bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice
Authors: Li Ziwei , Yu Juehua , Hosohama Linzi , Nee Kevin , Gkountela Sofia , Chaudhari Sonal , Cass Ashley A , Xiao Xinshu , Clark Amander T 
Published: December 2014

AbstractPRMT5 is a type II protein arginine methyltransferase with roles in stem cell biology, reprograming, cancer and neurogenesis. During embryogenesis in the mouse, it was hypothesized that PRMT5 functions with the master germline determinant BLIMP1 to promote primordial germ cell (PGC) specification. Using a Blimp1‐Cre germline conditional knockout, we discovered that Prmt5 has no major role in murine germline specification, or the first global epigenetic reprograming event involving depletion of cytosine methylation from DNA and histone H3 lysine 9 dimethylation from chromatin. Instead, we discovered that PRMT5 functions at the conclusion of PGC reprograming I to promote proliferation, survival and expression of the gonadal germline program as marked by MVH. We show that PRMT5 regulates gene expression by promoting methylation of the Sm spliceosomal proteins and significantly altering the spliced repertoire of RNAs in mammalian embryonic cells and primordial cells.
Superoxide anion radicals induce IGF‐1 resistance through concomitant activation of PTP1B and PTEN
Authors: Singh Karmveer , Maity Pallab , Krug Linda , Meyer Patrick , Treiber Nicolai , Lucas Tanja , Basu Abhijit , Kochanek Stefan , Wlaschek Meinhard , Geiger Hartmut , Scharffetter‐Kochanek Karin 
Published: December 2014

AbstractThe evolutionarily conserved IGF‐1 signalling pathway is associated with longevity, metabolism, tissue homeostasis, and cancer progression. Its regulation relies on the delicate balance between activating kinases and suppressing phosphatases and is still not very well understood. We report here that IGF‐1 signalling in vitro and in a murine ageing model in vivo is suppressed in response to accumulation of superoxide anions () in mitochondria, either by chemical inhibition of complex I or by genetic silencing of ‐dismutating mitochondrial Sod2. The ‐dependent suppression of IGF‐1 signalling resulted in decreased proliferation of murine dermal fibroblasts, affected translation initiation factors and suppressed the expression of α1(I), α1(III), and α2(I) collagen, the hallmarks of skin ageing. Enhanced led to activation of the phosphatases PTP1B and PTEN, which via dephosphorylation of the IGF‐1 receptor and phosphatidylinositol 3,4,5‐triphosphate dampened IGF‐1 signalling. Genetic and pharmacologic inhibition of PTP1B and PTEN abrogated ‐induced IGF‐1 resistance and rescued the ageing skin phenotype. We thus identify previously unreported signature events with , PTP1B, and PTEN as promising targets for drug development to prevent IGF‐1 resistance‐related pathologies.
Detection of Alternative Splice and Gene Duplication by RNA Sequencing in Japanese Flounder, Paralichthys olivaceus
Authors: Wang Wenji , Wang Jing , You Feng , Ma Liman , Yang Xiao , Gao Jinning , He Yan , Qi Jie , Yu Haiyang , Wang Zhigang , Wang Xubo , Wu Zhihao , Zhang Quanqi 
Published: December 2014

Abstract
Japanese flounder (Paralichthys olivaceus) is one of the economic important fish in China. Sexual dimorphism, especially the different growth rates and body sizes between two sexes, makes this fish a good model to investigate mechanisms responsible for such dimorphism for both fundamental questions in evolution and applied topics in aquaculture. However, the lack of “omics” data has hindered the process. The recent advent of RNA-sequencing technology provides a robust tool to further study characteristics of genomes of nonmodel species. Here, we performed de novo transcriptome sequencing for a double haploid Japanese flounder individual using Illumina sequencing. A single lane of paired-end sequencing produced more than 27 million reads. These reads were assembled into 107,318 nonredundant transcripts, half of which (51,563; 48.1%) were annotated by blastx to public protein database. A total of 1051 genes that had potential alternative splicings were detected by Chrysalis implemented in Trinity software. Four of 10 randomly picked genes were verified truly containing alternative splicing by cloning and Sanger sequencing. Notably, using a doubled haploid Japanese flounder individual allow us to analyze gene duplicates. In total, 3940 “single-nucleotide polymorphisms” were detected form 1859 genes, which may have happened gene duplicates. This study lays the foundation for structural and functional genomics studies in Japanese flounder.
Too Much of a Good Thing: The Unique and Repeated Paths Toward Copper Adaptation
Authors: Gerstein Aleeza C , Ono Jasmine , Lo Dara S , Campbell Marcus L , Kuzmin Anastasia , Otto Sarah P 
Published: December 2014

