Constraints on the Miocene landscape evolution of the Eastern Alps from the Kalkspitze region, Niedere Tauern (Austria)

NASA Astrophysics Data System (ADS)

Dertnig, Florian; Stüwe, Kurt; Woodhead, Jon; Stuart, Finlay M.; Spötl, Christoph

2017-12-01

In order to unravel aspects of the Miocene landscape evolution of the eastern European Alps, we present geomorphic and isotopic data from the western Niedere Tauern region (Austria). The region is critical for such interpretations, because it is one of the few regions along the topographic axis of the Eastern Alps where the highest peaks (up to 2500 m a.s.l.) are dominated by limestone. As such, the region contains a record of Miocene landscape-forming events that survived the Pleistocene glaciations, not preserved elsewhere in the central Eastern Alps. This record includes karst caves, karstified planation surfaces and crystalline fluvial pebbles (Augenstein Formation) preserved on planation surfaces and in karst caves. Caves in the region occur in three distinct levels that correlate with well-known cave levels in the Northern Calcareous Alps, although they are somewhat higher in the Niedere Tauern. In part, these cave elevations also correlate with three planation surfaces and knickpoints of major streams draining the region, testifying their pre-glacial origin. We report details of a karst cave (Durchgangshöhle) from the highest cave level located at 2340 m a.s.l. In this cave, allochthonous fluvial gravels are present, overgrown by speleothems. One speleothem yielded an early middle Pleistocene U-Pb age (682 ± 17 ka). We regard this as a minimum age for the erosion of the fluvial cave deposits during Marine Isotope Stages 17 or 16. Carbon and oxygen isotope data of these speleothems imply a climate that is consistent with this interpretation. Cosmogenic 21Ne data of fluvial quartz clasts collected from the surface on plateaus of the Northern Calcareous Alps suggest minimum exposure durations of 115 and 262 ka. They probably reflect successive exposure since removal of the sediment cover of the Oligocene Augenstein Formation during the Pleistocene. While our geochronological data fail to record aspects of the earlier Miocene uplift history, they are consistent with the overall geomorphic history inferred from the geomorphic markers. This suggests that the Niedere Tauern share a common uplift history with the Northern Calcareous Aps and implies a moderate south-north topographic gradient that has been maintained since the Miocene.

Synchronous mid-Holocene climate deteriorations in circum-Mediterranean and their links with ancient civilizations: first speloethem and archeological evidences from N-Algeria

NASA Astrophysics Data System (ADS)

Ruan, Jiaoyang; Kherbouche, Farid; Genty, Dominique; Cheng, Hai; Dewilde, Fabien; Blamart, Dominique

2015-04-01

Over the last decades, ancient civilizations during the Holocene were heavily studied at many places around the Mediterranean region such as Libya and Italy, and changes in the past social activities were widely assumed to be linked to regional climate variability. However, in many cases the climatic records were apart from the archaeological sites and the archaeological chronologies were not well constrained, which makes these links uncertain. Here we present a 230Th-dated decadal resolution climate record for 6034-3185yr BP based on the δ18O and δ13C analyses of two overlapping stalagmites from Gueldaman GLD1 Cave (36°26'N, 4°34'E, 507 m asl), N-Algeria. Recent archaeological work in this cave brought first information about the Neolithisation process since ca 7000yr cal BP in the region where little was known before. Together with new charcoal 14C dates from the digging sections we test the link between past climate change and human activities in the cave. GLD1 stalagmite records reveal a dry event at ca 5700-5500yr BP and a drying trend toward extreme aridity, since ca 4700yr BP, peaking at ca 4200yr BP. These climatic deteriorations in N-Algeria, within dating errors, are synchronous with dry phases observed on speleothem records from central (Corchia Cave and Renella Cave, Italy) and eastern (Soreq Cave, Israel) Mediterranean. Specifically, climatic condition was harsher at ca 4200yr BP than at ca 5700-5500yr BP in central and W-Mediterranean; while it was harsher at ca 5700-5500yr BP in E-Mediterranean. The new 14C dates relatively well anchor the age of sediment layers with the richest anthropogenic deposits (i.e. charcoal, bone and Neolithic pottery) to ca 4900-4400yr cal BP, coinciding with the wettest period inferred from the stalagmite records. Shortly following this period, archaeological remains were becoming very rare in the sediments, which might be the consequence of establishing extremely arid phase at ca 4200yr BP. This suggests a possible causal relationship between the cave abandonment and aridity. Similarly, a drought at ca 4200yr BP was inferred to cause the cultural collapse of the Uruk society in Mesopotamia and the Akkadian Empire in N-Africa. In the E-Mediterranean, although the early to late Bronze Age transition was coincident with the dry phase at that time, the major cultural transform from the Chalcolithic to the Bronze Age occurred at ca 5700-5500yr BP when the more severe drought was established. These observations suggest close links between past climate changes and ancient civilizations even though they might evolve independently at different sites.

Integrated detection of fractures and caves in carbonate fractured-vuggy reservoirs based on seismic data and well data

NASA Astrophysics Data System (ADS)

Cao, Zhanning; Li, Xiangyang; Sun, Shaohan; Liu, Qun; Deng, Guangxiao

2018-04-01

Aiming at the prediction of carbonate fractured-vuggy reservoirs, we put forward an integrated approach based on seismic and well data. We divide a carbonate fracture-cave system into four scales for study: micro-scale fracture, meso-scale fracture, macro-scale fracture and cave. Firstly, we analyze anisotropic attributes of prestack azimuth gathers based on multi-scale rock physics forward modeling. We select the frequency attenuation gradient attribute to calculate azimuth anisotropy intensity, and we constrain the result with Formation MicroScanner image data and trial production data to predict the distribution of both micro-scale and meso-scale fracture sets. Then, poststack seismic attributes, variance, curvature and ant algorithms are used to predict the distribution of macro-scale fractures. We also constrain the results with trial production data for accuracy. Next, the distribution of caves is predicted by the amplitude corresponding to the instantaneous peak frequency of the seismic imaging data. Finally, the meso-scale fracture sets, macro-scale fractures and caves are combined to obtain an integrated result. This integrated approach is applied to a real field in Tarim Basin in western China for the prediction of fracture-cave reservoirs. The results indicate that this approach can well explain the spatial distribution of carbonate reservoirs. It can solve the problem of non-uniqueness and improve fracture prediction accuracy.

Long-term Quaternary uplift rates inferred from limestone caves in Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Farrant, Andrew R.; Smart, Peter L.; Whitaker, Fiona F.; Tarling, Donald H.

1995-04-01

The rate of long-term (2 m.y.) base-level lowering estimated in an extensive sequence of limestone caves in Sarawak, Malaysia, from uranium series, electron spin resonance, and paleomagnetic dating is 0.19 +0.03/-0.04 m/ka. This rate has remained constant over at least the last 700 ka, as shown by comparison of the number and spacing of wall notches formed during phases of interstadial and interglacial aggradation with peaks in the deep-sea oxygen isotope curve. It is argued that base-level lowering occurs in response to epirogenic uplift of the more resistant limestones due to regional denudation of the softer shales, and to flexural isostacy associated with high rates of offshore sedimentation.

Climate variability during the Holocene inferred from northeastern Iberian speleothems

NASA Astrophysics Data System (ADS)

Moreno, A.; Bartolomé, M.; Sancho, C.; Belmonte, Á.; Stoll, H.; Cacho, I.; Edwards, R. L.; Hellstrom, J.

2012-04-01

Although the general climate trends during the Holocene in the Iberian Peninsula have been well described after the study of marine and lacustrine records, many questions regarding the timing of some of the events together with the characterization of the higher-frequency climate variability are still poorly understood. New speleothem records from several caves in northeastern Iberia provide data to explore Holocene climate changes. The selected caves are located in a latitudinal transect from the Pyrenees to the Iberian Range and placed at different altitude. Two of them, 5 de Agosto and Pot au Feu, belong to the same karstic complex in Cotiella massif (Central Pyrenees, 1600 m asl). Seso Cave, also in the Central Pyrenees but at 781 m of altitude, and Molinos cave, a cavity very rich in speleothems located at 1040 m in the Iberian Range, complete the transect. Although in all the caves precipitation coming from Atlantic fronts dominates over the year, a significant Mediterranean influence, specially in summer months, is identified after rainfall monitoring. Speleothem formation during the Holocene occurred at a very low pace in 5 de Agosto cave (80yrs/mm) and increased dramatically at low-altitude caves and during particular periods proved to be wetter (eg. Early Holocene in Molinos cave, less than 10yr/mm). In Seso and Pot au Feu caves, up to seven studied speleothems only grew during short climatic events such as the Iron Cold Period (3000-2500 cal yr BP) or the Little Ice Age (1300-1850 yr AD) that, although cold, were particularly humid periods in northeastern Spain. First stable isotope results highlight the importance of comparing speleothems with similar growing rates and from the same cave to extract climate information and discard other influences. From the integration of four stalagmites from Molinos cave covering since the Holocene onset to 2000 cal yrs BP, the Early Holocene (11.7-8.5 ka BP) with d13C values between -11 and - 9‰ appears as the wetter interval. The highest isotopic values are reached during Middle Holocene (8.5-5.5 ka BP) while there is a tendency towards more negative values during Late Holocene (last 5000 yrs). The range of d18O values is low (about 2‰) but still lighter values during Early Holocene and heavier afterwards are well marked. Shorter events characterized by more negative d13C values are observed at 4 ka, 6 ka, 7.5 ka, 8.2, 8.7, 9.2, 10.3 ka and interpreted as cold but probably wetter periods with denser vegetation cover and soil development over the cave. However, changes in the source of precipitation (Atlantic vs Mediterranean) or the influence of fresh-water outbursts in North Atlantic can not be neglected.

Under the Skin of a Lion: Unique Evidence of Upper Paleolithic Exploitation and Use of Cave Lion (Panthera spelaea) from the Lower Gallery of La Garma (Spain).

PubMed

Cueto, Marián; Camarós, Edgard; Castaños, Pedro; Ontañón, Roberto; Arias, Pablo

2016-01-01

Pleistocene skinning and exploitation of carnivore furs have been previously inferred from archaeological evidence. Nevertheless, the evidence of skinning and fur processing tends to be weak and the interpretations are not strongly sustained by the archaeological record. In the present paper, we analyze unique evidence of patterned anthropic modification and skeletal representation of fossil remains of cave lion (Panthera spelaea) from the Lower Gallery of La Garma (Cantabria, Spain). This site is one of the few that provides Pleistocene examples of lion exploitation by humans. Our archaeozoological study suggests that lion-specialized pelt exploitation and use might have been related to ritual activities during the Middle Magdalenian period (ca. 14800 cal BC). Moreover, the specimens also represent the southernmost European and the latest evidence of cave lion exploitation in Iberia. Therefore, the study seeks to provide alternative explanations for lion extinction in Eurasia and argues for a role of hunting as a factor to take into account.

Under the Skin of a Lion: Unique Evidence of Upper Paleolithic Exploitation and Use of Cave Lion (Panthera spelaea) from the Lower Gallery of La Garma (Spain)

PubMed Central

Camarós, Edgard; Castaños, Pedro; Ontañón, Roberto; Arias, Pablo

2016-01-01

Pleistocene skinning and exploitation of carnivore furs have been previously inferred from archaeological evidence. Nevertheless, the evidence of skinning and fur processing tends to be weak and the interpretations are not strongly sustained by the archaeological record. In the present paper, we analyze unique evidence of patterned anthropic modification and skeletal representation of fossil remains of cave lion (Panthera spelaea) from the Lower Gallery of La Garma (Cantabria, Spain). This site is one of the few that provides Pleistocene examples of lion exploitation by humans. Our archaeozoological study suggests that lion-specialized pelt exploitation and use might have been related to ritual activities during the Middle Magdalenian period (ca. 14800 cal BC). Moreover, the specimens also represent the southernmost European and the latest evidence of cave lion exploitation in Iberia. Therefore, the study seeks to provide alternative explanations for lion extinction in Eurasia and argues for a role of hunting as a factor to take into account. PMID:27783697

Genetic spatial structure of an anchialine cave annelid indicates connectivity within - but not between - islands of the Great Bahama Bank.

PubMed

Gonzalez, Brett C; Martínez, Alejandro; Borda, Elizabeth; Iliffe, Thomas M; Fontaneto, Diego; Worsaae, Katrine

2017-04-01

Land-locked anchialine blue holes are karstic sinkholes and caves with tidally influenced, vertically stratified water bodies that harbor endemic fauna exhibiting variable troglomorphic features. These habitats represent island-like systems, which can serve to elucidate evolutionary and biogeographic processes at local scales. We investigated whether the 'continuous spelean corridor' hypothesis may elucidate the biogeographical distributions of the stygobitic annelid Pelagomacellicephala iliffei (Polynoidae) collected from the Great Bahama and Caicos Banks of the Bahamas Archipelago. Phylogenetic reconstructions were performed using Bayesian Inference on individual and combined datasets of three molecular markers (16S rDNA, COI, 18S rDNA) and species delimitation employed three widely accepted methods in DNA taxonomy, namely GMYC, bPTP, and ABGD. Mantel tests were used to test the effect of geography on genetic structure. Using these analyses, we recovered five independently evolving entities of the focal species across four islands of the Great Bahama Bank including Cat, Eleuthera, Exumas, and Long. Genetic data yielded strong correlations between islands and phylogenetic entities, signifying independent evolutionary histories within anchialine caves across the platform. The island of Eleuthera showed intra-island gene flow and dispersal capabilities between blue holes separated by 115km, providing evidence of a crevicular spelean corridor within the island. However, no evidence of inter-island dispersal is present in the analyzed system. Consistent with previous biogeographic studies of cave crustaceans, the major barriers shaping the cave biota of the Bahamas Archipelago appears to be the deep trenches and channels separating the Bahamian banks. Copyright © 2017 Elsevier Inc. All rights reserved.

Inferring Gene Regulatory Networks by Singular Value Decomposition and Gravitation Field Algorithm

PubMed Central

Zheng, Ming; Wu, Jia-nan; Huang, Yan-xin; Liu, Gui-xia; Zhou, You; Zhou, Chun-guang

2012-01-01

Reconstruction of gene regulatory networks (GRNs) is of utmost interest and has become a challenge computational problem in system biology. However, every existing inference algorithm from gene expression profiles has its own advantages and disadvantages. In particular, the effectiveness and efficiency of every previous algorithm is not high enough. In this work, we proposed a novel inference algorithm from gene expression data based on differential equation model. In this algorithm, two methods were included for inferring GRNs. Before reconstructing GRNs, singular value decomposition method was used to decompose gene expression data, determine the algorithm solution space, and get all candidate solutions of GRNs. In these generated family of candidate solutions, gravitation field algorithm was modified to infer GRNs, used to optimize the criteria of differential equation model, and search the best network structure result. The proposed algorithm is validated on both the simulated scale-free network and real benchmark gene regulatory network in networks database. Both the Bayesian method and the traditional differential equation model were also used to infer GRNs, and the results were used to compare with the proposed algorithm in our work. And genetic algorithm and simulated annealing were also used to evaluate gravitation field algorithm. The cross-validation results confirmed the effectiveness of our algorithm, which outperforms significantly other previous algorithms. PMID:23226565

Little Ice Age versus Present Day: Comparison of Temperature, Precipitation and Seasonality in Speleothem Records from the Han-sur-Lesse Cave, Belgium.

NASA Astrophysics Data System (ADS)

Vansteenberge, S.; Van Opdenbosch, J.; Van Rampelbergh, M.; Verheyden, S.; Keppens, E.; Cheng, H.; Edwards, R. L.; Claeys, P. F.

2015-12-01

The Proserpine stalagmite is a 2 m large, tabular-shaped speleothem located in the Han-sur-Lesse cave in Belgium. The speleothem formed over the last 1000 years and is still growing. High-accuracy U/Th datings have indicated exceptionally high growth-rates of up to 2 mm per year. This, together with a well expressed annual layering, makes the Proserpine stalagmite an ideal candidate for high-resolution paleoclimate reconstructions of the last millennium. Previous work, including over 10 years of cave monitoring, has already learned us how short-term, i.e. decadal to seasonal, climate variations are incorporated within speleothem calcite from the Han-sur-Lesse cave system. It has been shown that δ18O and δ13C stable isotopes and trace element proxies of recently formed calcite reflect seasonal variations in temperature and precipitation of the near-cave environment (Verheyden et al, 2008; Van Rampelbergh et al., 2014). Now, this knowledge was used to infer local climate parameters further back in time to the period of +/- 1620-1630 CE, corresponding to one of the cold peaks within the Little Ice Age. Speleothem calcite was sampled at sub-annual resolution, with approximately 11 samples per year, for stable isotope analysis. LA-ICP-MS and µXRF analyses resulted in time series of trace elements. Preliminary results indicate a well expressed seasonal signal in δ13C and trace element composition but a multi-annual to decadal trend in δ18O. This combined proxy study eventually enables comparison of the expression of seasonality and longer term climate variations between a Little Ice Age cold peak and Present Day. References: Verheyden, S. et al., 2008, Monitoring climatological, hydrological and geochemical parameters in the Père Noël cave (Belgium): implication for the interpretation of speleothem isotopic and geochemical time-series. International Journal of Speleology, 37(3), 221-234. Van Rampelbergh, M. et al., 2014, Seasonal variations recorded in cave monitoring results and a 10-year monthly resolved speleothem δ13C and δ18O record from the Han-sur-Lesse cave, Belgium. Climate of the Past, 10, 1-15, 2014.

An Integrated Hydrogeologic and Geophysical Investigation to Characterize the Hydrostratigraphy of the Edwards Aquifer in an Area of Northeastern Bexar County, Texas

USGS Publications Warehouse

Shah, Sachin D.; Smith, Bruce D.; Clark, Allan K.; Payne, Jason

2008-01-01

In August 2007, the U.S. Geological Survey, in cooperation with the San Antonio Water System, did a hydrogeologic and geophysical investigation to characterize the hydrostratigraphy (hydrostratigraphic zones) and also the hydrogeologic features (karst features such as sinkholes and caves) of the Edwards aquifer in a 16-square-kilometer area of northeastern Bexar County, Texas, undergoing urban development. Existing hydrostratigraphic information, enhanced by local-scale geologic mapping in the area, and surface geophysics were used to associate ranges of electrical resistivities obtained from capacitively coupled (CC) resistivity surveys, frequency-domain electromagnetic (FDEM) surveys, time-domain electromagnetic (TDEM) soundings, and two-dimensional direct-current (2D-DC) resistivity surveys with each of seven hydrostratigraphic zones (equivalent to members of the Kainer and Person Formations) of the Edwards aquifer. The principal finding of this investigation is the relation between electrical resistivity and the contacts between the hydrostratigraphic zones of the Edwards aquifer and the underlying Trinity aquifer in the area. In general, the TDEM data indicate a two-layer model in which an electrical conductor underlies an electrical resistor, which is consistent with the Trinity aquifer (conductor) underlying the Edwards aquifer (resistor). TDEM data also show the plane of Bat Cave fault, a well-known fault in the area, to be associated with a local, nearly vertical zone of low resistivity that provides evidence, although not definitive, for Bat Cave fault functioning as a flow barrier, at least locally. In general, the CC resistivity, FDEM survey, and 2D-DC resistivity survey data show a sharp electrical contrast from north to south, changing from high resistivity to low resistivity across Bat Cave fault as well as possible karst features in the study area. Interpreted karst features that show relatively low resistivity within a relatively high-resistivity area likely are attributable to clay or soil filling a sinkhole. In general, faults are inferred where lithologic incongruity indicates possible displacement. Along most inferred faults, displacement was not sufficient to place different members of the Kainer or Person Formations (hydrostratigraphic zones) adjacent across the inferred fault plane. In general, the Kainer Formation (hydrostratigraphic zones V through VIII) has a higher resistivity than the Person Formation (hydrostratigraphic zones II through IV). Although resistivity variations from the CC resistivity, FDEM, and 2D-DC resistivity surveys, with mapping information, were sufficient to allow surface mapping of the lateral extent of hydrostratigraphic zones in places, resistivity variations from TDEM data were not sufficient to allow vertical delineation of hydrostratigraphic zones; however, the Edwards aquifer-Trinity aquifer contact could be identified from the TDEM data.

Image-Data Compression Using Edge-Optimizing Algorithm for WFA Inference.

ERIC Educational Resources Information Center

Culik, Karel II; Kari, Jarkko

1994-01-01

Presents an inference algorithm that produces a weighted finite automata (WFA), in particular, the grayness functions of graytone images. Image-data compression results based on the new inference algorithm produces a WFA with a relatively small number of edges. Image-data compression results alone and in combination with wavelets are discussed.…

Fish remains from Homestead Cave and lake levels of the past 13,000 years in the Bonneville basin

USGS Publications Warehouse

Broughton, J.M.; Madsen, D.B.; Quade, Jay

2000-01-01

A late Quaternary ichthyofauna from Homestead Cave, Utah, provides a new source of information on lake history in the Bonneville basin. The fish, represented by 11 freshwater species, were accumulated between ~11,200 and ~1000 14C yr B.P. by scavenging owls. The 87Sr/86Sr ratio of Lake Bonneville varied with its elevation; 87Sr/86Sr values of fish from the lowest stratum of the cave suggest they grew in a lake near the terminal Pleistocene Gilbert shoreline. In the lowest deposits, a decrease in fish size and an increase in species tolerant of higher salinities or temperatures suggest multiple die-offs associated with declining lake levels. An initial, catastrophic, post-Provo die-off occurred at 11,300-11,200 14C yr B.P. and was followed by at least one rebound or recolonization of fish populations, but fish were gone from Lake Bonneville sometime before ~10,400 14C yr B.P. This evidence is inconsistent with previous inferences of a near desiccation of Lake Bonneville between 13,000 and 12,000 14C yr B.P. Peaks in Gila atraria frequencies in the upper strata suggest the Great Salt Lake had highstands at ~3400 and ~1000 14C yr B.P. (C) 2000 University of Washington.

Unraveling the effects of sex and dispersal: Ozark big-eared bat (Corynorhinus townsendii ingens) conservation genetics

USGS Publications Warehouse

Weyandt, S.E.; Van Den Bussche, Ronald A.; Hamilton, M.J.; Leslie, David M.

2005-01-01

The Ozark big-eared bat (Corynorhinus townsendii ingens) is federally listed as endangered and is found in only a small number of caves in eastern Oklahoma and northwestern Arkansas. Previous studies suggested site fidelity of females to maternity caves; however, males are solitary most of the year, and thus specific information on their behavior and roosting patterns is lacking. Population genetic variation often provides the necessary data to make inferences about gene flow or mating behavior within that population. We used 2 types of molecular data: DNA sequences from the mitochondrial D loop and alleles at 5 microsatellite loci. Approximately 5% of the population, 24 males and 39 females (63 individuals), were sampled. No significant differentiation between 5 sites was present in nuclear microsatellite variation, but distribution of variation in maternally inherited markers differed among sites. This suggests limited dispersal of female Ozark big-eared bats and natal philopatry. Areas that experience local extinctions are unlikely to be recolonized by species that show strong site fidelity. These results provide a greater understanding of the population dynamics of Ozark big-eared bats and highlight the importance of cave protection relative to maintaining genetic integrity during recovery activities for this listed species. ?? 2005 American Society of Mammalogists.

Karst system vadose zone hydrodynamics highlighted by an integrative geophysical and hydrogeological monitoring

NASA Astrophysics Data System (ADS)

Watlet, A.; Van Camp, M. J.; Francis, O.; Poulain, A.; Hallet, V.; Rochez, G.; Kaufmann, O.

2015-12-01

The vadose zone of karst systems plays an important role on the water dynamics. In particular, temporary perched aquifers can appear in the subsurface due to changes of climate conditions, diminished evapotranspiration and differences of porosity relative to deeper layers. It is therefore crucial, but challenging, to separate the hydrological signature of the vadose zone from the one of the saturated zone for understanding hydrological processes that occur in the vadose zone. Although many difficulties are usually encountered when studying karst environments due to their heterogeneities, cave systems offer an outstanding opportunity to investigate vadose zone from the inside with various techniques. We present results covering two years of hydrogeological and geophysical monitoring at the Rochefort Cave Laboratory (RCL), located in the Variscan fold-and-thrust belt (Belgium), a region that shows many karstic networks within Devonian limestone units. Hydrogeological data such as flows and levels monitoring or tracer tests performed in both vadose and saturated zones bring valuable information on the hydrological context of the studied area. Combining those results with geophysical measurements allows validating and imaging them with more integrative techniques. A microgravimetric monitoring involves a superconducting gravimeter continuously measuring at the surface of the RCL. Early in 2015, a second relative gravimeter was installed in the underlying cave system located 35 meters below the surface. This set up allows highlighting vadose gravity changes. These relative measurements are calibrated using an absolute gravimeter. 12 additional stations (7 at the surface, 5 in the cave) are monitored on a monthly basis by a spring gravimeter. To complete these gravimetric measurements, the site has been equipped with a permanent Electrical Resistivity Tomography (ERT) monitoring system comprising an uncommon array of surface, borehole and cave electrodes. Although such an unconventional ERT setup is challenging in terms of data processing and interpretation, it provides valuable data for inferring variations of the vadose zone saturation rate.

Win-Stay, Lose-Sample: a simple sequential algorithm for approximating Bayesian inference.

PubMed

Bonawitz, Elizabeth; Denison, Stephanie; Gopnik, Alison; Griffiths, Thomas L

2014-11-01

People can behave in a way that is consistent with Bayesian models of cognition, despite the fact that performing exact Bayesian inference is computationally challenging. What algorithms could people be using to make this possible? We show that a simple sequential algorithm "Win-Stay, Lose-Sample", inspired by the Win-Stay, Lose-Shift (WSLS) principle, can be used to approximate Bayesian inference. We investigate the behavior of adults and preschoolers on two causal learning tasks to test whether people might use a similar algorithm. These studies use a "mini-microgenetic method", investigating how people sequentially update their beliefs as they encounter new evidence. Experiment 1 investigates a deterministic causal learning scenario and Experiments 2 and 3 examine how people make inferences in a stochastic scenario. The behavior of adults and preschoolers in these experiments is consistent with our Bayesian version of the WSLS principle. This algorithm provides both a practical method for performing Bayesian inference and a new way to understand people's judgments. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.

PubMed

Song, Jia; Zheng, Sisi; Nguyen, Nhung; Wang, Youjun; Zhou, Yubin; Lin, Kui

2017-10-03

Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca 2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

PubMed

Lee, Wei-Po; Hsiao, Yu-Ting; Hwang, Wei-Che

2014-01-16

To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high quality solutions can be obtained within relatively short time. This integrated approach is a promising way for inferring large networks.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment

PubMed Central

2014-01-01

Background To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. Results This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Conclusions Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high quality solutions can be obtained within relatively short time. This integrated approach is a promising way for inferring large networks. PMID:24428926

Parametric inference for biological sequence analysis.

PubMed

Pachter, Lior; Sturmfels, Bernd

2004-11-16

One of the major successes in computational biology has been the unification, by using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied to these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems that are associated with different statistical models. This article introduces the polytope propagation algorithm for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.

Accurate HLA type inference using a weighted similarity graph.

PubMed

Xie, Minzhu; Li, Jing; Jiang, Tao

2010-12-14

The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transplantations. Numerous studies have demonstrated that variation in HLA genes is associated with many autoimmune, inflammatory and infectious diseases. However, typing HLA genes by serology or PCR is time consuming and expensive, which limits large-scale studies involving HLA genes. Since it is much easier and cheaper to obtain single nucleotide polymorphism (SNP) genotype data, accurate computational algorithms to infer HLA gene types from SNP genotype data are in need. To infer HLA types from SNP genotypes, the first step is to infer SNP haplotypes from genotypes. However, for the same SNP genotype data set, the haplotype configurations inferred by different methods are usually inconsistent, and it is often difficult to decide which one is true. In this paper, we design an accurate HLA gene type inference algorithm by utilizing SNP genotype data from pedigrees, known HLA gene types of some individuals and the relationship between inferred SNP haplotypes and HLA gene types. Given a set of haplotypes inferred from the genotypes of a population consisting of many pedigrees, the algorithm first constructs a weighted similarity graph based on a new haplotype similarity measure and derives constraint edges from known HLA gene types. Based on the principle that different HLA gene alleles should have different background haplotypes, the algorithm searches for an optimal labeling of all the haplotypes with unknown HLA gene types such that the total weight among the same HLA gene types is maximized. To deal with ambiguous haplotype solutions, we use a genetic algorithm to select haplotype configurations that tend to maximize the same optimization criterion. Our experiments on a previously typed subset of the HapMap data show that the algorithm is highly accurate, achieving an accuracy of 96% for gene HLA-A, 95% for HLA-B, 97% for HLA-C, 84% for HLA-DRB1, 98% for HLA-DQA1 and 97% for HLA-DQB1 in a leave-one-out test. Our algorithm can infer HLA gene types from neighboring SNP genotype data accurately. Compared with a recent approach on the same input data, our algorithm achieved a higher accuracy. The code of our algorithm is available to the public for free upon request to the corresponding authors.

“Of Sheep and Men”: Earliest Direct Evidence of Caprine Domestication in Southern Africa at Leopard Cave (Erongo, Namibia)

PubMed Central

Pleurdeau, David; Imalwa, Emma; Détroit, Florent; Lesur, Joséphine; Veldman, Anzel; Bahain, Jean-Jacques; Marais, Eugène

2012-01-01

The origins of herding practices in southern Africa remain controversial. The first appearance of domesticated caprines in the subcontinent is thought to be c. 2000 years BP; however, the origin of this cultural development is still widely debated. Recent genetic analyses support the long-standing hypothesis of herder migration from the north, while other researchers have argued for a cultural diffusion hypothesis where the spread of herding practices took place without necessarily implicating simultaneous and large population movements. Here we document the Later Stone Age (LSA) site of Leopard Cave (Erongo, Namibia), which contains confirmed caprine remains, from which we infer that domesticates were present in the southern African region as early as the end of the first millennium BC. These remains predate the first evidence of domesticates previously recorded for the subcontinent. This discovery sheds new light on the emergence of herding practices in southern Africa, and also on the possible southward routes used by caprines along the western Atlantic coast. PMID:22808138

"Of sheep and men": earliest direct evidence of caprine domestication in southern Africa at Leopard Cave (Erongo, Namibia).

PubMed

Pleurdeau, David; Imalwa, Emma; Détroit, Florent; Lesur, Joséphine; Veldman, Anzel; Bahain, Jean-Jacques; Marais, Eugène

2012-01-01

The origins of herding practices in southern Africa remain controversial. The first appearance of domesticated caprines in the subcontinent is thought to be c. 2000 years BP; however, the origin of this cultural development is still widely debated. Recent genetic analyses support the long-standing hypothesis of herder migration from the north, while other researchers have argued for a cultural diffusion hypothesis where the spread of herding practices took place without necessarily implicating simultaneous and large population movements. Here we document the Later Stone Age (LSA) site of Leopard Cave (Erongo, Namibia), which contains confirmed caprine remains, from which we infer that domesticates were present in the southern African region as early as the end of the first millennium BC. These remains predate the first evidence of domesticates previously recorded for the subcontinent. This discovery sheds new light on the emergence of herding practices in southern Africa, and also on the possible southward routes used by caprines along the western Atlantic coast.

Object-oriented feature-tracking algorithms for SAR images of the marginal ice zone

NASA Technical Reports Server (NTRS)

Daida, Jason; Samadani, Ramin; Vesecky, John F.

1990-01-01

An unsupervised method that chooses and applies the most appropriate tracking algorithm from among different sea-ice tracking algorithms is reported. In contrast to current unsupervised methods, this method chooses and applies an algorithm by partially examining a sequential image pair to draw inferences about what was examined. Based on these inferences the reported method subsequently chooses which algorithm to apply to specific areas of the image pair where that algorithm should work best.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

PubMed

Audain, Enrique; Uszkoreit, Julian; Sachsenberg, Timo; Pfeuffer, Julianus; Liang, Xiao; Hermjakob, Henning; Sanchez, Aniel; Eisenacher, Martin; Reinert, Knut; Tabb, David L; Kohlbacher, Oliver; Perez-Riverol, Yasset

2017-01-06

In mass spectrometry-based shotgun proteomics, protein identifications are usually the desired result. However, most of the analytical methods are based on the identification of reliable peptides and not the direct identification of intact proteins. Thus, assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Currently, different protein inference algorithms and tools are available for the proteomics community. Here, we evaluated five software tools for protein inference (PIA, ProteinProphet, Fido, ProteinLP, MSBayesPro) using three popular database search engines: Mascot, X!Tandem, and MS-GF+. All the algorithms were evaluated using a highly customizable KNIME workflow using four different public datasets with varying complexities (different sample preparation, species and analytical instruments). We defined a set of quality control metrics to evaluate the performance of each combination of search engines, protein inference algorithm, and parameters on each dataset. We show that the results for complex samples vary not only regarding the actual numbers of reported protein groups but also concerning the actual composition of groups. Furthermore, the robustness of reported proteins when using databases of differing complexities is strongly dependant on the applied inference algorithm. Finally, merging the identifications of multiple search engines does not necessarily increase the number of reported proteins, but does increase the number of peptides per protein and thus can generally be recommended. Protein inference is one of the major challenges in MS-based proteomics nowadays. Currently, there are a vast number of protein inference algorithms and implementations available for the proteomics community. Protein assembly impacts in the final results of the research, the quantitation values and the final claims in the research manuscript. Even though protein inference is a crucial step in proteomics data analysis, a comprehensive evaluation of the many different inference methods has never been performed. Previously Journal of proteomics has published multiple studies about other benchmark of bioinformatics algorithms (PMID: 26585461; PMID: 22728601) in proteomics studies making clear the importance of those studies for the proteomics community and the journal audience. This manuscript presents a new bioinformatics solution based on the KNIME/OpenMS platform that aims at providing a fair comparison of protein inference algorithms (https://github.com/KNIME-OMICS). Six different algorithms - ProteinProphet, MSBayesPro, ProteinLP, Fido and PIA- were evaluated using the highly customizable workflow on four public datasets with varying complexities. Five popular database search engines Mascot, X!Tandem, MS-GF+ and combinations thereof were evaluated for every protein inference tool. In total >186 proteins lists were analyzed and carefully compare using three metrics for quality assessments of the protein inference results: 1) the numbers of reported proteins, 2) peptides per protein, and the 3) number of uniquely reported proteins per inference method, to address the quality of each inference method. We also examined how many proteins were reported by choosing each combination of search engines, protein inference algorithms and parameters on each dataset. The results show that using 1) PIA or Fido seems to be a good choice when studying the results of the analyzed workflow, regarding not only the reported proteins and the high-quality identifications, but also the required runtime. 2) Merging the identifications of multiple search engines gives almost always more confident results and increases the number of peptides per protein group. 3) The usage of databases containing not only the canonical, but also known isoforms of proteins has a small impact on the number of reported proteins. The detection of specific isoforms could, concerning the question behind the study, compensate for slightly shorter reports using the parsimonious reports. 4) The current workflow can be easily extended to support new algorithms and search engine combinations. Copyright © 2016. Published by Elsevier B.V.

An algebra-based method for inferring gene regulatory networks.

