Geology and Ground-Water Hydrology of the Valleys of the Republican and Frenchman Rivers Nebraska

The geology and ground-water resources of the upper Republican River valley west of the town of Alma, Nebr., to the Nebraska-Colorado State line and of the Frenchman River valley from its confluence with the Republican River to a point about 12 miles upstream from Wauneta, Nebr., were studied from January 1950 to April 1951. The purpose of the study was to relate the occurrence of ground water to irrigation and flood control and to aid in the evaluation of the effects of irrigation on the land in the area. The area included in this study consists of 370 square miles of flat or gently sloping terraces and bottom land that border the Republican and Frenchman Rivers on either side. The Republican River is a comparatively shallow stream, ranging in width from about 150 feet at the western end of the area to about 300 feet at the eastern end. The channel banks are low, except where the river cuts into bordering terraces. In many places, natural levees of loose sand and gravel have been formed adjacent to the river banks. The bedrock formations exposed in the area are the Niobrara formation and the Pierre shale of Cretaceous age and the Ogallala formation of Tertiary age. Deposits of sand and gravel, of early Pleistocene age, are present in the bottom of the ancestral Republican River valley and along the north side of the present valley. These coarse deposits are mantled by finer sediments of later Pleistocene and Recent age. Large quantities of ground water are available from the Pleistocene and Recent deposits throughout most of the Republican River valley. In the center of the valley as much as 40 to 60 feet of the deposits are saturated. The ground-water reservoir is recharged principally by precipitation. Ground water also enters the Republican River valley by underflow through the fill of tributary valleys. Ground water is discharged by evaporation, transpiration, and effluent streams; ground water also is drawn upon extensively for irrigation, for municipal supplies, and for domestic and stock use in rural areas

Geology and Ground-Water Hydrology of the Valleys of the Republican and Frenchman Rivers Nebraska

The geology and ground-water resources of the upper Republican River valley west of the town of Alma, Nebr., to the Nebraska-Colorado State line and of the Frenchman River valley from its confluence with the Republican River to a point about 12 miles upstream from Wauneta, Nebr., were studied from January 1950 to April 1951. The purpose of the study was to relate the occurrence of ground water to irrigation and flood control and to aid in the evaluation of the effects of irrigation on the land in the area. The area included in this study consists of 370 square miles of flat or gently sloping terraces and bottom land that border the Republican and Frenchman Rivers on either side. The Republican River is a comparatively shallow stream, ranging in width from about 150 feet at the western end of the area to about 300 feet at the eastern end. The channel banks are low, except where the river cuts into bordering terraces. In many places, natural levees of loose sand and gravel have been formed adjacent to the river banks. The bedrock formations exposed in the area are the Niobrara formation and the Pierre shale of Cretaceous age and the Ogallala formation of Tertiary age. Deposits of sand and gravel, of early Pleistocene age, are present in the bottom of the ancestral Republican River valley and along the north side of the present valley. These coarse deposits are mantled by finer sediments of later Pleistocene and Recent age. Large quantities of ground water are available from the Pleistocene and Recent deposits throughout most of the Republican River valley. In the center of the valley as much as 40 to 60 feet of the deposits are saturated. The ground-water reservoir is recharged principally by precipitation. Ground water also enters the Republican River valley by underflow through the fill of tributary valleys. Ground water is discharged by evaporation, transpiration, and effluent streams; ground water also is drawn upon extensively for irrigation, for municipal supplies, and for domestic and stock use in rural areas

Application of ¹⁴C analyses to source apportionment of carbonaceous PM_2.5 in the UK

Determination of the radiocarbon (<sup>14</sup>C) content of airborne particulate matter yields insight into the proportion of the carbonaceous material derived from fossil and contemporary carbon sources. Daily samples of PM<sub>2.5</sub> were collected by high-volume sampler at an urban background site in Birmingham, UK, and the fraction of <sup>14</sup>C in both the total carbon, and in the organic and elemental carbon fractions, determined by two-stage combustion to CO<sub>2</sub>, graphitisation and quantification by accelerator mass spectrometry. OC and EC content was also determined by Sunset Analyzer. The mean fraction contemporary TC in the PM<sub>2.5</sub> samples was 0.50 (range 0.27–0.66, n = 26). There was no seasonality to the data, but there was a positive trend between fraction contemporary TC and magnitude of SOC/TC ratio and for the high values of these two parameters to be associated with air-mass back trajectories arriving in Birmingham from over land. Using a five-compartment mass balance model on fraction contemporary carbon in OC and EC, the following average source apportionment for the TC in these PM<sub>2.5</sub> samples was derived: 27% fossil EC; 20% fossil OC; 2% biomass EC; 10% biomass OC; and 41% biogenic OC. The latter category will comprise, in addition to BVOC-derived SOC, other non-combustion contemporary carbon sources such as biological particles, vegetative detritus, humic material and tyre wear. The proportion of total PM<sub>2.5</sub> at this location estimated to derive from BVOC-derived secondary organic aerosol was 9–29%. The findings from this work are consistent with those from elsewhere in Europe and support the conclusion of a significant and ubiquitous contribution from non-fossil biogenic sources to the carbon in terrestrial aerosol