Abstract
Copper is a micronutrient essential for growth due to its role as a cofactor in enzymes involved in respiration, defense against oxidative damage, and iron uptake. Yet too much of a good thing can be lethal, and yeast cells typically do not have tolerance to copper levels much beyond the concentration in their ancestral environment. Here, we report a short-term evolutionary study of Saccharomyces cerevisiae exposed to levels of copper sulfate that are inhibitory to the initial strain. We isolated and identified adaptive mutations soon after they arose, reducing the number of neutral mutations, to determine the first genetic steps that yeast take when adapting to copper. We analyzed 34 such strains through whole-genome sequencing and by assaying fitness within different environments; we also isolated a subset of mutations through tetrad analysis of four lines. We identified a multilayered evolutionary response. In total, 57 single base-pair mutations were identified across the 34 lines. In addition, gene amplification of the copper metallothionein protein, CUP1-1, was rampant, as was chromosomal aneuploidy. Four other genes received multiple, independent mutations in different lines (the vacuolar transporter genes VTC1 and VTC4; the plasma membrane H+-ATPase PMA1; and MAM3, a protein required for normal mitochondrial morphology). Analyses indicated that mutations in all four genes, as well as CUP1-1 copy number, contributed significantly to explaining variation in copper tolerance. Our study thus finds that evolution takes both common and less trodden pathways toward evolving tolerance to an essential, but highly toxic, micronutrient.
An Evaluation of Voluntary 2-Dose Varicella Vaccination Coverage in New York City Public Schools
Authors: Doll Margaret K. , Rosen Jennifer B. , Bialek Stephanie R. , Szeto Hiram , Zimmerman Christopher M. 
Published: December 2014

Objectives. We assessed coverage for 2-dose varicella vaccination, which is not required for school entry, among New York City public school students and examined characteristics associated with receipt of 2 doses. Methods. We measured receipt of either at least 1 or 2 doses of varicella vaccine among students aged 4 years and older in a sample of 336 public schools (n = 223 864 students) during the 2010 to 2011 school year. Data came from merged student vaccination records from 2 administrative data systems. We conducted multivariable regression to assess associations of age, gender, race/ethnicity, and school location with 2-dose prevalence. Results. Coverage with at least 1 varicella dose was 96.2% (95% confidence interval [CI] = 96.2%, 96.3%); coverage with at least 2 doses was 64.8% (95% CI = 64.6%, 64.9%). Increasing student age, non-Hispanic White race/ethnicity, and attendance at school in Staten Island were associated with lower 2-dose coverage. Conclusions. A 2-dose varicella vaccine requirement for school entry would likely improve 2-dose coverage, eliminate coverage disparities, and prevent disease.
Debris-flow hazards in the Blue Ridge of central Virginia
Authors: Wieczorek G. F. , Morgan B. A. , Campbell R. H. 
Published: December 2014

Abstract
The June 27, 1995, storm in Madison County, Virginia produced debris flows and floods that devastated a small (130 km 2 ) area of the Blue Ridge in the eastern United States. Although similar debris-flow inducing storm events may return only approximately once every two thousand years to the same given locale, these events affecting a similar small-sized area occur about every three years somewhere in the central and southern Appalachian Mountains. From physical examinations and mapping of debris-flow sources, paths, and deposits in Madison County, we develop methods for identifying areas subject to debris flows using Geographic Information Systems (GIS) technology. We examined the rainfall intensity and duration characteristics of the June 27, 1995, and other storms, in the Blue Ridge of central Virginia, and have defined a minimum threshold necessary to trigger debris flows in granitic rocks. In comparison with thresholds elsewhere, longer and more intense rainfall is necessary to trigger debris flows in the Blue Ridge.
Bedrock knobs, San Francisco Bay; do navigation hazards outweigh other environmental problems?
Authors: Carlson Paul R. , Chin John L. , Wong Florence L. 
Published: December 2014