PubMed

Vera-Licona, Paola; Jarrah, Abdul; Garcia-Puente, Luis David; McGee, John; Laubenbacher, Reinhard

2014-03-26

The inference of gene regulatory networks (GRNs) from experimental observations is at the heart of systems biology. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that infer network dynamics. Furthermore, since the network inference problem is typically underdetermined, it is essential to have the option of incorporating into the inference process, prior knowledge about the network, along with an effective description of the search space of dynamic models. Finally, it is also important to have an understanding of how a given inference method is affected by experimental and other noise in the data used. This paper contains a novel inference algorithm using the algebraic framework of Boolean polynomial dynamical systems (BPDS), meeting all these requirements. The algorithm takes as input time series data, including those from network perturbations, such as knock-out mutant strains and RNAi experiments. It allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS. The BPDS framework allows an effective representation of the search space for algebraic dynamic models that improves computational performance. The algorithm is validated with both simulated and experimental microarray expression profile data. Robustness to noise is tested using a published mathematical model of the segment polarity gene network in Drosophila melanogaster. Benchmarking of the algorithm is done by comparison with a spectrum of state-of-the-art network inference methods on data from the synthetic IRMA network to demonstrate that our method has good precision and recall for the network reconstruction task, while also predicting several of the dynamic patterns present in the network. Boolean polynomial dynamical systems provide a powerful modeling framework for the reverse engineering of gene regulatory networks, that enables a rich mathematical structure on the model search space. A C++ implementation of the method, distributed under LPGL license, is available, together with the source code, at http://www.paola-vera-licona.net/Software/EARevEng/REACT.html.

Carbon cycle dynamics and solar activity embedded in a high-resolution 14C speleothem record from Belize, Central America

NASA Astrophysics Data System (ADS)

Lechleitner, Franziska A.; Breitenbach, Sebastian F. M.; McIntyre, Cameron; Asmerom, Yemane; Prufer, Keith M.; Polyak, Victor; Culleton, Brendan J.; Kennett, Douglas J.; Eglinton, Timothy I.; Baldini, James U. L.

2015-04-01

Speleothem 14C has recently emerged as a potentially powerful proxy for climate reconstruction. Several studies have highlighted the link between karst hydrology and speleothem 14C content, and a number of possible causes for this relationship have been proposed, such as dripwater flow dynamics in the karst and changes in soil organic matter (SOM) turnover time (e.g. Griffiths et al., 2012). Here we present a high resolution 14C record for a stalagmite (YOK-I) from Yok Balum cave in southern Belize, Central America. YOK-I grew continuously over the last 2000 years, and has been dated very precisely with the U-Th method (40 dates, mean uncertainty < 10 years). The excellent chronological control for this stalagmite allows us to calculate 14C activity (a14C) at the time of speleothem deposition (a14Cinit), as well as the dead carbon fraction (DCF), predominantly a measure of the reservoir effect introduced by limestone dissolution in the karst (Genty et al., 2001). Both records show striking similarities to atmospheric a14C (IntCal13) and reconstructions of solar activity and 14C production rate. We infer close coupling between cave environment and atmosphere, with minimal signal dampening, an observation supported by monitoring data (Ridley et al., in press). DCF fluctuates between approximately 10% and 16% over the entire record, with distinctly lower DCF values and higher a14Cinit during a period of reduced rainfall between ca. 700-1100 AD (linked to the Classic Maya Collapse). This behavior is consistent with observations made elsewhere, and suggests that DCF responds to karst hydrological variability, specifically open-closed system transitions. YOK-I a14Cinit typically lags atmospheric values by 10-100 cal years. A shorter lag appears to be linked to periods of drought, suggesting a response of SOM dynamics above the cave to rainfall reduction. Specifically, drought is inferred to lead to reduced bioproductivity and soil carbon turnover, lowering contributions of old recalcitrant carbon to the soil water, and resulting in closer coupling between atmosphere and cave environment. The resolution of the record (0.3-0.7 mm/sample) permits identification of the dominant drivers of stalagmite 14C during different intervals. For example, hydrologic control on 14C appears dominant during the 11th century drought, while in the 16th to 18th century a clear solar influence exists. Solar activity is reflected in YOK-I as lower a14Cinit, reflecting the atmospheric a14C. We apply simple hydrological models to investigate the different factors influencing 14C in YOK-I. We estimate the importance of mean SOM age to signal dampening, and quantify the strength of the solar influence and the global carbon cycle on the record. References: Genty, D., Baker, A., Massault, M., Proctor, C., Gilmour, M., Pons-Branchu, E., Hamelin, B. (2001) Dead carbon in stalagmites: carbonate bedrock paleodissolution vs. ageing of soil organic matter. Implications for 13C variations in speleothems, GCA, 65 Griffiths, M.L., Fohlmeister, J., Drysdale, R.N., Hua, Q., Johnson, K.R., Hellstrom, J.C., Gagan, M.K., Zhao, J.-x. (2012) Hydrological control of the dead carbon fraction in a Holocene tropical speleothem, Quat. Geochron. 14 Ridley, H.E., Baldini, J.U.L., Prufer, K.M., Walczak, I.W., Breitenbach, S.F.M. (in press) High resolution monitoring of a tropical cave system reveals dynamic ventilation and hydrologic resilience to seismic activity, Journal of Cave and Karst Studies

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

PubMed

Wu, Yufeng

2012-03-01

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

Constraints on Long-Term Seismic Hazard From Vulnerable Stalagmites from Vacska cave, Pilis Mountains of Hungary

NASA Astrophysics Data System (ADS)

Gribovszki, Katalin; Bokelmann, Götz; Kovács, Károly; Mónus, Péter; Konecny, Pavel; Lednicka, Marketa; Novák, Attila

2017-04-01

Damaging earthquakes in central Europe are infrequent, but do occur. This raises the important issue for society of how to react to this hazard: potential damages are enormous, and infrastructure costs for addressing these hazards are huge as well. Obtaining an unbiased expert knowledge of the seismic hazard (and risk) is therefore very important. Seismic activity in the Pannonian Basin is moderate. In territories with low or moderate seismic activity the recurrence time of large earthquakes can be as long as 10,000 years. Therefore, we cannot draw well-grounded inferences in the field of seismic hazard assessment exclusively from the seismic data of 1,000- to 2,000-years observational period, that we have in our earthquake catalogues. Long-term information can be gained from intact and vulnerable stalagmites (IVSTM) in natural karstic caves. These fragile formations survived all earthquakes that have occurred, over thousands of years - depending on the age of them. Their "survival" requires that the horizontal ground acceleration has never exceeded a certain critical value within that time period. Here we present such a stalagmite-based case study from the Pilis Mountains of Hungary. Evidence of historic events and of differential uplifting (incision of Danube at the River Bend and in Buda and Gerecse Hills) exists in the vicinity of investigated cave site. These observations imply that a better understanding of possible co-seismic ground motions in the nearby densely populated areas of Budapest is needed. A specially shaped (high, slim and more or less cylindrical form), intact and vulnerable stalagmites in the Vacska cave, Pilis Mountains were examined. The method of our investigation includes in-situ examination of the IVSTM and mechanical laboratory measurements of broken stalagmite samples. The used approach can yield significant new constraints on the seismic hazard of the investigated area, since tectonic structures close to Vacska cave could not have generated strong paleoearthquakes in the last few thousand years, which would have produced a horizontal ground acceleration larger than the upper acceleration threshold that we can determined from the intact and vulnerable stalagmites. A particular importance of this study results from the seismic hazard of the capital of Hungary.

Algorithm of OMA for large-scale orthology inference

PubMed Central

Roth, Alexander CJ; Gonnet, Gaston H; Dessimoz, Christophe

2008-01-01

Background OMA is a project that aims to identify orthologs within publicly available, complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects of its kind. Results The algorithm of OMA improves upon standard bidirectional best-hit approach in several respects: it uses evolutionary distances instead of scores, considers distance inference uncertainty, includes many-to-many orthologous relations, and accounts for differential gene losses. Herein, we describe in detail the algorithm for inference of orthology and provide the rationale for parameter selection through multiple tests. Conclusion OMA contains several novel improvement ideas for orthology inference and provides a unique dataset of large-scale orthology assignments. PMID:19055798

Gene-network inference by message passing

NASA Astrophysics Data System (ADS)

Braunstein, A.; Pagnani, A.; Weigt, M.; Zecchina, R.

2008-01-01

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms.

PubMed

Ruyssinck, Joeri; Huynh-Thu, Vân Anh; Geurts, Pierre; Dhaene, Tom; Demeester, Piet; Saeys, Yvan

2014-01-01

One of the long-standing open challenges in computational systems biology is the topology inference of gene regulatory networks from high-throughput omics data. Recently, two community-wide efforts, DREAM4 and DREAM5, have been established to benchmark network inference techniques using gene expression measurements. In these challenges the overall top performer was the GENIE3 algorithm. This method decomposes the network inference task into separate regression problems for each gene in the network in which the expression values of a particular target gene are predicted using all other genes as possible predictors. Next, using tree-based ensemble methods, an importance measure for each predictor gene is calculated with respect to the target gene and a high feature importance is considered as putative evidence of a regulatory link existing between both genes. The contribution of this work is twofold. First, we generalize the regression decomposition strategy of GENIE3 to other feature importance methods. We compare the performance of support vector regression, the elastic net, random forest regression, symbolic regression and their ensemble variants in this setting to the original GENIE3 algorithm. To create the ensemble variants, we propose a subsampling approach which allows us to cast any feature selection algorithm that produces a feature ranking into an ensemble feature importance algorithm. We demonstrate that the ensemble setting is key to the network inference task, as only ensemble variants achieve top performance. As second contribution, we explore the effect of using rankwise averaged predictions of multiple ensemble algorithms as opposed to only one. We name this approach NIMEFI (Network Inference using Multiple Ensemble Feature Importance algorithms) and show that this approach outperforms all individual methods in general, although on a specific network a single method can perform better. An implementation of NIMEFI has been made publicly available.

Inter-annual precipitation variabiity inferred from late Holocene speleothem records from Fiji: implications for SPCZ localisation and ENSO behaviour

NASA Astrophysics Data System (ADS)

Mattey, D.; Stephens, M.; Hoffmann, D.; Brett, M.

2015-12-01

The modern tropical Fiji climate is characterised by seasonal rainfall controlled by the position of the South Pacific Convergence Zone (SPCZ). Interannual rainfall is strongly modulated on decadal timescales by ENSO with higher rainfall associated with La Nina events. Voli Voli cave near Sigatoga (Viti Levu) is a stream passage that has been monitored since 2009. A U-Th dated laminated speleothem spans a 1500 year interval across the transition from the Medieval Warm Period into the Little Ice Age marked by a fabric change from finely laminated calcite with thin clay layers, to white well-laminated calcite. The older record is characterised by rising δ13C values followed by a rapid decrease in δ13C around 1200 AD. Evidence from cave monitoring shows that cave air CO2 levels are strongly seasonal as a result of greater ventilation by winter trade winds and high resolution δ13C record shows regularly spaced peaks correlated with paired laminae and cycles in P and S which provide annual markers driven by rainfall and seasonal ventilation. δ18O values remain relatively unchanged throughout the record but micromilling at sub-annual resolution reveals systematic cycles in δ18O that span groups of paired laminae with an inferred periodicity of 3-7 years i.e. a similar frequency to modern ENSO. The presence of these sub-decadal cycles in δ18O may be a result of a combination of factors. The amplitude of 2-3‰ would be equivalent to an amount-effect related change in annual precipitation of around 50% but an additional smoothing process, perhaps a result of aquifer storage, is required to attenuate interannual variance in precipitation. The Voli Voli record provides evidence of an underlying climatic change to more frequent La Niña conditions from 1200 AD and may be associated with increased conflict, shifts in settlements and changes in subsistence strategies on the island. Coeval speleothem isotope records from tropical Pacific Islands provide a provide a powerful means of locating the mean position and intensity of the SPCZ and changes in regional coupling of ocean-atmospheric circulation patterns.

An algebra-based method for inferring gene regulatory networks

PubMed Central

2014-01-01

Background The inference of gene regulatory networks (GRNs) from experimental observations is at the heart of systems biology. This includes the inference of both the network topology and its dynamics. While there are many algorithms available to infer the network topology from experimental data, less emphasis has been placed on methods that infer network dynamics. Furthermore, since the network inference problem is typically underdetermined, it is essential to have the option of incorporating into the inference process, prior knowledge about the network, along with an effective description of the search space of dynamic models. Finally, it is also important to have an understanding of how a given inference method is affected by experimental and other noise in the data used. Results This paper contains a novel inference algorithm using the algebraic framework of Boolean polynomial dynamical systems (BPDS), meeting all these requirements. The algorithm takes as input time series data, including those from network perturbations, such as knock-out mutant strains and RNAi experiments. It allows for the incorporation of prior biological knowledge while being robust to significant levels of noise in the data used for inference. It uses an evolutionary algorithm for local optimization with an encoding of the mathematical models as BPDS. The BPDS framework allows an effective representation of the search space for algebraic dynamic models that improves computational performance. The algorithm is validated with both simulated and experimental microarray expression profile data. Robustness to noise is tested using a published mathematical model of the segment polarity gene network in Drosophila melanogaster. Benchmarking of the algorithm is done by comparison with a spectrum of state-of-the-art network inference methods on data from the synthetic IRMA network to demonstrate that our method has good precision and recall for the network reconstruction task, while also predicting several of the dynamic patterns present in the network. Conclusions Boolean polynomial dynamical systems provide a powerful modeling framework for the reverse engineering of gene regulatory networks, that enables a rich mathematical structure on the model search space. A C++ implementation of the method, distributed under LPGL license, is available, together with the source code, at http://www.paola-vera-licona.net/Software/EARevEng/REACT.html. PMID:24669835

Ensemble stacking mitigates biases in inference of synaptic connectivity.

PubMed

Chambers, Brendan; Levy, Maayan; Dechery, Joseph B; MacLean, Jason N

2018-01-01

A promising alternative to directly measuring the anatomical connections in a neuronal population is inferring the connections from the activity. We employ simulated spiking neuronal networks to compare and contrast commonly used inference methods that identify likely excitatory synaptic connections using statistical regularities in spike timing. We find that simple adjustments to standard algorithms improve inference accuracy: A signing procedure improves the power of unsigned mutual-information-based approaches and a correction that accounts for differences in mean and variance of background timing relationships, such as those expected to be induced by heterogeneous firing rates, increases the sensitivity of frequency-based methods. We also find that different inference methods reveal distinct subsets of the synaptic network and each method exhibits different biases in the accurate detection of reciprocity and local clustering. To correct for errors and biases specific to single inference algorithms, we combine methods into an ensemble. Ensemble predictions, generated as a linear combination of multiple inference algorithms, are more sensitive than the best individual measures alone, and are more faithful to ground-truth statistics of connectivity, mitigating biases specific to single inference methods. These weightings generalize across simulated datasets, emphasizing the potential for the broad utility of ensemble-based approaches.

A novel gene network inference algorithm using predictive minimum description length approach.

PubMed

Chaitankar, Vijender; Ghosh, Preetam; Perkins, Edward J; Gong, Ping; Deng, Youping; Zhang, Chaoyang

2010-05-28

Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold which defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to find the optimal parameter. In this work, we proposed a new inference algorithm which incorporated mutual information (MI), conditional mutual information (CMI) and predictive minimum description length (PMDL) principle to infer gene regulatory networks from DNA microarray data. In this algorithm, the information theoretic quantities MI and CMI determine the regulatory relationships between genes and the PMDL principle method attempts to determine the best MI threshold without the need of a user-specified fine tuning parameter. The performance of the proposed algorithm was evaluated using both synthetic time series data sets and a biological time series data set for the yeast Saccharomyces cerevisiae. The benchmark quantities precision and recall were used as performance measures. The results show that the proposed algorithm produced less false edges and significantly improved the precision, as compared to the existing algorithm. For further analysis the performance of the algorithms was observed over different sizes of data. We have proposed a new algorithm that implements the PMDL principle for inferring gene regulatory networks from time series DNA microarray data that eliminates the need of a fine tuning parameter. The evaluation results obtained from both synthetic and actual biological data sets show that the PMDL principle is effective in determining the MI threshold and the developed algorithm improves precision of gene regulatory network inference. Based on the sensitivity analysis of all tested cases, an optimal CMI threshold value has been identified. Finally it was observed that the performance of the algorithms saturates at a certain threshold of data size.

Efficient Exact Inference With Loss Augmented Objective in Structured Learning.

PubMed

Bauer, Alexander; Nakajima, Shinichi; Muller, Klaus-Robert

2016-08-19

Structural support vector machine (SVM) is an elegant approach for building complex and accurate models with structured outputs. However, its applicability relies on the availability of efficient inference algorithms--the state-of-the-art training algorithms repeatedly perform inference to compute a subgradient or to find the most violating configuration. In this paper, we propose an exact inference algorithm for maximizing nondecomposable objectives due to special type of a high-order potential having a decomposable internal structure. As an important application, our method covers the loss augmented inference, which enables the slack and margin scaling formulations of structural SVM with a variety of dissimilarity measures, e.g., Hamming loss, precision and recall, Fβ-loss, intersection over union, and many other functions that can be efficiently computed from the contingency table. We demonstrate the advantages of our approach in natural language parsing and sequence segmentation applications.

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.

PubMed

Stolzer, Maureen; Lai, Han; Xu, Minli; Sathaye, Deepa; Vernot, Benjamin; Durand, Dannie

2012-09-15

Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. mstolzer@andrew.cmu.edu.

Algorithm Optimally Orders Forward-Chaining Inference Rules

NASA Technical Reports Server (NTRS)

James, Mark

2008-01-01

People typically develop knowledge bases in a somewhat ad hoc manner by incrementally adding rules with no specific organization. This often results in a very inefficient execution of those rules since they are so often order sensitive. This is relevant to tasks like Deep Space Network in that it allows the knowledge base to be incrementally developed and have it automatically ordered for efficiency. Although data flow analysis was first developed for use in compilers for producing optimal code sequences, its usefulness is now recognized in many software systems including knowledge-based systems. However, this approach for exhaustively computing data-flow information cannot directly be applied to inference systems because of the ubiquitous execution of the rules. An algorithm is presented that efficiently performs a complete producer/consumer analysis for each antecedent and consequence clause in a knowledge base to optimally order the rules to minimize inference cycles. An algorithm was developed that optimally orders a knowledge base composed of forwarding chaining inference rules such that independent inference cycle executions are minimized, thus, resulting in significantly faster execution. This algorithm was integrated into the JPL tool Spacecraft Health Inference Engine (SHINE) for verification and it resulted in a significant reduction in inference cycles for what was previously considered an ordered knowledge base. For a knowledge base that is completely unordered, then the improvement is much greater.

Simulation Study on Missile Penetration Based on LS - DYNA

NASA Astrophysics Data System (ADS)

Tang, Jue; Sun, Xinli

2017-12-01

Penetrating the shell armor is an effective means of destroying hard targets with multiple layers of protection. The penetration process is a high-speed impact dynamics research category, involving high pressure, high temperature, high speed and internal material damage, including plugging, penetration, spalling, caving, splashing and other complex forms, therefore, Analysis is one of the difficulties in the study of impact dynamics. In this paper, the Lagrang algorithm and the SPH algorithm are used to analyze the penetrating steel plate, and the penetration model of the rocket penetrating the steel plate, the failure mode of the steel plate and the missile and the advantages and disadvantages of Lagrang algorithm and SPH algorithm in the simulation of high-speed collision problem are analyzed and compared, which provides a reference for the study of simulation collision problem.

Comparison of 3D point clouds produced by LIDAR and UAV photoscan in the Rochefort cave (Belgium)

NASA Astrophysics Data System (ADS)

Watlet, Arnaud; Triantafyllou, Antoine; Kaufmann, Olivier; Le Mouelic, Stéphane

2016-04-01

Amongst today's techniques that are able to produce 3D point clouds, LIDAR and UAV (Unmanned Aerial Vehicle) photogrammetry are probably the most commonly used. Both methods have their own advantages and limitations. LIDAR scans create high resolution and high precision 3D point clouds, but such methods are generally costly, especially for sporadic surveys. Compared to LIDAR, UAV (e.g. drones) are cheap and flexible to use in different kind of environments. Moreover, the photogrammetric processing workflow of digital images taken with UAV becomes easier with the rise of many affordable software packages (e.g. Agisoft, PhotoModeler3D, VisualSFM). We present here a challenging study made at the Rochefort Cave Laboratory (South Belgium) comprising surface and underground surveys. The site is located in the Belgian Variscan fold-and-thrust belt, a region that shows many karstic networks within Devonian limestone units. A LIDAR scan has been acquired in the main chamber of the cave (~ 15000 m³) to spatialize 3D point cloud of its inner walls and infer geological beds and structures. Even if the use of LIDAR instrument was not really comfortable in such caving environment, the collected data showed a remarkable precision according to few control points geometry. We also decided to perform another challenging survey of the same cave chamber by modelling a 3D point cloud using photogrammetry of a set of DSLR camera pictures taken from the ground and UAV pictures. The aim was to compare both techniques in terms of (i) implementation of data acquisition and processing, (ii) quality of resulting 3D points clouds (points density, field vs cloud recovery and points precision), (iii) their application for geological purposes. Through Rochefort case study, main conclusions are that LIDAR technique provides higher density point clouds with slightly higher precision than photogrammetry method. However, 3D data modeled by photogrammetry provide visible light spectral information for each modeled voxel and interpolated vertices that can be a useful attributes for clustering during data treatment. We thus illustrate such applications to the Rochefort cave by using both sources of 3D information to quantify the orientation of inaccessible geological structures (e.g. faults, tectonic and gravitational joints, and sediments bedding), cluster these structures using color information gathered from UAV's 3D point cloud and compare these data to structural data surveyed on the field. An additional drone photoscan was also conducted in the surface sinkhole giving access to the surveyed underground cavity to seek geological bodies' connections.

Hydraulics of epiphreatic flow of a karst aquifer

NASA Astrophysics Data System (ADS)

Gabrovšek, Franci; Peric, Borut; Kaufmann, Georg

2018-05-01

The nature of epiphreatic flow remains an important research challenge in karst hydrology. This study focuses on the flood propagation along the epiphreatic system of Reka-Timavo system (Kras/Carso Plateau, Slovenia/Italy). It is based on long-term monitoring of basic physical parameters (pressure/level, temperature, specific electric conductivity) of ground water in six active caves belonging to the flow system. The system vigorously responds to flood events, with stage rising >100 m in some of the caves. Besides presenting the response of the system to flood events of different scales, the work focuses on the interpretation of recorded hydrographs in view of the known distribution and size of conduits and basic hydraulic relations. Furthermore, the hydrographs were used to infer the unknown geometry between the observation points. This way, the main flow restrictors, overflow passages and large epiphreatic storages were identified. The assumptions were tested with a hydraulic model, where the inversion procedure was used for an additional parameter optimisation. Time series of temperature and specific electric conductivity were used to assess the apparent velocities of flow between consecutive points.

Modeling Paragenesis: Erosion Opposite to Gravity in Cave Channels

NASA Astrophysics Data System (ADS)

Cooper, M. P.; Covington, M. D.

2017-12-01

Sediment plays an important role in bedrock channels, providing both tools and cover that influence patterns of bed erosion. It has also been shown that sediment load influences bedrock channel width, with increased sediment leading to wider channels. A variety of models have been developed to explore these effects. In caves, it is hypothesized that sediments covering the floors of fully flooded channels that are forming beneath the water table (phreatic zone) can force dissolution upwards towards the water table, leading to upward erosion balanced by gradual deposition of sediment within the channel bottom. This strange process is termed paragenesis, and while there are conceptual and experimental models of the process, no prior mathematical models of cave passage evolution has captured these effects. Consequently, there is little quantitative understanding of the processes that drive paragenesis and how they link to the morphology of the cave channels that develop. We adapt a previously developed algorithm for estimating boundary shear stress within channels with free-surface flows to enable calculation of boundary shear stress in pipe-full conditions. This model successfully duplicates scaling relationships in surface channels, and geometries of caves formed in the phreatic zone such as phreatic tubes. Once sediment flux is incorporated the model successfully duplicates the hypothesized processes of paragenetic gallery formation: the cover effect prevents dissolution in the direction of gravity; passages are enlarged upwards reducing the sediment transport capacity; sediment is deposited and the process drives a continuing feedback loop. Simulations reveal that equilibrium paragenetic channel widths scale with both sediment flux and discharge. Unlike in open channel settings, increased sediment load actually narrows paragenetic channels. The cross section evolution model also reveals that the existence of equilibrium widths in such galleries requires erosion to scale with shear stress, suggesting a role of either mechanical erosion or transport limited dissolution. These types of erosion contrast with current numerical models of speleogenesis, where chemically limited dissolution, a process independent of shear stress, is predicted to occur in most turbulent flow settings.

The Manhattan Frame Model-Manhattan World Inference in the Space of Surface Normals.

PubMed

Straub, Julian; Freifeld, Oren; Rosman, Guy; Leonard, John J; Fisher, John W

2018-01-01

Objects and structures within man-made environments typically exhibit a high degree of organization in the form of orthogonal and parallel planes. Traditional approaches utilize these regularities via the restrictive, and rather local, Manhattan World (MW) assumption which posits that every plane is perpendicular to one of the axes of a single coordinate system. The aforementioned regularities are especially evident in the surface normal distribution of a scene where they manifest as orthogonally-coupled clusters. This motivates the introduction of the Manhattan-Frame (MF) model which captures the notion of an MW in the surface normals space, the unit sphere, and two probabilistic MF models over this space. First, for a single MF we propose novel real-time MAP inference algorithms, evaluate their performance and their use in drift-free rotation estimation. Second, to capture the complexity of real-world scenes at a global scale, we extend the MF model to a probabilistic mixture of Manhattan Frames (MMF). For MMF inference we propose a simple MAP inference algorithm and an adaptive Markov-Chain Monte-Carlo sampling algorithm with Metropolis-Hastings split/merge moves that let us infer the unknown number of mixture components. We demonstrate the versatility of the MMF model and inference algorithm across several scales of man-made environments.

Statistical Signal Models and Algorithms for Image Analysis

DTIC Science & Technology

1984-10-25

In this report, two-dimensional stochastic linear models are used in developing algorithms for image analysis such as classification, segmentation, and object detection in images characterized by textured backgrounds. These models generate two-dimensional random processes as outputs to which statistical inference procedures can naturally be applied. A common thread throughout our algorithms is the interpretation of the inference procedures in terms of linear prediction

Coping with brackish water: A new species of cave-dwelling Protosuberites Porifera: Demospongiae: Suberitidae) from the Western Mediterranean and a first contribution to the phylogenetic relationships within the genus.

PubMed

Melis, Paolo; Riesgo, Ana; Taboada, Sergio; Manconi, Renata

2016-12-18

We used both morphological and genetic approaches to investigate and to describe a new Mediterranean sponge species of the genus Protosuberites from the estuarine-anchialine Bue Marino Cave of Sardinia (Tyrrhenian Sea). The morphotraits of the specimens were compared versus congeneric species with the strongest affinities, covering the genus geographic range worldwide. Protosuberites mereui sp. nov. is light yellow, thinly encrusting, devoid of any special ectosomal skeleton, with spicular complement of tylostyles of three size classes, single or arranged in bundles/tufts, with round to suboval heads. The new species is characterized by an exclusive diagnostic trait recorded for any cave-dwelling Protosuberites i.e. suboval and basally plated resting bodies with a foraminal aperture ornate by a collar. Resting bodies were found in the basal spongin plate firmly adhering to the substratum singly or in small groups. Also the rare, small tylostyles with a sinuous shaft and a typical mushroom-like head were never recorded in the Western Mediterranean and Atlantic species of the genus. The phylogenetic reconstruction using maximum likelihood (ML) and Bayesian Inference (BI) analyses (COI, 18S rRNA, and 28S rRNA) recovered a robustly supported sister relationship between the Mediterranean P. mereui sp. nov. and Protosuberites sp. 'Panama' from the Eastern Pacific Ocean. The genetic distances based on COI sequences between all compared Protosuberites species were always higher than 2%, a value sufficient to confirm that P. mereui sp. nov. is a distinct species within the genus. Morphological and genetic analyses confirm unanimously P. mereui sp. nov. as a new species. Our results contribute to the assessment of biodiversity in anchialine/estuarine caves and increase data on sponge adaptive strategies in these extreme ecosystems.

The architecture of adaptive neural network based on a fuzzy inference system for implementing intelligent control in photovoltaic systems

NASA Astrophysics Data System (ADS)

Gimazov, R.; Shidlovskiy, S.

2018-05-01

In this paper, we consider the architecture of the algorithm for extreme regulation in the photovoltaic system. An algorithm based on an adaptive neural network with fuzzy inference is proposed. The implementation of such an algorithm not only allows solving a number of problems in existing algorithms for extreme power regulation of photovoltaic systems, but also creates a reserve for the creation of a universal control system for a photovoltaic system.

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks

PubMed Central

Yamanaka, Ryota; Kitano, Hiroaki

2013-01-01

Elucidating gene regulatory network (GRN) from large scale experimental data remains a central challenge in systems biology. Recently, numerous techniques, particularly consensus driven approaches combining different algorithms, have become a potentially promising strategy to infer accurate GRNs. Here, we develop a novel consensus inference algorithm, TopkNet that can integrate multiple algorithms to infer GRNs. Comprehensive performance benchmarking on a cloud computing framework demonstrated that (i) a simple strategy to combine many algorithms does not always lead to performance improvement compared to the cost of consensus and (ii) TopkNet integrating only high-performance algorithms provide significant performance improvement compared to the best individual algorithms and community prediction. These results suggest that a priori determination of high-performance algorithms is a key to reconstruct an unknown regulatory network. Similarity among gene-expression datasets can be useful to determine potential optimal algorithms for reconstruction of unknown regulatory networks, i.e., if expression-data associated with known regulatory network is similar to that with unknown regulatory network, optimal algorithms determined for the known regulatory network can be repurposed to infer the unknown regulatory network. Based on this observation, we developed a quantitative measure of similarity among gene-expression datasets and demonstrated that, if similarity between the two expression datasets is high, TopkNet integrating algorithms that are optimal for known dataset perform well on the unknown dataset. The consensus framework, TopkNet, together with the similarity measure proposed in this study provides a powerful strategy towards harnessing the wisdom of the crowds in reconstruction of unknown regulatory networks. PMID:24278007

Spiking neuron network Helmholtz machine.

PubMed

Sountsov, Pavel; Miller, Paul

2015-01-01

An increasing amount of behavioral and neurophysiological data suggests that the brain performs optimal (or near-optimal) probabilistic inference and learning during perception and other tasks. Although many machine learning algorithms exist that perform inference and learning in an optimal way, the complete description of how one of those algorithms (or a novel algorithm) can be implemented in the brain is currently incomplete. There have been many proposed solutions that address how neurons can perform optimal inference but the question of how synaptic plasticity can implement optimal learning is rarely addressed. This paper aims to unify the two fields of probabilistic inference and synaptic plasticity by using a neuronal network of realistic model spiking neurons to implement a well-studied computational model called the Helmholtz Machine. The Helmholtz Machine is amenable to neural implementation as the algorithm it uses to learn its parameters, called the wake-sleep algorithm, uses a local delta learning rule. Our spiking-neuron network implements both the delta rule and a small example of a Helmholtz machine. This neuronal network can learn an internal model of continuous-valued training data sets without supervision. The network can also perform inference on the learned internal models. We show how various biophysical features of the neural implementation constrain the parameters of the wake-sleep algorithm, such as the duration of the wake and sleep phases of learning and the minimal sample duration. We examine the deviations from optimal performance and tie them to the properties of the synaptic plasticity rule.

Spiking neuron network Helmholtz machine

PubMed Central

Sountsov, Pavel; Miller, Paul

2015-01-01

An increasing amount of behavioral and neurophysiological data suggests that the brain performs optimal (or near-optimal) probabilistic inference and learning during perception and other tasks. Although many machine learning algorithms exist that perform inference and learning in an optimal way, the complete description of how one of those algorithms (or a novel algorithm) can be implemented in the brain is currently incomplete. There have been many proposed solutions that address how neurons can perform optimal inference but the question of how synaptic plasticity can implement optimal learning is rarely addressed. This paper aims to unify the two fields of probabilistic inference and synaptic plasticity by using a neuronal network of realistic model spiking neurons to implement a well-studied computational model called the Helmholtz Machine. The Helmholtz Machine is amenable to neural implementation as the algorithm it uses to learn its parameters, called the wake-sleep algorithm, uses a local delta learning rule. Our spiking-neuron network implements both the delta rule and a small example of a Helmholtz machine. This neuronal network can learn an internal model of continuous-valued training data sets without supervision. The network can also perform inference on the learned internal models. We show how various biophysical features of the neural implementation constrain the parameters of the wake-sleep algorithm, such as the duration of the wake and sleep phases of learning and the minimal sample duration. We examine the deviations from optimal performance and tie them to the properties of the synaptic plasticity rule. PMID:25954191

A linear programming model for protein inference problem in shotgun proteomics.

PubMed

Huang, Ting; He, Zengyou

2012-11-15

Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is an important issue in shotgun proteomics. The objective of protein inference is to find a subset of proteins that are truly present in the sample. Although many methods have been proposed for protein inference, several issues such as peptide degeneracy still remain unsolved. In this article, we present a linear programming model for protein inference. In this model, we use a transformation of the joint probability that each peptide/protein pair is present in the sample as the variable. Then, both the peptide probability and protein probability can be expressed as a formula in terms of the linear combination of these variables. Based on this simple fact, the protein inference problem is formulated as an optimization problem: minimize the number of proteins with non-zero probabilities under the constraint that the difference between the calculated peptide probability and the peptide probability generated from peptide identification algorithms should be less than some threshold. This model addresses the peptide degeneracy issue by forcing some joint probability variables involving degenerate peptides to be zero in a rigorous manner. The corresponding inference algorithm is named as ProteinLP. We test the performance of ProteinLP on six datasets. Experimental results show that our method is competitive with the state-of-the-art protein inference algorithms. The source code of our algorithm is available at: https://sourceforge.net/projects/prolp/. zyhe@dlut.edu.cn. Supplementary data are available at Bioinformatics Online.

Inferring nonlinear gene regulatory networks from gene expression data based on distance correlation.

PubMed

Guo, Xiaobo; Zhang, Ye; Hu, Wenhao; Tan, Haizhu; Wang, Xueqin

2014-01-01

Nonlinear dependence is general in regulation mechanism of gene regulatory networks (GRNs). It is vital to properly measure or test nonlinear dependence from real data for reconstructing GRNs and understanding the complex regulatory mechanisms within the cellular system. A recently developed measurement called the distance correlation (DC) has been shown powerful and computationally effective in nonlinear dependence for many situations. In this work, we incorporate the DC into inferring GRNs from the gene expression data without any underling distribution assumptions. We propose three DC-based GRNs inference algorithms: CLR-DC, MRNET-DC and REL-DC, and then compare them with the mutual information (MI)-based algorithms by analyzing two simulated data: benchmark GRNs from the DREAM challenge and GRNs generated by SynTReN network generator, and an experimentally determined SOS DNA repair network in Escherichia coli. According to both the receiver operator characteristic (ROC) curve and the precision-recall (PR) curve, our proposed algorithms significantly outperform the MI-based algorithms in GRNs inference.

Inferring Nonlinear Gene Regulatory Networks from Gene Expression Data Based on Distance Correlation

PubMed Central

Guo, Xiaobo; Zhang, Ye; Hu, Wenhao; Tan, Haizhu; Wang, Xueqin

2014-01-01

Nonlinear dependence is general in regulation mechanism of gene regulatory networks (GRNs). It is vital to properly measure or test nonlinear dependence from real data for reconstructing GRNs and understanding the complex regulatory mechanisms within the cellular system. A recently developed measurement called the distance correlation (DC) has been shown powerful and computationally effective in nonlinear dependence for many situations. In this work, we incorporate the DC into inferring GRNs from the gene expression data without any underling distribution assumptions. We propose three DC-based GRNs inference algorithms: CLR-DC, MRNET-DC and REL-DC, and then compare them with the mutual information (MI)-based algorithms by analyzing two simulated data: benchmark GRNs from the DREAM challenge and GRNs generated by SynTReN network generator, and an experimentally determined SOS DNA repair network in Escherichia coli. According to both the receiver operator characteristic (ROC) curve and the precision-recall (PR) curve, our proposed algorithms significantly outperform the MI-based algorithms in GRNs inference. PMID:24551058

The Science of Exploring Caves.

