provenance. Spatial distribution maps reflecting heterogeneity in isotopic signatures across large geographical regions are helpful for discerning the provenance and mobility of organisms. In this national-scale study conducted across South Korea, we investigated the spatial distribution patterns of 87Sr/86Sr ratios in human hair and tap water samples to determine their spatial variabilities and the relationships of isotopic signatures between hair and tap water. The strontium isoscapes of tap water and hair showed similar spatial distribution patterns. Non-parametric comparison indicated no significant differences in isotopic ratios between the two sample types. The 87Sr/86Sr ratios in human hair showed a significant and strong correlation with the ratios in tap water in eastern Korea, suggesting potential use of 87Sr/86Sr ratios in provenance studies. However, tap water and hair samples from western Korea did not show significant correlation between them, overall reducing the predictive power of the hair 87Sr/86Sr ratios for provenance studies. The deviation between 87Sr/86Srtap water and 87Sr/86Srhair was much larger in western coastal areas than in eastern Korea. Relatively high utilization of groundwater or exogenous materials, such as Asian dust, may have been responsible for this pattern. To fully utilize the potential of the strontium isotope signature as a biorecorder in provenance studies, it is essential to evaluate the effects of groundwater and other exogenous materials on the isotope signatures of hair and other biological samples. In this study, only hair samples from males were used to develop 87Sr/86Sr isoscapes. Therefore, further studies are required to examine the applicability of 87Sr/86Sr hair isoscapes based solely on human hair samples from males to forensic and provenance studies of human hair samples from females.

Tectonic Growth of the Late Paleozoic‐Middle Mesozoic Northwestern Margin of Laurentia and Implications for the Farewell Terrane: Stratigraphic, Structural, and Provenance Records From the Central Alaska Range

AbstractAnalysis of upper Paleozoic‐Jurassic strata in the central Alaska Range provides new insights into the following: the configuration of Late Triassic‐Jurassic depocenters along the northwestern Laurentian margin, the late Paleozoic paleogeographic position of the Farewell terrane, and the timing of accretion of the Farewell terrane to the Laurentian margin. Results from geologic mapping, stratigraphic analysis, and U‐Pb detrital zircon geochronology document two juxtaposed Paleozoic‐Jurassic stratigraphic assemblages. The Southern package consists of Permian‐Middle Triassic submarine fan strata and Upper Triassic pillow basalts that can be correlated with the Farewell terrane of the western Alaska Range. This package yields Ordovician‐Silurian and Late Pennsylvanian‐Early Permian detrital zircons linked to the Alexander and Wrangellia terranes. This detrital connection suggests that the Farewell terrane most likely collided with the Insular terranes in the paleo‐Pacific basin during the late Paleozoic. The Northern package, in contrast, consists of Upper Triassic‐Jurassic submarine fan strata deposited along the northwestern margin of Laurentia. An abundance of Neoproterozoic and early Paleozoic detrital zircons suggests recycling of Caledonian and Baltican zircons from the Ellesmerian clastic wedge of northwestern Canada. An influx of Late Triassic‐Early Jurassic detrital zircons in Upper Jurassic strata of the Northern package records the development of Mesozoic arc magmatism along the continental margin. Our findings document deformation consistent with latest Jurassic‐earliest Cretaceous accretion of the Farewell terrane to the Laurentian margin. Our results also suggest that the Farewell terrane may underlie much of the central Alaska Range, and played an important role in the construction of the northern Cordillera.