Age‐related changes in the biophysical and morphological characteristics of mouse cochlear outer hair cells

Outer hair cells (OHCs) are electromotile sensory receptors that provide sound amplification within the mammalian cochlea. Although OHCs appear susceptible to ageing, the progression of the pathophysiological changes in these cells is still poorly understood. By using mouse strains with a different progression of hearing loss (C57BL/6J, C57BL/6NTac, C57BL/6NTacCdh23+ , C3H/HeJ), we have identified morphological, physiological and molecular changes in ageing OHCs (9–12 kHz cochlear region). We show that by 6 months of age, OHCs from all strains underwent a reduction in surface area, which was not a sign of degeneration. Although the ageing OHCs retained a normal basolateral membrane protein profile, they showed a reduction in the size of the K+ current and non‐linear capacitance, a readout of prestin‐dependent electromotility. Despite these changes, OHCs have a normal V m and retain the ability to amplify sound, as distortion product otoacoustic emission thresholds were not affected in aged, good‐hearing mice (C3H/HeJ, C57BL/6NTacCdh23+ ). The loss of afferent synapses was present in all strains at 15 months. The number of efferent synapses per OHCs, defined as postsynaptic SK2 puncta, was reduced in aged OHCs of all strains apart from C3H mice. Several of the identified changes occurred in aged OHCs from all mouse strains, thus representing a general trait in the pathophysiological progression of age‐related hearing loss, possibly aimed at preserving functionality. We have also shown that the mechanoelectrical transduction (MET) current from OHCs of mice harbouring the Cdh23ahl allele is reduced with age, highlighting the possibility that changes in the MET apparatus could play a role in cochlear ageing

Vapor−Wall Deposition in Chambers: Theoretical Considerations

In order to constrain the effects of vapor–wall deposition on measured secondary organic aerosol (SOA) yields in laboratory chambers, researchers recently varied the seed aerosol surface area in toluene oxidation and observed a clear increase in the SOA yield with increasing seed surface area (Zhang, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 5802). Using a coupled vapor–particle dynamics model, we examine the extent to which this increase is the result of vapor–wall deposition versus kinetic limitations arising from imperfect accommodation of organic species into the particle phase. We show that a seed surface area dependence of the SOA yield is present only when condensation of vapors onto particles is kinetically limited. The existence of kinetic limitation can be predicted by comparing the characteristic time scales of gas-phase reaction, vapor–wall deposition, and gas–particle equilibration. The gas–particle equilibration time scale depends on the gas–particle accommodation coefficient α_p. Regardless of the extent of kinetic limitation, vapor–wall deposition depresses the SOA yield from that in its absence since vapor molecules that might otherwise condense on particles deposit on the walls. To accurately extrapolate chamber-derived yields to atmospheric conditions, both vapor–wall deposition and kinetic limitations must be taken into account

Monitoring contractility in cardiac tissue with cellular resolution using biointegrated microlasers

Funding: This research was financially supported by the European Research Council under the European Union’s Horizon 2020 Framework Programme (FP/2014-2020)/ERC grant agreement no. 640012 (ABLASE), by EPSRC (grant no. EP/P030017/1) and by the RS Macdonald Charitable Trust. S.J.P. acknowledges funding by the Royal Society of Edinburgh (Biomedical Fellowship) and the British Heart Foundation (grant no. FS/17/9/32676). S.J.P. and G.B.R. acknowledge support from The Wellcome Trust Institutional Strategic Support Fund to the University of St Andrews (grant no. 204821/Z/16/A). M.S. acknowledges funding by the European Commission (Marie Skłodowska-Curie Individual Fellowship, 659213) and the Royal Society (Dorothy Hodgkin Fellowship, DH160102; grant no. RGF\R1\180070).The contractility of cardiac cells is a key parameter that describes the biomechanical characteristics of the beating heart, but functional monitoring of three-dimensional cardiac tissue with single-cell resolution remains a major challenge. Here, we introduce microscopic whispering-gallery-mode lasers into cardiac cells to realize all-optical recording of transient cardiac contraction profiles with cellular resolution. The brilliant emission and high spectral sensitivity of microlasers to local changes in refractive index enable long-term tracking of individual cardiac cells, monitoring of drug administration, accurate measurements of organ-scale contractility in live zebrafish, and robust contractility sensing through hundreds of micrometres of rat heart tissue. Our study reveals changes in sarcomeric protein density as an underlying factor to cardiac contraction. More broadly, the use of novel micro- and nanoscopic lasers as non-invasive, biointegrated optical sensors brings new opportunities to monitor a wide range of physiological parameters with cellular resolution.PostprintPeer reviewe