ERIC Educational Resources Information Center

Reid, Frank S.

1991-01-01

An introduction to the science of speleology is presented. Discussed is why people explore caves--for the physical challenge, the thrill of discovery, and the joy of viewing their beauty. Cave conservation, cave biology, caving safety, and caving equipment are topics of discussion. A reading list on caves is included. (KR)

Inferring genetic interactions via a nonlinear model and an optimization algorithm.

PubMed

Chen, Chung-Ming; Lee, Chih; Chuang, Cheng-Long; Wang, Chia-Chang; Shieh, Grace S

2010-02-26

Biochemical pathways are gradually becoming recognized as central to complex human diseases and recently genetic/transcriptional interactions have been shown to be able to predict partial pathways. With the abundant information made available by microarray gene expression data (MGED), nonlinear modeling of these interactions is now feasible. Two of the latest advances in nonlinear modeling used sigmoid models to depict transcriptional interaction of a transcription factor (TF) for a target gene, but do not model cooperative or competitive interactions of several TFs for a target. An S-shape model and an optimization algorithm (GASA) were developed to infer genetic interactions/transcriptional regulation of several genes simultaneously using MGED. GASA consists of a genetic algorithm (GA) and a simulated annealing (SA) algorithm, which is enhanced by a steepest gradient descent algorithm to avoid being trapped in local minimum. Using simulated data with various degrees of noise, we studied how GASA with two model selection criteria and two search spaces performed. Furthermore, GASA was shown to outperform network component analysis, the time series network inference algorithm (TSNI), GA with regular GA (GAGA) and GA with regular SA. Two applications are demonstrated. First, GASA is applied to infer a subnetwork of human T-cell apoptosis. Several of the predicted interactions are supported by the literature. Second, GASA was applied to infer the transcriptional factors of 34 cell cycle regulated targets in S. cerevisiae, and GASA performed better than one of the latest advances in nonlinear modeling, GAGA and TSNI. Moreover, GASA is able to predict multiple transcription factors for certain targets, and these results coincide with experiments confirmed data in YEASTRACT. GASA is shown to infer both genetic interactions and transcriptional regulatory interactions well. In particular, GASA seems able to characterize the nonlinear mechanism of transcriptional regulatory interactions (TIs) in yeast, and may be applied to infer TIs in other organisms. The predicted genetic interactions of a subnetwork of human T-cell apoptosis coincide with existing partial pathways, suggesting the potential of GASA on inferring biochemical pathways.

Theoretic derivation of directed acyclic subgraph algorithm and comparisons with message passing algorithm

NASA Astrophysics Data System (ADS)

Ha, Jeongmok; Jeong, Hong

2016-07-01

This study investigates the directed acyclic subgraph (DAS) algorithm, which is used to solve discrete labeling problems much more rapidly than other Markov-random-field-based inference methods but at a competitive accuracy. However, the mechanism by which the DAS algorithm simultaneously achieves competitive accuracy and fast execution speed, has not been elucidated by a theoretical derivation. We analyze the DAS algorithm by comparing it with a message passing algorithm. Graphical models, inference methods, and energy-minimization frameworks are compared between DAS and message passing algorithms. Moreover, the performances of DAS and other message passing methods [sum-product belief propagation (BP), max-product BP, and tree-reweighted message passing] are experimentally compared.

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms

PubMed Central

Ruyssinck, Joeri; Huynh-Thu, Vân Anh; Geurts, Pierre; Dhaene, Tom; Demeester, Piet; Saeys, Yvan

2014-01-01

One of the long-standing open challenges in computational systems biology is the topology inference of gene regulatory networks from high-throughput omics data. Recently, two community-wide efforts, DREAM4 and DREAM5, have been established to benchmark network inference techniques using gene expression measurements. In these challenges the overall top performer was the GENIE3 algorithm. This method decomposes the network inference task into separate regression problems for each gene in the network in which the expression values of a particular target gene are predicted using all other genes as possible predictors. Next, using tree-based ensemble methods, an importance measure for each predictor gene is calculated with respect to the target gene and a high feature importance is considered as putative evidence of a regulatory link existing between both genes. The contribution of this work is twofold. First, we generalize the regression decomposition strategy of GENIE3 to other feature importance methods. We compare the performance of support vector regression, the elastic net, random forest regression, symbolic regression and their ensemble variants in this setting to the original GENIE3 algorithm. To create the ensemble variants, we propose a subsampling approach which allows us to cast any feature selection algorithm that produces a feature ranking into an ensemble feature importance algorithm. We demonstrate that the ensemble setting is key to the network inference task, as only ensemble variants achieve top performance. As second contribution, we explore the effect of using rankwise averaged predictions of multiple ensemble algorithms as opposed to only one. We name this approach NIMEFI (Network Inference using Multiple Ensemble Feature Importance algorithms) and show that this approach outperforms all individual methods in general, although on a specific network a single method can perform better. An implementation of NIMEFI has been made publicly available. PMID:24667482

Numerical simulation of formation and preservation of Ningwu ice cave, Shanxi, China

NASA Astrophysics Data System (ADS)

Yang, S.; Shi, Y.

2015-04-01

Ice caves exist in locations where annual average temperature in higher than 0 °C. An example is Ningwu ice cave, Shanxi Province, the largest ice cave in China. In order to quantitatively explain the mechanism of formation and preservation of the ice cave, we use Finite Element Method to simulate the heat transfer process at this ice cave. There are two major control factors. First, there is the seasonal asymmetric heat transfer. Heat is transferred into the ice cave from outside, very inefficiently by conduction in spring, summer and fall. In winter, thermal convection occurs that transfers heat very efficiently out of the ice cave, thus cooling it down. Secondly, ice-water phase change provides a heat barrier for heat transfer into the cave in summer. The calculation also helps to evaluate effects of global warming, tourists, etc. for sustainable development of ice cave as tourism resource. In some other ice caves in China, managers installed air-tight doors at these ice caves entrance intending to "protect" these caves, but this prevent cooling down these caves in winters and these cave ices will entirely melt within tens of years.

Geologic controls on cave development in Burnsville Cove, Bath and Highland Counties, Virginia

USGS Publications Warehouse

Swezey, Christopher; Haynes, John T.; Lucas, Philip C.; Lambert, Richard A.

2017-01-01

Burnsville Cove in Bath and Highland Counties (Virginia, USA) is a karst region in the Valley and Ridge Province of the Appalachian Mountains. The region contains many caves in Silurian to Devonian limestone, and is well suited for examining geologic controls on cave location and cave passage morphology. In Burnsville Cove, many caves are located preferentially near the axes of synclines and anticlines. For example, Butler Cave is an elongate cave where the trunk channel follows the axis of Sinking Creek syncline and most of the side passages follow joints at right angles to the syncline axis. In contrast, the Water Sinks Subway Cave, Owl Cave, and Helictite Cave have abundant maze patterns, and are located near the axis of Chestnut Ridge anticline. The maze patterns may be related to fact that the anticline axis is the site of the greatest amount of flexure, leading to more joints and (or) greater enlargement of joints. Many of the larger caves of Burnsville Cove (e.g., Breathing Cave, Butler Cave–Sinking Creek Cave System, lower parts of the Water Sinks Cave System) are developed in the Silurian Tonoloway Limestone, the stratigraphic unit with the greatest surface exposure in the area. Other caves are developed in the Silurian to Devonian Keyser Limestone of the Helderberg Group (e.g., Owl Cave, upper parts of the Water Sinks Cave System) and in the Devonian Shriver Chert and (or) Licking Creek Limestone of the Helderberg Group (e.g., Helictite Cave). Within the Tonoloway Limestone, the larger caves are developed in the lower member of the Tonoloway Limestone immediately below a bed of silica-cemented sandstone. In contrast, the larger caves in the Keyser Limestone are located preferentially in limestone beds containing stromatoporoid reefs, and some of the larger caves in the Licking Creek Limestone are located in beds of cherty limestone below the Devonian Oriskany Sandstone. Geologic controls on cave passage morphology include joints, bedding planes, and folds. The influence of joints results in tall and narrow cave passages, whereas the influence of bedding planes results in cave passages with flat ceilings and (or) floors. The influence of folds is less common, but a few cave passages follow fold axes and have distinctive arched ceilings.

Fundamentals and Recent Developments in Approximate Bayesian Computation

PubMed Central

Lintusaari, Jarno; Gutmann, Michael U.; Dutta, Ritabrata; Kaski, Samuel; Corander, Jukka

2017-01-01

Abstract Bayesian inference plays an important role in phylogenetics, evolutionary biology, and in many other branches of science. It provides a principled framework for dealing with uncertainty and quantifying how it changes in the light of new evidence. For many complex models and inference problems, however, only approximate quantitative answers are obtainable. Approximate Bayesian computation (ABC) refers to a family of algorithms for approximate inference that makes a minimal set of assumptions by only requiring that sampling from a model is possible. We explain here the fundamentals of ABC, review the classical algorithms, and highlight recent developments. [ABC; approximate Bayesian computation; Bayesian inference; likelihood-free inference; phylogenetics; simulator-based models; stochastic simulation models; tree-based models.] PMID:28175922

Bubble-induced cave collapse.

PubMed

Girihagama, Lakshika; Nof, Doron; Hancock, Cathrine

2015-01-01

Conventional wisdom among cave divers is that submerged caves in aquifers, such as in Florida or the Yucatan, are unstable due to their ever-growing size from limestone dissolution in water. Cave divers occasionally noted partial cave collapses occurring while they were in the cave, attributing this to their unintentional (and frowned upon) physical contact with the cave walls or the aforementioned "natural" instability of the cave. Here, we suggest that these cave collapses do not necessarily result from cave instability or contacts with walls, but rather from divers bubbles rising to the ceiling and reducing the buoyancy acting on isolated ceiling rocks. Using familiar theories for the strength of flat and arched (un-cracked) beams, we first show that the flat ceiling of a submerged limestone cave can have a horizontal expanse of 63 meters. This is much broader than that of most submerged Florida caves (~ 10 m). Similarly, we show that an arched cave roof can have a still larger expanse of 240 meters, again implying that Florida caves are structurally stable. Using familiar bubble dynamics, fluid dynamics of bubble-induced flows, and accustomed diving practices, we show that a group of 1-3 divers submerged below a loosely connected ceiling rock will quickly trigger it to fall causing a "collapse". We then present a set of qualitative laboratory experiments illustrating such a collapse in a circular laboratory cave (i.e., a cave with a circular cross section), with concave and convex ceilings. In these experiments, a metal ball represented the rock (attached to the cave ceiling with a magnet), and the bubbles were produced using a syringe located at the cave floor.

Poisson-Based Inference for Perturbation Models in Adaptive Spelling Training

ERIC Educational Resources Information Center

Baschera, Gian-Marco; Gross, Markus

2010-01-01

We present an inference algorithm for perturbation models based on Poisson regression. The algorithm is designed to handle unclassified input with multiple errors described by independent mal-rules. This knowledge representation provides an intelligent tutoring system with local and global information about a student, such as error classification…

Late Glacial Tropical Savannas in Sundaland Inferred From Stable Carbon Isotope Records of Cave Guano

NASA Astrophysics Data System (ADS)

Wurster, C. M.; Bird, M. I.; Bull, I.; Dungait, J.; Bryant, C. L.; Ertunç, T.; Hunt, C.; Lewis, H. A.; Paz, V.

2008-12-01

During the Last Glacial Period (LGP), reduced global sea level exposed the continental shelf south of Thailand to Sumatra, Java, and Borneo to form the contiguous continent of Sundaland. However, the type and extent of vegetation that existed on much of this exposed landmass during the LGP remains speculative. Extensive bird and bat guano deposits in caves throughout this region span beyond 40,000 yr BP, and contain a wealth of untapped stratigraphic palaeoenvironmental information. Stable carbon isotope ratios of insectivorous bird and bat guano contain a reliable record of the animal's diet and, through non-specific insect predation, reflect the relative abundance of major physiological pathways in plants. Various physiological pathways of carbon fixation in plants yield differing stable carbon isotope ratios. Stable carbon isotope values of C3 plants are lower than C4 vegetation due to different enzymatic discriminations of the heavy isotope through the carbon fixing pathways. In tropical locales, grasses nearly always follow the C4 photosynthetic pathway, whereas tropical rainforest uses C3 photosynthesis, providing a proxy for vegetation and therefore climate change in the past. Here we discuss four guano stable-isotope records, based on insect cuticle and n-alkane analysis, supplemented by pollen analysis. All sites suggest a C3 dominated ecosystem for the Holocene, consistent with the wet tropical forest vegetation present at all locations. Two sites from Palawan Island, Philippines, record stable carbon isotope values of guano that document a drastic change from C3 (forest) to C4 (savanna) dominated ecosystems during the Last Glacial Maximum (LGM). A third location, at Niah Great Cave, Malaysia, indicates C3-dominant vegetation throughout the record, but does display variation in stable carbon isotope values likely linked to humidity changes. A fourth location, Batu Caves in Peninsular Malaysia, also indicates open vegetation during the LGM. Vegetation models disagree as to the nature of vegetation during the LGM in Sundaland, but our results suggest major contraction of forest area with significant implications for carbon storage during the LGM and also for understanding the development of modern biogeographic and genetic patterns in the region. Additional cave guano sites will provide further constraints on the nature of environmental change in the region over the last glacial cycle.

Microbially induced iron precipitation associated with a neutrophilic spring at Borra Caves, Vishakhapatnam, India.

PubMed

Baskar, Sushmitha; Baskar, Ramanathan; Thorseth, Ingunn H; Ovreås, Lise; Pedersen, Rolf B

2012-04-01

The present investigation uncovers various pieces of evidence for the possible biologically induced mineralization in iron mats associated with a pH-neutral spring in the Borra caves, Vishakhapatnam, India. Electron microscopy [scanning electron microscopy (SEM) and transmission electron microscopy (TEM)] demonstrated large numbers of (i) hollow tubes (diameter ∼1 μm) resembling sheaths of the iron-oxidizing bacteria Leptothrix, (ii) thin (diameter <1 μm) solid fibers of uncertain origin, (iii) nanoscale subspherical to irregularly shaped particles encrusting tubes and fibers, and (iv) aggregates of broken and partially disintegrated sheaths, fibers, and particles embedded in extracellular polymeric substances (EPS) occasionally including microbial cells. X-ray microanalyses by energy dispersive spectroscopy (EDS) revealed that the mat accumulated largely Fe but also smaller amounts of Si and traces of P and Ca. Particles rich in Si and Al (possibly kaolinite) and Ca (carbonate) were also observed. High-resolution TEM/EDS of unstained ultrathin sections suggests that microbial sheaths were highly mineralized by amorphous to cryptocrystalline Fe-rich phases and less frequently by other fine-grained and fibrous authigenic claylike minerals. Total number of microorganisms in the iron mats was 5.8×10(5) cells, g sed(-1) (wet weight). Analysis of the 16S rRNA gene diversity revealed microorganisms assigned to eight different phyla [Proteobacteria (62%), Chloroflexi (8%), Bacteroidetes (7%), Planctomycetes (1%), Actinobacteria (5%), Acidobacteria (6%), Nitrospira (1%), Firmicutes (5%)]. Within the Proteobacteria, Betaproteobacteria was the predominant class, which accounted for 28% of the sequences. Within this class some obvious similarities between the obtained sequences and sequences from other cave systems could be seen, especially sequences affiliated with Leptothrix, Siderooxidans, Crenothrix, Comamonadaceae, Dechloromonas, and many uncultured Betaproteobacteria. Four (4%) of the sequences could not be assigned to phylum level but were affiliating with the candidate division TM7 (2%), candidate division OP11 (1%), and candidate division WWE3 (1%). The results allow us to infer a possible relationship of microbial sheaths, EPS, and the iron precipitates to microbial community diversity in the Borra cave springs. Understanding biogenic iron oxides in caves has important astrobiological applications as it provides a potential tool for the detection of extraterrestrial life.

Flowstone compositions as indicators of centennial fluctuations of hydrological balance in Central Europe during the late Holocene

NASA Astrophysics Data System (ADS)

Demény, Attila; Kern, Zoltán; Molnár, Mihály; Czuppon, György; Leél-Őssy, Szabolcs; Surányi, Gergely; Gilli, Adrian

2017-04-01

Flowstones formed from springs in the Baradla and Béke Caves, North-east Hungary were drilled at several locations, and their sites were monitored for temperature, CO2 level in cave air, water and carbonate compositions for three years. The monitoring results suggest that the carbonate precipitated close to equilibrium with the local water. The non-systematic distribution of stable isotope and chemical compositions along sections on the surfaces of flowstone occurrences indicate irregular formation and the possibility of hiatuses within the flowstones' edifices. Approximately 40 cm long drill cores were extracted from the „Nagy-tufa" flowstone of the Béke Cave (BNT-2 core) and the Havasok flowstone of the Baradla Cave. U-Th dating efforts resulted in very large age uncertainties for the BNT-2 core, owing to detrital Th contamination. Therefore, in addition to the U-Th dating, AMS radiocarbon analyses were conducted to establish reliable age-depth models. The raw 14C ages were corrected for the dead carbon fraction (dfc) using radiocarbon results obtained for samples that yielded also accurate U-Th ages. Calibration and age-depth modeling have been performed using the OxCal v4.2.4. software. The data prove that the flowstones in the studied caves were formed contemporarily, covering the last 4 ka with two major hiatuses around 3.5 and 1 ka BP. Inclusion-hosted water contents, stable carbon and oxygen isotope compositions of carbonate, and hydrogen isotope composition of inclusion-hosted water as well as Si contents were determined for the two cores and compared with regional paleoclimate records for the period of 3.5 to 1 ka BP. The water contents, δ13Ccarb values and Si contents show correspondence with paleoprecipitation proxies from Central Europe to western Anatolia, while the paleotemperature estimates obtained using the δDwater values were in agreement with temperature reconstructions derived from paleobiological proxies from nearby lake sediments. The inferred paleohumidity variations agree also with water level changes of Lake Balaton (Western Hungary) assumed on the base of settlement migrations revealed by archeological excavations. These correlations indicate that the flowstone data provide valuable information about the regional water balance fluctuations for the late Holocene. The study was financed by the Hungarian Research Fund (OTKA NK 101664).

Sulphate partitioning into calcite: Experimental verification of pH control and application to seasonality in speleothems

NASA Astrophysics Data System (ADS)

Wynn, Peter M.; Fairchild, Ian J.; Borsato, Andrea; Spötl, Christoph; Hartland, Adam; Baker, Andy; Frisia, Silvia; Baldini, James U. L.

2018-04-01

Carbonate-associated sulphate (CAS) is a useful carrier of palaeoenvironmental information throughout the geologic record, particularly through its stable isotope composition. However, a paucity of experimental data restricts quantitative understanding of sulphate incorporation into carbonates, and consequently CAS concentrations and their diagenetic modifications are rarely interpreted. However, in the case of calcite speleothems, the remarkably high-resolution CAS records which are obtainable via modern microanalytical techniques represent a potentially invaluable source of palaeoenvironmental information. Here, we describe the results of controlled experiments of sulphate co-precipitation with calcite in freshwater solutions where pH, saturation state, and sulphate concentration were varied independently of each other. Solution pH is confirmed as the principal control on sulphate incorporation into calcite. The relative efficiency of incorporation was calculated as a partition coefficient DSO4 = (mSO4/mCO3)solid/(mSO4/mCO3)solution. High crystal growth rates (driven by either pH or saturation state) encouraged higher values of DSO4 because of an increasing concentration of defect sites on crystal surfaces. At low growth rates, DSO4 was reduced due to an inferred competition between sulphate and bicarbonate at the calcite surface. These experimental results are applied to understand the incorporation of sulphate into speleothem calcite. The experimentally determined pH-dependence suggests that strong seasonal variations in cave air PCO2 could account for annual cycles in sulphate concentration observed in stalagmites. Our new experimentally determined values of DSO4 were compared with DSO4 values calculated from speleothem-drip water monitoring from two caves within the Austrian and Italian Alps. At Obir cave, Austria, DSO4 (×105) varies between 11.1 (winter) and 9.0 (summer) and the corresponding figures for Ernesto cave, Italy, are 15.4 (winter) and 14.9 (summer). These values approximate predicted DSO4 values based on our chamber experiments containing both low (2 ppm) and high (20 ppm) sulphate concentrations. Our experimental values of DSO4 obtained at crystal growth rates typical of stalagmites, closely match those observed in other cave sites from around the world. This validates the universality of the controls behind DSO4 and will enhance the use of speleothem CAS as a palaeoenvironmental proxy.

Spotted hyena and steppe lion predation behaviours on cave bears of Europe - ?Late Quaternary cave bear extinction as result of predator stress

NASA Astrophysics Data System (ADS)

Diedrich, Cajus G.

2010-05-01

Cave bears hibernated in caves all over Eurasia (e.g. Rabeder et al., 2000) including alpine regions using mainly larger caves for this purpose. Late Quaternary spotted hyenas Crocuta crocuta spelaea instead occupied mainly areas close to the cave entrances as their dens (Diedrich and Žák 2006, Diedrich 2010). The largest predator, the steppe lion Panthera leo spelaea was only a sporadic cave dweller (Diedrich 2007b, 2009b). His presence and its remains from caves all over Europe can be recently explained best as result of imported carcasses after killing by their largest antagonists, the Late Quaternary spotted hyenas. In some cases the kill might have happened in the hyena den cave itself during the theft of prey remains by lions (Diedrich 2009a). Another reason of their remains in caves of Europe is the hunting onto the herbivorous cave bears, especially during hibernation times, when megafauna prey was less available in the open environments (Diedrich 2009c). These lion remains from caves of Europe, nearly all of which were from adult animals, provide evidence of active predation by lions onto cave bears even in medium high alpine regions (Diedrich 2009b, in review). Lion skeletons in European cave bear dens were therefore often found amongst originally articulated cave bear skeletons or scattered cave bear remains and even close to their hibernation nests (Diedrich et al. 2009c, in review). Not only lions fed on cave bears documented mainly by the large quantities of chewed, punctured and crushed cave bear long-bones; even damaged skulls reveal that hyenas scavenged primarily on cave bear carcasses which were mainly responsible for the destruction of their carcasses and bones (Diedrich 2005, 2009d). Predation and scavenging on cave bears by the two largest Late Quaternary predators C. c. spelaea and P. l. spelaea explains well the large quantity of fragmented cave bear bones over all European caves in low to medium high mountainous elevations, whereas in high alpine regions the leopard Panthera pardus seem to have used the ecological niche of the absent hyenas (Diedrich 2009d, in review a). At open air sites cave bear scavenging by the largest Late Quaternary predators were proven, too (Diedrich 2006, 2009e). The predation stress caused by the three main and largest Late Quaternary predators seem to have provided cave bears to hibernate often deeply in many European caves, and here especially in larger and longer cave systems (e.g. Diedrich et al 2009, in review, Diedrich and Moldovan 2010) to protect themselves against the largest Quaternary predators. In conflicts with those large felids must have been killed by adult cave bears, which explains why those predator carcasses remained as complete skeletons or as partly disarticulated ones even deep in caves all over Europe which were finally not scavenged by the herbivorous cave bears (Diedrich in review). In such cave bear den caves the amount of lion bones generally take only 1-3% of the total bone amount being highly dominated by cave bear bones (Diedrich 2009c, in review). Lions and hyenas seem to have focussed onto the hunt of cave bears all over Europe, especially with the reduction of the biomass in the open environments at the maximum cold period during around 26.000-24.000 BP (Solutrean). The slow extinction of their largest prey was an important motor of the predation pressure onto cave bears. This might be one reason for the cave bear extinction in the final Late Quaternary (early Late Weichselian, maximum cold period) at least in northern Europe, but it seem to have happened in a combination of climatic change, and also human impact (cf. Diedrich, this volume). References Diedrich, C., 2005. Cracking and nibbling marks as indicators for the Upper Pleistocene spotted hyena as a scavenger of cave bear (Ursus spelaeus Rosenmüller, 1794) carcasses in the Perick Caves den of Northwest Germany. Abhandlungen der Naturhistorischen Gesellschaft Nürnberg, 45, 73-90. Diedrich, C., 2006. Ice age spotted hyenas ?hunting or only scavenging on a cave bear Ursus spelaeus Rosenmüller at the Ice Age spotted hyena freeland den and prey deposit site Bad Wildungen-Biedensteg (Hessia, Germany). Scientific Annals, School of Geology Aristotle University of Thessaloniki (AUTH) special volume, 98, 193-199. Diedrich, C., 2007b. The fairy tale about the "cave lions" Panthera leo spelaea (Goldfuss 1810) of Europe - Late Ice Age spotted hyenas and Ice Age steppe lions in conflict - lion killers and scavengers around Prague (Central Bohemia). Scripta Facultatis Scientiarum Universitatis Masarykianae Geology, 35 (2005), 107-112. Diedrich, C., 2009a. Steppe lion remains imported by Ice Age spotted hyenas into the Late Pleistocene Perick Caves hyena den in Northern Germany. Quaternary Research, 71 (3), 361-374. Diedrich, C., 2009b. Upper Pleistocene Panthera leo spelaea (Goldfuss, 1810) remains from the Bilstein Caves (Sauerland Karst) and contribution to the steppe lion taphonomy, palaeobiology and sexual dimorphism. Annales de Paléontologie, 95, 117-138. Diedrich, C. 2009c. Steppe lion predation - another reason for cave bears to protect during hibernation against carnivores in deepest parts of large cave systems in Europe. Abstractc 15th International Cave Bear Symposium, Spisska Nova Ves Slovakia, 8-9. Diedrich, C., 2009d. Cave bear killers, scavengers between the Scandinavian and Alpine Ice shields - the last hyenas and cave bears in antagonism - and the reason why cave bears hibernated deeply in caves. Stalactite, 58(2), 54-63. Diedrich, C. 2009e. Late Pleistocene Cave bear remains from the open air hyena den Emscher River terrace site Bottrop (NW Germany). - Stalactite, 58 (2): 42-47. Diedrich, C. 2010. The Crocuta crocuta spelaea (GOLDFUSS 1823) population from the Late Pleistocene Rösenbeck Cave den in NW Germany and contribution to the sexual dimorphism and palaeobiogeography of the last hyenas of Europe. - Annales de Paléontologie. Diedrich, C. (in review). Cave bear killers and scavengers from the last European Ice Age. Palaeogeography Palaeoclimatology Palaeoecology. Diedrich, C., Žák, K. 2006. Prey deposits and den sites of the Upper Pleistocene hyena Crocuta crocuta spelaea (Goldfuss, 1823) in horizontal and vertical caves of the Bohemian Karst (Czech Republic). Bulletin of Geosciences, 81 (4), 237-276. Diedrich, C., Robu, M., Dragusin, V., Constantin, S., Moldovan, O., 2009. New Upper Pleistocene steppe lion skeleton finds between the cave bear hibernation plateaus of the Ursilor Cave bear den, Romania. Abstractc 15th International Cave Bear Symposium, Spisska Nova Ves Slovakia, 10. Diedrich, C., Moldovan, O., Constantin, S. 2009. Cave bear tracks, scratch marks, hair traces and hibernation nests in the Ursilor Cave (Transylvania, Romania) - preliminary report from a famous European cave bear den. - Stalactite, 58 (2): 48-52. Diedrich, C., Moldovan, O. 2010. Ichnological and ethological studies in one of Europe's famous bear den in the Ursilor Cave (Carpathians, Romania). - Quarternary International (accepted). Rabeder, G., Nagel, D., Pacher, M., 2000. Der Höhlenbär. Stuttgart: Thorbecke.

Numerical simulation of formation and preservation of Ningwu ice cave, Shanxi, China

NASA Astrophysics Data System (ADS)

Yang, S.; Shi, Y.

2015-10-01

Ice caves exist in locations where annual average air temperature is higher than 0 °C. An example is Ningwu ice cave, Shanxi Province, the largest ice cave in China. In order to quantitatively investigate the mechanism of formation and preservation of the ice cave, we use the finite-element method to simulate the heat transfer process at this ice cave. There are two major control factors. First, there is the seasonal asymmetric heat transfer. Heat is transferred into the ice cave from outside very inefficiently by conduction in spring, summer and fall. In winter, thermal convection occurs that transfers heat very efficiently out of the ice cave, thus cooling it down. Secondly, ice-water phase change provides a heat barrier for heat transfer into the cave in summer. The calculation also helps to evaluate effects of global warming, tourists, colored lights, climatic conditions, etc. for sustainable development of the ice cave as a tourism resource. In some other ice caves in China, managers have installed airtight doors at these ice caves' entrances with the intention of "protecting" these caves, but this in fact prevents cooling in winter and these cave ices will entirely melt within tens of years.

Bubble-Induced Cave Collapse

PubMed Central

Girihagama, Lakshika; Nof, Doron; Hancock, Cathrine

2015-01-01

Conventional wisdom among cave divers is that submerged caves in aquifers, such as in Florida or the Yucatan, are unstable due to their ever-growing size from limestone dissolution in water. Cave divers occasionally noted partial cave collapses occurring while they were in the cave, attributing this to their unintentional (and frowned upon) physical contact with the cave walls or the aforementioned “natural” instability of the cave. Here, we suggest that these cave collapses do not necessarily result from cave instability or contacts with walls, but rather from divers bubbles rising to the ceiling and reducing the buoyancy acting on isolated ceiling rocks. Using familiar theories for the strength of flat and arched (un-cracked) beams, we first show that the flat ceiling of a submerged limestone cave can have a horizontal expanse of 63 meters. This is much broader than that of most submerged Florida caves (~ 10 m). Similarly, we show that an arched cave roof can have a still larger expanse of 240 meters, again implying that Florida caves are structurally stable. Using familiar bubble dynamics, fluid dynamics of bubble-induced flows, and accustomed diving practices, we show that a group of 1-3 divers submerged below a loosely connected ceiling rock will quickly trigger it to fall causing a “collapse”. We then present a set of qualitative laboratory experiments illustrating such a collapse in a circular laboratory cave (i.e., a cave with a circular cross section), with concave and convex ceilings. In these experiments, a metal ball represented the rock (attached to the cave ceiling with a magnet), and the bubbles were produced using a syringe located at the cave floor. PMID:25849088

36 CFR 290.3 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., DEPARTMENT OF AGRICULTURE CAVE RESOURCES MANAGEMENT § 290.3 Nomination, evaluation, and designation of... humans, biota, or development of cave resources. (5) Recreational. The cave provides or could provide... consultation with individuals and organizations interested in the management and use of caves and cave...

A multi-method approach for speleogenetic research on alpine karst caves. Torca La Texa shaft, Picos de Europa (Spain)

NASA Astrophysics Data System (ADS)

Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; Giralt, Santiago; García-Sansegundo, Joaquín; Meléndez-Asensio, Mónica

2015-10-01

Speleogenetic research on alpine caves has advanced significantly during the last decades. These investigations require techniques from different geoscience disciplines that must be adapted to the methodological constraints of working in deep caves. The Picos de Europa mountains are one of the most important alpine karsts, including 14% of the World's Deepest Caves (caves with more than 1 km depth). A speleogenetic research is currently being developed in selected caves in these mountains; one of them, named Torca La Texa shaft, is the main goal of this article. For this purpose, we have proposed both an optimized multi-method approach for speleogenetic research in alpine caves, and a speleogenetic model of the Torca La Texa shaft. The methodology includes: cave surveying, dye-tracing, cave geometry analyses, cave geomorphological mapping, Uranium series dating (234U/230Th) and geomorphological, structural and stratigraphical studies of the cave surroundings. The SpeleoDisc method was employed to establish the structural control of the cavity. Torca La Texa (2653 m length, 215 m depth) is an alpine cave formed by two cave levels, vadose canyons and shafts, soutirage conduits, and gravity-modified passages. The cave was formed prior to the Middle Pleistocene and its development was controlled by the drop of the base level, producing the development of the two cave levels. Coevally to the cave levels formation, soutirage conduits originated connecting phreatic and epiphreatic conduits and vadose canyons and shafts were formed. Most of the shafts were created before the local glacial maximum (43-45 ka) and only two cave passages are related to dolines developed in recent times. The cave development is strongly related to the structure, locating the cave in the core of a gentle fold with the conduits' geometry and orientation controlled by the bedding and five families of joints.

Caving in the Classroom

ERIC Educational Resources Information Center

Yoder, Holly

2010-01-01

During Cave Week, more than 200 students explore a simulated cave environment and participate in cave-related activities. Active cavers from a local club bring in equipment and photos and speak about their caving experiences. As student groups explore the simulated cave, other groups participate in different activities where they can create bat…

Hypogene caves of the central Appalachian Shenandoah Valley in Virginia

USGS Publications Warehouse

Doctor, Daniel H.; Orndorff, Wil

2017-01-01

Several caves in the Shenandoah Valley in Virginia show evidence for early hypogenic conduit development with later-enhanced solution under partly confined phreatic conditions guided by geologic structures. Many (but not all) of these caves have been subsequently invaded by surface waters as a result of erosion and exhumation. Those not so affected are relict phreatic caves, bearing no relation to modern drainage patterns. Field and petrographic evidence shows that carbonate rocks hosting certain relict phreatic caves were dolomitized and/or silicified by early hydrothermal fluid migration in zones that served to locally enhance rock porosity, thus providing preferential pathways for later solution by groundwater flow, and making the surrounding bedrock more resistant to surficial weathering to result in caves that reside within isolated hills on the land surface. Features suggesting that deep phreatic processes dominated the development of these relict caves include (1) cave passage morphologies indicative of ascending fluids, (2) cave plans of irregular pattern, reflecting early maze or anastomosing development, (3) a general lack of cave breakdown and cave streams or cave stream deposits, and (4) calcite wall and pool coatings within isolated caves intersecting the local water table, and within unroofed caves at topographic locations elevated well above the local base level. Episodes of deep karstification were likely separated by long periods of geologic time, encompassing multiple phases of sedimentary fill and excavation within caves, and reflect a complex history of deep fluid migration that set the stage for later shallow speleogenesis that continues today.

Studies of Cave Sediments: Physical and Chemical Records of Paleoclimate (Revised Edition)

NASA Astrophysics Data System (ADS)

Baker, Andy

2007-10-01

Caves have long fascinated humankind, from prehistory to present-day tourism. Caves are also a subject for a range of scientific investigations, including cave biology, archaeology, paleoclimatology, geology, hydrology, and geomorphology. One of the benefits caves provide is their role as a repository of material that might not otherwise survive on the Earth's surface, due to caves' interiors being protected from physical erosion by nature of their underground locations. Studies of Cave Sediments focuses on this role as a repository, in particular on Quaternary (historic to 1.8 million years old) paleoclimate information preserved in cave sediments.

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

PubMed Central

Read, Kaitlyn J. H.; Hughes, Evan M.; Spilde, Michael N.

2017-01-01

Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community. PMID:28199330

Personalized recommendation via unbalance full-connectivity inference

NASA Astrophysics Data System (ADS)

Ma, Wenping; Ren, Chen; Wu, Yue; Wang, Shanfeng; Feng, Xiang

2017-10-01

Recommender systems play an important role to help us to find useful information. They are widely used by most e-commerce web sites to push the potential items to individual user according to purchase history. Network-based recommendation algorithms are popular and effective in recommendation, which use two types of elements to represent users and items respectively. In this paper, based on consistence-based inference (CBI) algorithm, we propose a novel network-based algorithm, in which users and items are recognized with no difference. The proposed algorithm also uses information diffusion to find the relationship between users and items. Different from traditional network-based recommendation algorithms, information diffusion initializes from users and items, respectively. Experiments show that the proposed algorithm is effective compared with traditional network-based recommendation algorithms.

Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm.