Syn‐Subduction Strike‐Slip Faults Shape an Accretionary Orogen and its Provenance Signatures: Insights From Sikhote‐Alin in NE Asia During the Late Jurassic to Early Cretaceous

AbstractSedimentary rocks provide key information on source‐to‐sink systems and the regional expression of plate tectonics. The abruptly changing provenance signature of sedimentary rocks is commonly ascribed to changes in the source regions, such as continental collision events, the rise of mountain chains, reorganization of river systems and climatic change. However, moving the positions of the sinks (depocenters) geographically can also change the provenance record, but this is rarely considered. Typically, large‐scale strike‐slip faults can transport depocenters for long distances, thus altering the provenance information. In this study, we present a systematic investigation of the provenance changes in the Sikhote‐Alin orogenic belt in the Russian Far East to evaluate this process. The Central Sikhote‐Alin Fault is a margin‐parallel strike‐slip fault that developed along the NE Asian continental margin from the late Mesozoic. Our new detrital zircon U‐Pb data, together with a compilation of geochronological data, indicate two different types of provenance signatures available: the sediments to the west of the fault were mainly derived from the adjacent Central Asian Orogenic Belt, but to the east of the fault, they were mainly supplied from the Korean Peninsula, which is several hundred kilometers away. It is proposed that these different sedimentary rocks were juxtaposed by syn‐ and post‐subduction sinistral displacements along the fault, and were not related to local variations in the source regions. Thus, understanding the shifting positions of depocenters is important when decoding provenance change because lateral displacement is critical for reconstructing regional paleogeography along oblique convergent plate margins.

Changes in sedimentary provenance and climate off the coast of Northeast Brazil since the Last Interglacial

Neodymium (Nd) and strontium (Sr) isotopic signatures in marine sediments reflect the geology of the associated drainage basin from which those sediments are supplied. These signatures are significantly affected by relief, weathering, transport, and deposition of sedimentary contributions from the respective sources. This work makes available new data of SrNd isotope ratios and Rare Earth Element (REE) concentrations, which provides a record of the sedimentary provenance of marine sediment supplied to the continental slope off the coast of northeastern Brazil since the last 130 thousand years. Our results indicate the main source of sediments to this site was the Parnaíba sedimentary basin. Furthermore, the fluctuations in Fe/K, Al/Si ratios, and Sr values are explained by geochemical processes operating within the region, which likely reflects changes in the hydrological regime and relative sea-level, and intensity of weathering in continental rocks in glacial-interglacial timescales. We suggest that low values of 87Sr/86Sr ratios during glacial are a result of dry conditions. Also, minor fluctuations within the last glacial period may be a consequence of displacements of the Intertropical Convergence Zone (ITCZ). Such displacements cause changes in rainfall and consequently variations in chemical weathering which affect Sr isotopic fractionation. During past humid intervals, the low Nd (non-radiogenic) signal observed could be explained as a process of penetration of rainwater into the deepest non-radiogenic sediment and subsequent replacement of the isotopic signal in the environment in glacial-interglacial timescales.

Partitioning maternal and exogenous diet contributions to otolith 87Sr/86Sr in kokanee salmon (Oncorhynchus nerka)

Strontium isotopes (87Sr/86Sr) recorded in the otoliths of Pacific salmon (Oncorhynchus spp.) are commonly used to identify natal origin. For species that migrate at or soon after emergence, the embryonic region of the otolith provides the only record of provenance. However, maternal contribution of Sr from the yolk can confound the isotopic signature of the natal site. We experimentally quantified maternal and exogenous diet contributions to otolith 87Sr/86Sr over embryonic development in kokanee salmon (Oncorhynchus nerka). Eggs from two populations in isotopically distinct lakes were incubated and reared in a common water source. Timing of developmental events and proportional contribution from yolk to otolith 87Sr/86Sr differed significantly between the two populations. We suggest that the magnitude of difference in 87Sr/86Sr between yolk and water, the relative concentrations of Sr and Ca in these isotopic sources, and population-specific effects on otolith growth and composition contribute to this variation. Understanding how these factors affect otolith 87Sr/86Sr could extend the use of otolith geochemistry for determining provenance to species and populations in which natal site rearing is limited.

