Predicting suitable environments and potential occurrences for coelacanths (Latimeria spp.)

This is the author's accepted manuscript. The original publication is available at www.springerlink.com.Extant coelacanths (Latimeria chalumnae) were first discovered in the western Indian Ocean in 1938; in 1998, a second species of coelacanth, Latimeria menadoensis, was discovered off the north coast of Sulawesi, Indonesia, expanding the known distribution of the genus across the Indian Ocean Basin. This study uses ecological niche modeling techniques to estimate dimensions of realized niches of coelacanths and generate hypotheses for additional sites where they might be found. Coelacanth occurrence information was integrated with environmental and oceanographic data using the Genetic Algorithm for Rule-set Production (GARP) and a maximum entropy algorithm (Maxent). Resulting models were visualized as maps of relative suitability of sites for coelacanths throughout the Indian Ocean, as well as scatterplots of ecological variables. Our findings suggest that the range of coelacanths could extend beyond their presently known distribution and suggests alternative mechanisms for currently observed distributions. Further investigation into these hypotheses could aid in forming a more complete picture of the distributions and populations of members of genus Latimeria, which in turn could aid in developing conservation strategies, particularly in the case of L. menadoensis

Developing a Prototype for a Microcontroller-Based Coin-Counting Machine

Coins have become a significant part of today\u27s economy and are continuously being distributed, along with banknotes, for daily transactions in the most conventional methods. The modernized circulating currency method relies heavily on coin sorting and counting machines to prevent inconsistencies when handling and calculating coins. While the innovation reduces the need for human resources and revolutionizes the way establishments work with large sums of coins, accuracy in differentiating coins becomes an issue in some existing designs. The prototype uses light occlusion and measures the energy of the coin impact to identify the denomination. The prototype shows promise in being able to identify four Philippine coin denominations

Lck is a relevant target in chronic lymphocytic leukaemia cells whose expression variance is unrelated to disease outcome.

Pathogenesis of chronic lymphocytic leukaemia (CLL) is contingent upon antigen receptor (BCR) expressed by malignant cells of this disease. Studies on somatic hypermutation of the antigen binding region, receptor expression levels and signal capacity have all linked BCR on CLL cells to disease prognosis. Our previous work showed that the src-family kinase Lck is a targetable mediator of BCR signalling in CLL cells, and that variance in Lck expression associated with ability of BCR to induce signal upon engagement. This latter finding makes Lck similar to ZAP70, another T-cell kinase whose aberrant expression in CLL cells also associates with BCR signalling capacity, but also different because ZAP70 is not easily pharmacologically targetable. Here we describe a robust method of measuring Lck expression in CLL cells using flow cytometry. However, unlike ZAP70 whose expression in CLL cells predicts prognosis, we find Lck expression and disease outcome in CLL are unrelated despite observations that its inhibition produces effects that biologically resemble the egress phenotype taken on by CLL cells treated with idelalisib. Taken together, our findings provide insight into the pathobiology of CLL to suggest a more complex relationship between expression of molecules within the BCR signalling pathway and disease outcome

Biotic and abiotic factors influencing forage fish and pelagic nekton community in the Columbia River plume (USA) throughout the upwelling season 1999–2009

Large river plumes modify coastal environments and can impact production across multiple trophic levels. From 1999 to 2009, the assemblages of forage fish, predator fish, and other pelagic nekton were monitored in coastal waters associated with the Columbia River plume. Surveys were conducted at night to target vertically migrating species, and community structure evaluated to better understand ecological interactions. Distinct inshore and offshore communities were identified during spring and summer that were correlated with ocean temperature, salinity, plume volume, and upwelling intensity. Resident euryhaline forage fish species, such as smelts, anchovy, herring, market squid, juvenile salmon, and spiny dogfish, showed a high affinity for inshore habitat and the lower salinity plume during spring. Highly migratory species, such as sardine, piscivorous hake, sharks, and mackerels, were associated with warmer, saltier waters offshore, during strong upwelling periods in summer. Overall, our study of pelagic nekton revealed that temporal dynamics in abundance and community composition were associated with seasonal abiotic phenomenon, but not interannual, large-scale oceanographic processes. Forage fish assemblages differed seasonally and spatially from the assemblages of major piscivorous predators. This finding suggests a potential role of the plume as refuge for forage fish from predation by piscivorous fish in the northern California Current.Keywords: Predator fish, Columbia River plume, California current, Community analysis, Forage fishKeywords: Predator fish, Columbia River plume, California current, Community analysis, Forage fis