PubMed

Mandal, Sudip; Saha, Goutam; Pal, Rajat Kumar

2017-08-01

Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN). This algorithm is mainly based on the water search strategy of intelligent and social elephants during drought, utilizing the different types of communication techniques. Initially, the algorithm is tested against benchmark small and medium scale artificial genetic networks without and with presence of different noise levels and the efficiency was observed in term of parametric error, minimum fitness value, execution time, accuracy of prediction of true regulation, etc. Next, the proposed algorithm is tested against the real time gene expression data of Escherichia Coli SOS Network and results were also compared with others state of the art optimization methods. The experimental results suggest that ESWSA is very efficient for GRN inference problem and performs better than other methods in many ways.

Detection of Cheating by Decimation Algorithm

NASA Astrophysics Data System (ADS)

Yamanaka, Shogo; Ohzeki, Masayuki; Decelle, Aurélien

2015-02-01

We expand the item response theory to study the case of "cheating students" for a set of exams, trying to detect them by applying a greedy algorithm of inference. This extended model is closely related to the Boltzmann machine learning. In this paper we aim to infer the correct biases and interactions of our model by considering a relatively small number of sets of training data. Nevertheless, the greedy algorithm that we employed in the present study exhibits good performance with a few number of training data. The key point is the sparseness of the interactions in our problem in the context of the Boltzmann machine learning: the existence of cheating students is expected to be very rare (possibly even in real world). We compare a standard approach to infer the sparse interactions in the Boltzmann machine learning to our greedy algorithm and we find the latter to be superior in several aspects.

Stalagmite-inferred centennial variability of the Asian summer monsoon in southwest China between 58 and 79 ka BP

NASA Astrophysics Data System (ADS)

Zhang, Tao-Tao; Li, Ting-Yong; Cheng, Hai; Edwards, R. Lawrence; Shen, Chuan-Chou; Spötl, Christoph; Li, Hong-Chun; Han, Li-Yin; Li, Jun-Yun; Huang, Chun-Xia; Zhao, Xin

2017-03-01

We use a new spliced stalagmite oxygen isotope record from Yangkou Cave and Xinya Cave, Chongqing, southwest China, to reconstruct the centennial-millennial-scale changes in Asian Summer Monsoon (ASM) intensity between 58.0 and 79.3 thousand years before present (ka BP, before AD 1950). This multidecadally resolved record shows four strong ASM periods, corresponding to Greenland Interstadials (GIS) 17-20, and three weak ASM episodes, among which, the one starting at 61.5 ± 0.2 ka BP and ending at 59.4 ± 0.2 ka BP that may correlate with Heinrich Event 6. The close agreement of climate events between China and Greenland supports the notion that the ASM is dominantly governed by high-latitude forcings in the Northern Hemisphere. The short-lived interstadial GIS 18, however, lasted for over 3 kyr in the records derived from ASM region, reflecting a gradual decline of ASM intensity, which coincides with a millennial-scale warming trend in Antarctica. This suggests an additional forcing of the ASM by the Southern Hemisphere, which also affected GIS 8-12, H4 and H5, as shown by previous speleothem studies from the ASM region.

Hydro-climate variability and teleconnection patterns during the last millennium in NW Africa, inferred from speleothem records

NASA Astrophysics Data System (ADS)

Ait Brahim, Y.; Cheng, H.; Sifeddine, A.; Wassenburg, J. A.; Khodri, M.; Cruz, F. W., Sr.

2017-12-01

In this study, we present new paleoclimate records from two well dated Moroccan speleothems. Our stalagmites were sampled from Ifoulki cave in the Western High Atlas Mountains in SW Morocco and Chaara cave in the Eastern Middle Atlas Mountains in NE Morocco. The new paleo-records cover the last 1000 years with a high resolution and reveal substantial swings of dry and humid periods with decadal to multidecadal frequencies. The Medieval Climate Anomaly (MCA) is characterized by generally dry conditions, while wetter conditions are recorded during the Little Ice Age (LIA) and a trend towards dry conditions during the 20th century. These observations are consistent with regional climate signals, providing new insights on common climate controls and teleconnection patterns in NW Africa. We emphasize that the hydro-climate conditions in Morocco remained under the influence of the Atlantic Multidecadal Oscillation (AMO) and the North Atlantic Oscillation (NAO). At longer timescales, we hypothesize that the generally warmer MCA and colder LIA influenced the regional climate in NW Africa through interactions with local mechanisms, such as the Sahara Low, which weakened and strengthened the mean moisture inflow from the Atlantic Ocean during the MCA and LIA respectively.

Late Pleistocene leopards across Europe - northernmost European German population, highest elevated records in the Swiss Alps, complete skeletons in the Bosnia Herzegowina Dinarids and comparison to the Ice Age cave art

NASA Astrophysics Data System (ADS)

Diedrich, Cajus G.

2013-09-01

European leopard sites in Europe demonstrate Early/Middle Pleistocene out of Africa lowland, and Late Pleistocene Asian alpine migrations being driven by climatic changes. Four different European Pleistocene subspecies are known. The final European Late Pleistocene “Ice Age leopard” Panthera pardus spelaea (Bächler, 1936) is validated taxonomically. The skull shows heavy signs of sexual dimorphism with closest cranial characters to the Caucasian Panthera pardus ciscaucasica (Persian leopard). Late Pleistocene leopards were distributed northernmost, up to S-England with the youngest stratigraphic records by skeletons and cave art in the MIS 2/3 (about 32,000-26,000 BP). The oldest leopard painting left by Late Palaeolithics (Aurignacians/Gravettians) in the Chauvet Cave (S-France) allows the reconstruction of the Ice Age leopard fur spot pattern being close to the snow or Caucasian leopards. The last Ice Age glacial leopard habitat was the mountain/alpine boreal forest (not mammoth steppe lowland), where those hunted even larger prey such as alpine game (Ibex, Chamois). Into some lairs, those imported their prey by short-term cave dwelling (e.g. Baumann's Cave, Harz Mountains, Germany). Only Eurasian Ice Age leopards specialized, similar as other Late Pleistocene large felids (steppe lions), on cave bear predation/scavenging partly very deep in caves. In Vjetrenica Cave (Dinarid Mountains, Bosnia Herzegovina), four adult leopards (two males/two females) of the MIS 3 were found about two km deep from the entrance in a cave bear den, near to one cave bear skeleton, that remained articulated in its nest. Leopards died there, partly being trapped by raising water levels of an active ponor stream, but seem to have been killed possibly either, similar as for lions known, in battles with cave bears in several cave bear den sites of Europe (e.g. Baumann's Cave, Wildkirchli Cave, Vjetrenica Cave). At other large cave sites, with overlap of hyena, wolf and dhole dens at the cave entrances, leopard bones with bite damages indicate their remains to have been imported and consumed by predators in alpine regions due to reduced prey availability. The best models for the competition/taphonomy of large predators - felids, hyenids, canids - within large cave bear dens of Europe is represented in combination of the Zoolithen Cave and Vjetrenica Cave taphonomy.

Characterization of Microbial Community in Lascaux Cave by High Throughput Sequencing

NASA Astrophysics Data System (ADS)

Alonso, Lise; Dubost, Audrey; Luis, Patricia; Pommier, Thomas; Moënne-Loccoz, Yvan

2017-04-01

The Lascaux Cave in South-Est France is an archeological landmark renowned for its Paleolithic paintings dating back c.18.000 years. Extensive touristic frequenting and repeated chemical treatments have resulted in the development of microbial stains on cave walls, which is a major issue in terms of art conservation. Therefore, it is of prime importance to better understand the microbial ecology of Lascaux Cave. Like many other caves, Lascaux is quite heterogeneous in terms of the nature and surface properties of rock walls within cave rooms, as well as the succession of rooms/galleries from the entrance to deeper areas of the cave. Lascaux Cave displays an additional levels of heterogeneity related to the presence of discontinuous stains on certain types of cave walls. We compared the microbial community (i.e. both prokaryotic and eukaryotic microbial populations) colonizing cave walls of different rooms/galleries, in and outside stains and in different cave layers, in successive years. Quantitative PCR analysis of cave wall samples gave in the order of 102 copies of 18S rRNA genes and 105 copies of 16S rRNA genes per ng of DNA, indicating significant colonization of all cave walls by micro-eukaryotes and especially bacteria. Illumina metagenomic analyses of cave wall samples was carried out based on four ribosomal DNA markers targeting bacteria, archaea, fungi, and other micro-eukaryotes. The results showed that the four microbial communities were highly diverse in and outside stains, as several hundred genera of microorganisms were identified in each. Proteobacteria were more prominent within stains whereas Bacteroidetes and Sordariomycetes were more prominent outside stains. High-throughput sequencing also showed that the nature/surface properties of cave walls were the main factor determining the structure and composition of microbial communities, ahead of the other heterogeneity factors studied i.e. location within the cave, presence of stain and sampling season. This work provides a global view of the microbial community of Lascaux Cave, which could be useful to guide conservation efforts.

Reinforce: An Ensemble Approach for Inferring PPI Network from AP-MS Data.

PubMed

Tian, Bo; Duan, Qiong; Zhao, Can; Teng, Ben; He, Zengyou

2017-05-17

Affinity Purification-Mass Spectrometry (AP-MS) is one of the most important technologies for constructing protein-protein interaction (PPI) networks. In this paper, we propose an ensemble method, Reinforce, for inferring PPI network from AP-MS data set. The new algorithm named Reinforce is based on rank aggregation and false discovery rate control. Under the null hypothesis that the interaction scores from different scoring methods are randomly generated, Reinforce follows three steps to integrate multiple ranking results from different algorithms or different data sets. The experimental results show that Reinforce can get more stable and accurate inference results than existing algorithms. The source codes of Reinforce and data sets used in the experiments are available at: https://sourceforge.net/projects/reinforce/.

Developing JSequitur to Study the Hierarchical Structure of Biological Sequences in a Grammatical Inference Framework of String Compression Algorithms.

PubMed

Galbadrakh, Bulgan; Lee, Kyung-Eun; Park, Hyun-Seok

2012-12-01

Grammatical inference methods are expected to find grammatical structures hidden in biological sequences. One hopes that studies of grammar serve as an appropriate tool for theory formation. Thus, we have developed JSequitur for automatically generating the grammatical structure of biological sequences in an inference framework of string compression algorithms. Our original motivation was to find any grammatical traits of several cancer genes that can be detected by string compression algorithms. Through this research, we could not find any meaningful unique traits of the cancer genes yet, but we could observe some interesting traits in regards to the relationship among gene length, similarity of sequences, the patterns of the generated grammar, and compression rate.

A Prize-Collecting Steiner Tree Approach for Transduction Network Inference

NASA Astrophysics Data System (ADS)

Bailly-Bechet, Marc; Braunstein, Alfredo; Zecchina, Riccardo

Into the cell, information from the environment is mainly propagated via signaling pathways which form a transduction network. Here we propose a new algorithm to infer transduction networks from heterogeneous data, using both the protein interaction network and expression datasets. We formulate the inference problem as an optimization task, and develop a message-passing, probabilistic and distributed formalism to solve it. We apply our algorithm to the pheromone response in the baker’s yeast S. cerevisiae. We are able to find the backbone of the known structure of the MAPK cascade of pheromone response, validating our algorithm. More importantly, we make biological predictions about some proteins whose role could be at the interface between pheromone response and other cellular functions.

GPU Computing in Bayesian Inference of Realized Stochastic Volatility Model

NASA Astrophysics Data System (ADS)

Takaishi, Tetsuya

2015-01-01

The realized stochastic volatility (RSV) model that utilizes the realized volatility as additional information has been proposed to infer volatility of financial time series. We consider the Bayesian inference of the RSV model by the Hybrid Monte Carlo (HMC) algorithm. The HMC algorithm can be parallelized and thus performed on the GPU for speedup. The GPU code is developed with CUDA Fortran. We compare the computational time in performing the HMC algorithm on GPU (GTX 760) and CPU (Intel i7-4770 3.4GHz) and find that the GPU can be up to 17 times faster than the CPU. We also code the program with OpenACC and find that appropriate coding can achieve the similar speedup with CUDA Fortran.

Application of a cave inventory system to stimulate development of management strategies: the case of west-central Florida, USA.

PubMed

Harley, Grant L; Polk, Jason S; North, Leslie A; Reeder, Philip P

2011-10-01

The active management of air-filled cave systems is virtually non-existent within the karst landscape of west-central Florida. As in every karst landscape, caves are important because they contain a wide variety of resources (e.g., biota, speleothems) and can act as direct connections between surface and subsurface hydrological processes, potentially exacerbating the pollution of groundwater. Before sound management policies can be drafted, implemented, and enforced, stakeholders must first have knowledge of the management requirements of each cave. However, there is an informational disconnect between researchers, stakeholders, and the recreational caving community. Here, we present a cave inventory system that simplifies the dissemination of resource knowledge to stakeholders so that cave management and protection policies can be drafted and implemented at the state and local level. We inventoried 36 caves in west-central Florida, located on both public and private land, and analyzed cave resource data to provide insights on cave sensitivity and disturbance using two standardized indices. The data revealed that both public and private caves exhibit a wide range of sensitivity and disturbance, and before management strategies can be drafted, the ownership of each cave must be considered. Our inventory geodatabase serves as a link between researchers, landowners, and the public. To ensure the conservation and protection of caves, support from county or state government, combined with cave inventory data, is crucial in developing sound management policy. Copyright © 2011 Elsevier Ltd. All rights reserved.

Book Review: Caves and Karst of the Yorkshire Dales

NASA Astrophysics Data System (ADS)

Westaway, Rob

2015-10-01

The British Cave Research Association (BCRA) is the research division of the British Caving Association (BCA), itself the principal society in Britain for those interested in caving, with activities including provision of training and safety certification for cavers and managing access to caves. Although some UK cave-related research is carried out by academics, this tends to be restricted to archaeological investigations of caves that have served as human habitations, and to be focused more on the occupants than the caves themselves. In contrast, most cave exploration is undertaken as a leisure activity, under the auspices of clubs affiliated to the BCA/BCRA, this being indeed virtually the only field of Earth science where amateur investigators can continue to make significant discoveries. Many cave explorers are also affiliated with academic researchers, such as managers of dating laboratories; the synergy between these two groups is highly productive, having resulted for instance in the discovery and exploration in recent years of the vast Ogof Draenen cave system in South Wales, which probably dates back to the Early Pleistocene (e.g., Farrant et al., 2014).

Metis: A Pure Metropolis Markov Chain Monte Carlo Bayesian Inference Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bates, Cameron Russell; Mckigney, Edward Allen

The use of Bayesian inference in data analysis has become the standard for large scienti c experiments [1, 2]. The Monte Carlo Codes Group(XCP-3) at Los Alamos has developed a simple set of algorithms currently implemented in C++ and Python to easily perform at-prior Markov Chain Monte Carlo Bayesian inference with pure Metropolis sampling. These implementations are designed to be user friendly and extensible for customization based on speci c application requirements. This document describes the algorithmic choices made and presents two use cases.

Assessment of Local Recharge Area Characteristics of Four Caves in Northern Arkansas and Northeastern Oklahoma, 2004-07

USGS Publications Warehouse

Gillip, Jonathan A.; Galloway, Joel M.; Hart, Rheannon M.

2009-01-01

A study was conducted from 2004 to 2007 by the U.S. Geological Survey in cooperation with the U.S. Fish and Wildlife Service to assess the characteristics of the local recharge areas of four caves in northern Arkansas and northeastern Oklahoma that provide habitat for a number of unique organisms. Characterization of the local recharge areas are important because the caves occur in a predominately karst system and because land use proximal to the caves, including areas suspected to lie within the local recharge areas, may include activities with potentially deleterious effects to cave water quality. An integrated approach was used to determine the hydrogeologic characteristics and the extent of the local recharge areas of Civil War Cave, January-Stansbury Cave, Nesbitt Spring Cave, and Wasson's Mud Cave. This approach incorporated methods of hydrology, structural geology, geomorphology, and geochemistry. Continuous water-level and water-temperature data were collected at each cave for various periods to determine recharge characteristics. Field investigations were conducted to determine surficial controls affecting the groundwater flow and connections of the groundwater system to land-surface processes in each study area. Qualitative groundwater tracing also was conducted at each cave to help define the local recharge areas. These independent methods of investigation provided multiple lines of evidence for effectively describing the behavior of these complex hydrologic systems. Civil War Cave is located near the city of Bentonville in Benton County, Arkansas, and provides habitat for the Ozark cavefish. Civil War Cave is developed entirely within the epikarst of the upper Boone Formation, and recharge to Civil War Cave occurs from the Boone Formation (Springfield Plateau aquifer). The daily mean discharge for the period of study was 0.59 cubic feet per second and ranged from 0.19 to 2.8 cubic feet per second. The mean water temperature for Civil War Cave was 14.0 degrees Celsius. The calculated recharge area for Civil War Cave ranged from 0.13 to 2.5 square miles using the water-balance equation to 3.80 square miles using a normalized base-flow method. Tracer tests indicated a portion of the water within Civil War Cave was from across a major topographic divide located to the southwest. January-Stansbury Cave is located in Delaware County in northeastern Oklahoma, and provides habitat for the Oklahoma cave crayfish and the Ozark cavefish. January-Stansbury Cave is developed in the St. Joe Limestone member of the Boone Formation. The daily mean discharge for the period of study was 1.0 cubic foot per second and ranged from 0.35 to 8.7 cubic feet per second. The mean water temperature for January-Stansbury Cave was 14.3 degrees. The calculated recharge area for January-Stansbury Cave using the water-balance equation ranged from approximately 0.04 to 0.83 square miles. Tracer tests generally showed water discharging from January-Stansbury Cave during high flow originates from within the topographic drainage area and from an area outside the topographic drainage area to the southwest. Nesbitt Spring Cave is located near the city of Mountain View in north-central Arkansas and provides habitat for the Hell Creek cave crayfish. Nesbitt Spring Cave is developed in the Plattin Limestone (Ozark aquifer) and is recharged through the Boone Formation (Springfield Plateau aquifer). The mean daily discharge for the period of study was 4.5 cubic feet per second and ranged from 0.39 to 70.7 cubic feet per second. The mean water temperature for Nesbitt Spring Cave was 14.2 degrees Celsius. The calculated recharge area for Nesbitt Spring Cave using the water-balance equation ranged from 0.49 square mile to 4.0 square miles. Tracer tests generally showed a portion of water discharging from Nesbitt Spring during high flow originates from outside the topographic drainage area. Wasson's Mud Cave is located near the city of Springtown

Magnetostratigraphy of cave sediments, Wyandotte Ridge, Crawford County, southern Indiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pease, P.P.; Gomez, B.; Schmidt, V.A.

1992-01-01

The field polarities of 42 sediment samples obtained from 21 sites in Wyandotte Cave, and five smaller satellite caves in Wyandotte Ridge, southern Indiana, have been determined and correlated with magnetostratigraphic data from Mammoth Cave, Kentucky. In Wyandotte Cave sediment samples obtained between 137 m and 162 m in elevation possessed a normal field polarity, while samples obtained between 168 m and 171 m exhibited a field reversal. The reversal was interpreted to represent the most recent polarity change, dating the sediment fill and the end of the active period of the upper level of Wyandotte Cave at ca 0.788more » Ma. There is a temporal correlation between the active period of the upper level in Wyandotte Cave and the C-level in Mammoth Cave, which lies at a similar elevation. Such a correlation is most likely a consequence of the contemporaneous abandonment of passages in the two cave systems during the early Pleistocene reconstruction of the Ohio River system, which acts as the base level control in both caves. Samples from two caves near the top of Wyandotte Ridge, located between elevations of 236 m and 241 m, exhibited a normal polarity. These caves are located at a higher elevation than any of the sample sites in Mammoth Cave and their location suggests that the fill predates sediments from that system. It appears most likely that the fill in these caves is a minimum of ca 2.48 Ma. old and correlates with the residuum of the upper Mitchell Plain surface, not with the fill in the upper (A- or B-levels) in Mammoth Cave.« less

Local adaptation and pronounced genetic differentiation in an extremophile fish, Poecilia mexicana, inhabiting a Mexican cave with toxic hydrogen sulphide.

PubMed

Plath, M; Hauswaldt, J S; Moll, K; Tobler, M; García De León, F J; Schlupp, I; Tiedemann, R

2007-03-01

We investigated genetic differentiation and migration patterns in a small livebearing fish, Poecilia mexicana, inhabiting a sulfidic Mexican limestone cave (Cueva del Azufre). We examined fish from three different cave chambers, the sulfidic surface creek draining the cave (El Azufre) and a nearby surface creek without the toxic hydrogen sulphide (Arroyo Cristal). Using microsatellite analysis of 10 unlinked loci, we found pronounced genetic differentiation among the three major habitats: Arroyo Cristal, El Azufre and the cave. Genetic differentiation was also found within the cave between different pools. An estimation of first-generation migrants suggests that (i) migration is unidirectional, out of the cave, and (ii) migration among different cave chambers occurs to some extent. We investigated if the pattern of genetic differentiation is also reflected in a morphological trait, eye size. Relatively large eyes were found in surface habitats, small eyes in the anterior cave chambers, and the smallest eyes were detected in the innermost cave chamber (XIII). This pattern shows some congruence with a previously proposed morphocline in eye size. However, our data do not support the proposed mechanism for this morphocline, namely that it would be maintained by migration from both directions into the middle cave chambers. This would have led to an increased variance in eye size in the middle cave chambers, which we did not find. Restricted gene flow between the cave and the surface can be explained by local adaptations to extreme environmental conditions, namely H2S and absence of light. Within the cave system, habitat properties are patchy, and genetic differentiation between cave chambers despite migration could indicate local adaptation at an even smaller scale.

On developing thermal cave detection techniques for earth, the moon and mars

USGS Publications Warehouse

Wynne, J. Judson; Titus, Timothy N.; Chong Diaz, Guillermo

2008-01-01

The purpose of this study is to (1) demonstrate the viability of detecting terrestrial caves at thermal-infrared wavelengths, (2) improve our understanding of terrestrial cave thermal behavior, (3) identify times of day when cave openings have the maximum thermal contrast with the surrounding surface regolith, and (4) further our understanding of how to detect caves on Earth, the Moon and Mars. We monitored the thermal behavior of two caves in the Atacama Desert of northern Chile. Through this work, we identified times when temperature contrasts between entrance and surface were greatest, thus enabling us to suggest optimal overflight times. The largest thermal contrast for both caves occurred during mid-day. One cave demonstrated thermal behavior at the entrance suggestive of cold-trapping, while the second cave demonstrated temperature shifts suggestive of airflow. We also collected thermograms without knowing optimal detection times; these images suggest both caves may also be detectable during off-peak times. We suggest cave detection using thermal remote sensing on Earth and other planetary objects will be limited by (1) capturing imagery in the appropriate thermal wavelength, (2) the size of cave entrance vs. the sensor's spatial resolution, (3) the viewing angle of the platform in relation to the slope trajectory of the cave entrance, (4) the strength of the thermal signal associated with the cave entrance, and (5) the time of day and season of thermal image capture. Through this and other studies, we will begin to identify the range of conditions under which caves are detectable in the thermal infrared and thus improve our detection capabilities of these features on Earth, the Moon and Mars. ?? 2008 Elsevier B.V.

Classification of complex information: inference of co-occurring affective states from their expressions in speech.

PubMed

Sobol-Shikler, Tal; Robinson, Peter

2010-07-01

We present a classification algorithm for inferring affective states (emotions, mental states, attitudes, and the like) from their nonverbal expressions in speech. It is based on the observations that affective states can occur simultaneously and different sets of vocal features, such as intonation and speech rate, distinguish between nonverbal expressions of different affective states. The input to the inference system was a large set of vocal features and metrics that were extracted from each utterance. The classification algorithm conducted independent pairwise comparisons between nine affective-state groups. The classifier used various subsets of metrics of the vocal features and various classification algorithms for different pairs of affective-state groups. Average classification accuracy of the 36 pairwise machines was 75 percent, using 10-fold cross validation. The comparison results were consolidated into a single ranked list of the nine affective-state groups. This list was the output of the system and represented the inferred combination of co-occurring affective states for the analyzed utterance. The inference accuracy of the combined machine was 83 percent. The system automatically characterized over 500 affective state concepts from the Mind Reading database. The inference of co-occurring affective states was validated by comparing the inferred combinations to the lexical definitions of the labels of the analyzed sentences. The distinguishing capabilities of the system were comparable to human performance.

Recreational Impacts on the Microclimate of the Gorilla Limestone Cave in Shoushan National Nature Park of Taiwan

NASA Astrophysics Data System (ADS)

Chen, Chun; Ho, Lih-Der

2017-04-01

This study reports a continuous microclimate monitoring carried out in the Gorilla Cave (Kaohsiung, Taiwan) between December 2015 and December 2016. This limestone cave is located in the Mt. Shoushan, which is mainly composed of limestone and mudstone. This study tried to assess the recreational impacts to the microclimate of the cave by monitoring the CO2, temperature, humidity and barometric pressure. Two monitoring stations were set up respectively at the front part (station A) and the end of the cave (station B). We also set up an auto-operated time-lapse camera at the entrance of the cave to record the numbers of tourists, and their entering time and the durations in cave. As carbon dioxide in the limestone cave may have negative impact to both speleothems and visitors, our presentation focuses on the variations of CO2 concentration in the Gorilla Cave. Daily and seasonal fluctuations of CO2 concentration were observed. The fluctuations are closely related with the temperature outside the cave. In summer, when the temperature outside the cave maintained at 30。C, fluctuations of CO2 concentration in the cave will become chaotic. The CO2 concentration would fluctuate around 1000ppm most of the day, but it would be relatively low ( 500ppm) during the noon. In winter, when temperature outside the cave maintained below 25゜C, the fluctuation of CO2 concentration in cave presented a steady state ( 400-500 ppm). Only at the noon, the temperature outside the cave rose above 25 ゜C, the CO2 concentration inside the cave would increase. There were 1,517 tourists entered the cave during the monitoring period. The average number of visitors in a group is 13, and each group averagely stayed for 15 minutes. Over half of the visitors (776 tourists) entered the cave in December, due to lower humidity, drier in the cave and less dripping water in winter. After tourists entered the cave, the CO2 concentration value of station A rose instantly. However, most tourists stayed at the end of the cave longer, so the CO2 concentration of station B would be higher due to the CO2 accumulation. Therefore, it took a long time to return to the background level of CO2 concentration. In summer, because the CO2 concentration in the cave was already high, the value fluctuated less when the tourists entered the cave, but it took a longer time to return to the background CO2 level. On the contrary, the CO2 concentration increased significantly after tourists entered the cave during the winter time, but the recovery time was shorter. Based on the monitoring results, we suggest that (1) the buffering time between each visiting group should be longer in summer, but shorter in winter. (2) Consider to the limited space of the cave, each group should not exceed 20 tourists and stays no longer than 30 minutes to avoid the CO2 concentration exceeding 2400 ppm to discomfort tourists. However, the degradation of speleothems by increasing CO2 concentration in the Gorilla Cave is still unclear and further research is needed.

High resolution pCO2 monitoring reveals ventilation of Bunker Cave (NW Germany) and its impact on speleothem growth

NASA Astrophysics Data System (ADS)

Riechelmann, Sylvia; Breitenbach, Sebastian F. M.; Schröder-Ritzrau, Andrea; Immenhauser, Adrian

2017-04-01

Understanding the environmental processes that influence geochemical proxies archived in speleothems depends critically on detailed cave monitoring. Cave air pCO2 is one of the most important factors controlling speleothem growth. The pCO2 concentration of cave air depends on (i) the productivity of its source(s), (ii) CO2-transport dynamics through the epikarst and (iii) cave ventilation processes. We monitored the pCO2 concentration ca. 100 m from the lower entrance of the Bunker-Emst-Cave system (NW Germany) with a CORA CO2-logger at a two-hourly resolution between April 2012 and February 2014. Near-atmospheric minimum pCO2 concentrations of 408 ppm are observed in winter, while higher values up to 811 ppm are recorded in summer. Higher summer concentrations are due to increased plant and soil microbial activity, resulting in elevated CO2 in the soil, which is transferred to the cave with infiltrating water. Generally, the front passages of Bunker Cave are well ventilated. Besides the seasonal pattern, pCO2 concentrations vary at diurnal scale. Correlations of pCO2 with the temperature difference between surface and cave air are positive during summer and negative in winter, with no clear pattern for spring and autumn months. Thus, Bunker Cave ventilation is driven by temperature and density differences between cave and surface air, with two entrances at different elevations allowing dynamic ventilation. During summer, relatively cooler cave air flows from the upper to the lower entrance, while in winter this pattern is reversed due to ascending warm cave air. The situation is further complicated by preferential south/southwestern winds that point directly on the cave entrances. Thus, cave ventilation is frequently disturbed, especially during periods of higher wind speed. Modern ventilation systematics only developed when the two cave entrances were artificially opened (1863 and 1926). Before that, ventilation was restricted and cave pCO2 concentrations were presumably higher under natural conditions. Thus, the present-day ventilation system of Bunker Cave is not a direct analogue for natural ventilation conditions. pCO2 concentrations are relatively low compared to other caves, and because the difference between summer and winter pCO2 is relatively low (max. 400 ppm), a significant effect on seasonal speleothem growth rate is unlikely. In case of Bunker Cave, it is rather a combination of the availability of water, and thus of calcium and carbonate ions and pCO2 concentrations that allow higher carbonate precipitation during winter than summer. Holocene speleothems from Bunker Cave display relatively slow growth rates. We suggest that - with absence of major entrances to the cave system during the Holocene - ventilation was minimal and pCO2 concentrations significantly higher, making winterly water supply the governing factor regulating speleothem growth. Thus, stalagmites from Bunker Cave are likely to record a climatic signal biased towards the winter season.

Contextualizing Cave Maps as Geospatial Information: Case Study of Indonesia

NASA Astrophysics Data System (ADS)

Reinhart, H.

2017-12-01

Caves are the result of solution processes. Because they are happened from geochemical and tectonic activity, they can be considered as geosphere phenomena. As one of the geosphere phenomena, especially at karst landform, caves have spatial dimensions and aspects. Cave’s utilizations and developments are increasing in many sectors such as hydrology, earth science, and tourism industry. However, spatial aspects of caves are poorly concerned dues to the lack of recognition toward cave maps. Many stakeholders have not known significances and importance of cave maps in determining development of a cave. Less information can be considered as the cause. Therefore, it is strongly necessary to put cave maps into the right context in order to make stakeholders realize the significance of it. Also, cave maps will be officially regarded as tools related to policy, development, and conservation act of caves hence they will have regulation in the usages and applications. This paper aims to make the contextualization of cave maps toward legal act. The act which is used is Act Number 4 Year 2011 About Geospatial Information. The contextualization is done by scrutinizing every articles and clauses related to cave maps and seek the contextual elements from both of them. The results are that cave maps can be regarded as geospatial information and classified as thematic geospatial information. The usages of them can be regulated through the Act Number 4 Year 2011. The regulations comprised by data acquisition, database, authorities, surveyor, and the obligation of providing cave maps in planning cave’s development and the environment surrounding.

Gravity for Detecting Caves: Airborne and Terrestrial Simulations Based on a Comprehensive Karstic Cave Benchmark

NASA Astrophysics Data System (ADS)

Braitenberg, Carla; Sampietro, Daniele; Pivetta, Tommaso; Zuliani, David; Barbagallo, Alfio; Fabris, Paolo; Rossi, Lorenzo; Fabbri, Julius; Mansi, Ahmed Hamdi

2016-04-01

Underground caves bear a natural hazard due to their possible evolution into a sink hole. Mapping of all existing caves could be useful for general civil usages as natural deposits or tourism and sports. Natural caves exist globally and are typical in karst areas. We investigate the resolution power of modern gravity campaigns to systematically detect all void caves of a minimum size in a given area. Both aerogravity and terrestrial acquisitions are considered. Positioning of the gravity station is fastest with GNSS methods the performance of which is investigated. The estimates are based on a benchmark cave of which the geometry is known precisely through a laser-scan survey. The cave is the Grotta Gigante cave in NE Italy in the classic karst. The gravity acquisition is discussed, where heights have been acquired with dual-frequency geodetic GNSS receivers and Total Station. Height acquisitions with non-geodetic low-cost receivers are shown to be useful, although the error on the gravity field is larger. The cave produces a signal of -1.5 × 10-5 m/s2, with a clear elliptic geometry. We analyze feasibility of airborne gravity acquisitions for the purpose of systematically mapping void caves. It is found that observations from fixed wing aircraft cannot resolve the caves, but observations from slower and low-flying helicopters or drones do. In order to detect the presence of caves the size of the benchmark cave, systematic terrestrial acquisitions require a density of three stations on square 500 by 500 m2 tiles. The question has a large impact on civil and environmental purposes, since it will allow planning of urban development at a safe distance from subsurface caves. The survey shows that a systematic coverage of the karst would have the benefit to recover the position of all of the greater existing void caves.

Survey and hydrogeology of Carroll Cave

USDA-ARS?s Scientific Manuscript database

Carroll Cave, located in Camden County, Missouri, is the largest known cave formed in the Gasconade Dolomite of the Salem Plateau. Despite extensive visitation over the last 50 years and multiple survey efforts, a comprehensive map of the cave has never been produced. In 2002, the Carroll Cave Conse...

Quantitative evaluation of the underground Geoheritage in karst areas: The Picos de Europa National Park, North Spain

NASA Astrophysics Data System (ADS)

Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; José Domínguez-Cuestra, María; García-Sansegundo, Joaquín; Meléndez-Asensio, Mónica

2014-05-01

Karst areas show a lot of kilometers of cave conduits with a hidden Geoheritage poorly investigated in previous works that concerning with their cultural, scientific and education values. The evaluation of cave Geoheritage is complex due to methodological constrains. One of the most important karst areas in the World is the Picos de Europa National Park (North Spain) that was declared as a Global Geosite in 2007 and includes 14 % of the World's Deepest Caves. The GEOCAVE research project is being developed in several caves from the Picos de Europa National Park since 2012 in order to characterize geomorphology and geochronology of the cavities, proposing and validating new methodologies adapted to these environments. The aim of this work is to evaluate the Geoheritage of the Picos de Europa caves based on the studies made in nine selected caves. The methodology includes: 1) elaboration of geomorphological maps of the nine selected caves, projecting geomorphological, geological, hydrogeological, paleontological and cultural forms on the caves surveys; and 2) definition and calculation of three indexes useful to evaluate the Geoheritage of the caves. The indexes are: a) Cave Geoheritage Extension Index (CGhEI), defined as the percentage of the area occupied by the entire features divided by the cave area (excluding the forms that represent the conduits themselves), b) Feature Extension Index (FEI), defined as the area occupied by each group of form divided by the cave area, and c) Cave Geodiversity Index (CGdI), defined as the number of forms divided by the cave area. The nine cave geomorphological maps cover 178,639 m2 of caves and include a whole of 14.9 km of karst conduits, representing these caves the 4.1 % of the conduits of the Picos de Europa. The values of the Cave Geoheritage Extension Index range from 22 to 82 %, while the values of the Feature Extension Indexes for each group of features reach the following values: Geomorphological FEI take values of 20-80 % (speleothems FEI is 15-60 %, fluviokarst FEI is 5-25 %, gravity FEI is 10-40 %); Geological FEI is 4-5 %; Hydrogeological FEI is 0-3 %; Paleontological FEI is 0-0.1% and cultural FEI is 0-4 %. the On the other hand, 84 features are recognized into the caves and the Cave Geodiversity Index ranges from 0.3 to 1.1 features/cm2. These results evidence that 22 to 82 % of the cave conduits are occupy with Geoheritage features, being most of them geomorphological forms (speleothems, fluviokarst and gravity forms). The Geodiversity of the karst caves is high, recognizing a whole of 84 features into the caves and showing a high density of forms. Consequently, underground Geoheritage from karst areas can be estimated combining geomorphological maps few selected caves and three indexes based on number and extensions of the features. These indexes allow us to assign a preliminary weight of the geomorphological, geological, hydrogeological, paleontological and cultural features in a karst area.