Cenozoic to modern-day source to sink systems of Senegal: A record of provenance, transport, recycling and climate controls

This study presents an integrated mineralogical assessment for the provenance of sediments derived from modern-day rivers and Cenozoic deposits in Senegal and Gambia. Two distinct populations are identified from discrimination of the heavy mineral assemblages; the Senegal River sediment, sourced from the West African Craton and Mauritanides and Meso-Cenozoic sediment sourced from the onshore Senegal Basin, demonstrating prevalent recycling of Senegal Basin sediments by the Ferlo, Saloum, Gambia and Casamance Rivers throughout the Quaternary.The Senegal River records the occurrence of amphibole, epidote, garnet and pyroxene, which indicates denudation of Neo to Paleo-Proterozoic granites, low-medium grade meta-sediments and a skarn-type lithology. Meso-Cenozoic recycled sediments within the onshore Senegal Basin exhibit a heavy mineral component which has been modified through the chemical-weathering and diagenesis of less-stable amphibole, pyroxene and garnet. U/Pb dating of zircons from the Casamance and Gambia provinces indicates that, at least in part, the Mesozoic sediments of the onshore Senegal basin may have been ultimately derived from the Leo-Man Shield.Kaolin occurrence is associated with tropical weathering of laterites. The occurrence of terrigenous-smectite sourced from high altitude regions of the Mauritanides and West African Craton is interpreted to have formed under hyper-arid conditions prior to erosion and transportation, during the African humid periods of the Holocene.This integrated mineralogical study of modern-day and Cenozoic sediments has established prevalent recycling of Senegal Basin-sediments by the Ferlo, Saloum, Gambia and Casamance Rivers and continued erosion and recycling of hinterland-sediments via the modern-day Senegal River. This identification of two distinct provenance groups and the strong climatic signal provides the important framework for future studies assessing the source to sink systems during the Meso-Cenozoic.

Addressing Regulatory Requirements on Explanations for Automated Decisions with Provenance—A Case Study

AI-based automated decisions are increasingly used as part of new services being deployed to the general public. This approach to building services presents significant potential benefits, such as the reduced speed of execution, increased accuracy, lower cost, and ability to adapt to a wide variety of situations. However, equally significant concerns have been raised and are now well documented such as concerns about privacy, fairness, bias, and ethics. On the consumer side, more often than not, the users of those services are provided with no or inadequate explanations for decisions that may impact their lives. In this article, we report the experience of developing a socio-technical approach to constructing explanations for such decisions from their audit trails, or provenance, in an automated manner. The work has been carried out in collaboration with the UK Information Commissioner’s Office. In particular, we have implemented an automated Loan Decision scenario, instrumented its decision pipeline to record provenance, categorized relevant explanations according to their audience and their regulatory purposes, built an explanation-generation prototype, and deployed the whole system in an online demonstrator.

New Record of Dust Input and Provenance During Glacial Periods in Western Australia Shelf (IODP Expedition 356, Site U1461) from the Middle to Late Pleistocene

International Ocean Discovery Program (IODP) Expedition 356 Site U1461 represents one of the few records from the North West Australian shelf that provides information about aridity fluctuations in Australia during the Quaternary. A combination of chronostratigraphic indicators revealed the (partial) preservation of two major glaciations (Marine Isotope Stage (MIS) 2 and MIS 12) in the sedimentary record. The faunal content (mainly benthic foraminifera, corals and bryozoans) was analyzed to estimate paleo-environments and paleo-depths in order to determine if these sediments have been remobilized by reworking processes. Despite the occurrence of a depositional hiatus (including MIS 5d to MIS 9-time interval), the excellent preservation of faunal content suggests that the preserved sediment is in situ. The geochemical composition of the sediments (Nd and major elements) indicates that during MIS 12 riverine input was likely reduced because of enhanced aridity, and the sediment provenance (mainly atmospheric dust) is likely in the central (Lake Eyre) or eastern (Murray Darling Basin) parts of the Australian continent. MIS 2 is confirmed to be one of the driest periods recorded in Australia but with mixed dust sources from the eastern and western parts of the continent. More humid conditions followed the glacial maximum, which might correspond to the peak of the Indian-Australian Summer Monsoon.