Abstract
Three bedrock knobs (Arch, Harding, and Shag rocks) rise above the unconsolidated sediment of central San Francisco Bay to a water depth of less than -12 m (<-39.4 ft MLLW). These rocks are within the westbound vessel traffic area, and the northernmost, Harding Rock, is approximately 300 m (984 ft) from the two-way deep water traffic lane. The rocks pose a hazard to deep-draft vessels. Large ships with drafts deeper than -17 m (-55.8 ft) cross central San Francisco Bay bound for and returning from major port cities of the Bay estuary. Acoustic profiling data show that bedrock extends at a gentle to moderate slope away from the knobs. These data also show that two of the knobs, Harding and Shag, may be part of a bedrock ridge that extends to Alcatraz Island and perhaps southeast to Blossom Rock. The tops of these rocks should be lowered to a depth of -17 m (-55.8 ft), with a total volume of as much as 245,000 m 3 (320,460 yd 3 ), at an estimated cost of nearly 27 million dollars, to eliminate the possibility that a tanker would strike one and rupture. A resulting large oil spill would likely cost many times more than the 10 million dollars needed to clean up a small 1996 spill. If the rocks were removed, local habitat for striped bass and other game fish would be altered, with potential negative impact on sport fishing. Currently, public officials are studying the benefits to the Bay environment of lowering the rock knobs.
Rock bursts and associated neotectonic forms at Minnipa Hill, northwestern Eyre Peninsula, South Australia
Authors: Twidale C. R. , Bourne J. A. 
Published: December 2014

Abstract
Disturbance of the surface of Minnipa Hill Southeast, a low granite dome located on the northwestern Eyre Peninsula, on 19 January 1999, coincided with a shallow earth tremor, and it is suggested that the two events are causally related. The disturbance, which affected an area 170X100 m, took the form of rock bursts, reverse fault scarps, low angle planes of dislocation and overriding sheets, A-tents, dislocated slabs and blocks and widespread surficial flaking. Evidence of two earlier disturbances was noted. The event directly confirms the association of A-tents and dislocated slabs with compressive stress and by implication links bornhardts and sheet fractures with similar strain environments.
Detection of buried faults and fractures using soil gas analysis
Authors: Fountain John C. , Jacobi Robert D. 
Published: December 2014

Abstract
Detection of fractures in bedrock, which is essential for hazardous waste site evaluation and for modeling of local ground-water flow in fractured terranes, is difficult where exposure is poor, but may be accomplished using a newly developed method based on soil gas analysis. This method is based upon the accumulation of thermogenic gas in soil above open bedrock fractures. Fractures may provide high permeability pathways through bedrock; if the underlying units contain natural gas, gas will migrate upward through open fractures, producing anomalously high methane concentrations in the soil above. Over ten thousand soil gas analyses from western New York demonstrated that fractures of the Clarendon-Linden Fault System could be traced with soil gas analyses through an area largely covered with unconsolidated glacial deposits. Interpretation of soil gas anomalies as indicators of underlying fractures was confirmed by correlation with outcrop, well log, seismic, and remote sensing data. Samples were collected at a spacing of 10 m, from a depth of approximately 60 cm, using a stainless steel probe driven with a sledgehammer. Analysis of the 60 cc samples was done on-site with a portable gas chromatograph. Ethane/methane ratios were used to distinguish thermogenic gas from biogenic methane. The excellent correlation of linear soil gas anomalies with mapped fractures suggests that where gas-bearing units underlie an area, soil gas analysis may provide a method of mapping faults and fractures where exposure is too poor for conventional mapping.
A standard method for sinkhole detection in the Tampa, Florida, area
Authors: Zisman E. D. 
Published: December 2014