Process Mining for Individualized Behavior Modeling Using Wireless Tracking in Nursing Homes

PubMed Central

Fernández-Llatas, Carlos; Benedi, José-Miguel; García-Gómez, Juan M.; Traver, Vicente

2013-01-01

The analysis of human behavior patterns is increasingly used for several research fields. The individualized modeling of behavior using classical techniques requires too much time and resources to be effective. A possible solution would be the use of pattern recognition techniques to automatically infer models to allow experts to understand individual behavior. However, traditional pattern recognition algorithms infer models that are not readily understood by human experts. This limits the capacity to benefit from the inferred models. Process mining technologies can infer models as workflows, specifically designed to be understood by experts, enabling them to detect specific behavior patterns in users. In this paper, the eMotiva process mining algorithms are presented. These algorithms filter, infer and visualize workflows. The workflows are inferred from the samples produced by an indoor location system that stores the location of a resident in a nursing home. The visualization tool is able to compare and highlight behavior patterns in order to facilitate expert understanding of human behavior. This tool was tested with nine real users that were monitored for a 25-week period. The results achieved suggest that the behavior of users is continuously evolving and changing and that this change can be measured, allowing for behavioral change detection. PMID:24225907

43 CFR 37.11 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2010 CFR

2010-10-01

... organizations interested in the management and use of cave resources, within the limits imposed by the... caves are afforded protection and will be managed in compliance with approved resource management plans... in part due to cave resources found therein, all caves within the so-designated special management...

Exploring caves: teaching packet for grades K-3

USGS Publications Warehouse

,

1998-01-01

"Exploring Caves" is an interdisciplinary set of materials on caves for grades K-3. Caves entail at least five scientific disciplines: earth science, hydrology, mapping, biology, and anthropology. Each of these disciplines involves a unique content area as well as the development of particular intellectual skills. This unit aims at helping teachers to sort and organize the most important ideas in this rich scientific area. Detailed lesson plans serve as ways to pass these ideas on to very young students. Most American caves are big holes that form in limestone rock. The holes begin as cracks in limestone. The cracks get bigger and bigger. They grow into underground streams, rivers, and even lakes. When water drains away, the waterways turn into open cave tunnels, passages, and caverns. It takes 10,000 to 100,000 years to form a cave big enough for people to move around inside. Water drips constantly in caves. The drips dissolve limestone minerals in one part of the cave. As water dries out, the minerals build up in other places. In this way, beautiful cave rock formations and crystals grow over thousands of years. These rock formations change dark limestone caves into hidden fantasy lands.

Magnetic Susceptibility and Heavy Metals in Guano from South Sulawesi Caves

NASA Astrophysics Data System (ADS)

Rifai, H.; Putra, R.; Fadila, M. R.; Erni, E.; Wurster, C. M.

2018-04-01

Measurement of some magnetic properties have been performed on vertical profile from South Sulawesi caves (Mampu and Bubau) by using low cost, rapid, sensitive and non destructive magnetic method. The aim is to attempt to use magnetic characters as a fingerprint for anthropogenic pollution in the caves. Guano samples were collected every 5 cm at a certain section of Mampu and Bubau cave, South Sulawesi, starting from surface through 300 cm in depth of mampu Cave and 30 cm of Bubau Cave. The magnetic parameters such as magnetic susceptibility and percentage frequency dependence susceptibility were measured using the Bartington MS2-MS2B instruments and supported by X-Ray Fluoroscence (XRF) to know their element composition. The results show that the samples had variations in magnetic susceptibility from 3.5 to 242.6 x 10‑8 m3/kg for Mampu Cave and from 8.6 to 106.5 x 10‑8 m3/kg for Bubau Cave and also magnetic domain. Then, the XRF results show that the caves contain several heavy metals. Magnetic and heavy metal analyses showing that the magnetic minerals in caves are lithogenic (Fe-bearing minerals) in origin and anthropogenic (Zn content) in the caves.

Fish mitigate trophic depletion in marine cave ecosystems.

PubMed

Bussotti, Simona; Di Franco, Antonio; Bianchi, Carlo Nike; Chevaldonné, Pierre; Egea, Lea; Fanelli, Emanuela; Lejeusne, Christophe; Musco, Luigi; Navarro-Barranco, Carlos; Pey, Alexis; Planes, Serge; Vieux-Ingrassia, Jean Vincent; Guidetti, Paolo

2018-06-15

Dark marine habitats are often characterized by a food-limited condition. Peculiar dark habitats include marine caves, characterized by the absence of light and limited water flow, which lead to reduced fluxes of organic matter for cave-dwelling organisms. We investigated whether the most abundant and common cave-dwelling fish Apogon imberbis has the potential to play the role of trophic vector in Mediterranean marine caves. We first analysed stomach contents to check whether repletion changes according to a nycthemeral cycle. We then identified the prey items, to see whether they belong to species associated with cave habitats or not. Finally, we assessed whether A. imberbis moves outside marine caves at night to feed, by collecting visual census data on A. imberbis density both inside and outside caves, by day and by night. The stomach repletion of individuals sampled early in the morning was significantly higher than later in the day. Most prey were typical of habitats other than caves. A. imberbis was on average more abundant within caves during the day and outside during the night. Our study supports the hypothesis regarding the crucial trophic role of A. imberbis in connecting Mediterranean marine caves with external habitats.

Climatic and environmental controls on speleothem oxygen-isotope values

NASA Astrophysics Data System (ADS)

Lachniet, Matthew S.

2009-03-01

Variations in speleothem oxygen-isotope values ( δ18O) result from a complicated interplay of environmental controls and processes in the ocean, atmosphere, soil zone, epikarst, and cave system. As such, the controls on speleothem δ18O values are extremely complex. An understanding of the processes that control equilibrium and kinetic fractionation of oxygen isotopes in water and carbonate species is essential for the proper interpretation of speleothem δ18O as paleoclimate and paleoenvironmental proxies, and is best complemented by study of site-specific cave processes such as infiltration, flow routing, drip seasonality and saturation state, and cave microclimate, among others. This review is a process-based summary of the multiple controls on δ18O in the atmosphere, soil, epikarst, and speleothem calcite, illustrated with case studies. Primary controls of δ18O in the atmosphere include temperature and relative humidity through their role in the multiple isotope "effects". Variability and modifications of water δ18O values in the soil and epikarst zones are dominated by evaporation, mixing, and infiltration of source waters. The isotopically effective recharge into a cave system consists of those waters that participate in precipitation of CaCO 3, resulting in calcite deposition rates which may be biased to time periods with optimal dripwater saturation state. Recent modeling, experimental, and observational data yield insight into the significance of kinetic fractionation between dissolved carbonate phases and solid CaCO 3, and have implications for the 'Hendy' test. To assist interpretation of speleothem δ18O time series, quantitative and semi-quantitative δ18O-climate calibrations are discussed with an emphasis on some of the difficulties inherent in using modern spatial and temporal isotope gradients to interpret speleothems as paleoclimate proxy records. Finally, several case studies of globally significant speleothem paleoclimate records are discussed that show the utility of δ18O to reconstruct past climate changes in regions that have been typically poorly represented in paleoclimate records, such as tropical and subtropical terrestrial locations. The new approach to speleothem paleoclimatology emphasizes climate teleconnections between regions and attribution of forcing mechanisms. Such investigations allow paleoclimatologists to infer regional to global-scale climate dynamics.

MultiNest: Efficient and Robust Bayesian Inference

NASA Astrophysics Data System (ADS)

Feroz, F.; Hobson, M. P.; Bridges, M.

2011-09-01

We present further development and the first public release of our multimodal nested sampling algorithm, called MultiNest. This Bayesian inference tool calculates the evidence, with an associated error estimate, and produces posterior samples from distributions that may contain multiple modes and pronounced (curving) degeneracies in high dimensions. The developments presented here lead to further substantial improvements in sampling efficiency and robustness, as compared to the original algorithm presented in Feroz & Hobson (2008), which itself significantly outperformed existing MCMC techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MultiNest algorithm is demonstrated by application to two toy problems and to a cosmological inference problem focusing on the extension of the vanilla LambdaCDM model to include spatial curvature and a varying equation of state for dark energy. The MultiNest software is fully parallelized using MPI and includes an interface to CosmoMC. It will also be released as part of the SuperBayeS package, for the analysis of supersymmetric theories of particle physics, at this http URL.

Bayesian inference of interaction properties of noisy dynamical systems with time-varying coupling: capabilities and limitations

NASA Astrophysics Data System (ADS)

Wilting, Jens; Lehnertz, Klaus

2015-08-01

We investigate a recently published analysis framework based on Bayesian inference for the time-resolved characterization of interaction properties of noisy, coupled dynamical systems. It promises wide applicability and a better time resolution than well-established methods. At the example of representative model systems, we show that the analysis framework has the same weaknesses as previous methods, particularly when investigating interacting, structurally different non-linear oscillators. We also inspect the tracking of time-varying interaction properties and propose a further modification of the algorithm, which improves the reliability of obtained results. We exemplarily investigate the suitability of this algorithm to infer strength and direction of interactions between various regions of the human brain during an epileptic seizure. Within the limitations of the applicability of this analysis tool, we show that the modified algorithm indeed allows a better time resolution through Bayesian inference when compared to previous methods based on least square fits.

Recursive algorithms for phylogenetic tree counting.

PubMed

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Long-term climate record inferred from early-middle Pleistocene amphibian and squamate reptile assemblages at the Gran Dolina Cave, Atapuerca, Spain.

PubMed

Blain, Hugues-Alexandre; Bailon, Salvador; Cuenca-Bescós, Gloria; Arsuaga, Juan Luis; Bermúdez de Castro, José Maria; Carbonell, Eudald

2009-01-01

The Gran Dolina cave site is famous for having delivered some of the oldest hominin remains of Western Europe (Homo antecessor, ca. 960 ka). Moreover, the evidence of lithic industries throughout the long vertical section suggests occupation on the part of hominins from the latest early Pleistocene (levels TD3/4, TD5, and TD6) to the late middle Pleistocene (level TD10). The Gran Dolina Sondeo Sur (TDS) has furnished a great number of small-vertebrate remains; among them some 40,000 bones are attributed to amphibians and squamates. Although they do not differ specifically from the extant herpetofauna of the Iberian Peninsula, the overlap of their current distribution areas (= mutual climatic range method) in Spain can provide mean annual temperatures (MAT), the mean temperatures of the coldest (MTC) and warmest (MTW) months, and mean annual precipitation (MAP) estimations for each sub-level, and their change can be studied throughout the sequence. Results from the squamate and amphibian study indicate that during hominin occupation the MAT (10-13 degrees C) was always slightly warmer than at present in the vicinity of the Gran Dolina Cave, and the MAP (800-1000mm) was greater than today in the Burgos area. Climatic differences between "glacial" and "interglacial" phases are poorly marked. Summer temperatures (MTW) show stronger oscillations than winter temperatures (MTC), but seasonality remains almost unchanged throughout the sequence. These results are compared with those for large mammals, small mammals, and pollen analysis, giving a scenario for the palaeoclimatic conditions that occurred during the early to middle Pleistocene in Atapuerca, and hence a scenario for the hominins that once lived in the Sierra de Atapuerca.

Middle Stone Age Ochre Processing and Behavioural Complexity in the Horn of Africa: Evidence from Porc-Epic Cave, Dire Dawa, Ethiopia

PubMed Central

Rosso, Daniela Eugenia; Pitarch Martí, Africa; d’Errico, Francesco

2016-01-01

Ochre is a common feature at Middle Stone Age (MSA) sites and has often been interpreted as a proxy for the origin of modern behaviour. However, few ochre processing tools, ochre containers, and ochre-stained artefacts from MSA contexts have been studied in detail within a theoretical framework aimed at inferring the technical steps involved in the acquisition, production and use of these artefacts. Here we analyse 21 ochre processing tools, i.e. upper and lower grindstones, and two ochre-stained artefacts from the MSA layers of Porc-Epic Cave, Dire Dawa, Ethiopia, dated to ca. 40 cal kyr BP. These tools, and a large proportion of the 4213 ochre fragments found at the site, were concentrated in an area devoted to ochre processing. Lower grindstones are made of a variety of raw materials, some of which are not locally available. Traces of use indicate that different techniques were employed to process ochre. Optical microscopy, XRD, μ-Raman spectroscopy, and SEM-EDS analyses of residues preserved on worn areas of artefacts show that different types of ferruginous rocks were processed in order to produce ochre powder of different coarseness and shades. A round stone bearing no traces of having been used to process ochre is half covered with residues as if it had been dipped in a liquid ochered medium to paint the object or to use it as a stamp to apply pigment to a soft material. We argue that the ochre reduction sequences identified at Porc-Epic Cave reflect a high degree of behavioural complexity, and represent ochre use, which was probably devoted to a variety of functions. PMID:27806067

South-France caves monitoring : present day cave air dynamics characterization,paleoclimatic and archaeological interests

NASA Astrophysics Data System (ADS)

Bourges, F.; Genty, D.; Genthon, P.; Mangin, A.; D'Hulst, D.

2012-04-01

Cave climatic environment survey covers different sort of analyses on air and water, and has various interests from the conservation of prehistoric caves to the study of paleoclimates. Depending on the purpose, the cave monitoring can be entirely automatic or combine both automatic and manual data acquisitions. Apparatus are adapted to cave environment to measure specific parameters (i.e. drip rate, air humidity, CO2) and during the long-term monitorings, several generations of techniques have been used. We present here examples of cave monitoring (1996 →) from South-France: Chauvet, Orgnac (Ardèche), Esparros (Hautes-Pyrénées) and Villars (Dordogne). In all these sites, we obtained among the longest series of climatic parameters of inside the caves, coupled sometimes with geochemical and isotopic analyses on air and seepage water, which allow to better understand cave air circulation behaviour and their sensitivity to the external climatic and environmental variations. High precision temperature measurements in Orgnac and Chauvet caves, coupled with pCO2 and radon analyses, allowed the reconstruction of seasonal air circulation patterns in each cave. While the Chauvet and Esparros caves are quite confined environments with temperature changes mainly controlled by air pressure variations, the Orgnac cave, like most caves, shows a well marked summer/winter regime alternation. Quantification of air flows of known CO2 concentration allowed the calculation of carbon fluxes toward the earth atmosphere which is estimated to about 340 gm-2yr-1. Since 15 years, the monitoring made in the Villars cave at two different levels has shown that the air temperature displays small seasonal variations in the upper galleries while it is not detectable in the lower ones. Average annual temperature difference between these two levels is of more than 1°C, showing that local differences in a single cave can be significant. A global warming trend likely correlated with local external temperature changes is observed in both levels since the beginning of the monitoring in 1996 which is not the case in Chauvet and Esparros caves. The stable isotope composition of the seepage water of the Villars cave and drip rates measured under several stalactites give precious information about the mixture of the rainfall infiltration signal in the unsaturated zone; these long isotopic series are discussed and compared with the rainfall (quantity and isotopic composition) sampled at this site.

The Unicorn Cave, Southern Harz Mountains, Germany: From known passages to unknown extensions with the help of geophysical surveys

NASA Astrophysics Data System (ADS)

Kaufmann, Georg; Nielbock, Ralf; Romanov, Douchko

2015-12-01

In soluble rocks (limestone, dolomite, anhydrite, gypsum, …), fissures and bedding partings can be enlarged with time by both physical and chemical dissolution of the host rock. With time, larger cavities evolve, and a network of cave passages can evolve. If the enlarged cave voids are not too deep under the surface, geophysical measurements can be used to detect, identify and trace these karst structures, e.g.: (i) gravity revealing air- and sediment-filled cave voids through negative Bouguer anomalies, (ii) electrical resistivity imaging (ERI) mapping different infillings of cavities either as high resistivities from air-filled voids or dry soft sediments, or low resistivities from saturated sediments, and (iii) groundwater flow through electrical potential differences (SP) arising from dislocated ionic charges from the walls of the underground flow paths. We have used gravity, ERI, and SP methods both in and above the Unicorn Cave located in the southern Harz Mountains in Germany. The Unicorn Cave is a show cave developed in the Werra dolomite formation of the Permian Zechstein sequence, characterised by large trunk passages interrupted by larger rooms. The overburden of the cave is only around 15 m, and passages are filled with sediments reaching infill thicknesses up to 40 m. We present results from our geophysical surveys above the known cave and its northern and southern extension, and from the cave interior. We identify the cave geometry and its infill from gravity and ERI measurements, predict previously unknown parts of the cave, and subsequently confirm the existence of these new passages through drilling. From the wealth of geophysical data acquired we derive a three-dimensional structural model of the Unicorn Cave and its surrounding, especially the cave infill.

Reconciling Mining with the Conservation of Cave Biodiversity: A Quantitative Baseline to Help Establish Conservation Priorities.

PubMed

Jaffé, Rodolfo; Prous, Xavier; Zampaulo, Robson; Giannini, Tereza C; Imperatriz-Fonseca, Vera L; Maurity, Clóvis; Oliveira, Guilherme; Brandi, Iuri V; Siqueira, José O

2016-01-01

Caves pose significant challenges for mining projects, since they harbor many endemic and threatened species, and must therefore be protected. Recent discussions between academia, environmental protection agencies, and industry partners, have highlighted problems with the current Brazilian legislation for the protection of caves. While the licensing process is long, complex and cumbersome, the criteria used to assign caves into conservation relevance categories are often subjective, with relevance being mainly determined by the presence of obligate cave dwellers (troglobites) and their presumed rarity. However, the rarity of these troglobitic species is questionable, as most remain unidentified to the species level and their habitats and distribution ranges are poorly known. Using data from 844 iron caves retrieved from different speleology reports for the Carajás region (South-Eastern Amazon, Brazil), one of the world's largest deposits of high-grade iron ore, we assess the influence of different cave characteristics on four biodiversity proxies (species richness, presence of troglobites, presence of rare troglobites, and presence of resident bat populations). We then examine how the current relevance classification scheme ranks caves with different biodiversity indicators. Large caves were found to be important reservoirs of biodiversity, so they should be prioritized in conservation programs. Our results also reveal spatial autocorrelation in all the biodiversity proxies assessed, indicating that iron caves should be treated as components of a cave network immersed in the karst landscape. Finally, we show that by prioritizing the conservation of rare troglobites, the current relevance classification scheme is undermining overall cave biodiversity and leaving ecologically important caves unprotected. We argue that conservation efforts should target subterranean habitats as a whole and propose an alternative relevance ranking scheme, which could help simplify the assessment process and channel more resources to the effective protection of overall cave biodiversity.

Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders.

PubMed

Zhang, Yuanyuan; Li, Shuqiang

2013-09-04

The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly distributed in the Yunnan-Guizhou Plateau, China. With comprehensive sampling and phylogenetic and coalescent-based analyses, we investigated the tempo and mode of diversification and the origins of these troglobites. We also aimed to determine which factors have influenced the diversification of this little-known group. Coalescent-based species delimitation validated the 18 species recognized by morphological inspection and also suggested the existence of cryptic lineages. Divergence time estimates suggested that Nesticella cave spiders in the Yunnan-Guizhou Plateau constituted a monophyletic troglobite clade that originated in the middle Miocene (11.1-18.6 Ma). Although the Yunnan-Guizhou Plateau clade was composed exclusively of troglobite species, suggesting an ancient common subterranean ancestor, we favor multiple, independent cave colonizations during the Pleistocene over a single ancient cave colonization event to explain the origin of these cave faunas. The diversification of plateau Nesticella has been greatly influenced by the sequential uplift of the plateau and likely reflects multiple cave colonizations over time by epigean ancestors during Pleistocene glacial advances. We concluded that plateau cave Nesticella represent an ancient group of spiders, but with young troglobite lineages that invaded caves only recently. The absence of extant epigean relatives and nearly complete isolation among caves supported their relict status. Our work highlights the importance of comprehensive sampling for studies of subterranean diversity and the evolution of cave organisms. The existence of potentially cryptic species and the relict status of Nesticella highlight the need to conserve these cave spiders.

Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders

PubMed Central

2013-01-01

Background The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly distributed in the Yunnan–Guizhou Plateau, China. With comprehensive sampling and phylogenetic and coalescent-based analyses, we investigated the tempo and mode of diversification and the origins of these troglobites. We also aimed to determine which factors have influenced the diversification of this little-known group. Results Coalescent-based species delimitation validated the 18 species recognized by morphological inspection and also suggested the existence of cryptic lineages. Divergence time estimates suggested that Nesticella cave spiders in the Yunnan–Guizhou Plateau constituted a monophyletic troglobite clade that originated in the middle Miocene (11.1–18.6 Ma). Although the Yunnan–Guizhou Plateau clade was composed exclusively of troglobite species, suggesting an ancient common subterranean ancestor, we favor multiple, independent cave colonizations during the Pleistocene over a single ancient cave colonization event to explain the origin of these cave faunas. The diversification of plateau Nesticella has been greatly influenced by the sequential uplift of the plateau and likely reflects multiple cave colonizations over time by epigean ancestors during Pleistocene glacial advances. Conclusions We concluded that plateau cave Nesticella represent an ancient group of spiders, but with young troglobite lineages that invaded caves only recently. The absence of extant epigean relatives and nearly complete isolation among caves supported their relict status. Our work highlights the importance of comprehensive sampling for studies of subterranean diversity and the evolution of cave organisms. The existence of potentially cryptic species and the relict status of Nesticella highlight the need to conserve these cave spiders. PMID:24006950

Potential effects of recurrent low oxygen conditions on the Illinois Cave amphipod

USGS Publications Warehouse

Panno, S.V.; Hackley, Keith C.; Kelly, W.R.; Hwang, H.-H.; Wilhelm, F.M.; Taylor, S.J.; Stiff, B.J.

2006-01-01

The caves of Illinois' sinkhole plain are the sole habitat of the Illinois Cave amphipod (Gammarus acherondytes), a federally endangered species. The sinkhole plain is a hydrologically-connected sequence of karstified limestone that constitutes an extensive karst aquifer which serves as an important source of potable water for area residents. During this investigation, we examined the ground-water quality in caves within two ground-water basins: 1) Illinois Caverns, where the amphipod is now present after previously reported to have been extirpated from the lower reaches, and 2) Stemler Cave, where the amphipod is reported to have been extirpated. The chemical composition of cave streams in Illinois Caverns and Stemler Cave were compared to determine which parameters, if any, could have contributed to the loss of G. acherondytes from Stemler Cave. Stream water in Stemler Cave contained higher concentrations of organic carbon, potassium, silica, chloride, fluoride, sulfate, iron and manganese than Illinois Caverns. Perhaps most importantly, dissolved oxygen (DO) concentrations in Stemler Cave were, during periods of low flow, substantially lower than in Illinois Caverns. Based on land use, there are probably at least eight times more private septic systems in the Stemler Cave ground-water basin than in the Illinois Caverns ground-water basin. Low DO concentrations were likely the result of microbial breakdown of soil organic matter and wastewater treatment system effluent, and the oxidation of pyrite in bedrock. The near-hypoxic DO in Stemler Cave that occurred during low-flow conditions, and, we speculate, a limited range of G. acherondytes within the Stemler Cave ground-water basin due to a metabolic advantage of the stygophilic aquatic invertebrates over the stygobitic G. acherodytes, resulted in the apparent loss of G. acherondytes from Stemler Cave.

Natural-trap ursid mortality and the Kurtén Response.

PubMed

Wolverton, Steve

2006-05-01

Ursid mortality data have long been used to evaluate associations between cave-bear remains (Ursus deningeri and U. spelaeus) and hominin (Homo sp.) remains. Typically, such ursid assemblages produce mortality patterns that indicate that juvenile and old bears died during hibernation, a pattern that is used to suggest that humans and bears occupied the same caves at different times. However, a different kind of mortality pattern can also be used to suggest human influence on cave bears, particularly under circumstances when bears and humans compete for habitat. In particular, data from Lawson Cave and Jerry Long Cave, Missouri indicate that young-adult North American black bears (Ursus americanus) are prone to capture in natural-trap caves. Similar faunal data from Sima de los Huesos in Spain, where cave-bear and hominin remains are found in the same deposit, might also suggest that the bears died from falling into a natural trap. It is concluded that mortality analysis of ursid remains from caves is a useful tool with which to evaluate accumulation histories of cave deposits and relations between humans, artifacts, and cave-bear remains. In particular, ursid mortality data are relevant to the Kurtén Response, a hypothesis reiterated in the recent literature that implicates human encroachment on ursid habitat (e.g., cave den sites) as a potential cause in cave-bear extinction.

The role of natural ventilation in the exposure to radon in the Postojna Cave

NASA Astrophysics Data System (ADS)

Gregorič, A.; Smerajec, M.; Vaupotič, J.

2012-04-01

Postojna Cave is the biggest of 21 show caves in Slovenia and one of present day's most visited show caves in the world. Long and branched out cave system, large entrances at different levels, inflow of the Pivka river, and large variation of the outdoor air temperature and precipitation, make the Postojna Cave also a very complex climatic system in which each part shows different conditions. The cave is only naturally ventilated and it is therefore characterised by high radon concentration, which depends on the ventilation regime in different seasons, resulting in typical annual cycles of radon levels in the cave air. Postojna Cave is a typical horizontal cave, where the difference between outside and cave air temperature represents the main driving force for air circulation. In winter, when the cave temperature is higher than outside, cave air is released from the cave into the outdoor atmosphere due to the air draught caused by the 'chimney effect', thus allowing fresh and cold outdoor air to enter the cave through low lying openings. This effect is not operative in summer, when the outside temperature is higher than in the cave, and air draught is minimal or reversed. In addition, air circulation can be locally altered due to other processes, like changing level of Pivka river during the rainy season and local geomorphologic characteristics of cave passages. High radon concentration in the Postojna Cave is the reason for thorough studies of the methodology for dose estimates of the personnel working in the cave. Due to high relative humidity and low air circulation, the cave air is characterised by very low particle concentration, which play an important role in radon dosimetry. Therefore parallel monitoring of radioactive aerosols of radon decay products (RnDP) and general (non-radioactive) aerosols in the particle size range of 10-1100 nm was performed in the air of Postojna Cave at the lowest point of tourist path in summer, winter and both transitional periods (spring and autumn), focusing on the unattached fraction of RnDP (fun), a key parameter in radon dosimetry. Dose conversion factors (DCF) were calculated (using Porstendörfer approach) from measured fun for the four periods and compared with recommended DCF, based on the results of epidemiological studies. Results of calculated DCF are in the range from 8-18 mSV WLM-1, much higher that recommended values, and differ significantly for summer and winter period. The lowest value of DCF was calculated for winter period, when the enhanced inflow of cold outside air introduces outdoor aerosols into the cave and consequently lowers fun. On the other hand, calculated DCF during summer period was significantly higher, caused by high fun, which is the consequence of very low particle concentration in cave air during summer ventilation regime. Taking into account also significantly higher radon concentration during summer, when about 70 % of visits is recorded, it is evident, that personnel receives the highest annual dose during summer months.

Carroll Cave: a Missouri legend

USDA-ARS?s Scientific Manuscript database

Carroll Cave is one of the premiere caves of Missouri and the Ozarks region. At over 20 miles of surveyed passage, it is the 2nd longest cave in the state and 33rd longest in the nation. It is also the largest known cave formed in the Ordovician aged (443-485 million years ago) Gasconade Dolomite o...

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.

PubMed

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J; Thomas, David J

2017-09-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.

Predictive minimum description length principle approach to inferring gene regulatory networks.

PubMed

Chaitankar, Vijender; Zhang, Chaoyang; Ghosh, Preetam; Gong, Ping; Perkins, Edward J; Deng, Youping

2011-01-01

Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold that defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to find the optimal parameter. In this work, we propose a new inference algorithm that incorporates mutual information (MI), conditional mutual information (CMI), and predictive minimum description length (PMDL) principle to infer gene regulatory networks from DNA microarray data. In this algorithm, the information theoretic quantities MI and CMI determine the regulatory relationships between genes and the PMDL principle method attempts to determine the best MI threshold without the need of a user-specified fine tuning parameter. The performance of the proposed algorithm is evaluated using both synthetic time series data sets and a biological time series data set (Saccharomyces cerevisiae). The results show that the proposed algorithm produced fewer false edges and significantly improved the precision when compared to existing MDL algorithm.

Radon as a natural tracer for underwater cave exploration and hypogenic cave formation

NASA Astrophysics Data System (ADS)

Csondor, Katalin; Erőss, Anita; Horváth, Ákos; Szieberth, Dénes

2017-04-01

Using 222Rn as a natural tracer is a novel approach in underwater cave exploration and in the research of active hypogenic caves. The research area, the Molnár János cave is one of the largest caves of an unique hypogenic karst system, the Buda Thermal Karst (Budapest, Hungary). The cave system is mainly characterized by water-filled passages. The cave is located at one of the main discharge areas of the Buda Thermal Karst and the major outflow point of the waters of the cave system is the Boltív spring, which feeds the artificial Malom Lake. Previous complex hydrogeological studies and radon measurements in the cave system and in the spring established the highest radon concentration (71 Bq/L, where the average is 44 Bq/L) in the springwater. The origin of radon was identified in the form of iron-hydroxide containing biofilms, which form by mixing of waters and efficiently adsorb radium from the thermal water component and cause local radon anomalies. Since mixing of waters is responsible for the formation of the cave as well, these iron-hydroxide containing biofilms and consequently high radon concentrations mark the active cave forming zones. The aim of the study was to use the radon as a natural tracer to locate active mixing and cave forming zones. Based on previous radon measurements it is supposed that the active mixing and cave forming zone has to be close to the spring, since the highest radon concentration was measured there. Therefore, the radon activity concentration mapping was carried out with the help of divers and involving that part of the cave which closest to the spring. Based on our measurements the highest radon concentration (84 Bq/L) ever was achieved in the springwater. Based on the radon concentration distribution direct connection and active karst conduit was established between the spring and the deepest room of the researched part of the cave, which was verified by artificial tracer as well. However, the distribution of radon in the cave passages shows lower concentrations (18-46 Bq/L) compared to the spring, therefore an addition deep inflow from a hitherto unknown cave passages is assumed, from which waters with high radon content arrive to the spring. These passages are supposed to be in the active cave formation (mixing) zone. The Buda Thermal Karst research was funded by the Hungarian Scientific Research Fund under the grant agreement no. NK 101356.

Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain).

PubMed

Portillo, M Carmen; Gonzalez, Juan M

2009-01-15

The conservation of paleolithic paintings such as those in Altamira Cave (Spain) is a primary objective. Recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. Herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (SRB), from Altamira Cave with potential negative effects on painting conservation. In the present work, the communities of bacteria and SRB were studied through PCR-DGGE analysis. Data suggest that SRB communities represent a significant, highly diverse bacterial group in Altamira Cave. These findings represent a first report on this physiological group on caves with paleolithic paintings and their potential biodegradation consequences. Expanding our knowledge on microbial communities in Altamira Cave is a priority to design appropriate conservation strategies.

Visual Inference Programming

NASA Technical Reports Server (NTRS)

Wheeler, Kevin; Timucin, Dogan; Rabbette, Maura; Curry, Charles; Allan, Mark; Lvov, Nikolay; Clanton, Sam; Pilewskie, Peter

2002-01-01

The goal of visual inference programming is to develop a software framework data analysis and to provide machine learning algorithms for inter-active data exploration and visualization. The topics include: 1) Intelligent Data Understanding (IDU) framework; 2) Challenge problems; 3) What's new here; 4) Framework features; 5) Wiring diagram; 6) Generated script; 7) Results of script; 8) Initial algorithms; 9) Independent Component Analysis for instrument diagnosis; 10) Output sensory mapping virtual joystick; 11) Output sensory mapping typing; 12) Closed-loop feedback mu-rhythm control; 13) Closed-loop training; 14) Data sources; and 15) Algorithms. This paper is in viewgraph form.

Energy and speleogenesis: Key determinants of terrestrial species richness in caves.

PubMed

Jiménez-Valverde, Alberto; Sendra, Alberto; Garay, Policarp; Reboleira, Ana Sofia P S

2017-12-01

The aim of this study was to unravel the relative role played by speleogenesis (i.e., the process in which a cave is formed), landscape-scale variables, and geophysical factors in the determination of species richness in caves. Biological inventories from 21 caves located in the southeastern Iberian Peninsula along with partial least square (PLS) regression analysis were used to assess the relative importance of the different explanatory variables. The caves were grouped according to the similarity in their species composition; the effect that spatial distance could have on similarity was also studied using correlation between matrices. The energy and speleogenesis of caves accounted for 44.3% of the variation in species richness. The trophic level of each cave was the most significant factor in PLS regression analysis, and epigenic caves (i.e., those formed by the action of percolating water) had significantly more species than hypogenic ones (i.e., those formed by the action of upward flows in confined aquifers). Dissimilarity among the caves was very high (multiple-site β sim  = 0.92). Two main groups of caves were revealed through the cluster analysis, one formed by the western caves and the other by the eastern ones. The significant-but low-correlation found between faunistic dissimilarity and geographical distance ( r  =   .16) disappeared once the caves were split into the two groups. The extreme beta-diversity suggests a very low connection among the caves and/or a very low dispersal capacity of the species. In the region under study, two main factors are intimately related to the richness of terrestrial subterranean species in caves: the amount of organic material (trophic level) and the formation process (genesis). This is the first time that the history of a cave genesis has been quantitatively considered to assess its importance in explaining richness patterns in comparison with other factors more widely recognized.

Morphometry and distribution of isolated caves as a guide for phreatic and confined paleohydrological conditions

NASA Astrophysics Data System (ADS)

Frumkin, Amos; Fischhendler, Itay

2005-04-01

Isolated caves are a special cave type common in most karst terrains, formed by prolonged slow water flow where aggressivity is locally boosted. The morphometry and distribution of isolated caves are used here to reconstruct the paleohydrology of a karstic mountain range. Within a homogenous karstic rock sequence, two main types of isolated caves are distinguished, and each is associated with a special hydrogeologic setting: maze caves form by rising water in the confined zone of the aquifer, under the Mt. Scopus Group (Israel) confinement, while chamber caves are formed in phreatic conditions, apparently by lateral flow mixing with a vadose input from above.

Effect of diurnal and seasonal temperature variation on Cussac cave ventilation using co2 assessment

NASA Astrophysics Data System (ADS)

Peyraube, Nicolas; Lastennet, Roland; Villanueva, Jessica Denila; Houillon, Nicolas; Malaurent, Philippe; Denis, Alain

2017-08-01

Cussac cave was investigated to assess the cave air temperature variations and to understand its ventilation regime. This cave is located in an active karst system in the south west part of France. It has a single entrance and is considered as a cold air trap. In this study, air mass exchanges were probed. Measurements of temperature and Pco2 with a 30-min frequency were made in several locations close to the cave entrance. Speed of the air flow was also measured at the door of cave entrance. Results show that cave air Pco2 varies from 0.18 to 3.33 %. This cave appears to be a CO2 source with a net mass of 2319 tons blown in 2009. Carbon-stable isotope of CO2 (13Cco2) ranges from -20.6 ‰ in cold season to -23.8 ‰ in warm season. Cave air is interpreted as a result of a mix between external air and an isotopically depleted air, coming from the rock environment. The isotopic value of the light member varies through time, from -23.9 to -22.5 ‰. Furthermore, this study ascertains that the cave never stops in communicating with the external air. The ventilation regime is identified. (1) In cold season, the cave inhales at night and blows a little at the warmest hours. However, in warm season, (2) cave blows at night, but (3) during the day, a convection loop takes place in the entrance area and prevents the external air from entering the cave, confirming the cold air trap.