Scratching the Surface: A Marine Sediment Provenance Record From the Continental Slope of Central Wilkes Land, East Antarctica

AbstractThe geology of Wilkes Land, East Antarctica, is masked by kilometers of ice and remains largely unexplored. Defining the sediment provenance adjacent to this hidden region is important for distinguishing the proximal subglacial basement terranes and refining the dynamic regional glaciological history. This study presents a detrital sediment provenance record spanning c. 23.5 ka from the continental slope of central Wilkes Land. Sediment provenance was characterized using U‐Pb geochronology and trace element geochemistry from detrital zircon, titanite and apatite, and Pb isotopic signatures from detrital feldspar. These data were compared with new feldspar Pb‐isotopic signatures and existing U‐Pb zircon data sets from rare nearby coastal outcrop. A principally igneous source was revealed with dominant age populations between c. 1,360‐1,100 Ma and c. 1,620‐1,490 Ma, characteristic of rocks of the proximal Wilkes and Banzare provinces, respectively. Minor detritus was additionally sourced from the proximal Nuyina Province (c. 1,450‐1,390 Ma). Temporal variation in the climate and ice sheet configuration are likely responsible for subtle downcore changes observed in detrital sediment provenance. High sedimentation rates during the glacial period suggest reworking of continental shelf sediments and downslope transport in debris flows during ice sheet advance. Glacial meltwater fluxes fed largely by the Totten Glacier were responsible for supplying detritus during deglaciation. During interglacials, detritus was derived from a broad coastal region and delivered to the slope via multiple glacial outlets. These results present the first substantial offshore evidence to support recent interpretations that the subglacial crust of central Wilkes Land has a dominantly Mesoproterozoic history.

Pagoda: A Hybrid Approach to Enable Efficient Real-Time Provenance Based Intrusion Detection in Big Data Environments

Efficient intrusion detection and analysis of the security landscape in big data environments present challenge for today's users. Intrusion behavior can be described by provenance graphs that record the dependency relationships between intrusion processes and the infected files. Existing intrusion detection methods typically analyze and identify the anomaly either in a single provenance path or the whole provenance graph, neither of which can achieve the benefit on both detection accuracy and detection time. We propose Pagoda, a hybrid approach that takes into account the anomaly degree of both a single provenance path and the whole provenance graph. It can identify intrusion quickly if a serious compromise has been found on one path, and can further improve the detection rate by considering the behavior representation in the whole provenance graph. Pagoda uses a persistent memory database to store provenance and aggregates multiple similar items into one provenance record to maximumly reduce unnecessary I/O during the detection analysis. In addition, it encodes duplicate items in the rule database and filters noise that does not contain intrusion information. The experimental results on a wide variety of real-world applications demonstrate its performance and efficiency.

The clastic record of a Wilson Cycle: Evidence from detrital apatite petrochronology of the Grampian-Taconic fore-arc