Participative decision making and the sharing of benefits: laws, ethics, and data protection for building extended global communities

Transdisciplinary and cross-cultural cooperation and collaboration are needed to build extended, densely interconnected information resources. These are the prerequisites for the successful implementation and execution of, for example, an ambitious monitoring framework accompanying the post-2020 Global Biodiversity Framework (GBF) of the Convention on Biological Diversity (CBD; SCBD 2021). Data infrastructures that meet the requirements and preferences of concerned communities can focus and attract community involvement, thereby promoting participatory decision making and the sharing of benefits. Community acceptance, in turn, drives the development of the data resources and data use. Earlier this year, the alliance for biodiversity knowledge (2021a) conducted forum-based consultations seeking community input on designing the next generation of digital specimen representations and consequently enhanced infrastructures. The multitudes of connections that arise from extending the digital specimen representations through linkages in all “directions” will form a powerful network of information for research and application. Yet, with the power of an extended, accessible data network comes the responsibility to protect sensitive information (e.g., the locations of threatened populations, culturally context-sensitive traditional knowledge, or businesses’ fundamental data and infrastructure assets). In addition, existing legislation regulates access and the fair and equitable sharing of benefits. Current negotiations on ‘Digital Sequence Information’ under the CBD suggest such obligations might increase and become more complex in the context of extensible information networks. For example, in the case of data and resources funded by taxpayers in the EU, such access should follow the general principle of being “as open as possible; as closed as is legally necessary” (cp. EC 2016). At the same time, the international regulations of the CBD Nagoya Protocol (SCBD 2011) need to be taken into account. Summarizing main outcomes from the consultation discussions in the forum thread “Meeting legal/regulatory, ethical and sensitive data obligations” (alliance for biodiversity knowledge 2021b), we propose a framework of ten guidelines and functionalities to achieve community building and drive application: Substantially contribute to the conservation and protection of biodiversity (cp. EC 2020). Use language that is CBD conformant. Show the importance of the digital and extensible specimen infrastructure for the continuing design and implementation of the post-2020 GBF, as well as the mobilisation and aggregation of data for its monitoring elements and indicators. Strive to openly publish as much data and metadata as possible online. Establish a powerful and well-thought-out layer of user and data access management, ensuring security of ‘sensitive data’. Encrypt data and metadata where necessary at the level of an individual specimen or digital object; provide access via digital cryptographic keys. Link obligations, rights and cultural information regarding use to the digital key (e.g. CARE principles (Carroll et al. 2020), Local Context-labels (Local Contexts 2021), licenses, permits, use and loan agreements, etc.). Implement a transactional system that records every transaction. Amplify workforce capacity across the digital realm, its work areas and workflows. Do no harm (EC 2020): Reduce the social and ecological footprint of the implementation, aiming for a long-term sustainable infrastructure across its life-cycle, including development, implementation and management stages. Balancing the needs for open access, as well as protection, accountability and sustainability, the framework is designed to function as a robust interface between the (research) infrastructure implementing the extensible network of digital specimen representations, and the myriad of applications and operations in the real world. With the legal, ethical and data protection layers of the framework in place, the infrastructure will provide legal clarity and security for data providers and users, specifically in the context of access and benefit sharing under the CBD and its Nagoya Protocol. Forming layers of protection, the characteristics and functionalities of the framework are envisioned to be flexible and finely-grained, adjustable to fulfill the needs and preferences of a wide range of stakeholders and communities, while remaining focused on the protection and rights of the natural world. Respecting different value systems and national policies, the framework is expected to allow a divergence of views to coexist and balance differing interests. Thus, the infrastructure of the digital extensible specimen network is fair and equitable to many providers and users. This foundation has the capacity and potential to bring together the diverse global communities using, managing and protecting biodiversity