Radon levels in Romanian caves: an occupational exposure survey.

PubMed

Cucoş Dinu, Alexandra; Călugăr, Monica I; Burghele, Bety D; Dumitru, Oana A; Cosma, Constantin; Onac, Bogdan P

2017-10-01

A comprehensive radon survey has been carried out in seven caves located in the western half of Romania's most significant karst regions. Touristic and non-touristic caves were investigated with the aim to provide a reliable distribution of their radon levels and evaluate the occupational exposure and associated effective doses. Radon gas concentrations were measured with long-term diffusion-type detectors during two consecutive seasons (warm and cold). All investigated caves exceed the European Union reference level of radon gas at workplaces (300 Bq/m 3 ). The radon concentration in these caves ranges between 53 and 2866 Bq/m 3 , reflecting particular cave topography, season-related cave ventilation, and complex tectonic and geological settings surrounding each location. Relatively homogeneous high radon levels occur in all investigated touristic caves and in Tăuşoare and Vântului along their main galleries. Except for Muierii, in all the other caves radon levels are higher during the warm season, compared to the cold one. This suggests that natural cave ventilation largely controls the underground accumulation of radon. The results reported here reveal that the occupational exposure in Urşilor, Vadu Crişului, Tăuşoare, Vântului, and Muierii caves needs to be carefully monitored. The effective doses to workers vary between an average of 0.25 and 4.39 mSv/year depending on the measuring season. The highest values were recorded in show caves, ranging from 1.15 to 6.15 mSv/year, well above the European recommended limit, thus posing a potential health hazard upon cave guides, cavers, and scientists.

Critical level setting of continuous air monitor.

PubMed

Li, Huibin; Jia, Mingyan; Wang, Kailiang

2013-01-01

Algorithms used to compensate the radon and thoron progeny's interference are one of the key technologies for continuous air monitors (CAMs). In this study, a CAM that can automatically change filter was manufactured, and equations used to calculate the transuranic aerosol concentration and the corresponding critical level were derived. The parameters used in calculation were acquired by continuous measurement in a high radon environment. At last, validation of the calculation was tested in a cave where the radon concentration fluctuated frequently, and the results were analysed.

Analysis of Bioactive Amino Acids from Fish Hydrolysates with a New Bioinformatic Intelligent System Approach.

PubMed

Elaziz, Mohamed Abd; Hemdan, Ahmed Monem; Hassanien, AboulElla; Oliva, Diego; Xiong, Shengwu

2017-09-07

The current economics of the fish protein industry demand rapid, accurate and expressive prediction algorithms at every step of protein production especially with the challenge of global climate change. This help to predict and analyze functional and nutritional quality then consequently control food allergies in hyper allergic patients. As, it is quite expensive and time-consuming to know these concentrations by the lab experimental tests, especially to conduct large-scale projects. Therefore, this paper introduced a new intelligent algorithm using adaptive neuro-fuzzy inference system based on whale optimization algorithm. This algorithm is used to predict the concentration levels of bioactive amino acids in fish protein hydrolysates at different times during the year. The whale optimization algorithm is used to determine the optimal parameters in adaptive neuro-fuzzy inference system. The results of proposed algorithm are compared with others and it is indicated the higher performance of the proposed algorithm.

78 FR 59923 - Cave Run Energy, LLC; Notice of Intent To File License Application, Filing of Pre-Application...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 14376-001] Cave Run Energy...: July 21, 2013. d. Submitted By: Cave Run Energy, LLC. e. Name of Project: Cave Run Hydroelectric...: 18 CFR 5.3 of the Commission's regulations. h. Potential Applicant Contact: Mark Boumansour, Cave Run...

A prior-based integrative framework for functional transcriptional regulatory network inference

PubMed Central

Siahpirani, Alireza F.

2017-01-01

Abstract Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to infer regulatory networks, however, networks inferred from such methods have low overlap with experimentally derived (e.g. ChIP-chip and transcription factor (TF) knockouts) networks. Currently we have a limited understanding of this discrepancy. To address this gap, we first develop a regulatory network inference algorithm, based on probabilistic graphical models, to integrate expression with auxiliary datasets supporting a regulatory edge. Second, we comprehensively analyze our and other state-of-the-art methods on different expression perturbation datasets. Networks inferred by integrating sequence-specific motifs with expression have substantially greater agreement with experimentally derived networks, while remaining more predictive of expression than motif-based networks. Our analysis suggests natural genetic variation as the most informative perturbation for network inference, and, identifies core TFs whose targets are predictable from expression. Multiple reasons make the identification of targets of other TFs difficult, including network architecture and insufficient variation of TF mRNA level. Finally, we demonstrate the utility of our inference algorithm to infer stress-specific regulatory networks and for regulator prioritization. PMID:27794550

Picos de Europa National and Regional parks (Northern Spain): the karst underground landscape

NASA Astrophysics Data System (ADS)

Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; Rodríguez-Rodríguez, Laura; José Domínguez-Cuesta, María; Meléndez-Asensio, Mónica; García-Sansegundo, Joaquín

2015-04-01

Karst caves represent an environmental with a high value from the Geoheritage and Geodiversity points of view given by hidden underground landscape practically reserved to the speleologists. Nevertheless, cave surveys, 3d models of caves and DEMs, and pictures can be used to approach the endokarst geoheritage characterization. The Picos de Europa National and Regional parks include the 14% of World's Deepest Caves (>1 km depth); moreover these parks shows a high environmental value related with seven protection figures: Biosphere Reserve, Special Protection Area, the Site of Community Importance, and four Natural Monument. The aim of this work is to present the Geoheritage values of the underground landscape of the Picos de Europa National and Regional parks. These parks involve several alpine karst massifs up to 700 km2 and 2,600 m asl, as the Picos de Europa mountains (declared Global Geosite by its geomorphological interest), the Mampodre Massif, and the Peñas Pintas and Yordas peaks (sited in Riaño dam area). The alpine karst involves a large underground landscape formed by more than 3,700 epigenic caves with 403 km of conduits. The 95 % of the cave conduits are located in the Picos de Europa mountains and correspond to caves up to 18.9 km length and 1.6 km depth; the 5 % of cave conduits are sited in other small karst areas and include caves up to 1.5 km length and 200 m depth. The karst caves present high natural, scientific and cultural values. The natural value corresponds to the singularity and the spectacular vertical development of the caves and a very high Geodiversity of cave features. The karst shows a high concentration of deep caves (81 caves deeper than 500 m) that is twice higher than the concentration of other karst areas, as Arabika Massif (Western Caucasus). The natural value is mainly related to the presence of geomorphological and hydrogeological features, highlighting high vadose canyons and shafts, old phreatic and epiphreatic conduits, few fluvial deposits, some speleothems (dripstone, flowstone), few ice caves, many underground streams, and karst springs. The scientific value corresponds to the cave records related to the regional evolution of the Cantabrian Range. The scientific studies evidence that the caves are originated prior to, at least, the Middle Pleistocene, in relation to mountain uplift, glaciations, fluvial incision, and the erosion of the alpine lithological seriesthat were above the karst. The cultural value is related with the specific uses of the cavities by shepherds and speleologists, and the singularity of cave names. The uses include traditional customs, as the livestock farming, the water collection, the elaboration of five types of cheese with Certificated of Origin, and sport uses by speleologists from many countries of Europe. The educative values are low due to the limitations of access inside the caves, although two caves are touristic and the entrance of some caves can be used to explain vadose shafts, relations between caves and glaciers and rivers or the underground water flow. GEOCAVE project (MAGRAMA-580/12 OAPN)

Discovery of a diverse cave flora in China.

PubMed

Monro, Alexandre K; Bystriakova, Nadia; Fu, Longfei; Wen, Fang; Wei, Yigang

2018-01-01

Few studies document plants in caves. Our field observations of a widespread and seemingly angiosperm-rich cave flora in SW China lead us to test the following hypotheses, 1) SW China caves contain a diverse vascular plant flora, 2) that this is a relic of a largely absent forest type lacking endemic species, and 3) that the light environment plants occupy in caves is not distinct from non-cave habitats. To do so we surveyed 61 caves and used species accumulation curves (SAC) to estimate the total diversity of this flora and used a subsample of 14 caves to characterise the light environment. We used regional floras and existing conservation assessments to evaluate the conservation value of this flora. We used observations on human disturbance within caves to evaluate anthropogenic activities. Four-hundred-and-eighteen vascular plant species were documented with SACs predicting a total diversity of 529-846. Ninety-three percent of the species documented are known karst forest species, 7% are endemic to caves and 81% of the species are angiosperms. We demonstrate that the light environment in caves is distinct to that of terrestrial habitats and that a subset of the flora likely grow in the lowest light levels documented for vascularised plants. Our results suggest that the proportion of species threatened with extinction is like that for the terrestrial habitat and that almost half of the entrance caverns sampled showed signs of human disturbance. We believe that this is the first time that such an extensive sample of cave flora has been undertaken and that such a diverse vascular plant flora has been observed in caves which we predict occurs elsewhere in SE Asia. We argue that the cave flora is an extension of the karst forest understory present prior to catastrophic deforestation in the 20thC. We suggest that within SW China caves serve as both refuges and a valuable source of germplasm for the restoration of karst forest. We also propose that caves represent a distinct habitat for plants that is most similar to that of the forest understory, but distinct with respect to the absence of trees, leaf litter, root mats, higher levels of atmospheric CO2, and lower diurnal and annual variation in temperature and humidity. We highlight tourism, agriculture and the absence of legislated protection of caves as the main current threats to this flora.

Discovery of a diverse cave flora in China

PubMed Central

Wen, Fang

2018-01-01

Few studies document plants in caves. Our field observations of a widespread and seemingly angiosperm-rich cave flora in SW China lead us to test the following hypotheses, 1) SW China caves contain a diverse vascular plant flora, 2) that this is a relic of a largely absent forest type lacking endemic species, and 3) that the light environment plants occupy in caves is not distinct from non-cave habitats. To do so we surveyed 61 caves and used species accumulation curves (SAC) to estimate the total diversity of this flora and used a subsample of 14 caves to characterise the light environment. We used regional floras and existing conservation assessments to evaluate the conservation value of this flora. We used observations on human disturbance within caves to evaluate anthropogenic activities. Four-hundred-and-eighteen vascular plant species were documented with SACs predicting a total diversity of 529–846. Ninety-three percent of the species documented are known karst forest species, 7% are endemic to caves and 81% of the species are angiosperms. We demonstrate that the light environment in caves is distinct to that of terrestrial habitats and that a subset of the flora likely grow in the lowest light levels documented for vascularised plants. Our results suggest that the proportion of species threatened with extinction is like that for the terrestrial habitat and that almost half of the entrance caverns sampled showed signs of human disturbance. We believe that this is the first time that such an extensive sample of cave flora has been undertaken and that such a diverse vascular plant flora has been observed in caves which we predict occurs elsewhere in SE Asia. We argue that the cave flora is an extension of the karst forest understory present prior to catastrophic deforestation in the 20thC. We suggest that within SW China caves serve as both refuges and a valuable source of germplasm for the restoration of karst forest. We also propose that caves represent a distinct habitat for plants that is most similar to that of the forest understory, but distinct with respect to the absence of trees, leaf litter, root mats, higher levels of atmospheric CO2, and lower diurnal and annual variation in temperature and humidity. We highlight tourism, agriculture and the absence of legislated protection of caves as the main current threats to this flora. PMID:29415039

Stan: Statistical inference

NASA Astrophysics Data System (ADS)

Stan Development Team

2018-01-01

Stan facilitates statistical inference at the frontiers of applied statistics and provides both a modeling language for specifying complex statistical models and a library of statistical algorithms for computing inferences with those models. These components are exposed through interfaces in environments such as R, Python, and the command line.

The architectural form of Qikou Cave dwellings in Chinese "Earth" culture

NASA Astrophysics Data System (ADS)

Chen, Xuanchen; Feng, Xinqun

2018-03-01

Cave building is not only a kind of architecture with unique style, but also a manifestation of Chinese traditional culture. Cave culture is an important part of Chinese traditional culture. The main purpose of this thesis which studies the architectural form of Qikou Cave, is to analyze how the cave building plays a positive role in promoting the development and application of modern resources and in cultural transmission. Based on a large amount of literature material, and taking Qikou Cave as an example, by studying the morphological characteristics of cave building, the paper takes an optimistic outlook on its future development and the sustainable development of the resources. It is expected that the cave culture can be further explored to promote the traditional Chinese culture and to drive the development of modern construction industry and resource conservation.

Karst development and speleogenesis, Isla de Mona, Puerto Rico

USGS Publications Warehouse

Frank, E.F.; Mylroie, J.; Troester, J.; Alexander, E.C.; Carew, J.L.

1998-01-01

Isla de Mona consists of a raised table-top Miocene-Pliocene reef platform bounded on three sides by vertical cliffs, up to 80 m high. Hundreds of caves ring the periphery of the island and are preferentially developed in, but not limited to, the Lirio Limestone/Isla de Mona Dolomite contact. These flank margin caves originally formed at sea level and are now exposed at various levels by tectonic uplift of the island (Franbk 1983; Mylroie et al. 1995b). Wall cusps, a characteristic feature of flank margin caves, are ubiquitois features. Comparisons among similar caves formed in the Bahamas and Isla de Mona reveal the same overall morphology throughout the entire range of sizes and complexities. The coincidence of the primary cave development zone with the Lirio Limestone/Isla de Mona Dolomite contact may result from syngenetic speleogenesis and dolomitization rather than preferential dissolution along a lithologic boundary. Tectonic uplift and glacioeustatic sea level fluctuations produced caves at a variety of elevations. Speleothem dissolution took place in many caves under phreatic conditions, evidence these caves were flooded after an initial period of subaerial exposure and speleothem growth. Several features around the perimeter of the island are interpreted to be caves whose roofs were removed by surficial denudation processes. Several large closed depressions and dense pit cave fields are further evidence of surficial karst features. The cliff retreat around the island perimeter since the speleogenesis of the major cave systems is small based upon the distribution of the remnant cave sections.

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

PubMed Central

Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui

2015-01-01

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments. PMID:25870592

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China.

PubMed

Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui

2015-01-01

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.

Semantic Health Knowledge Graph: Semantic Integration of Heterogeneous Medical Knowledge and Services.

PubMed

Shi, Longxiang; Li, Shijian; Yang, Xiaoran; Qi, Jiaheng; Pan, Gang; Zhou, Binbin

2017-01-01

With the explosion of healthcare information, there has been a tremendous amount of heterogeneous textual medical knowledge (TMK), which plays an essential role in healthcare information systems. Existing works for integrating and utilizing the TMK mainly focus on straightforward connections establishment and pay less attention to make computers interpret and retrieve knowledge correctly and quickly. In this paper, we explore a novel model to organize and integrate the TMK into conceptual graphs. We then employ a framework to automatically retrieve knowledge in knowledge graphs with a high precision. In order to perform reasonable inference on knowledge graphs, we propose a contextual inference pruning algorithm to achieve efficient chain inference. Our algorithm achieves a better inference result with precision and recall of 92% and 96%, respectively, which can avoid most of the meaningless inferences. In addition, we implement two prototypes and provide services, and the results show our approach is practical and effective.

Semantic Health Knowledge Graph: Semantic Integration of Heterogeneous Medical Knowledge and Services

PubMed Central

Yang, Xiaoran; Qi, Jiaheng; Pan, Gang; Zhou, Binbin

2017-01-01

With the explosion of healthcare information, there has been a tremendous amount of heterogeneous textual medical knowledge (TMK), which plays an essential role in healthcare information systems. Existing works for integrating and utilizing the TMK mainly focus on straightforward connections establishment and pay less attention to make computers interpret and retrieve knowledge correctly and quickly. In this paper, we explore a novel model to organize and integrate the TMK into conceptual graphs. We then employ a framework to automatically retrieve knowledge in knowledge graphs with a high precision. In order to perform reasonable inference on knowledge graphs, we propose a contextual inference pruning algorithm to achieve efficient chain inference. Our algorithm achieves a better inference result with precision and recall of 92% and 96%, respectively, which can avoid most of the meaningless inferences. In addition, we implement two prototypes and provide services, and the results show our approach is practical and effective. PMID:28299322

An inference engine for embedded diagnostic systems

NASA Technical Reports Server (NTRS)

Fox, Barry R.; Brewster, Larry T.

1987-01-01

The implementation of an inference engine for embedded diagnostic systems is described. The system consists of two distinct parts. The first is an off-line compiler which accepts a propositional logical statement of the relationship between facts and conclusions and produces data structures required by the on-line inference engine. The second part consists of the inference engine and interface routines which accept assertions of fact and return the conclusions which necessarily follow. Given a set of assertions, it will generate exactly the conclusions which logically follow. At the same time, it will detect any inconsistencies which may propagate from an inconsistent set of assertions or a poorly formulated set of rules. The memory requirements are fixed and the worst case execution times are bounded at compile time. The data structures and inference algorithms are very simple and well understood. The data structures and algorithms are described in detail. The system has been implemented on Lisp, Pascal, and Modula-2.

Environmental change at Kartchner Caverns: trying to separate natural and anthropogenic changes

Treesearch

Rickard S. Toomey; Ginger Nolan

2005-01-01

Cave temperature and moisture levels are important factors in the environmental health of Kartchner Caverns. Monitoring indicates the cave has warmed and moisture levels have fallen over the past 14 years. Timing and patterns of change within the cave suggest that changes are due to development as a show cave. However, changes in other caves, surface temperature and...

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria

PubMed Central

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A.; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J.; Thomas, David J.

2018-01-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa. PMID:29551950

Steppe lion remains imported by Ice Age spotted hyenas into the Late Pleistocene Perick Caves hyena den in northern Germany

NASA Astrophysics Data System (ADS)

Diedrich, Cajus G.

2009-05-01

Upper Pleistocene remains of the Ice Age steppe lion Panthera leo spelaea (Goldfuss, 1810) have been found in the Perick Caves, Sauerland Karst, NW Germany. Bones from many hyenas and their imported prey dating from the Lower to Middle Weichselian have also been recovered from the Perick Cave hyena den. These are commonly cracked or exhibit deep chew marks. The absence of lion cub bones, in contrast to hyena and cave bear cub remains in the Perick Caves, and other caves of northern Germany, excludes the possibility that P. leo spelaea used the cave for raising cubs. Only in the Wilhelms Cave was a single skeleton of a cub found in a hyena den. Evidence of the chewing, nibbling and cracking of lion bones and crania must have resulted from the importation and destruction of lion carcasses (4% of the prey fauna). Similar evidence was preserved at other hyena den caves and open air sites in Germany. The bone material from the Perick and other Central European caves points to antagonistic hyena and lion conflicts, similar to clashes of their modern African relatives.

Investigation of Sediment Pathways and Concealed Sedimentological Features in Hidden River Cave, Kentucky

NASA Astrophysics Data System (ADS)

Feist, S.; Maclachlan, J. C.; Reinhardt, E. G.; McNeill-Jewer, C.; Eyles, C.

2016-12-01

Hidden River Cave is part of a cave system hydrogeologically related to Mammoth Cave in Kentucky and is a multi-level active cave system with 25km of mapped passages. Upper levels experience flow during flood events and lower levels have continuously flowing water. Improper industrial and domestic waste disposal and poor understanding of local hydrogeology lead to contamination of Hidden River Cave in the early 1940s. Previously used for hydroelectric power generation and as a source of potable water the cave was closed to the public for almost 50 years. A new sewage treatment plant and remediation efforts since 1989 have improved the cave system's health. This project focuses on sedimentological studies in the Hidden River Cave system. Water and sediment transport in the cave are being investigated using sediment cores, surface sediment samples and water level data. An Itrax core scanner is used to analyze sediment cores for elemental concentrations, magnetic susceptibility, radiography, and high resolution photography. Horizons of metal concentrations in the core allow correlation of sedimentation events in the cave system. Thecamoebian (testate amoebae) microfossils identified in surface samples allow for further constraint of sediment sources, sedimentation rates, and paleoclimatic analysis. Dive recorders monitor water levels, providing data to further understand the movement of sediment through the cave system. A general time constraint on the sediment's age is based on the presence of microplastic in the surface samples and sediment cores, and data from radiocarbon and lead-210 dating. The integration of various sedimentological data allows for better understanding of sedimentation processes and their record of paleoenvironmental change in the cave system. Sediment studies and methodologies from this project can be applied to other karst systems, and have important applications for communities living on karst landscapes and their water management policies.

A Brief Analysis on the Redesign of Traditional Cave Dwellings

NASA Astrophysics Data System (ADS)

Chen, Xuanchen; Feng, Xinqun

2018-05-01

Cave dwelling, the treasure of ancient architecture, is the unique product of Chinese Loess Plateau. However, recently due to the continuous development of social economy and industrial civilization, traditional cave dwelling in our country has represented the backwardness and poverty of the country, and it had been gradually abandoned in the history. In order to effectively avoid this phenomenon and protect the traditional cave dwelling to the greatest extent. This paper makes relevant introduction about traditional cave dwelling, and meanwhile, the redesign of traditional cave dwelling houses has also been studied in detail.

Analytic continuation of quantum Monte Carlo data by stochastic analytical inference.

PubMed

Fuchs, Sebastian; Pruschke, Thomas; Jarrell, Mark

2010-05-01

We present an algorithm for the analytic continuation of imaginary-time quantum Monte Carlo data which is strictly based on principles of Bayesian statistical inference. Within this framework we are able to obtain an explicit expression for the calculation of a weighted average over possible energy spectra, which can be evaluated by standard Monte Carlo simulations, yielding as by-product also the distribution function as function of the regularization parameter. Our algorithm thus avoids the usual ad hoc assumptions introduced in similar algorithms to fix the regularization parameter. We apply the algorithm to imaginary-time quantum Monte Carlo data and compare the resulting energy spectra with those from a standard maximum-entropy calculation.

Inferring microbial interaction networks from metagenomic data using SgLV-EKF algorithm.

PubMed

Alshawaqfeh, Mustafa; Serpedin, Erchin; Younes, Ahmad Bani

2017-03-27

Inferring the microbial interaction networks (MINs) and modeling their dynamics are critical in understanding the mechanisms of the bacterial ecosystem and designing antibiotic and/or probiotic therapies. Recently, several approaches were proposed to infer MINs using the generalized Lotka-Volterra (gLV) model. Main drawbacks of these models include the fact that these models only consider the measurement noise without taking into consideration the uncertainties in the underlying dynamics. Furthermore, inferring the MIN is characterized by the limited number of observations and nonlinearity in the regulatory mechanisms. Therefore, novel estimation techniques are needed to address these challenges. This work proposes SgLV-EKF: a stochastic gLV model that adopts the extended Kalman filter (EKF) algorithm to model the MIN dynamics. In particular, SgLV-EKF employs a stochastic modeling of the MIN by adding a noise term to the dynamical model to compensate for modeling uncertainties. This stochastic modeling is more realistic than the conventional gLV model which assumes that the MIN dynamics are perfectly governed by the gLV equations. After specifying the stochastic model structure, we propose the EKF to estimate the MIN. SgLV-EKF was compared with two similarity-based algorithms, one algorithm from the integral-based family and two regression-based algorithms, in terms of the achieved performance on two synthetic data-sets and two real data-sets. The first data-set models the randomness in measurement data, whereas, the second data-set incorporates uncertainties in the underlying dynamics. The real data-sets are provided by a recent study pertaining to an antibiotic-mediated Clostridium difficile infection. The experimental results demonstrate that SgLV-EKF outperforms the alternative methods in terms of robustness to measurement noise, modeling errors, and tracking the dynamics of the MIN. Performance analysis demonstrates that the proposed SgLV-EKF algorithm represents a powerful and reliable tool to infer MINs and track their dynamics.

Bacterial Activity and Geochemical Reactions in Submerged Cave Development -- Impact on Karst Aquifers in Florida

NASA Astrophysics Data System (ADS)

Herman, J. S.; Franklin, R. B.; Mills, A. L.; Giannotti, A. L.; Tysall, T. N.

2008-05-01

Elucidation of coupled mechanisms of sulfide oxidation and biomass generation supports an improved understanding the driving forces behind acid production, calcite dissolution, cave development, and karst aquifers characterization. Wekiwa Springs Cave and DeLeon Springs Cave, located in central Florida, both contain prolific bacterial mats from which sulfur-oxidizing bacteria have been identified. Wekiwa Springs Cave, a submerged cave developed in the Hawthorne Formation and located near Orlando, Florida, has groundwater discharge from the Floridian aquifer system, with some contribution from surficial and intermediate aquifers. The spring is the headwater of the Wekiwa River and releases a total of 170,000 m3 of water per day. The ceiling and walls are heavily covered (10 cm thick) with three morphologically distinct types of microbial mats largely comprising sulfur-oxidizing bacteria. Analysis of nearby groundwater collected from wells confirms sulfide concentrations in the regional groundwater of ~ 1.5 mg/L, though sulfide concentrations for water collected in the cave are below detection. Dissolved oxygen concentration in the water is low (<0.5 mg/L). DeLeon Springs Cave, a submerged cave located in Volusia County, Florida, is a single conduit with an average discharge of ~ 70,000 m3 of water per day, and water chemistry data suggest the presence of a saline seep in the system. Dense microbial mats cover the rock surfaces of the cave; the mats are highly filamentous, with long white streamers that often extend 1-2 feet from the cave wall. Microscopic analysis has confirmed the presence of sulfur granules within these bacterial cells, similar to those observed in the Wekiwa cave organisms. The water chemistry in DeLeon Springs Cave, however, is distinct from that of Wekiwa Springs Cave. Though DO, Fetotal, and HS- values are similar for the two sites, the concentration of ions such as Cl-, Na+, and SO42- are considerably higher at DeLeon. A similar contrast exists for the other major cations (Ca2+, Mg2+, K+), although the difference is less pronounced. An important difference between the two cave systems is the considerable spatial variability associated with water chemistry along the flowpath in the DeLeon system, whereas water chemistry is fairly constant at all locations sampled in Wekiwa Springs Cave. Microbial communities were characterized based on the on overall genetic similarity between whole-community DNA samples as compared using T-RFLP analysis of 16S rRNA genes. The microbial communities found at each sampling station in the Wekiwa Springs Cave are relatively similar to one another, while the communities found at the different sampling stations in the DeLeon Springs Cave are distinct from one another and from the Wekiwa community. This examination of submerged caves with respect to the specific speleogenic mechanisms and the importance of biological processes in their generation informs our understanding of caves and karst environments.

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

PubMed Central

Riquelme, Cristina; Marshall Hathaway, Jennifer J.; Enes Dapkevicius, Maria de L. N.; Miller, Ana Z.; Kooser, Ara; Northup, Diana E.; Jurado, Valme; Fernandez, Octavio; Saiz-Jimenez, Cesareo; Cheeptham, Naowarat

2015-01-01

Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems. PMID:26696966

Conservation of prehistoric caves and stability of their inner climate: lessons from Chauvet and other French caves.

PubMed

Bourges, F; Genthon, P; Genty, D; Lorblanchet, M; Mauduit, E; D'Hulst, D

2014-09-15

In the last 150 years, some prehistoric painted caves suffered irreversible degradations due to misperception of conservation issues and subsequent mismanagement. These sites presented naturally an exceptional stability of their internal climate allowing conservation in situ of outstanding fragile remains, some for nearly 40,000 years. This is for a large part due to exchanges of air, CO2, heat and water with the karstic system in which these caves are included. We introduce the concept of underground confinement, based on the stability of the inner cave climate parameters, especially its temperature. Confined caves present the best conservative properties. It is emphasized that this confined state implies slow exchanges with the surrounding karst and that a stable cave cannot be viewed as a closed system. This is illustrated on four case studies of French caves of various confinement states evidenced by long term continuous monitoring and on strategies to improve their conservation properties. The Chauvet cave presents optimal conservation properties. It is wholly confined as shown by the stability of its internal parameters since its discovery in 1994. In Marsoulas cave, archeological works removed the entrance scree and let a strong opening situation of the decorated zone. Remediation is expected by adding a buffer structure at the entrance. In Pech Merle tourist cave, recurrent painting fading was related to natural seasonal drying of walls. Improvement of the cave closure system restored a confined state insuring optimal visibility of the paintings. In Gargas tourist cave, optimization of closures, lighting system and number of visitors, allowed it to gradually reach a semi-confined state that improved the conservation properties. Conclusions are drawn on the characterization of confinement state of caves and on the ways to improve their conservation properties by restoring their initial regulation mechanisms and to avoid threats to their stability. Copyright © 2013 Elsevier B.V. All rights reserved.

Reconciling Mining with the Conservation of Cave Biodiversity: A Quantitative Baseline to Help Establish Conservation Priorities

PubMed Central

Prous, Xavier; Zampaulo, Robson; Giannini, Tereza C.; Imperatriz-Fonseca, Vera L.; Maurity, Clóvis; Oliveira, Guilherme; Brandi, Iuri V.; Siqueira, José O.

2016-01-01

Caves pose significant challenges for mining projects, since they harbor many endemic and threatened species, and must therefore be protected. Recent discussions between academia, environmental protection agencies, and industry partners, have highlighted problems with the current Brazilian legislation for the protection of caves. While the licensing process is long, complex and cumbersome, the criteria used to assign caves into conservation relevance categories are often subjective, with relevance being mainly determined by the presence of obligate cave dwellers (troglobites) and their presumed rarity. However, the rarity of these troglobitic species is questionable, as most remain unidentified to the species level and their habitats and distribution ranges are poorly known. Using data from 844 iron caves retrieved from different speleology reports for the Carajás region (South-Eastern Amazon, Brazil), one of the world's largest deposits of high-grade iron ore, we assess the influence of different cave characteristics on four biodiversity proxies (species richness, presence of troglobites, presence of rare troglobites, and presence of resident bat populations). We then examine how the current relevance classification scheme ranks caves with different biodiversity indicators. Large caves were found to be important reservoirs of biodiversity, so they should be prioritized in conservation programs. Our results also reveal spatial autocorrelation in all the biodiversity proxies assessed, indicating that iron caves should be treated as components of a cave network immersed in the karst landscape. Finally, we show that by prioritizing the conservation of rare troglobites, the current relevance classification scheme is undermining overall cave biodiversity and leaving ecologically important caves unprotected. We argue that conservation efforts should target subterranean habitats as a whole and propose an alternative relevance ranking scheme, which could help simplify the assessment process and channel more resources to the effective protection of overall cave biodiversity. PMID:27997576

Radon as a natural tracer for underwater cave exploration.

PubMed

Csondor, Katalin; Erőss, Anita; Horváth, Ákos; Szieberth, Dénes

2017-07-01

The Molnár János cave is one of the largest hypogenic caves of the Buda Thermal Karst (Budapest, Hungary) and mainly characterized by water-filled passages. The major outflow point of the waters of the cave system is the Boltív spring, which feeds the artificial Malom Lake. Previous radon measurements in the cave system and in the spring established the highest radon concentration (71 BqL -1 ) in the springwater. According to previous studies, the origin of radon was identified as iron-hydroxide containing biofilms, which form where there is mixing of cold and thermal waters, and these biofilms efficiently adsorb radium from the thermal water component. Since mixing of waters is responsible for the formation of the cave as well, these iron-hydroxide containing biofilms and the consequent high radon concentrations mark the active cave forming zones. Based on previous radon measurements, it is supposed that the active mixing and cave forming zone has to be close to the spring, since the highest radon concentration was measured there. Therefore radon mapping was carried out with the help of divers in order to get a spatial distribution of radon in the cave passages closest to the spring. Based on our measurements, the highest radon activity concentration (84 BqL -1 ) was found in the springwater. Based on the distribution of radon activity concentrations, direct connection was established between the spring and the István-room of the cave, which was verified by an artificial tracer. However, the distribution of radon in the cave passages shows lower concentrations (18-46 BqL -1 ) compared to the spring, therefore an additional deep inflow from hitherto unknown cave passages is assumed, from which waters with high radon content arrive to the spring. These passages are assumed to be in the active cave formation zone. This study proved that radon activity concentration distribution is a useful tool in underwater cave exploration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variations on seepage water geochemistry induced by natural and anthropogenic microclimatic changes: Implications for the speleothems growth conditions

NASA Astrophysics Data System (ADS)

Fernandez-Cortes, A.; Sanchez-Moral, S.; Canaveras, J. C.; Cuevas, J.; Cuezva, S.; Andreu, J. M.; Abella, R.

2009-04-01

During an annual cycle the effect of microclimatic changes (natural and anthropogenic origin) on the geochemical characteristics of seepage water and mineral precipitation rates was analyzed, for two karstic caves under opposing environmental stability and energy exchange with exterior. On the one hand Castañar cave (Caceres, Spain), an extremely controlled show cave with limited visitation showing a minimum exchange rate of energy with the outer atmosphere and, secondly, Canelobre cave (Alicante, Spain), a widely visited cave where the anthropogenic impact generates both high-speed and high-energy environmental changes. Microclimatic variations play a key role in CO2-dessgasing caused by the imbalance of pCO2 between the karstic water and the cave air, favoring the slow processes of mineral precipitation. Thus, a pCO2-range of seepage water have been detected for each cave (from 10-2.30/-2.35 to 10-2.47/-2.52 bar for Castañar cave, and from 10-2.8/-2.85 to 10-2.95/-3.0 bar for Canelobre cave) where the mineral oversaturation prevails, determining the type and rate of mineral precipitation in each cave. Finally, it analyzes how the changes on the oversaturation/ precipitation states are controlled by microclimatic variations, such as: 1) natural underground air renewal through the porous system of upper soil and the network of host-rock fissures (isolating membranes), or else through the cave entrance, 2) cumulative disruptions in the pCO2 levels of cave air due to the presence of visitors, and 3) forced ventilation of the subterranean atmosphere due to the uncontrolled opening of cave entrances. The obtained results reinforce the significance of the microclimatic fluctuations on short time scales in the dynamic and evolution of the subterranean karst system, in terms of rates of mineral precipitation and growth of speleothems. Likewise the interpretations are useful in order to ensure the constant climate required for the conservation of caves.

Speleogenesis, geometry, and topology of caves: A quantitative study of 3D karst conduits

NASA Astrophysics Data System (ADS)

Jouves, Johan; Viseur, Sophie; Arfib, Bruno; Baudement, Cécile; Camus, Hubert; Collon, Pauline; Guglielmi, Yves

2017-12-01

Karst systems are hierarchically spatially organized three-dimensional (3D) networks of conduits behaving as drains for groundwater flow. Recently, geostatistical approaches proposed to generate karst networks from data and parameters stemming from analogous observed karst features. Other studies have qualitatively highlighted relationships between speleogenetic processes and cave patterns. However, few studies have been performed to quantitatively define these relationships. This paper reports a quantitative study of cave geometries and topologies that takes the underlying speleogenetic processes into account. In order to study the spatial organization of caves, a 3D numerical database was built from 26 caves, corresponding to 621 km of cumulative cave passages representative of the variety of karst network patterns. The database includes 3D speleological surveys for which the speleogenetic context is known, allowing the polygenic karst networks to be divided into 48 monogenic cave samples and classified into four cave patterns: vadose branchwork (VB), water-table cave (WTC), looping cave (LC), and angular maze (AM). Eight morphometric cave descriptors were calculated, four geometrical parameters (width-height ratio, tortuosity, curvature, and vertical index) and four topological ones (degree of node connectivity, α and γ graph indices, and ramification index) respectively. The results were validated by statistical analyses (Kruskal-Wallis test and PCA). The VB patterns are clearly distinct from AM ones and from a third group including WTC and LC. A quantitative database of cave morphology characteristics is provided, depending on their speleogenetic processes. These characteristics can be used to constrain and/or validate 3D geostatistical simulations. This study shows how important it is to relate the geometry and connectivity of cave networks to recharge and flow processes. Conversely, the approach developed here provides proxies to estimate the evolution of the vadose zone to epiphreatic and phreatic zones in limestones from the quantitative analysis of existing cave patterns.