Detrital apatite deposited before, during and after Grampian-Taconic arc accretion in western Ireland reveals dramatic changes in source provenance and provides a detailed detrital petrochronological record of a Wilson Cycle sited on the Laurentian margin. These determinations are made possible by recent improvements in source rock type diagnosis by apatite trace element analysis. In addition, by interrogating the proportion of apatite derived from peraluminous vs metaluminous melt and felsic vs mafic melt in detritus, temporal changes can be seen in the relative proportions of these magma compositions over time. We present combined trace element and U-Pb age data for detrital apatite in clastic formations from the South Mayo Trough, a uniquely well-preserved fore-arc basin accreted to the Laurentian margin during the Grampian-Taconic orogeny (∼ 475 – 460 Ma), which records the early phase of closing of the Iapetus Ocean. Apatite deposited before collision is derived from the Laurentian margin and mafic igneous rocks of the Central Iapetus Magmatic Province associated with the Neoproterozoic break-up of Rodinia / Pannotia leading to the birth of the Iapteus Ocean. Following the onset of ocean closure in the Cambrian, igneous apatite derived from the nascent Grampian-Taconic arc is detected. Apatite derived from felsic and peraluminous melts becomes progressively more dominant over apatite from more mafic and metaluminous sources as the arc evolves from an intra-oceanic to continental arc setting after collision. The subsequent Grampian-Taconic unroofing history recorded by detrital apatite records the transition from ancient Laurentian margin- and intra-oceanic arc-derived detritus, to the exhumation of the high-grade metamorphic core of the Grampian-Taconic orogen and the exposure of post-collisional continental-arc granitoids. Our results are in broad agreement with both the Grampian fore-arc provenance record (heavy mineral analysis, detrital zircon U-Pb and white mica Ar-Ar) and the Laurentian crustal reworking record derived from the geochemistry of volcaniclastic units in the South Mayo Trough. However, we also obtain novel provenance information undetected by detrital zircon in the South Mayo Trough, such as apatite derived from the Central Iapetus Magmatic Province. Critically this information is obtained from a single mineral system, which eliminates the need to consider differing mineral stabilities during weathering, transport and diagenesis. The high preservation potential for apatite in similar tectonic environments illustrates the potential to employ detrital apatite as a record of Earth's lithological composition in deep time.

Provenance Record of Late Mesoproterozoic to Early Neoproterozoic Units, West Hainan, South China, and Implications for Rodinia Reconstruction

AbstractUnraveling the character and source of late Mesoproterozoic‐early Neoproterozoic sedimentary sequences is crucial in constraining Rodinia reconstructions. We carried out an integrated geochemical, zircon U‐Pb geochronological and Lu‐Hf isotopic study of the Shilu Group and the overlying Shihuiding Formation in Hainan, South China. These two successions are chemically mature and dominated by siliceous components. The Shilu Group was mainly derived from felsic arc lithologies whereas the Shihuiding Formation was from recycled sedimentary materials and records a transition from convergent to passive margin settings during the late Mesoproterozoic‐early Neoproterozoic in Hainan. Detrital zircons from the Shilu Group and Shihuiding Formation yield similar age populations, with maximum depositional ages of ~1,100–1,000 Ma and ~900 Ma, respectively. The Shilu Group matches well with the Kunyang Group outcropped in the Yangtze Block in depositional age, detrital zircon age populations and Lu‐Hf isotopic compositions, and geochemical characteristics, whereas the Shihuiding Formation exhibits significantly different detrital age populations from the Wanquan Group in the Cathaysia Block. This indicates that Hainan was linked to the Yangtze Block rather than the Cathaysia Block in the late Mesoproterozoic‐early Neoproterozoic. The Shilu and Kunyang groups have similar detrital age patterns to the late Mesoproterozoic to early Neoproterozoic strata in northwest India and are distinct from their equivalents in west Laurentia, suggesting an external location of Hainan‐Yangtze in Rodinia.

Deciphering relationships between the Nicobar and Bengal submarine fans, Indian Ocean

The Nicobar Fan and Bengal fans can be considered as the eastern and western parts, respectively, of the largest submarine-fan system in the world. This study presents the integrated results of petrographic and provenance studies from the Nicobar Fan and evaluates these in the context of controls on sedimentation. Both fans were predominantly supplied by Himalaya-derived material from the main tectono-stratigraphic sequences as well as the Gangdese arc. A lack of volcanic material in the Nicobar Fan rules out sources from the Sumatra magmatic arc. Overall, the petrographic data shows a progressive decrease in sedimentary detritus and corresponding increase of higher-grade metamorphic detritus up-section. Changes in sediment provenance and exhumation rates in the Himalaya are seen to track changes in sediment accumulation rates. High sediment accumulation rates in the Bengal Fan occurred at ∼13.5–8.3 Ma, and in the Nicobar Fan from ∼9.5–5 Ma. Both fans show peak accumulation rates at 9.5–8.3 Ma (but with the Nicobar Fan being about twice as high), and both record a sharp drop from ∼5.5–5.2 Ma, that coincided with a change in river drainage associated with the Brahmaputra River diverting west of the uplifting Shillong Plateau. At ∼5 Ma, the Nicobar Fan was supplied by an eastern drainage route that finally closed at ∼2 Ma, when sediment accumulation rates in the Nicobar Fan significantly decreased. Sediment provenance record these changes in routing whereby Bengal Fan deposits include granitoid sources from the Namche Barwa massif in the eastern syntaxis that are not seen in the Nicobar Fan, likely due to a more localised eastern drainage that included material from the Indo-Burman wedge. Prior to ∼3 Ma, source exhumation rates were rapid and constant and the short lag-time rules out significant intermediate storage and mixing. In terms of climate versus tectonic controls, tectonically driven changes in the river network have had most influence on fan sedimentation.