Prediction of epigenetically regulated genes in breast cancer cell lines

Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation of CpG islands may silence associated genes. Therefore, using high-throughput microarrays to measure CpG island methylation will lead to better understanding of tumor pathobiology and progression, while revealing potentially new biomarkers. We have examined a recently developed high-throughput technology for measuring genome-wide methylation patterns called mTACL. Here, we propose a computational pipeline for integrating gene expression and CpG island methylation profles to identify epigenetically regulated genes for a panel of 45 breast cancer cell lines, which is widely used in the Integrative Cancer Biology Program (ICBP). The pipeline (i) reduces the dimensionality of the methylation data, (ii) associates the reduced methylation data with gene expression data, and (iii) ranks methylation-expression associations according to their epigenetic regulation. Dimensionality reduction is performed in two steps: (i) methylation sites are grouped across the genome to identify regions of interest, and (ii) methylation profles are clustered within each region. Associations between the clustered methylation and the gene expression data sets generate candidate matches within a fxed neighborhood around each gene. Finally, the methylation-expression associations are ranked through a logistic regression, and their significance is quantified through permutation analysis. Our two-step dimensionality reduction compressed 90% of the original data, reducing 137,688 methylation sites to 14,505 clusters. Methylation-expression associations produced 18,312 correspondences, which were used to further analyze epigenetic regulation. Logistic regression was used to identify 58 genes from these correspondences that showed a statistically signifcant negative correlation between methylation profles and gene expression in the panel of breast cancer cell lines. Subnetwork enrichment of these genes has identifed 35 common regulators with 6 or more predicted markers. In addition to identifying epigenetically regulated genes, we show evidence of differentially expressed methylation patterns between the basal and luminal subtypes. Our results indicate that the proposed computational protocol is a viable platform for identifying epigenetically regulated genes. Our protocol has generated a list of predictors including COL1A2, TOP2A, TFF1, and VAV3, genes whose key roles in epigenetic regulation is documented in the literature. Subnetwork enrichment of these predicted markers further suggests that epigenetic regulation of individual genes occurs in a coordinated fashion and through common regulators

Potential controls of isoprene in the surface ocean

Isoprene surface ocean concentrations and vertical distribution, atmospheric mixing ratios, and calculated sea-to-air fluxes spanning approximately 125° of latitude (80°N–45°S) over the Arctic and Atlantic Oceans are reported. Oceanic isoprene concentrations were associated with a number of concurrently monitored biological variables including chlorophyll a (Chl a), photoprotective pigments, integrated primary production (intPP), and cyanobacterial cell counts, with higher isoprene concentrations relative to all respective variables found at sea surface temperatures greater than 20°C. The correlation between isoprene and the sum of photoprotective carotenoids, which is reported here for the first time, was the most consistent across all cruises. Parameterizations based on linear regression analyses of these relationships perform well for Arctic and Atlantic data, producing a better fit to observations than an existing Chl a-based parameterization. Global extrapolation of isoprene surface water concentrations using satellite-derived Chl a and intPP reproduced general trends in the in situ data and absolute values within a factor of 2 between 60% and 85%, depending on the data set and algorithm used

Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene

Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms.Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas.The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia

Intermediate-severity wind disturbance in mature temperate forests: legacy structure, carbon storage, and stand dynamics

Wind is one of the most important natural disturbances influencing forest structure, ecosystem function, and successional processes worldwide. This study quantifies the stand-scale effects of intermediate-severity windstorms (i.e., blowdowns) on (1) live and dead legacy structure, (2) aboveground carbon storage, and (3) tree regeneration and associated stand dynamics at four mature, mixed hardwood–conifer forest sites in the northeastern United States. We compare wind-affected forests to adjacent reference conditions (i.e., undisturbed portions of the same stands) 0–8 yr post-blowdown using parametric (ANOVA) and nonparametric (NMS ordination) analyses. We supplement inventory plots and downed coarse woody detritus (DCWD) transects with hemispherical photography to capture spatial variation in the light environment. Although recent blowdowns transferred a substantial proportion of live overstory trees to DCWD, residual live tree basal area was high (19–59% of reference areas). On average, the initial post-blowdown ratio of DCWD carbon to standing live tree carbon was 2.72 in blowdown stands and 0.18 in reference stands, indicating a large carbon transfer from live to dead pools. Despite these dramatic changes, structural complexity remained high in blowdown areas, as indicated by the size and species distributions of overstory trees, abundance of sound and rotten downed wood, spatial patterns of light availability, and variability of understory vegetation. Furthermore, tree species composition was similar between blowdown and reference areas at each site, with generally shade-tolerant species dominating across multiple canopy strata. Community response to intermediate-severity blowdown at these sites suggests a dynamic in which disturbance maintains late-successional species composition rather than providing a regeneration opportunity for shade-intolerant, pioneer species. Our findings suggest that intermediate-severity wind disturbances can contribute to stand-scale structural complexity as well as development toward late-successional species composition, at least when shade-tolerant regeneration is present pre-blowdown. Advance regeneration thus enhances structural and compositional resilience to this type of disturbance. This study provides a baseline for multi-cohort silvicultural systems designed to restore heterogeneity associated with natural disturbance dynamics