A Model for Integrating the Public into Scientific Research

Science progresses whenever new ways of explaining natural phenomena are revealed. New ideas can only be put to use after the results and significance of research have been brought to the attention of both the scientific and lay communities. The Milwaukee Public Museum Dig-A-Dinosaur Program is a model for scientists who want to conduct research as well as engage and educate the public in their field of study. An array of rewards is derived from including amateurs as members of a research team. Such collaborations strongly increase interest in and comprehension of science as a process. Active participation in scientific investigations promotes one\u27s ability to grasp the logic employed to construct scientific knowledge. Derivative to this, people who experience research enthusiastically share what they learn with diverse audiences. Moreover, the productivity of the scientist can be significantly increased, as exemplified in an extensive paleoecological research project conducted by the authors. In retrospect, the project provided an educational experience for the volunteers that should have been formalized. It would certainly be appropriate to earn college credit based on participation and formalization would validate this learning experience

Late Ordovician and early Silurian virgianid and stricklandioid brachiopods from North Greenland: implications for a warm‐water faunal province

An unusually rich and diverse suite of virgianid brachiopods, hitherto poorly known, is systematically described here for the first time from the Ordovician–Silurian boundary interval (late Katian – Aeronian) of North Greenland. The Late Ordovician virgianids comprise typical taxa of the warm‐water Tcherskidium fauna (e.g. Tcherskidium tenuicostatum, Proconchidium schleyi, Holorhynchus giganteus and Deloprosopus dawesi sp. nov.). Among the early Silurian taxa, Virgiana hursti sp. nov. occurs as abundant shell beds, similar to other congeneric species in Laurentia, but has somewhat larger internal skeletal structures, albeit not as extravagantly developed as in the late Katian virgianids; Borealoides balderi gen. et sp. nov. shows extreme thickening of the shell wall and internal structures, approaching the extravagant calcification of Katian virgianids. The highly distinctive mid‐Aeronian stricklandioid brachiopod genus, Kulumbella, characterized by a shell with criss‐cross (divaricate) ribbing, also occurs in North Greenland, represented by K. heimdali sp. nov., which has the largest and most strongly biconvex shells for the genus. Palaeogeographically, the Late Ordovician virgianid fauna of Laurentia was highly distinct, confined to the low–mid tropical latitudes north of the palaeoequator. In comparison, the early Silurian (Rhuddanian) Virgiana and some related taxa in Laurentia spanned the tropics of both hemispheres, forming extensive shell beds in carbonate basins, although Borealis and Borealoides gen. nov. remained confined largely to the northern hemisphere, suggesting a certain level of provincialism extending into the earliest Silurian. A palaeoecological preference for warm‐water carbonate settings would explain the unusual abundance and richness of the virgianid faunas in North Greenland

Weekly variability of hydrography and transport of northwestern inflows into the northern North Sea

Quantifying the variability of North Sea inflows and understanding the temporal variability of their physical properties are essential for understanding, modelling and managing the ecosystems of the North Sea. The Joint North Sea Information System (JONSIS) line hydrographic section crosses the path of the main inflows of Atlantic water into the northwestern North Sea. We use observations from an autonomous underwater glider to observe the inflows at high spatial and temporal resolutions. The glider completed 10 partial sections of the JONSIS line in October and November of 2013. Key water masses of the inflow are identified; their spatial distribution varies greatly from section to section. This is not apparent from long-running ship surveys of the JONSIS line, which are generally several months apart. In particular, the distribution of water of most recent Atlantic origin varies as summer stratification decays throughout autumn: at the start of the deployment it is present as a thin layer beneath the thermocline; at the end of the deployment, it occupies the full depth of the water column. Thermohaline flow, i.e. that which is driven by horizontal density gradients, is focused into three or four jets (approximately 10 km wide). Jets as narrow as these have not previously been observed in the region. We also observe baroclinic eddies. The thermohaline transport of the inflows is compared with the absolute transport that is derived by referencing geostrophic shear to the glider's dive-average current. Thermohaline transport (approximately 0.2 Sv) is consistently smaller than absolute transport (approximately 0.5 Sv). The week-to-week variability in hydrography and flow structure identified in this study is relevant to on-going efforts to define a background state against which the nature of anthropogenic changes can be assessed, and future modelling efforts should represent the spatial and temporal variability that we have identified