A voice for the voiceless: Improving provenance practice for working-class books

In recent years, libraries have become increasingly aware of the need to present a more diverse representation of society in their collections. While some efforts have been made to improve gender, race and sexuality representation, little attention has been paid to the working classes. The purpose of this research is to encourage a debate about the social class make-up of institutional collections and how fair representation and lack of diversity can be addressed. The research entails three stages: (1) Interviews with the 36 members of Research Libraries UK to investigate current challenges that prevent them from recording provenance information for working-class books; (2) The inclusive and fair cataloguing of the Janet Powney Collection – a working-class prize book collection in Cardiff University’s Special Collections and Archives; and (3) The organisation of impact and engagement events to promote the Janet Powney Collection. The study highlights that, while librarians face many challenges in terms of time, money and resources, as well as differences in guidelines and practices, the correct recording of provenance is essential in recovering the voices of working-class individuals, giving them agency as autonomous writers, and developing new narratives of working-class life and culture that challenge myths perpetuated by those in higher positions of power.

Sediment provenance of pre- and post-collisional Cretaceous–Paleogene strata from the frontal Himalaya of northwest India

Whereas the timing for India–Asia collision remains debated, contrasting collisional models provide testable predictions in terms of sediment source contributions during the accumulation of Paleocene to middle Eocene deposits now exposed in the frontal Himalayan system. Within the Lesser Himalaya and frontal thrust system of northwest India, discontinuous exposures of the Cretaceous Singtali Formation and upper Paleocene–middle Eocene Subathu Formation yield a record of these early collisional stages. To test competing collisional models, we analyze the provenance of these deposits with new detrital zircon U-Pb and Hf isotopic data which can distinguish among Indian plate, Asian plate, Kohistan-Ladahk arc, and various Himalayan sources. Detrital zircon age distributions for the Singtali Formation are dominated by Paleoproterozoic zircons with a distinct Cretaceous age component, whereas age data from the Subathu Formation record (1) a marked increase in the relative abundance of Cambrian–Neoproterozoic grains, (2) a decrease in the proportion of Paleoproterozoic grains, and (3) distinct Permian and Late Cretaceous–Paleocene age components. All Cretaceous grains from the Singtali Formation yielded crustal Hf isotopic signatures, indicating a distinctive pre-collisional source of Cretaceous grains of Indian affinity. Zircon Hf isotopic signatures from <320 Ma grains in the Subathu Formation show a significant lower to middle Eocene increase in source diversity, including juvenile grains most likely originating from the Asian plate and Kohistan-Ladakh arc. This requires inception of India-Asia collision by ∼44–50 Ma—the depositional age of the uppermost Subathu Formation. This major provenance shift is similar to that observed for pre- and post-collisional Tethyan Himalayan strata in the north, which is suggestive of a single contiguous basin linking the Lesser Himalaya by ∼44–50 Ma and contests the notion that the Lesser and Tethyan Himalaya were separated by a “Greater India Basin” during the Eocene. When coupled with the well documented Paleocene–early Eocene provenance record of the Tethyan Himalaya, these new data provide support for a collisional model in which Asian detritus reached the northernmost edge of India by ∼59 Ma with terminal closure of both the Shyok and Indus-Yarlung suture zones by ∼54 Ma.