Boolean network inference from time series data incorporating prior biological knowledge.

PubMed

Haider, Saad; Pal, Ranadip

2012-01-01

Numerous approaches exist for modeling of genetic regulatory networks (GRNs) but the low sampling rates often employed in biological studies prevents the inference of detailed models from experimental data. In this paper, we analyze the issues involved in estimating a model of a GRN from single cell line time series data with limited time points. We present an inference approach for a Boolean Network (BN) model of a GRN from limited transcriptomic or proteomic time series data based on prior biological knowledge of connectivity, constraints on attractor structure and robust design. We applied our inference approach to 6 time point transcriptomic data on Human Mammary Epithelial Cell line (HMEC) after application of Epidermal Growth Factor (EGF) and generated a BN with a plausible biological structure satisfying the data. We further defined and applied a similarity measure to compare synthetic BNs and BNs generated through the proposed approach constructed from transitions of various paths of the synthetic BNs. We have also compared the performance of our algorithm with two existing BN inference algorithms. Through theoretical analysis and simulations, we showed the rarity of arriving at a BN from limited time series data with plausible biological structure using random connectivity and absence of structure in data. The framework when applied to experimental data and data generated from synthetic BNs were able to estimate BNs with high similarity scores. Comparison with existing BN inference algorithms showed the better performance of our proposed algorithm for limited time series data. The proposed framework can also be applied to optimize the connectivity of a GRN from experimental data when the prior biological knowledge on regulators is limited or not unique.

On an adaptive preconditioned Crank-Nicolson MCMC algorithm for infinite dimensional Bayesian inference

NASA Astrophysics Data System (ADS)

Hu, Zixi; Yao, Zhewei; Li, Jinglai

2017-03-01

Many scientific and engineering problems require to perform Bayesian inference for unknowns of infinite dimension. In such problems, many standard Markov Chain Monte Carlo (MCMC) algorithms become arbitrary slow under the mesh refinement, which is referred to as being dimension dependent. To this end, a family of dimensional independent MCMC algorithms, known as the preconditioned Crank-Nicolson (pCN) methods, were proposed to sample the infinite dimensional parameters. In this work we develop an adaptive version of the pCN algorithm, where the covariance operator of the proposal distribution is adjusted based on sampling history to improve the simulation efficiency. We show that the proposed algorithm satisfies an important ergodicity condition under some mild assumptions. Finally we provide numerical examples to demonstrate the performance of the proposed method.

MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach.

PubMed

Abduallah, Yasser; Turki, Turki; Byron, Kevin; Du, Zongxuan; Cervantes-Cervantes, Miguel; Wang, Jason T L

2017-01-01

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections are known as gene regulatory networks (GRNs). Elucidating GRNs is crucial to understand the inner workings of the cell and the complexity of gene interactions. To date, numerous algorithms have been developed to infer gene regulatory networks. However, as the number of identified genes increases and the complexity of their interactions is uncovered, networks and their regulatory mechanisms become cumbersome to test. Furthermore, prodding through experimental results requires an enormous amount of computation, resulting in slow data processing. Therefore, new approaches are needed to expeditiously analyze copious amounts of experimental data resulting from cellular GRNs. To meet this need, cloud computing is promising as reported in the literature. Here, we propose new MapReduce algorithms for inferring gene regulatory networks on a Hadoop cluster in a cloud environment. These algorithms employ an information-theoretic approach to infer GRNs using time-series microarray data. Experimental results show that our MapReduce program is much faster than an existing tool while achieving slightly better prediction accuracy than the existing tool.

Cave Conservation Priority Index to Adopt a Rapid Protection Strategy: A Case Study in Brazilian Atlantic Rain Forest

NASA Astrophysics Data System (ADS)

Souza Silva, Marconi; Martins, Rogério Parentoni; Ferreira, Rodrigo Lopes

2015-02-01

Cave environments are characterized by possessing specialized fauna living in high environmental stability with limited food conditions. These fauna are highly vulnerable to impacts, because this condition can frequently be easily altered. Moreover, environmental determinants of the biodiversity patterns of caves remain poorly understood and protected. Therefore, the main goal of this work is to propose a cave conservation priority index (CCPi) for a rapid assessment for troglobiotic and troglophile protection. Furthermore, the troglobiotic diversity, distribution and threats have been mapped in the Brazilian Atlantic forest. To propose the CCPi, the human impacts and richness of troglobiotic and troglophile species of 100 caves were associated. Data related to troglomorphic/troglobiotic fauna from another 200 caves were used to map the troglobiotic diversity and distribution. The CCPi reveals extremely high conservation priority for 15 % of the caves, high for 36 % and average for 46 % of the caves. Fourteen caves with extremely high priorities should have urgent conservation and management actions. The geographical distribution of the 221 known troglobiotic/troglomorphic species allowed us to select 19 karst areas that need conservation actions. Seven areas were considered to have urgent priority for conservation actions. The two richest areas correspond to the "iron quadrangle" with iron ore caves (67 spp.) and the "Açungui limestone group" (56 spp.). Both areas have several caves and are important aquifers. The use of the CCPi can prevent future losses because it helps assessors to select caves with priorities for conservation which should receive emergency attention in relation to protection, management and conservation actions.

Winter distribution and use of high elevation caves as foraging sites by the endangered Hawaiian hoary bat, Lasiurus cinereus semotus

USGS Publications Warehouse

Bonaccorso, Frank; Montoya-Aiona, Kristina; Pinzari, Corinna A.; Todd, Christopher M.

2016-01-01

We examine altitudinal movements involving unusual use of caves by Hawaiian hoary bats, Lasiurus cinereus semotus, during winter and spring in the Mauna Loa Forest Reserve (MLFR), Hawai‘i Island. Acoustic detection of hoary bat vocalizations, were recorded with regularity outside 13 lava tube cave entrances situated between 2,200 to 3,600 m asl from November 2012 to April 2013. Vocalizations were most numerous in November and December with the number of call events and echolocation pulses decreasing through the following months. Bat activity was positively correlated with air temperature and negatively correlated with wind speed. Visual searches found no evidence of hibernacula nor do Hawaiian hoary bats appear to shelter by day in these caves. Nevertheless, bats fly deep into caves as evidenced by numerous carcasses found in cave interiors. The occurrence of feeding buzzes around cave entrances and visual observations of bats flying in acrobatic fashion in cave interiors point to the use of these spaces as foraging sites. Peridroma moth species (Noctuidae), the only abundant nocturnal, flying insect sheltering in large numbers in rock rubble and on cave walls in the MLFR, apparently serve as the principal prey attracting hoary bats during winter to lava tube caves in the upper MLFR. Caves above 3,000 m on Mauna Loa harbor temperatures suitable for Pseudogymnoascus destructansfungi, the causative agent of White-nose Syndrome that is highly lethal to some species of North American cave-dwelling bats. We discuss the potential for White-nose Syndrome to establish and affect Hawaiian hoary bats.

Chemical Ecology of Cave-Dwelling Millipedes: Defensive Secretions of the Typhloiulini (Diplopoda, Julida, Julidae).

PubMed

Makarov, Slobodan E; Bodner, Michaela; Reineke, Doris; Vujisić, Ljubodrag V; Todosijević, Marina M; Antić, Dragan Ž; Vagalinski, Boyan; Lučić, Luka R; Mitić, Bojan M; Mitov, Plamen; Anđelković, Boban D; Lucić, Sofija Pavković; Vajs, Vlatka; Tomić, Vladimir T; Raspotnig, Günther

2017-04-01

Cave animals live under highly constant ecological conditions and in permanent darkness, and many evolutionary adaptations of cave-dwellers have been triggered by their specific environment. A similar "cave effect" leading to pronounced chemical interactions under such conditions may be assumed, but the chemoecology of troglobionts is mostly unknown. We investigated the defensive chemistry of a largely cave-dwelling julid group, the controversial tribe "Typhloiulini", and we included some cave-dwelling and some endogean representatives. While chemical defense in juliform diplopods is known to be highly uniform, and mainly based on methyl- and methoxy-substituted benzoquinones, the defensive secretions of typhloiulines contained ethyl-benzoquinones and related compounds. Interestingly, ethyl-benzoquinones were found in some, but not all cave-dwelling typhloiulines, and some non-cave dwellers also contained these compounds. On the other hand, ethyl-benzoquinones were not detected in troglobiont nor in endogean typhloiuline outgroups. In order to explain the taxonomic pattern of ethyl-benzoquinone occurrence, and to unravel whether a cave-effect triggered ethyl-benzoquinone evolution, we classed the "Typhloiulini" investigated here within a phylogenetic framework of julid taxa, and traced the evolutionary history of ethyl-benzoquinones in typhloiulines in relation to cave-dwelling. The results indicated a cave-independent evolution of ethyl-substituted benzoquinones, indicating the absence of a "cave effect" on the secretions of troglobiont Typhloiulini. Ethyl-benzoquinones probably evolved early in an epi- or endogean ancestor of a clade including several, but not all Typhloiulus (basically comprising a taxonomic entity known as "Typhloiulus sensu stricto") and Serboiulus. Ethyl-benzoquinones are proposed as novel and valuable chemical characters for julid systematics.

Study of pulmonary functions of the tourist guides in two show caves in Slovenia

NASA Astrophysics Data System (ADS)

Debevec Gerjevic, V.; Jovanovič, P.

2009-04-01

Park Škocjan Caves is located in South Eastern part of Slovenia. It was established with aim of conserving and protecting exceptional geomorphological, geological and hydrological outstanding features, rare and endangered plant and animal species, paleontological and archaeological sites, ethnological and architectural characteristics and cultural landscape and for the purpose of ensuring opportunities for suitable development, by the National Assembly of the Republic of Slovenia in 1996. Due to their exceptional significance for cultural and natural heritage, the Škocjan Caves were entered on UNESCO's list of natural and cultural world heritage sites in 1986. Caves have always been special places for people all over the world. There has been a lot of research done in the field of speleology and also in medicine in relation to speleotherapy. There is still one field left partial unexplored and its main issue covers the interaction between special ecosystems as caves and human activities and living. Implementing the Slovene legislation in the field of radiation protection, we are obligated to perform special measurements in the caves and also having our guides and workers in the caves regularly examined according to established procedure. The medical exams are performed at Institution of Occupational Safety, Ljubljana in order to monitor the influence of Radon to the workers in the cave. The issue of epidemiologic research encompass several factors that are not necessarily related to the radon. Park Škocjan Caves established research monitoring projects such as caves microclimate parameters, quality of the water, every day's data from our meteorological station useful tool in public awareness related to pollution and climate change. Last year a special study was started in order to evaluate pulmonary functions of persons who work in the caves and those who work mostly in offices. Two groups of tourist guides from Škocjan Caves and Postojna Cave were included in the study. The promising results will highlight the need of medical survey of people working in the caves and help managers of the caves to adopt reactive management process. In order to facilitate decision process related to protection of people and caves environment, special recommendation in form of index of environment's use will be proposed after the study.

Evolution and development in cave animals: from fish to crustaceans.

PubMed

Protas, Meredith; Jeffery, William R

2012-01-01

Cave animals are excellent models to study the general principles of evolution as well as the mechanisms of adaptation to a novel environment: the perpetual darkness of caves. In this article, two of the major model systems used to study the evolution and development (evo-devo) of cave animals are described: the teleost fish Astyanax mexicanus and the isopod crustacean Asellus aquaticus. The ways in which these animals match the major attributes expected of an evo-devo cave animal model system are described. For both species, we enumerate the regressive and constructive troglomorphic traits that have evolved during their adaptation to cave life, the developmental and genetic basis of these traits, the possible evolutionary forces responsible for them, and potential new areas in which these model systems could be used for further exploration of the evolution of cave animals. Furthermore, we compare the two model cave animals to investigate the mechanisms of troglomorphic evolution. Finally, we propose a few other cave animal systems that would be suitable for development as additional models to obtain a more comprehensive understanding of the developmental and genetic mechanisms involved in troglomorphic evolution.

Recognition of microclimate zones through radon mapping, Lechuguilla Cave, Carlsbad Caverns National Park, New Mexico

USGS Publications Warehouse

Cunningham, K.I.; LaRock, E.J.

1991-01-01

Radon concentrations range from <185 to 3,515 Bq m-3 throughout Lechuguilla Cave, Carlsbad Caverns National Park, New Mexico. Concentrations in the entrance passages and areas immediately adjacent to these passages are controlled by outside air temperature and barometric pressure, similar to other Type 2 caves. Most of the cave is developed in three geographic branches beneath the entrance passages; these areas maintain Rn levels independent of surface effects, an indication that Rn levels in deep, complex caves or mines cannot be simply estimated by outside atmospheric parameters. These deeper, more isolated areas are subject to convective ventilation driven by temperature differences along the 477-m vertical extent of the cave. Radon concentrations are used to delineate six microclimate zones (air circulation cells) throughout the cave in conjunction with observed airflow data. Suspected surface connections contribute fresh air to remote cave areas demonstrated by anomalous Rn lows surrounded by higher values, the presence of mammalian skeletal remains, CO2 concentrations and temperatures lower than the cave mean, and associated surficial karst features.

Carbon dioxide budgets in cave air and carbon in speleothems; insights from a shallow cave in Ireland

NASA Astrophysics Data System (ADS)

McDermott, Frank; Phillips, Dominika

2017-04-01

The conventional view that hydrological inputs (e.g. drip-water degassing) comprise the dominant source of cave air CO2 has been challenged by recent studies that emphasise the importance of direct advection of gaseous CO2from above and beneath cave voids (e.g. 'soil air' and 'ground air'). A better understanding of CO2 gas budgets in caves is important, not only for the correct interpretation of δ13C values and 14C activity data in speleothems, but also for an understanding of the wider role of karst in the global carbon cycle as a source or sink of atmospheric CO2. This study presents new results from a combined air-temperature and CO2 monitoring programme at a small multi-chamber cave in SE Ireland (Ballynamintra cave, Co. Waterford), building on an earlier study at this cave (Baldini et al., 2006). Episodic, low-amplitude but temporally coherent diurnal-scale cave air temperature fluctuations detected almost simultaneously by a series of temperature loggers within the cave were used to detect air mass advection. The sequence and pattern of temperature fluctuations at different locations within the cave enabled the identification of discrete air-inflow and air-outflow events. These diurnal-scale events occur episodically throughout the year in the winter/ spring and summer/autumn temperature ventilation regimes of the cave. Importantly, changes in cave air pCO2 values recorded by an infra-red logger located in the inner chamber a few metres from the back of the cave occur contemporaneously with the air-mass displacement events, and are consistent with direct advection of CO2-rich soil air via fractures in the subjacent cave roof and walls. In the winter regime, episodic diurnal-scale air outflow events draw CO2-rich air over the logger, resulting in short-lived pulses of air, typically containing c. 0.7% CO2 (by volume), several times the ambient cave air CO2 values at this site. Similar events occur during the summer/autumn thermal regime, but these reach higher CO2values (1-1.2%), similar to those measured previously in the overlying soil. Overall, the data confirm an important role for soil and/or ground air sources at this cave and indicate that the episodic CO2 inputs are not controlled by drip-water inputs,. Some recent studies have additionally argued that advected 'ground-air' is not only an important constituent of cave air, but also an important source of carbon in speleothems. This claim is critically evaluated here using 14C activity measurements from actively growing zero-age soda-straw stalactites from the small inner chamber of the cave where the CO2 monitoring was carried out. Surprisingly, soda-straws collected from within a few metres of each other in this inner chamber exhibit quite different 14C activities (93-101 pMC), and are not identical as might be expected if complete carbon isotope exchange had occurred between the dissolved inorganic carbon and the cave atmosphere. The reasons for this will be discussed, drawing on the results of published kinetic models for degassing and isotope exchange. Overall, it is concluded that while the CO2 budget of the air in Ballynamintra cave is dominated by directly advected soil air, water transported dissolved inorganic carbon (DIC) likely remains an important carbon source for its speleothems. Baldini, J.U.L., Baldini, L.M., McDermott, F. and Clipson, N. (2006) Carbon dioxide sources, sinks, and spatial variability in shallow temperate zone caves: evidence from Ballynamintra Cave, Ireland. Journal of Cave and Karst Studies, 68, 4-11.

Occurrence of organic wastewater and other contaminants in cave streams in northeastern Oklahoma and northwestern Arkansas.

PubMed

Bidwell, Joseph R; Becker, Carol; Hensley, Steve; Stark, Richard; Meyer, Michael T

2010-02-01

The prevalence of organic wastewater compounds in surface waters of the United States has been reported in a number of recent studies. In karstic areas, surface contaminants might be transported to groundwater and, ultimately, cave ecosystems, where they might impact resident biota. In this study, polar organic chemical integrative samplers (POCISs) and semipermeable membrane devices (SPMDs) were deployed in six caves and two surface-water sites located within the Ozark Plateau of northeastern Oklahoma and northwestern Arkansas in order to detect potential chemical contaminants in these systems. All caves sampled were known to contain populations of the threatened Ozark cavefish (Amblyopsis rosae). The surface-water site in Oklahoma was downstream from the outfall of a municipal wastewater treatment plant and a previous study indicated a hydrologic link between this stream and one of the caves. A total of 83 chemicals were detected in the POCIS and SPMD extracts from the surface-water and cave sites. Of these, 55 chemicals were detected in the caves. Regardless of the sampler used, more compounds were detected in the Oklahoma surface-water site than in the Arkansas site or the caves. The organic wastewater chemicals with the greatest mass measured in the sampler extracts included sterols (cholesterol and beta-sitosterol), plasticizers [diethylhexylphthalate and tris(2-butoxyethyl) phosphate], the herbicide bromacil, and the fragrance indole. Sampler extracts from most of the cave sites did not contain many wastewater contaminants, although extracts from samplers in the Oklahoma surface-water site and the cave hydrologically linked to it had similar levels of diethylhexyphthalate and common detections of carbamazapine, sulfamethoxazole, benzophenone, N-diethyl-3-methylbenzamide (DEET), and octophenol monoethoxylate. Further evaluation of this system is warranted due to potential ongoing transport of wastewater-associated chemicals into the cave. Halogenated organics found in caves and surface-water sites included brominated flame retardants, organochlorine pesticides (chlordane and nonachlor), and polychlorinated biphenyls. The placement of samplers in the caves (near the cave mouth compared to farther in the system) might have influenced the number of halogenated organics detected due to possible aerial transport of residues. Guano from cave-dwelling bats also might have been a source of some of these chlorinated organics. Seven-day survival and growth bioassays with fathead minnows (Pimephales promelas) exposed to samples of cave water indicated initial toxicity in water from two of the caves, but these effects were transient, with no toxicity observed in follow-up tests.

Occurrence of organic wastewater and other contaminants in cave streams in northeastern Oklahoma and northwestern Arkansas

USGS Publications Warehouse

Bidwell, Joseph R.; Becker, C.; Hensley, S.; Stark, R.; Meyer, M.T.

2010-01-01

The prevalence of organic wastewater compounds in surface waters of the United States has been reported in a number of recent studies. In karstic areas, surface contaminants might be transported to groundwater and, ultimately, cave ecosystems, where they might impact resident biota. In this study, polar organic chemical integrative samplers (POCISs) and semipermeable membrane devices (SPMDs) were deployed in six caves and two surface-water sites located within the Ozark Plateau of northeastern Oklahoma and northwestern Arkansas in order to detect potential chemical contaminants in these systems. All caves sampled were known to contain populations of the threatened Ozark cavefish (Amblyopsis rosae). The surface-water site in Oklahoma was downstream from the outfall of a municipal wastewater treatment plant and a previous study indicated a hydrologic link between this stream and one of the caves. A total of 83 chemicals were detected in the POCIS and SPMD extracts from the surface-water and cave sites. Of these, 55 chemicals were detected in the caves. Regardless of the sampler used, more compounds were detected in the Oklahoma surface-water site than in the Arkansas site or the caves. The organic wastewater chemicals with the greatest mass measured in the sampler extracts included sterols (cholesterol and ??-sitosterol), plasticizers [diethylhexylphthalate and tris (2-butoxyethyl) phosphate], the herbicide bromacil, and the fragrance indole. Sampler extracts from most of the cave sites did not contain many wastewater contaminants, although extracts from samplers in the Oklahoma surfacewater site and the cave hydrologically linked to it had similar levels of diethylhexyphthalate and common detections of carbamazapine, sulfamethoxazole, benzophenone, N-diethyl-3-methylbenzamide (DEET), and octophenol monoethoxylate. Further evaluation of this system is warranted due to potential ongoing transport of wastewaterassociated chemicals into the cave. Halogenated organics found in caves and surface-water sites included brominated flame retardants, organochlorine pesticides (chlordane and nonachlor), and polychlorinated biphenyls. The placement of samplers in the caves (near the cave mouth compared to farther in the system) might have influenced the number of halogenated organics detected due to possible aerial transport of residues. Guano from cave-dwelling bats also might have been a source of some of these chlorinated organics. Seven-day survival and growth bioassays with fathead minnows (Pimephales promelas) exposed to samples of cave water indicated initial toxicity in water from two of the caves, but these effects were transient, with no toxicity observed in follow-up tests. ??Springer Science+Business Media, LLC 2009.

Efficient fuzzy Bayesian inference algorithms for incorporating expert knowledge in parameter estimation

NASA Astrophysics Data System (ADS)

Rajabi, Mohammad Mahdi; Ataie-Ashtiani, Behzad

2016-05-01

Bayesian inference has traditionally been conceived as the proper framework for the formal incorporation of expert knowledge in parameter estimation of groundwater models. However, conventional Bayesian inference is incapable of taking into account the imprecision essentially embedded in expert provided information. In order to solve this problem, a number of extensions to conventional Bayesian inference have been introduced in recent years. One of these extensions is 'fuzzy Bayesian inference' which is the result of integrating fuzzy techniques into Bayesian statistics. Fuzzy Bayesian inference has a number of desirable features which makes it an attractive approach for incorporating expert knowledge in the parameter estimation process of groundwater models: (1) it is well adapted to the nature of expert provided information, (2) it allows to distinguishably model both uncertainty and imprecision, and (3) it presents a framework for fusing expert provided information regarding the various inputs of the Bayesian inference algorithm. However an important obstacle in employing fuzzy Bayesian inference in groundwater numerical modeling applications is the computational burden, as the required number of numerical model simulations often becomes extremely exhaustive and often computationally infeasible. In this paper, a novel approach of accelerating the fuzzy Bayesian inference algorithm is proposed which is based on using approximate posterior distributions derived from surrogate modeling, as a screening tool in the computations. The proposed approach is first applied to a synthetic test case of seawater intrusion (SWI) in a coastal aquifer. It is shown that for this synthetic test case, the proposed approach decreases the number of required numerical simulations by an order of magnitude. Then the proposed approach is applied to a real-world test case involving three-dimensional numerical modeling of SWI in Kish Island, located in the Persian Gulf. An expert elicitation methodology is developed and applied to the real-world test case in order to provide a road map for the use of fuzzy Bayesian inference in groundwater modeling applications.

Cave Art: Reflections of Early Human Culture.

ERIC Educational Resources Information Center

Sullivan, Brother Nicholas

1981-01-01

Discusses Paleolithic and Neolithic cave art and artifacts, stressing the degree of intellectual ability exhibited by the creators of this art. Topics discussed include some misunderstandings about cave art intellect shown by cave artists and the use of light and color. (DS)

Dark Oligotrophic Volcanic Ecosystems (DOVEs) in Fumarolic Ice Caves of Mt. Erebus Volcano

NASA Astrophysics Data System (ADS)

Staudigel, H.; Anitori, R.; Davis, R.; Connell, L.; Tebo, B. M.

2011-12-01

Dark Oligotrophic Volcanic Ecosystems (DOVEs) in the earth's crust may host substantial biomass sustained by chemolithoautotrophic metabolic reactions. It may serve as the base of the foodweb at the surface via hydrothermal circulation, venting pore fluids, cold seeps or gases, and offer a means for primary carbon fixation. When compared to other crustal oligotrophic environments, DOVEs are particularly relevant due to their considerable reductive potential, high permeability and the substantial chemical exchange facilitated by their hydrothermal systems. We studied terrestrial DOVEs in fumarolic ice caves on the summit plateau of Mt Erebus, an active volcano on Ross Island, Antarctica (http://erebuscaves.nmt.edu/). Most of the ice caves on Mt Erebus are relatively shallow and illuminated by natural light, but some are deep enough to afford complete darkness. Fumarole gases forming these caves are mostly atmospheric, enriched with water vapor and CO2. The fumaroles were studied in three caves, Warren, Warren West and Harry's Dream; these displayed, respectively, temperatures of 18°C, 2°C and 11°C at our sampling sites. Both Warren caves were completely dark, while Harry's Dream received continuous indirect light during the Austral summer, and offered a control to the two dark caves. The composition of the resident microbial communities was assessed using 16S rRNA and ITS libraries, while metabolic and functional characteristics were analyzed by culturing. The latter results are presented by Anitori et al. (this session). The three cave soils displayed very low (Warren, Warren West) or moderate division-level diversity, with distinct communities in each environment. Acidobacteria was the only phylum detected in all three caves, and was a major component of each library. The phototroph-containing phyla Cyanobacteria, Chloroflexi, and Chlorophyta (latter eukaryotic) were only seen in Harry's Dream. A number of phyla whose members are known to oxidize Mn(II) or Fe(II) were also identified in the caves. The overall phylum and class-level composition of the cave libraries displayed certain similarities to other cave communities, with a notable exception being the dominance of Ktedonobacteria (63% of the Warren cave 16S rDNA library), a recently described, filamentous bacterial lineage. A large fraction of the database matches for the cave libraries were to uncultured or cultured bacteria from environments with one or more similarities to the Mt. Erebus ice caves, i.e, associated with volcanic rocks and soils, alpine soil types, glaciers, caves and other cold environments. A functional analysis of microbes from these caves (Anitori et al., this session) shows good evidence for chemolithotrophic metabolisms, autotrophic carbon fixation as well as nitrogen fixation. These studies validate fumarolic ice caves at Mt Erebus as viable experimental study sites for chemolithotrophic microbial communities in DOVEs.

Inverse Ising problem in continuous time: A latent variable approach

NASA Astrophysics Data System (ADS)

Donner, Christian; Opper, Manfred

2017-12-01

We consider the inverse Ising problem: the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form which allows for simple iterative inference algorithms with analytical updates. The variables are (1) Poisson variables to linearize an exponential term which is typical for point process likelihoods and (2) Pólya-Gamma variables, which make the likelihood quadratic in the coupling parameters. Using the augmented likelihood, we derive an expectation-maximization (EM) algorithm to obtain the maximum likelihood estimate of network parameters. Using a third set of latent variables we extend the EM algorithm to sparse couplings via L1 regularization. Finally, we develop an efficient approximate Bayesian inference algorithm using a variational approach. We demonstrate the performance of our algorithms on data simulated from an Ising model. For data which are simulated from a more biologically plausible network with spiking neurons, we show that the Ising model captures well the low order statistics of the data and how the Ising couplings are related to the underlying synaptic structure of the simulated network.

Črna Jama as a cold air trap cave within Postojna Cave, Slovenia

NASA Astrophysics Data System (ADS)

Šebela, Stanka; Turk, Janez

2017-10-01

Črna Jama is the coldest section of cave within the Postojna Cave System. Mean annual air temperatures at the Črna Jama 2 site are 5.6 °C (2015) and 5.7 °C (2016), and at the Črna Jama 3 site 7.1 °C (2015) and 7.2 (2016), whereas the mean external air temperature was 10.3 °C (2015) and 10.0 °C (2016). In Lepe Jame, the passage most heavily visited by tourists, the mean cave-air temperature is 10.7 °C (2014-2017). Črna Jama exhibits winter and summer temperature regimes. During warm periods (Tcave < Tout), it acts as a cold air trap, exchanging no air with the outside atmosphere. Under such conditions the cave-air temperature shows no short-term diurnal temperature oscillations. Cave-air temperature is significantly stable and affected only by elevation of the groundwater table, which is associated with precipitation. During cold periods (Tcave > Tout), ventilation takes place and dense, cold, outside air sinks into Črna Jama because of the favourable cave entrance morphology. Recent Črna Jama air temperature data (2014-2017) indicate a < 0.5 °C higher temperature than that recorded in historical data since 1933. Črna Jama is the most appropriate place within the Postojna Cave System to study long-term climatic changes. There are hardly any tourist visits to the cave, and human impacts on the cave climate are essentially reduced.

Aspergillus baeticus sp. nov. and Aspergillus thesauricus sp. nov., two species in section Usti from Spanish caves.

PubMed

Nováková, Alena; Hubka, Vit; Saiz-Jimenez, Cesareo; Kolarik, Miroslav

2012-11-01

Two novel species of Aspergillus that are clearly distinct from all known species in section Usti were revealed during a study of microfungal communities in Spanish caves. The novel species identified in this study and additional species of Aspergillus section Usti are associated with places and substrates related to human activities in caves. Novel species are described using data from four loci (ITS, benA, caM and rpb2), morphology and basic chemical and physiological analyses. Members of the species Aspergillus thesauricus sp. nov. were isolated from various substrates, including decaying organic matter, cave air and cave sediment of the Cueva del Tesoro Cave (the Treasure cave); the species is represented by twelve isolates and is most closely related to the recently described Aspergillus germanicus. Members of the species Aspergillus baeticus sp. nov. were isolated from cave sediment in the Gruta de las Maravillas Cave (the Grotto of the Marvels); the species is represented by two isolates. An additional isolate was found in the Cueva del Tesoro Cave and in the Demänovská Peace Cave (Slovakia), suggesting a potentially wide distribution of this micro-organism. The species is related to Aspergillus ustus and Aspergillus pseudoustus. Both species were unable to grow at 37 °C, and a weakly positive, light greenish yellow Ehrlich reaction was observed in A. thesauricus. Unique morphological features alone are sufficient to distinguish both species from related taxa.

Late Quaternary cave bears and brown bears in Europe: implications for distribution, chronology, and extinction based on a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Pacher, Martina

2010-05-01

Cave bear remains are one of the most numerous fossils found in European caves. Despite their frequency of occurrence, many aspects of cave bear palaeontology still remain poorly understood. New methodological approaches and ongoing studies led to controversial results and discussion about its taxonomy, palaeoecology, and final extinction. Are we dealing with one single or several species of cave bears? Was cave bear exclusively vegetarian or after all more omnivorous? Did he go extinct before or after the Late Glacial Maximum? Was cave bear restricted to Europe or did he also occur in Asia? Late Pleistocene brown bears, on the other hand, are often rare and little is known about the possible co-occurrence of cave and brown bears during the Late Pleistocene. Based on direct radiocarbon dates the distribution pattern of both, cave and brown bears is reconstructed during the Late Pleistocene in Europe. In addition, the reasons for the achieved pattern will be tested leading to the main question - why did cave bear become extinct while brown bears survived until today? To answer this question palaeobiological data of Late Pleistocene cave and brown bears will be tested against results from isotope analyses, while aDNA data may contribute to the question of distinct local population or even species of bears. The current state of evidence will be presented and on the basis of resulting pattern implications for further multi-disciplinary studies will be discussed.

A >400 kyrs archive of sedimentation in Scladina cave (Belgium)

NASA Astrophysics Data System (ADS)

Vonhof, Hubert; Bonjean, Dominique; Pirson, Stéphane; van der Lubbe, Jeroen; Hellstrom, John; Scholz, Denis; Verheyden, Sophie

2017-04-01

Scladina Cave, near the Meuse River in Belgium, is well-known for its well preserved Neanderthal fossils and stone tools. Cave research started in the 1970's, when archeological findings near the entrance of the cave initiated a long-running excavation programme in the -at that time- almost completely sediment-infilled cave. Over the past decades, a wealth of mammal fossils, stone tools, and a mandible of a Neanderthal child were found, and the complex sedimentary context of the cave strata was reconstructed in high detail. Crucial to understanding the cave stratigraphy is the construction of an absolutely dated age model. Until recently, this age model was based on a number of OSL ages, pollen stratigraphy and a few U-series ages on flowstone and stalagmite calcite. These U-series ages, however, had much lower precision than can be obtained by modern MC-ICP-MS techniques. In this study, we present new and more precise U-series ages for the major flow stone levels in Scladina Cave (upper stratigraphical sequence), and two flowstone levels from Sous-Saint-Paul Cave (lower stratigraphical sequence). The oldest flow stone layer dates back to > 400 ka, and the youngest represents the Holocene. The age model shows that flow stone formation typically occurred during warm climate conditions. These findings help to improve the existing age model for Scladina Cave significantly, and place better constraints on the age of individual fossils, and fossil assemblages in the cave.

75 FR 4417 - Wind Cave National Park, Custer County, SD

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-27

... DEPARTMENT OF THE INTERIOR Wind Cave National Park, Custer County, SD AGENCY: National Park... Final Environmental Impact Statement, Wind Cave National Park, Custer County, South Dakota. SUMMARY... Management Plan and Final Environmental Impact Statement (Plan), Wind Cave National Park, Custer County...

Inference of scale-free networks from gene expression time series.

PubMed

Daisuke, Tominaga; Horton, Paul

2006-04-01

Quantitative time-series observation of gene expression is becoming possible, for example by cell array technology. However, there are no practical methods with which to infer network structures using only observed time-series data. As most computational models of biological networks for continuous time-series data have a high degree of freedom, it is almost impossible to infer the correct structures. On the other hand, it has been reported that some kinds of biological networks, such as gene networks and metabolic pathways, may have scale-free properties. We hypothesize that the architecture of inferred biological network models can be restricted to scale-free networks. We developed an inference algorithm for biological networks using only time-series data by introducing such a restriction. We adopt the S-system as the network model, and a distributed genetic algorithm to optimize models to fit its simulated results to observed time series data. We have tested our algorithm on a case study (simulated data). We compared optimization under no restriction, which allows for a fully connected network, and under the restriction that the total number of links must equal that expected from a scale free network. The restriction reduced both false positive and false negative estimation of the links and also the differences between model simulation and the given time-series data.

Modeling and analysis of caves using voxelization

NASA Astrophysics Data System (ADS)

Szeifert, Gábor; Szabó, Tivadar; Székely, Balázs

2014-05-01

Although there are many ways to create three dimensional representations of caves using modern information technology methods, modeling of caves has been challenging for researchers for a long time. One of these promising new alternative modeling methods is using voxels. We are using geodetic measurements as an input for our voxelization project. These geodetic underground surveys recorded the azimuth, altitude and distance of corner points of cave systems relative to each other. The diameter of each cave section is estimated from separate databases originating from different surveys. We have developed a simple but efficient method (it covers more than 99.9 % of the volume of the input model on the average) to convert these vector-type datasets to voxels. We have also developed software components to make visualization of the voxel and vector models easier. Since each cornerpoint position is measured relative to another cornerpoints positions, propagation of uncertainties is an important issue in case of long caves with many separate sections. We are using Monte Carlo simulations to analyze the effect of the error of each geodetic instrument possibly involved in a survey. Cross-sections of the simulated three dimensional distributions show, that even tiny uncertainties of individual measurements can result in high variation of positions that could be reduced by distributing the closing errors if such data are available. Using the results of our simulations, we can estimate cave volume and the error of the calculated cave volume depending on the complexity of the cave. Acknowledgements: the authors are grateful to Ariadne Karst and Cave Exploring Association and State Department of Environmental and Nature Protection of the Hungarian Ministry of Rural Development, Department of National Parks and Landscape Protection, Section Landscape and Cave Protection and Ecotourism for providing the cave measurement data. BS contributed as an Alexander von Humboldt Research Fellow.

Insectivorous bat reproduction and human cave visitation in Cambodia: A perfect conservation storm?