Sources and pathways of glacial meltwater in the Bellingshausen Sea, Antarctica

Meltwater content and pathways determine the impact of Antarctica's melting ice shelves on ocean circulation and climate. Using ocean glider observations, we quantify meltwater distribution and transport within the Bellingshausen Sea's Belgica Trough. Meltwater is present at different densities and with different turbidities: both are indicative of a layer's ice shelf of origin. To investigate how ice-shelf origin separates meltwater into different export pathways, we compare these observations with high-resolution tracer-release model simulations. Meltwater filaments branch off the Antarctic Coastal Current into the southwestern trough. Meltwater also enters the Belgica Trough in the northwest via an extended western pathway, hence the greater observed southward (0.50 mSv) than northward (0.17 mSv) meltwater transport. Together, the observations and simulations reveal meltwater retention within a cyclonic in-trough gyre, which has the potential to promote climactically important feedbacks on circulation and future melting

Junctional diversification in the generation of the precursor of a discrete immune response

Phosphocholine (PC)-specific antibodies that arise in the mouse in response to Proteus morganii (PM) and use V1-DFL16.1-JH1 are characterized by a number of recurring mutations. Most striking is an invariant A for G substitution in codon 95 of VH which results in an asparagine instead of aspartate at that position. Because of the apparent importance of this substitution in an anti-PC(PM) response, we wanted to determine the molecular basis for this base change. A cDNA library derived from pre-immune splenic B cells was examined for the frequency of VDJ containing the A substitution at 95 and the presence of additional point mutations in these sequences. Six different cDNA were isolated which contained an A substitution at the VD junction (frequency 0.00009); a seventh positive cDNA could not be examined. The V segments of four of these cDNA matched known germline genes and were, therefore, unmutated. Two others closely matched V in families whose members have not all been characterized, hence, it is not known whether the mutations observed are somatic or germline in origin. Sequences of 35 cDNA clones, containing the same V segment but differing in D, J and junctional nucleotides, revealed no mutations. These results indicate that the A substitution generated at codon 95 is most likely a product of V-DJ joining.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30952/1/0000624.pd

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy

BACKGROUND: Preterm birth confers a high risk of adverse long term health outcomes for survivors, yet the underlying molecular mechanisms are unclear. We hypothesized that effects of preterm birth can be mediated through measurable epigenomic changes throughout development. We therefore used a longitudinal birth cohort to measure the epigenetic mark of DNA methylation at birth and 18 years comparing survivors of extremely preterm birth with infants born at term. METHODS: Using 12 extreme preterm birth cases and 12 matched, term controls, we extracted DNA from archived neonatal blood spots and blood collected in a similar way at 18 years of age. DNA methylation was measured at 347,789 autosomal locations throughout the genome using Infinium HM450 arrays. Representative methylation differences were confirmed by Sequenom MassArray EpiTYPER. RESULTS: At birth we found 1,555 sites with significant differences in methylation between term and preterm babies. At 18 years of age, these differences had largely resolved, suggesting that DNA methylation differences at birth are mainly driven by factors relating to gestational age, such as cell composition and/or maturity. Using matched longitudinal samples, we found evidence for an epigenetic legacy associated with preterm birth, identifying persistent methylation differences at ten genomic loci. Longitudinal comparisons of DNA methylation at birth and 18 years uncovered a significant overlap between sites that were differentially-methylated at birth and those that changed with age. However, we note that overlapping sites may either differ in the same (300/1,555) or opposite (431/1,555) direction during gestation and aging respectively. CONCLUSIONS: We present evidence for widespread methylation differences between extreme preterm and term infants at birth that are largely resolved by 18 years of age. These results are consistent with methylation changes associated with blood cell development, cellular composition, immune induction and age at these time points. Finally, we identified ten probes significantly associated with preterm individuals and with greater than 5% methylation discordance at birth and 18 years that may reflect a long term epigenetic legacy of preterm birth

Turbulent kinetic energy dissipation rate and associated fluxes in the western tropical Atlantic estimated from ocean glider observations