Subduction Polarity in Ancient Arcs: A Call to Integrate Geology and Geophysics to Decipher the Mesozoic Tectonic History of the Northern Cordillera of North America: REPLY

Subduction Polarity in Ancient Arcs: A Call to Integrate Geology and Geophysics to Decipher the Mesozoic Tectonic History of the Northern Cordillera of North America: REPLY

A Provenance Task Abstraction Framework.

Visual analytics tools integrate provenance recording to externalize analytic processes or user insights. Provenance can be captured on varying levels of detail, and in turn activities can be characterized from different granularities. However, current approaches do not support inferring activities that can only be characterized across multiple levels of provenance. We propose a task abstraction framework that consists of a three stage approach, composed of 1) initializing a provenance task hierarchy, 2) parsing the provenance hierarchy by using an abstraction mapping mechanism, and 3) leveraging the task hierarchy in an analytical tool. Furthermore, we identify implications to accommodate iterative refinement, context, variability, and uncertainty during all stages of the framework. We describe a use case which exemplifies our abstraction framework, demonstrating how context can influence the provenance hierarchy to support analysis. The article concludes with an agenda, raising and discussing challenges that need to be considered for successfully implementing such a framework.

Querying Attributed DL-Lite Ontologies Using Provenance Semirings

Attributed description logic is a recently proposed formalism, targeted for graph-based representation formats, which enriches description logic concepts and roles with finite sets of attribute-value pairs, called annotations. One of the most important uses of annotations is to record provenance information. In this work, we first investigate the complexity of satisfiability and query answering for attributed DL-LiteR ontologies. We then propose a new semantics, based on provenance semirings, for integrating provenance information with query answering. Finally, we establish complexity results for satisfiability and query answering under this semantics.

SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications.

Data consistency is necessary for effective bioinformatic analysis. SeqScrub is a web tool that parses and maintains consistent information about protein and DNA sequences in FASTA file format, checks if records are current, and adds taxonomic information by matching identifiers against entries in authoritative biological sequence databases. SeqScrub provides a powerful, yet simple workflow for managing, enrichingand exchanging data, which is crucial to establish a record of provenance for sequences found from broad and varied searches; for example, using BLAST on continually updated genome sequence sets. Headers standardized using SeqScrub can be parsed by a majority of bioinformatic tools, stay uniformly named between collaboratorsand contain informative labels to aid management of reproducible, scientific data. SeqScrub is available at http://bioinf.scmb.uq.edu.au/seqscrub.

Verified, Shared, Modular, and Provenance Based Research Communication with the Dat Protocol

A scholarly communication system needs to register, distribute, certify, archive, and incentivize knowledge production. The current article-based system technically fulfills these functions, but suboptimally. I propose a module-based communication infrastructure that attempts to take a wider view of these functions and optimize the fulfillment of the five functions of scholarly communication. Scholarly modules are conceptualized as the constituent parts of a research process as determined by a researcher. These can be text, but also code, data, and any other relevant pieces of information that are produced in the research process. The chronology of these modules is registered by iteratively linking to each other, creating a provenance record of parent and child modules (and a network of modules). These scholarly modules are linked to scholarly profiles, creating a network of profiles, and a network of how profiles relate to their constituent modules. All these scholarly modules would be communicated on the new peer-to-peer Web protocol Dat, which provides a decentralized register that is immutable, facilitates greater content integrity than the current system through verification, and is open-by-design. Open-by-design would also allow diversity in the way content is consumed, discovered, and evaluated to arise. This initial proposal needs to be refined and developed further based on the technical developments of the Dat protocol, its implementations, and discussions within the scholarly community to evaluate the qualities claimed here. Nonetheless, a minimal prototype is available today, and this is technically feasible.