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

In situ multi-frequency measurements of magnetic susceptibility as an indicator of planetary regolith maturity

Space weathering is now generally accepted to modify the optical and magnetic properties of airless planetary regoliths such as those on the Moon and Mercury. Under micrometeorite and ion bombardment, ferrous iron in such surfaces is reduced to metallic iron spheres, found in amorphous coatings on almost all exposed regolith grains. The size and number distribution of these particles and their location in the regolith all determine the nature and extent of the optical and magnetic changes. These parameters in turn reflect the formation mechanisms, temperatures, and durations involved in the evolution of the regolith. Studying them in situ is of intrinsic value to understanding the weathering process, and useful for determining the maturity of the regolith and providing supporting data for interpreting remotely sensed mineralogy. Fine-grained metallic iron has a number of properties that make it amenable to magnetic techniques, of which magnetic susceptibility is the simplest and most robust. The magnetic properties of the lunar regolith and laboratory regolith analogues are therefore reviewed and the theoretical basis for the frequency dependence of magnetic susceptibility presented. Proposed here is then an instrument concept using multi-frequency measurements of magnetic susceptibility to confirm the presence of fine grained magnetic material and attempt to infer its quantity and size distribution. Such an instrument would be invaluable on a future mission to an asteroid, the Moon, Mercury or other airless rocky Solar System body

Tissue sampling methods and standards for vertebrate genomics

The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 μg of DNA); and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota

Hormonal Risk Factors for Ovarian Cancer in Premenopausal and Postmenopausal Women

Ovarian cancer is most frequently diagnosed in postmenopausal women; however, the strongest risk predictors, pregnancy and oral contraceptive use, occur in most women in their twenties and thirties. Relatively few studies have examined how reproductive risk factors vary between pre- and postmenopausal ovarian cancer. The authors used data from a population-based, case-control study of ovarian cancer (896 cases, 967 controls) conducted in North Carolina from 1999 to 2006. Odds ratios and 95% confidence intervals were calculated by using unconditional logistic regression. Inverse associations with ovarian cancer were observed with duration of oral contraceptive use, later age at last use, and more recent use among premenopausal women; no significant associations were found for postmenopausal women. Analyses limited to oral contraceptive users showed that duration was a more significant predictor of risk than was timing of use. Parity was inversely associated with premenopausal but not postmenopausal ovarian cancer. Later age at pregnancy was associated with reduced risk for both pre- and postmenopausal women. Analyses among parous women showed that pregnancy timing was a stronger risk predictor than number of pregnancies. Findings suggest that associations between ovarian cancer and reproductive characteristics vary by menopausal status. Additional research is needed to further elucidate risk factors for postmenopausal disease

Preparation of amino-substituted indenes and 1,4-dihydronaphthalenes using a one-pot multireaction approach: total synthesis of oxybenzo[c]phenanthridine alkaloids

Allylic trichloroacetimidates bearing a 2-vinyl or 2-allylaryl group have been designed as substrates for a one-pot, two-step multi-bond-forming process leading to the general preparation of aminoindenes and amino-substituted 1,4-dihydronaphthalenes. The synthetic utility of the privileged structures formed from this one-pot process was demonstrated with the total synthesis of four oxybenzo[c]phenanthridine alkaloids, oxychelerythrine, oxysanguinarine, oxynitidine, and oxyavicine. An intramolecular biaryl Heck coupling reaction, catalyzed using the Hermann–Beller palladacycle was used to effect the key step during the synthesis of the natural products