Abstract
This paper presents a method for evaluating sinkhole potential based on eleven sinkhole characteristics that may be found during a subsurface investigation. In brief, the characteristics address the density of soil material at different depths, drilling properties, stratigraphic conditions and ground water levels. Each of the eleven-sinkhole characteristics is discussed in detail so the investigator can identify each characteristic during the subsurface investigation. Once the total number of sinkhole characteristics are identified the Sinkhole Score for the site is determined. The Sinkhole Score is the number of sinkhole characteristics found compared to the number of sinkhole characteristics possible. Also discussed is the Weighted Sinkhole Score, which is a modification to the Sinkhole Score that accounts for the importance of each characteristic. The significance of the sinkhole scoring method is discussed in determining the likelihood that a sinkhole has impacted existing construction or could impact future site development. The paper also discusses other factors that can cause sinkhole-like distress and discusses methods of detection.
Using an analytical solution to estimate the subsidence risk caused by ASR applications
Authors: Li J. , Helm D. C. 
Published: December 2014

Abstract
Land subsidence, due to the net compression of one or more semi-pervious clay beds, can be induced by the application of aquifer storage and recovery (ASR) technology. ASR technology involves periodically pumping and injecting water from or into adjacent aquifers for various purposes. In order to estimate the potential risk of aquifer system deformation in response to an injecting-pumping scheme, an analytic solution for the one-dimensional case (a sandwich model) is solved. The solution is analyzed for a unit column of an idealized compressible semipervious layer. A governing equation is invoked that is expressed directly in terms of the vertical displacement of the skeletal frame (Helm, 1987). For simplicity, the saturated aquifer system is assumed to behave like poroelastic material (both recoverable and nonrecoverable). The two idealized aquifers (one above the modeled semi-confining bed and the other beneath) can be pumped independently of each other. Analytical solutions are found for subsidence in response to selected stress/pumping patterns. Results from the analytic solution are applied in order to estimate and predict the potential risk of land subsidence due to ground-water withdrawal and injection, and to provide a first-estimate type of guideline for city and regional planning and the exploration of water resources.
Liquefaction evaluation guidelines for practicing engineering and geological professionals and regulators
Authors: Lew Marshall 
Published: December 2014

Abstract
Liquefaction is a seismic hazard that must be evaluated for a significant percentage of the developable areas of California. The combination of the presence of active seismic faults, young loose alluvium, and shallow ground water are the ingredients that could result in the occurrence of liquefaction in many areas of California. These ingredients are also found in other seismically active areas of the United States and the world. The state of California, through the Seismic Hazard Mapping Act of 1990, has mandated that liquefaction hazard be determined for new construction. On a parallel track, the Uniform Building Code, since 1994, has provisions requiring the determination of liquefaction potential and mitigation of related hazards, such as settlement, flow slides, lateral spreading, ground oscillation, sand boils, and loss of bearing capacity. Fortunately, the state of knowledge has now evolved to where there are field exploration methods and analytical techniques to estimate the liquefaction potential and the possible consequences arising from the occurrence of liquefaction. There are some areas that still need further research. Mitigation for liquefaction has become more commonplace and confidence in these techniques has been increased based on the relatively successful performance of improved sites in the past several major earthquakes. Unfortunately, not all practicing engineering and geological professionals and building officials are knowledgeable about the current state-of-practice in liquefaction hazard analysis and mitigation. Thus, it was considered necessary to develop a set of guidelines to aid professionals and building officials, based on California's experience with the current practice of liquefaction hazard analysis and mitigation. Although the guidelines reported in this paper were written specifically for practice in California, it is believed that guidelines can benefit practitioners to evaluate liquefaction hazard in all seismic regions.
Fracturing within anticlines and its kinematic control on slope stability
Authors: Badger Thomas C. 
Published: December 2014

Abstract
Anticlinal folding generates both bedding-parallel shear stresses and tensional stresses radial to the fold axis. These stresses typically produce two sets of discontinuities. Discontinuity set S 1 forms coincident with bedding (S 0 ) as a mode II fracture, and discontinuity set S 2 forms perpendicular to bedding and strikes parallel to the fold axis as a mode I fracture. For slopes that strike parallel to the fold axis, these two discontinuity sets may produce three structurally-controlled modes of slope failure. For slopes that are coincident with bedding, planar failures along S 0 /S 1 commonly occur and can be very large. Where bedding dips favorably into the slope, failures along joint set S 2 and across bedding can occur. Toppling failures are common to both of these slope configurations, along S 2 and S 0 /S 1 , respectively. Lastly, flat or shallow dipping S 0 /S 1 fractures, even those favorably oriented, and intersecting S 2 joints define blocks that can be mobilized by high ground-water pressures. An example is presented for each slope configuration to illustrate these kinematic controls on slope stability.
Silica transport in the high-level radioactive waste repository, Yucca Mountain, Nevada
Authors: Sun Zhuang , Rimstidt J. Donald 
Published: December 2014