Ocean gliders enable us to collect the high-resolution microstructure observations necessary to calculate the dissipation rate of turbulent kinetic energy, ε, on timescales of weeks to months: far longer than is normally possible using traditional ship-based platforms. Slocum gliders have previously been used to this end; here, we report the first detailed estimates of ε calculated using the Batchelor spectrum method on observations collected by a FP07 fast thermistor mounted on a Seaglider. We use these same fast thermistor observations to calculate ε following the Thorpe scale method and find very good agreement between the two methods. The Thorpe scale method yields larger values of ε, but the average difference, which is less than an order of magnitude, is smaller than reported elsewhere. The spatio-temporal distribution of ε is comparable for both methods. Maximum values of ε (10−7 W kg−1) are observed in the surface mixed layer; values of approximately 10−9 W kg−1 are observed between approximately 200 and 500 m depth. These two layers are separated by a 100 m thick layer of low ε (10−10 W kg−1), which is co-located with a high-salinity layer of Subtropical Underwater and a peak in the strength of stratification. We calculate the turbulent heat and salt fluxes associated with the observed turbulence. Between 200 and 500 m, ε induces downward fluxes of both properties that, if typical of the annual average, would have a very small influence on the heat and salt content of the overlying salinity-maximum layer. We compare these turbulent fluxes with two estimates of double-diffusive fluxes that occur in regions susceptible to salt fingers, such as the western tropical Atlantic. We find that the double-diffusive fluxes of both heat and salt are larger than the corresponding turbulent fluxes

Deep-Learning based segmentation and quantification in experimental kidney histopathology

BACKGROUND: Nephropathologic analyses provide important outcomes-related data in experiments with the animal models that are essential for understanding kidney disease pathophysiology. Precision medicine increases the demand for quantitative, unbiased, reproducible, and efficient histopathologic analyses, which will require novel high-throughput tools. A deep learning technique, the convolutional neural network, is increasingly applied in pathology because of its high performance in tasks like histology segmentation. METHODS: We investigated use of a convolutional neural network architecture for accurate segmentation of periodic acid-Schiff-stained kidney tissue from healthy mice and five murine disease models and from other species used in preclinical research. We trained the convolutional neural network to segment six major renal structures: glomerular tuft, glomerulus including Bowman\u27s capsule, tubules, arteries, arterial lumina, and veins. To achieve high accuracy, we performed a large number of expert-based annotations, 72,722 in total. RESULTS: Multiclass segmentation performance was very high in all disease models. The convolutional neural network allowed high-throughput and large-scale, quantitative and comparative analyses of various models. In disease models, computational feature extraction revealed interstitial expansion, tubular dilation and atrophy, and glomerular size variability. Validation showed a high correlation of findings with current standard morphometric analysis. The convolutional neural network also showed high performance in other species used in research-including rats, pigs, bears, and marmosets-as well as in humans, providing a translational bridge between preclinical and clinical studies. CONCLUSIONS: We developed a deep learning algorithm for accurate multiclass segmentation of digital whole-slide images of periodic acid-Schiff-stained kidneys from various species and renal disease models. This enables reproducible quantitative histopathologic analyses in preclinical models that also might be applicable to clinical studies

The Isoelectric Region of Proteins: A Systematic Analysis

Background: Binding of proteins in ion exchange chromatography is dominated by electrostatic interactions and can be tuned by adjusting pH and ionic strength of the solvent. Therefore, the isoelectric region (IER), the pH region of almost zero charge near the pI, has been used to predict the binding properties of proteins. Principal findings: Usually the IER is small and binding and elution is carried out at pH values near to the pI. However, some proteins with an extended IER have been shown to bind and elute far away from its pI. To analyze factors that mediate the size of the IER and to identify proteins with an extended IER, two protein families consisting of more than 7000 proteins were systematically investigated. Most proteins were found to have a small IER and thus are expected to bind or elute near to their pI, while only a small fraction of less than 2 % had a large IER. Conclusions: Only four factors, the number of histidines, the pI, the number of titratable amino acids and the ratio of acidic to basic residues, are sufficient to reliably classify proteins by their IER based on their sequence only, and thus to predict their binding and elution behaviour in ion exchange chromatography

Injection of oxygenated Persian Gulf Water into the southern Bay of Bengal

Persian Gulf Water (PGW) is an oxygenated, high-salinity water mass that has recently been detected in the Bay of Bengal (BoB). However, little is known about the transport pathways of PGW into the BoB. Ocean glider observations presented here demonstrate the presence of PGW in the southwestern BoB. Output from an ocean reanalysis product shows that this PGW signal is associated with a northward-flowing filament of high-salinity water. Particle tracking experiments reveal two pathways: one in the eastern Arabian Sea that takes a minimum of 2 years and another in the western Arabian Sea that takes a minimum of 3 years. The western pathway connects to the BoB via equatorial currents. The greatest influx of PGW occurs between 82° and 87°E during the southwest monsoon. We propose that injection of PGW to the BoB oxygen minimum zone (OMZ) contributes to keeping oxygen concentrations in the BoB above the level at which denitrification occurs