Abstract
The United States is currently planning to bury high-level radioactive wastes from commercial nuclear power plants and from weapons production in a mined repository in tuff deposits under Yucca Mountain, Nevada. Radioactive decay in these wastes will create steep thermal gradients in the rocks surrounding the repository. This heat might cause the pore water in these tuffs to evaporate, migrate as vapor to cooler areas, and condense to form a solution that can aggressively dissolve the surrounding tuff. Under certain circumstances the silica-rich, bicarbonate solutions produced by this process could migrate under the influence of gravity back toward the canisters where the water would again evaporate leaving amorphous silica behind to form a low permeability silica cap above the repository. Over time, a perched water table containing carbonate and colloidal silica-rich brine could develop above the repository. Thermoelastic fracturing of the silica cap might allow this brine to flow into the repository. We developed a vertical thermal gradient experiment that simulates the silica dissolution and transport processes and used it to determine that each Joule of heat can leach and transport as much as 1.85(+ or -0.56)X10 (super -8) g of silica from a crushed sample of the Topopah Springs Member of the Paintbrush Tuff. Based on this value and the thermal models of Moujaes and Lei (1995), we estimate that the heat from each canister of waste might transport as much as 31.7 kg of silica during the first 100 years and as much as 136 kg of silica during the first 1,000 years after emplacement. Assuming a reasonable fracture density and a 30 mX30 m area of influence for each canister, we estimate that the silica cap above the repository could grow to be 2.1 mm thick after 100 yr and 9.1 mm thick after 1,000 yr.
Rock mass characterization to indicate slope instability at Bandarban, Bangladesh; a rock engineering systems approach
Authors: Ali Khaled Mohammed , Hasan Khaled 
Published: December 2014

Abstract
A Rock Engineering Systems (RES) approach was adopted for rock mass characterization to indicate unstable slopes along the main roads of Bandarban Sadar Thana, Bandarban district of southeastern Bangladesh. The research work was based on a thorough field investigation, which was followed by geomathematical analyses of collected data. Fieldwork was carried out along two roads in Bandarban Sadar Thana of Bandarban. The slopes are composed of rocks of the lithostratigraphic units--the Surma and Tipam Group. Data on probable parameters related to slope instability were collected for the analyses. Based on the findings of the field investigation, literature review and collected ancillary data, 13 parameters were found relevant to slope instability. For the geomathematical analysis, matrix coding was done and rating values were designated for subcategories of each parameter to construct pull down menus. Finally, Rock Mass Instability Index (RMIIj) was calculated for each slope; higher values of RMIIj indicate higher degrees of slope instability. For the purpose of verification of the RES methodology and results, several stable slopes were included in the field study and geomathematical analyses. It was found that the unstable slopes had a RMIIj value ranging between 43.99 and 65.27, whereas the stable slopes were found to have RMIIj values between 14.04 and 39.10. Therefore, the adapted RES method of rock mass characterization based on RMIIj values was found effective in differentiating the studied slopes based on their degree of slope instability.
Contribution de la thermoluminescence a la paleogeographie de la Mediterrannee centrale
Authors: Beugnies Alphonse , Broquet Paul , Caire Andre , Charlet Jean Marie , Duee Gerard , Mascle Georges , Truillet Rene 
Published: December 2014

Abstract
Detrital sediments, quartz and feldspar types and distribution, Permian-Miocene, Sicily, Sardinia, Tunisia and Algeria
Les foraminiferes benthiques et planctoniques d'une carotte atlantique (golfe de Gascogne); variations climatiques du milieu marin au cours du Quaternaire recent
Authors: Caralp Michelle , Pujos Michel 
Published: December 2014

Abstract
Three planktonic assemblages, two benthonic assemblages indicate interglacial, glacial and postglacial stages of the Wurm glaciation