PubMed

Lim, Thona; Cappelle, Julien; Hoem, Thavry; Furey, Neil

2018-01-01

Cave roosting bats represent an important component of Southeast Asian bat diversity and are vulnerable to human disturbance during critical reproductive periods (pregnancy, lactation and weaning). Because dramatic growth of cave tourism in recent decades has raised concerns about impacts on cave bats in the region, we assessed the reproductive phenology of two insectivorous species (Hipposideros larvatus sensu lato and Taphozous melanopogon) at three caves in Cambodia for 23 months in 2014-2016 and evaluated human visitation to these sites between 2007 and 2014. Despite the differing foraging strategies employed by the two taxa, the temporal consistency observed in proportions of pregnant, lactating and juvenile bats indicates that their major birth peaks coincide with the time of greatest cave visitation annually, particularly for domestic visitors and namely during the Cambodian new year in April. They also reflect rainfall patterns and correspond with the reproductive phenology of insectivorous cave bats in Vietnam. These findings were predictable because 1) insect biomass and thus food availability for insectivorous bats are optimal for ensuring survival of young following this period, and 2) the Khmer new year is the most significant month for religious ceremonies and thus domestic cave visitation nationally, due to the abundance of Buddhist shrines and temples in Cambodian caves. While the impact of visitor disturbance on bat population recruitment cannot be empirically assessed due to lack of historical data, it is nonetheless likely to have been considerable and raises a conservation concern. Further, because growing evidence suggests that insectivorous cave bats exhibit reproductive synchrony across continental Southeast Asia where countless cave shrines are heavily frequented during April in Theravada Buddhist countries (e.g., Myanmar, Thailand, Cambodia and Laos), our results may have wider applicability in the region. We consequently advocate for increased emphasis on sustainable cave management practices in Cambodia and further investigations to determine whether our findings present a broader concern for cave bat conservation in Southeast Asia.

Insectivorous bat reproduction and human cave visitation in Cambodia: A perfect conservation storm?

PubMed Central

Cappelle, Julien; Hoem, Thavry

2018-01-01

Cave roosting bats represent an important component of Southeast Asian bat diversity and are vulnerable to human disturbance during critical reproductive periods (pregnancy, lactation and weaning). Because dramatic growth of cave tourism in recent decades has raised concerns about impacts on cave bats in the region, we assessed the reproductive phenology of two insectivorous species (Hipposideros larvatus sensu lato and Taphozous melanopogon) at three caves in Cambodia for 23 months in 2014–2016 and evaluated human visitation to these sites between 2007 and 2014. Despite the differing foraging strategies employed by the two taxa, the temporal consistency observed in proportions of pregnant, lactating and juvenile bats indicates that their major birth peaks coincide with the time of greatest cave visitation annually, particularly for domestic visitors and namely during the Cambodian new year in April. They also reflect rainfall patterns and correspond with the reproductive phenology of insectivorous cave bats in Vietnam. These findings were predictable because 1) insect biomass and thus food availability for insectivorous bats are optimal for ensuring survival of young following this period, and 2) the Khmer new year is the most significant month for religious ceremonies and thus domestic cave visitation nationally, due to the abundance of Buddhist shrines and temples in Cambodian caves. While the impact of visitor disturbance on bat population recruitment cannot be empirically assessed due to lack of historical data, it is nonetheless likely to have been considerable and raises a conservation concern. Further, because growing evidence suggests that insectivorous cave bats exhibit reproductive synchrony across continental Southeast Asia where countless cave shrines are heavily frequented during April in Theravada Buddhist countries (e.g., Myanmar, Thailand, Cambodia and Laos), our results may have wider applicability in the region. We consequently advocate for increased emphasis on sustainable cave management practices in Cambodia and further investigations to determine whether our findings present a broader concern for cave bat conservation in Southeast Asia. PMID:29709036

Glacioclimatological study of Perennial Ice in the Fuji Ice Cave, Japan. Part I. Seasonal variation and mechanism of maintenance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohata, Tetsuo; Furukawa, Teruo; Higuchi, Keiji

1994-08-01

Perennial cave ice in a cave located at Mt. Fuji in central Japan was studied to investigate the basic characteristics and the cause for existence of such ice under warm ground-level climate considering the ice cave as a thermal and hydrological system. Fuji Ice Cave is a lava tube cave 150 m in length with a collapsed part at the entrance. Measurements from 1984 to 1986 showed that the surface-level change of floor ice occurred due to freezing and melting at the surface and that melting at the bottom of the ice was negligible. The annual amplitude of change inmore » surface level was larger near the entrance. Meterological data showed that the cold air inflow to the cave was strong in winter, but in summer the cave was maintained near 0[degrees]C with only weak inflow of warm air. The predominant wind system was from the entrance to the interior in both winter and summer, but the spatial scale of the wind system was different. Heat budget consideration of the cave showed that the largest component was the strong inflow of subzero dry air mass in winter. Cooling in winter was compensated for by summer inflow of warm air, heat transport from the surrounding ground layer, and loss of sensible heat due to cooling of the cave for the observed year. Strong inflow of cold air and weak inflow of warm air, which is extremely low compared to the ground level air, seemed to be the most important condition. Thus the thermal condition of the cave is quasi-balanced at the presence condition below 0[degrees]C with ice. It can be said that the interrelated result of the climatological and special structural conditions makes this cave very cold, and allows perennial ice to exist in the cave. Other climatological factors such as precipitation seem to be minor factors. 17 refs., 3 figs., 3 tabs.« less

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China

PubMed Central

Man, Baiying; Wang, Hongmei; Xiang, Xing; Wang, Ruicheng; Yun, Yuan; Gong, Linfeng

2015-01-01

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems. PMID:26539184

Diversity and Function of Methanotrophic Bacteria in Caves

NASA Astrophysics Data System (ADS)

Webster, K.; Schimmelmann, A.; Lennon, J. T.

2016-12-01

Despite representing the second largest sink for the atmospheric greenhouse gas methane (CH4), the methanotrophic organisms responsible for atmospheric CH4 consumption have eluded cultivation. High-throughput studies of methanotrophic communities present an opportunity to learn novel details about the organisms responsible, yet such studies have rarely been conducted. Recent observations of subatmospheric CH4 concentrations in cave-air have led to the hypothesis that methanotrophs are active over large spatial scales in the subsurface. Karst terrains cover between 10 - 20 % of the terrestrial surface area and offer abundant cave-related methanotrophic habitat due to the exchange of air with the atmosphere. We collected 42 cave soil samples from 20 caves to test the hypothesis that subterranean methanotrophy removes CH4 from cave-air. Methanotrophs were found in 90 % of samples, notably in locations with subatmospheric CH4­ concentrations. Methylocystaceae were present in caves and accounted for 92 % of the methanotrophic community on average (median), however almost all of the observations were of unidentified Methylocystaceae. Abundances of uncultured and unidentified members of the Methylococcales were correlated with cave-air CH4 concentrations suggesting that some Methylococcales may contribute to atmospheric CH4 oxidation. Individual caves had a strong influence on the observed methanotrophic community composition accounting for 77 % of the variance in the assemblage. Nevertheless, cave-air CH4 concentrations were predictive of the methanotrophic community composition accounting for 5 % of the variation. Our findings also are suggestive of CH4-fueled microbial food webs. For example, abundances of known methylotrophic organisms were correlated with cave-air CH4 concentrations. This may suggest that some methylotrophs contribute to atmospheric CH4 oxidation or that molecules produced in the CH4 oxidation pathway, like methanol, are leaked from methanotrophic cells allowing for the growth of methylotrophs. Our results suggest that uncultivated and unidentified methanotrophs are responsible for subatmospheric CH4 concentrations in caves and have secondary influences on the cave-microbial community structure.

Cave air and hydrological controls on prior calcite precipitation and stalagmite growth rates: Implications for palaeoclimate reconstructions using speleothems

NASA Astrophysics Data System (ADS)

Sherwin, Catherine M.; Baldini, James U. L.

2011-07-01

Hourly resolved cave air P and cave drip water hydrochemical data illustrate that calcite deposition on stalagmites can be modulated by prior calcite precipitation (PCP) on extremely short timescales. A very clear second-order covariation between cave air P and drip water Ca 2+ concentrations during the winter months demonstrates the effects of degassing-induced PCP on drip water chemistry. Estimating the strength of the cave air P control on PCP is possible because the PCP signal is so clear; at our drip site a one ppm shift in Ca 2+ concentrations requires a P shift of between 333 and 667 ppm. This value will undoubtedly vary from site to site, depending on drip water flow rate, residence time, drip water-cave air P differential, and availability of low P void spaces in the vadose zone above the cave. High-resolution cave environmental measurements were used to model calcite deposition on one stalagmite in Crag Cave, SW Ireland, and modelled growth over the study period (222 μm over 171 days) is extremely similar to the amount of actual calcite growth (240 μm) over the same time interval, strongly suggesting that equations used to estimate stalagmite growth rates are valid. Although cave air P appears to control drip water hydrochemistry in the winter, drip water dilution caused by rain events may have played a larger role during the summer, as evidenced by a series of sudden drops in Ca 2+ concentrations (dilution) followed by much more gradual increases in drip water Ca 2+ concentrations (slow addition of diffuse water). This research demonstrates that PCP on stalactites, cave ceilings, and void spaces within the karst above the cave partially controls drip water chemistry, and that thorough characterisation of this process at individual caves is necessary to most accurately interpret climate records from those sites.

The NIFTy way of Bayesian signal inference

NASA Astrophysics Data System (ADS)

Selig, Marco

2014-12-01

We introduce NIFTy, "Numerical Information Field Theory", a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTy can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTy as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D3PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy.

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

PubMed

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies.

PubMed

Min, Xiaoping; Zhang, Mouzhao; Yuan, Sisi; Ge, Shengxiang; Liu, Xiangrong; Zeng, Xiangxiang; Xia, Ningshao

2017-12-26

In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms.

43 CFR 37.11 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2014 CFR

2014-10-01

... the public, including those who utilize caves for scientific, educational, and recreational purposes... where the cave is located as new cave discoveries are made or as new information becomes available...) Paleontologic resources with potential to contribute useful educational and scientific information. (4...

43 CFR 37.11 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2011 CFR

2011-10-01

... the public, including those who utilize caves for scientific, educational, and recreational purposes... where the cave is located as new cave discoveries are made or as new information becomes available...) Paleontologic resources with potential to contribute useful educational and scientific information. (4...

43 CFR 37.11 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2013 CFR

2013-10-01

... the public, including those who utilize caves for scientific, educational, and recreational purposes... where the cave is located as new cave discoveries are made or as new information becomes available...) Paleontologic resources with potential to contribute useful educational and scientific information. (4...

43 CFR 37.11 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2012 CFR

2012-10-01

... the public, including those who utilize caves for scientific, educational, and recreational purposes... where the cave is located as new cave discoveries are made or as new information becomes available...) Paleontologic resources with potential to contribute useful educational and scientific information. (4...

Diversity and role of cave-dwelling hematophagous insects in pathogen transmission in the Afrotropical region.

PubMed

Obame-Nkoghe, Judicaël; Leroy, Eric-Maurice; Paupy, Christophe

2017-04-12

The progressive anthropization of caves for food resources or economic purposes increases human exposure to pathogens that naturally infect cave-dwelling animals. The presence of wild or domestic animals in the immediate surroundings of caves also may contribute to increasing the risk of emergence of such pathogens. Some zoonotic pathogens are transmitted through direct contact, but many others require arthropod vectors, such as blood-feeding insects. In Africa, hematophagous insects often play a key role in the epidemiology of many pathogens; however, their ecology in cave habitats remains poorly known. During the last decades, several investigations carried out in Afrotropical caves suggested the medical and veterinary importance particularly of insect taxa of the Diptera order. Therefore, the role of some of these insects as vectors of pathogens that infect cave-dwelling vertebrates has been studied. The present review summarizes these findings, brings insights into the diversity of cave-dwelling hematophagous Diptera and their involvement in pathogen transmission, and finally discusses new challenges and future research directions.

The fungal colonisation of rock-art caves: experimental evidence.

PubMed

Jurado, Valme; Fernandez-Cortes, Angel; Cuezva, Soledad; Laiz, Leonila; Cañaveras, Juan Carlos; Sanchez-Moral, Sergio; Saiz-Jimenez, Cesareo

2009-09-01

The conservation of rock-art paintings in European caves is a matter of increasing interest. This derives from the bacterial colonisation of Altamira Cave, Spain and the recent fungal outbreak of Lascaux Cave, France-both included in the UNESCO World Heritage List. Here, we show direct evidence of a fungal colonisation of rock tablets in a testing system exposed in Altamira Cave. After 2 months, the tablets, previously sterilised, were heavily colonised by fungi and bacteria. Most fungi isolated were labelled as entomopathogens, while the bacteria were those regularly identified in the cave. Rock colonisation was probably promoted by the dissolved organic carbon supplied with the dripping and condensation waters and favoured by the displacement of aerosols towards the interior of the cave, which contributed to the dissemination of microorganisms. The role of arthropods in the dispersal of spores may also help in understanding fungal colonisation. This study evidences the fragility of rock-art caves and demonstrates that microorganisms can easily colonise bare rocks and materials introduced into the cavity.

Algorithms for database-dependent search of MS/MS data.

PubMed

Matthiesen, Rune

2013-01-01

The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather than providing software user manuals. The process of database-dependent search can be divided into search strategy, peptide scoring, protein scoring, and finally protein inference. Most efforts in the literature have been put in to comparing results from different software rather than discussing the underlining algorithms. Such practical comparisons can be cluttered by suboptimal implementation and the observed differences are frequently caused by software parameters settings which have not been set proper to allow even comparison. In other words an algorithmic idea can still be worth considering even if the software implementation has been demonstrated to be suboptimal. The aim in this chapter is therefore to split the algorithms for database-dependent searching of MS/MS data into the above steps so that the different algorithmic ideas become more transparent and comparable. Most search engines provide good implementations of the first three data analysis steps mentioned above, whereas the final step of protein inference are much less developed for most search engines and is in many cases performed by an external software. The final part of this chapter illustrates how protein inference is built into the VEMS search engine and discusses a stand-alone program SIR for protein inference that can import a Mascot search result.

Important caves to be identified

NASA Astrophysics Data System (ADS)

Criteria to identify significant caves on federal land are being developed by the Interior Department's Bureau of Land Management and the Agriculture Department's Forest Service under requirements of the Federal Cave Resources Protection Act of 1988. The departments gave advance notice of proposed rulemaking March 3 and invited suggestions and comments from the public for 30 days.The law requires protection, to the extent practical, of significant caves on lands administered by the Secretaries of Agriculture and Interior and includes authority to issue and revoke permits for collection and removal of cave resources and special provisions for regulation of cave resources on Indian lands. Final regulations must be published by August 18, 1989.

Combining stable isotope (δ13C) of trace gases and aerobiological data to monitor the entry and dispersion of microorganisms in caves.

PubMed

Garcia-Anton, E; Cuezva, S; Jurado, V; Porca, E; Miller, A Z; Fernandez-Cortes, A; Saiz-Jimenez, C; Sanchez-Moral, S

2014-01-01

Altamira Cave (north of Spain) contains one of the world's most prominent Paleolithic rock art paintings, which are threatened by a massive microbial colonization of ceiling and walls. Previous studies revealed that exchange rates between the cave and the external atmosphere through the entrance door play a decisive role in the entry and transport of microorganisms (bacteria and fungi) and nutrients to the interior of the cave. A spatial-distributed sampling and measurement of carrier (CO2) and trace (CH4) gases and isotopic signal of CO2 (δ(13)C) inside the cave supports the existence of a second connection (active gas exchange processes) with the external atmosphere at or near the Well Hall, the innermost and deepest area of the cave. A parallel aerobiological study also showed that, in addition to the entrance door, there is another connection with the external atmosphere, which favors the transport and increases microorganism concentrations in the Well Hall. This double approach provides a more complete knowledge on cave ventilation and revealed the existence of unknown passageways in the cave, a fact that should be taken into account in future cave management.

Quantitative food web analysis supports the energy-limitation hypothesis in cave stream ecosystems.

PubMed

Venarsky, Michael P; Huntsman, Brock M; Huryn, Alexander D; Benstead, Jonathan P; Kuhajda, Bernard R

2014-11-01

Energy limitation has long been the primary assumption underlying conceptual models of evolutionary and ecological processes in cave ecosystems. However, the prediction that cave communities are actually energy-limited in the sense that constituent populations are consuming all or most of their resource supply is untested. We assessed the energy-limitation hypothesis in three cave streams in northeastern Alabama (USA) by combining measurements of animal production, demand, and resource supplies (detritus, primarily decomposing wood particles). Comparisons of animal consumption and detritus supply rates in each cave showed that all, or nearly all, available detritus was required to support macroinvertebrate production. Furthermore, only a small amount of macroinvertebrate prey production remained to support other predatory taxa (i.e., cave fish and salamanders) after accounting for crayfish consumption. Placing the energy demands of a cave community within the context of resource supply rates provided quantitative support for the energy-limitation hypothesis, confirming the mechanism (limited energy surpluses) that likely influences the evolutionary processes and population dynamics that shape cave communities. Detritus-based surface ecosystems often have large detrital surpluses. Thus, cave ecosystems, which show minimal surpluses, occupy the extreme oligotrophic end of the spectrum of detritus-based food webs.

Identification of Martian Cave Skylights Using the Temperature Change During Day and Night

NASA Astrophysics Data System (ADS)

Jung, Jongil; Yi, Yu; Kim, Eojin

2014-06-01

Recently, cave candidates have been discovered on other planets besides the Earth, such as the Moon and Mars. When we go to other planets, caves could be possible human habitats providing natural protection from cosmic threats. In this study, seven cave candidates have been found on Pavonis Mons and Ascraeus Mons in Tharsis Montes on Mars. The cave candidates were selected using the images of the Context Camera (CTX) on the Mars Reconnaissance Orbiter (MRO). The Context Camera could provide images with the high resolution of 6 meter per pixel. The diameter of the candidates ranges from 50 to 100m. Cushing et al. (2007) have analyzed the temperature change at daytime and nighttime using the Thermal Emission Imaging System (THEMIS) for the sites of potential cave candidates. Similarly, we have examined the temperature change at daytime and at nighttime for seven cave candidates using the method of Cushing et al. (2007). Among those, only one candidate showed a distinct temperature change. However, we cannot verify a cave based on the temperature change only and further study is required for the improvement of this method to identify caves more clearly.

An Energy-Efficient and Scalable Deep Learning/Inference Processor With Tetra-Parallel MIMD Architecture for Big Data Applications.

PubMed

Park, Seong-Wook; Park, Junyoung; Bong, Kyeongryeol; Shin, Dongjoo; Lee, Jinmook; Choi, Sungpill; Yoo, Hoi-Jun

2015-12-01

Deep Learning algorithm is widely used for various pattern recognition applications such as text recognition, object recognition and action recognition because of its best-in-class recognition accuracy compared to hand-crafted algorithm and shallow learning based algorithms. Long learning time caused by its complex structure, however, limits its usage only in high-cost servers or many-core GPU platforms so far. On the other hand, the demand on customized pattern recognition within personal devices will grow gradually as more deep learning applications will be developed. This paper presents a SoC implementation to enable deep learning applications to run with low cost platforms such as mobile or portable devices. Different from conventional works which have adopted massively-parallel architecture, this work adopts task-flexible architecture and exploits multiple parallelism to cover complex functions of convolutional deep belief network which is one of popular deep learning/inference algorithms. In this paper, we implement the most energy-efficient deep learning and inference processor for wearable system. The implemented 2.5 mm × 4.0 mm deep learning/inference processor is fabricated using 65 nm 8-metal CMOS technology for a battery-powered platform with real-time deep inference and deep learning operation. It consumes 185 mW average power, and 213.1 mW peak power at 200 MHz operating frequency and 1.2 V supply voltage. It achieves 411.3 GOPS peak performance and 1.93 TOPS/W energy efficiency, which is 2.07× higher than the state-of-the-art.

Fracture Networks from a deterministic physical model as 'forerunners' of Maze Caves

NASA Astrophysics Data System (ADS)

Ferer, M. V.; Smith, D. H.; Lace, M. J.

2013-12-01

'Fractures are the chief forerunners of caves because they transmit water much more rapidly than intergranular pores.[1] Thus, the cave networks can follow the fracture networks from which the Karst caves formed by a variety of processes. Traditional models of continental Karst define water flow through subsurface geologic formations, slowly dissolving the rock along the pathways (e.g. water saturated with respect to carbon dioxide flowing through fractured carbonate formations). We have developed a deterministic, physical model of fracturing in a model geologic layer of a given thickness, when that layer is strained in one direction and subsequently in a perpendicular direction. It was observed that the connected fracture networks from our model visually resemble maps of maze caves. Since these detailed cave maps offer critical tools in modeling cave development patterns and conduit flow in Karst systems, we were able to test the qualitative resemblance by using statistical analyses to compare our model networks in geologic layers of four different thicknesses with the corresponding statistical analyses of four different maze caves, formed in a variety of geologic settings. The statistical studies performed are: i) standard box-counting to determine if either the caves or the model networks are fractal. We found that both are fractal with a fractal dimension Df ≈ 1.75 . ii) for each section inside a closed path, we determined the area and perimeter-length, enabling a study of the tortuosity of the networks. From the dependence of the section's area upon its perimeter-length, we have found a power-law behavior (for sufficiently large sections) characterized by a 'tortuosity' exponent. These exponents have similar values for both the model networks and the maze caves. The best agreement is between our thickest model layer and the maze-like part of Wind Cave in South Dakota where the data from the model and the cave overlie each other. For the present networks from the physical model, we assumed that the geologic layer was of uniform thickness and that the strain in both directions were the same. The latter may not be the case for the Brazilian, Toca de Boa Cave. These assumptions can be easily modified in our computer code to reflect different geologic histories. Even so the quantitative agreement suggests that our model networks are statistically realistic both for the 'forerunners' of caves and for general fracture networks in geologic layers, which should assist the study of underground fluid flow in many applications for which fracture patterns and fluid flow are difficult to determine (e.g., hydrology, watershed management, oil recovery, carbon dioxide sequestration, etc.). Keywords - Fracture Networks, Karst, Caves, Structurally Variable Pathways, hydrogeological modeling 1 Arthur N. Palmer, CAVE GEOLOGY, pub. Cave Books, Dayton OH, (2007).

Continuously Monitoring the Micrometeorology of a Natural Cave System: Hollow Ridge Speleoclimatology

NASA Astrophysics Data System (ADS)

Kowalczk, A.; Gaffka, C.; Froelich, P.

2008-05-01

A study of cave microclimatology has been underway since October 2007 in a protected karst cave system near Marianna Florida. We are monitoring cave air, drip water and climatology at Hollow Ridge Cave to help calibrate isotopic and chemical paleoproxies incorporated into actively growing speleothems in Northwest Florida. Multiple monitoring stations positioned in the interior and above the overburden of this 1000 m long cave continuously record temperature (T), relative humidity (RH), barometric pressure (BP), drip rates (precipitation), acoustic airflow (wind) direction and velocity, 222Rn activities and CO2 concentrations. Air samples for 13CO2 analyses are collected periodically along the cave axis. Positively correlated 13CO2 vs. 1/ CO2 indicate soil gas (δ13C= -22 ‰) is the dominant CO2 source. Rn-222 is likely sourced from decay of 226Ra (U-series) in the limestone bedrock. In general, this cave inhales and exhales diurnally. All cave parameters reflect the intensity and longitudinal gradients of each breath modulated by frontal passages and seasonal changes. The diurnal amplitudes of T, RH, 222Rn and CO2 are highest nearest the entrance and almost disappear at the back of the cave, which mostly senses small amplitude frontal and seasonal changes. Radon-222 (20-340 dpm/L) and CO2 (400-1500 ppm) rise and fall coherently. Both gases are higher in the poorly ventilated portions of the cave, but each shows temporal and spatial patterns that reflect different sources - emanation from the enclosing limestone vs. soil gas and dripwater infusion from above. A flooding event due to a rise of the adjacent Chipola River inadvertently sealed the cave entrances, allowing 222Rn to grow in nearly to secular equilibrium (steady-state) in the air trapped inside the cave. Rn-222 peaked at 1200 dpm/L, over three-fold higher than previously measured, while CO2 peaked at 1400 ppm, similar to the highest CO2 values observed during normal conditions. As airflow was fully restricted, decay of 222Rn is balanced only by 222Rn emanation into the cave. Assuming 222Rn emanation into the cave is constant and represented by the secular equilibrium value, we use a simple radon- deficiency model to estimate air exchange rates (fractional tidal air volumes) and CO2 exhalation rates to compare wet (rainy) and dry periods. Daily air exchange rates vary from 18 to 26% of the cave volume. Radon/ CO2 ratios are four-times higher during wet periods than during dry periods, indicating stronger CO2 sources during dry periods. This suggests the cave ventilation system may be entraining soil gas CO2 from overhead fissures when the overlying soil cap is not waterlogged. This is counter to presumptions that wet periods with faster drips and more CO2 degassing from dripwater might increase cave air CO2 levels.

Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference.

PubMed

Morcos, Faruck; Lamanna, Charles; Sikora, Marcin; Izaguirre, Jesús

2008-10-01

Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include maximum likelihood estimation (MLE) using expectation maximization (EM); the set cover approach maximum specificity set cover (MSSC) and the sum-product algorithm (SPA). After accepting an input set of proteins with Uniprot ID/Accession numbers and a selected prediction algorithm, Cytoprophet draws a network of potential interactions with probability scores and GO distances as edge attributes. A network of domain interactions between the domains of the initial protein list can also be generated. Cytoprophet was designed to take advantage of the visual capabilities of Cytoscape and be simple to use. An example of inference in a signaling network of myxobacterium Myxococcus xanthus is presented and available at Cytoprophet's website. http://cytoprophet.cse.nd.edu.

Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon

PubMed Central

Prous, Xavier; Calux, Allan; Gastauer, Markus; Nicacio, Gilberto; Zampaulo, Robson; Souza-Filho, Pedro W.M.; Oliveira, Guilherme; Brandi, Iuri V.; Siqueira, José O.

2018-01-01

The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole. PMID:29576987

Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon.

PubMed

Jaffé, Rodolfo; Prous, Xavier; Calux, Allan; Gastauer, Markus; Nicacio, Gilberto; Zampaulo, Robson; Souza-Filho, Pedro W M; Oliveira, Guilherme; Brandi, Iuri V; Siqueira, José O

2018-01-01

The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole.

Stratigraphic Evidence for Environmental Change in a Bermudian Coastal Underwater Cave (Palm Cave System) in Response to Holocene Sea-level Rise

NASA Astrophysics Data System (ADS)

Cresswell, J. N.; van Hengstum, P. J.; Iliffe, T. M.

2016-12-01

Unique environments exist worldwide in coastal underwater caves, including those from Bermuda, which has been a global epicenter for interdisciplinary cave research. However, the development of environments, ecosystems, and sedimentary deposits in coastal underwater caves, particularly over millennial timescales is poorly understood, with previous research from Bermuda indicating a critical role for sea-level rise in driving environmental change. A multi-proxy stratigraphic analysis of 14 sediment cores that were collected from the Palm Cave System in Bermuda from 2 m to 20 m water depths was conducted to better understand Holocene-scale environmental change in coastal underwater caves (e.g., textural analysis, x-radiographs, microfossil analysis, radiocarbon dating). The rate of deposition was found to be variable throughout time and dependent upon the proximity of core locations to cave openings (`karst windows') and conduit geometry. The oldest recovered sediment was likely Pleistocene-aged, terra-rosa soil deposits that predate the Holocene inundation. By 9500 Cal yrs BP, deposition was dominated by organic-rich facies (gyttja), with agglutinated brackish foraminifera (Trochammina, Polysaccammina) and bivalves indicating brackish aquatic conditions in the system by 9200 Cal yrs BP. A system-wide shift to carbonate deposition occurred 8500 Cal yrs BP, which indicates the onset of oxygenated marine water entering the cave and development of a marine-dominated (i.e., submarine) cave environment. Comparison with local maximum sea-level indicators shows that inundation of the Bermuda platform by Holocene sea-level rise likely drove environmental change in the Palm Cave System.

Computational statistics using the Bayesian Inference Engine

NASA Astrophysics Data System (ADS)

Weinberg, Martin D.

2013-09-01

This paper introduces the Bayesian Inference Engine (BIE), a general parallel, optimized software package for parameter inference and model selection. This package is motivated by the analysis needs of modern astronomical surveys and the need to organize and reuse expensive derived data. The BIE is the first platform for computational statistics designed explicitly to enable Bayesian update and model comparison for astronomical problems. Bayesian update is based on the representation of high-dimensional posterior distributions using metric-ball-tree based kernel density estimation. Among its algorithmic offerings, the BIE emphasizes hybrid tempered Markov chain Monte Carlo schemes that robustly sample multimodal posterior distributions in high-dimensional parameter spaces. Moreover, the BIE implements a full persistence or serialization system that stores the full byte-level image of the running inference and previously characterized posterior distributions for later use. Two new algorithms to compute the marginal likelihood from the posterior distribution, developed for and implemented in the BIE, enable model comparison for complex models and data sets. Finally, the BIE was designed to be a collaborative platform for applying Bayesian methodology to astronomy. It includes an extensible object-oriented and easily extended framework that implements every aspect of the Bayesian inference. By providing a variety of statistical algorithms for all phases of the inference problem, a scientist may explore a variety of approaches with a single model and data implementation. Additional technical details and download details are available from http://www.astro.umass.edu/bie. The BIE is distributed under the GNU General Public License.

An inference method from multi-layered structure of biomedical data.

PubMed

Kim, Myungjun; Nam, Yonghyun; Shin, Hyunjung

2017-05-18

Biological system is a multi-layered structure of omics with genome, epigenome, transcriptome, metabolome, proteome, etc., and can be further stretched to clinical/medical layers such as diseasome, drugs, and symptoms. One advantage of omics is that we can figure out an unknown component or its trait by inferring from known omics components. The component can be inferred by the ones in the same level of omics or the ones in different levels. To implement the inference process, an algorithm that can be applied to the multi-layered complex system is required. In this study, we develop a semi-supervised learning algorithm that can be applied to the multi-layered complex system. In order to verify the validity of the inference, it was applied to the prediction problem of disease co-occurrence with a two-layered network composed of symptom-layer and disease-layer. The symptom-disease layered network obtained a fairly high value of AUC, 0.74, which is regarded as noticeable improvement when comparing 0.59 AUC of single-layered disease network. If further stretched to whole layered structure of omics, the proposed method is expected to produce more promising results. This research has novelty in that it is a new integrative algorithm that incorporates the vertical structure of omics data, on contrary to other existing methods that integrate the data in parallel fashion. The results can provide enhanced guideline for disease co-occurrence prediction, thereby serve as a valuable tool for inference process of multi-layered biological system.

Psychological Benefits of Outdoor Adventure Activities.

ERIC Educational Resources Information Center

Teaff, Joseph; Kablach, John

1987-01-01

Reports psychological benefits of participation in caving, rock climbing, ropes, and teams course of 30-day adventure program by 56 delinquent youth (ages 11-18). Concludes rope course satisfied independence, rewards, and variety more than caving; rock climbing satisfied independence and rewards more than caving; caving less beneficial than other…

36 CFR 290.3 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2012 CFR

2012-07-01

... governmental agencies and the public, including those who utilize caves for scientific, educational, or... is located as new cave discoveries are made. Caves nominated but not approved for designation may be... mineralogic features that are fragile, represent formation processes that are of scientific interest, or that...

36 CFR 290.3 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2013 CFR

2013-07-01

... governmental agencies and the public, including those who utilize caves for scientific, educational, or... is located as new cave discoveries are made. Caves nominated but not approved for designation may be... mineralogic features that are fragile, represent formation processes that are of scientific interest, or that...

36 CFR 290.3 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2014 CFR

2014-07-01

... governmental agencies and the public, including those who utilize caves for scientific, educational, or... is located as new cave discoveries are made. Caves nominated but not approved for designation may be... mineralogic features that are fragile, represent formation processes that are of scientific interest, or that...

36 CFR 290.3 - Nomination, evaluation, and designation of significant caves.

Code of Federal Regulations, 2011 CFR

2011-07-01

... governmental agencies and the public, including those who utilize caves for scientific, educational, or... is located as new cave discoveries are made. Caves nominated but not approved for designation may be... mineralogic features that are fragile, represent formation processes that are of scientific interest, or that...

Ice Versus Rock

ERIC Educational Resources Information Center

Rule, Audrey C.; Olson, Eric A.; Dehm, Janet

2005-01-01

During a snow bank exploration, students noticed "ice caves," or pockets, in some of the larger snow banks, usually below darker layers. Most of these caves had many icicles hanging inside. Students offered reasonable explanations of ice cave formation--squirrels, kids, snow blowers--and a few students came close to the true ice cave-formation…

Statistical Inference and Reverse Engineering of Gene Regulatory Networks from Observational Expression Data

PubMed Central

Emmert-Streib, Frank; Glazko, Galina V.; Altay, Gökmen; de Matos Simoes, Ricardo

2012-01-01

In this paper, we present a systematic and conceptual overview of methods for inferring gene regulatory networks from observational gene expression data. Further, we discuss two classic approaches to infer causal structures and compare them with contemporary methods by providing a conceptual categorization thereof. We complement the above by surveying global and local evaluation measures for assessing the performance of inference algorithms. PMID:22408642

Control Algorithms For Liquid-Cooled Garments

NASA Technical Reports Server (NTRS)

Drew, B.; Harner, K.; Hodgson, E.; Homa, J.; Jennings, D.; Yanosy, J.

1988-01-01

Three algorithms developed for control of cooling in protective garments. Metabolic rate inferred from temperatures of cooling liquid outlet and inlet, suitably filtered to account for thermal lag of human body. Temperature at inlet adjusted to value giving maximum comfort at inferred metabolic rate. Applicable to space suits, used for automatic control of cooling in suits worn by workers in radioactive, polluted, or otherwise hazardous environments. More effective than manual control, subject to frequent, overcompensated adjustments as level of activity varies.

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. | Office of Cancer Genomics

Cancer.gov

We and others have shown that transition and maintenance of biological states is controlled by master regulator proteins, which can be inferred by interrogating tissue-specific regulatory models (interactomes) with transcriptional signatures, using the VIPER algorithm. Yet, some tissues may lack molecular profiles necessary for interactome inference (orphan tissues), or, as for single cells isolated from heterogeneous samples, their tissue context may be undetermined.

Vibrational spectroscopic analysis of taranakite (K,NH 4)Al 3(PO 4) 3(OH)·9(H 2O) from the Jenolan Caves, Australia

NASA Astrophysics Data System (ADS)

Frost, Ray L.; Xi, Yunfei; Palmer, Sara J.; Pogson, Ross E.

2011-12-01

Many phosphate containing minerals are found in the Jenolan Caves. Such minerals are formed by the reaction of bat guano and clays from the caves. Among these cave minerals is the mineral taranakite (K,NH 4)Al 3(PO 4) 3(OH)·9(H 2O) which has been identified by X-ray diffraction. Jenolan Caves taranakite has been characterised by Raman spectroscopy. Raman and infrared bands are assigned to H 2PO 4, OH and NH stretching vibrations. By using a combination of XRD and Raman spectroscopy, the existence of taranakite in the caves has been proven.

Geophysical exploration in vicinity of the Unicorn Cave, South Harz Mountains, Germany

NASA Astrophysics Data System (ADS)

Kaufmann, Georg; Romanov, Douchko; Nielbock, Ralf

2010-05-01

The Unicorn Cave in the southern Harz Mountains in Germany is located in an outcrop of dolomite from the Zechstein formation, which is underlain by Grauwacke rocks. The cave, about 600 meters long, consists of several large chambers, which are connected by a gallery following the main fault alignments in E/W, NE/SW, and NW/SE direction. The overburden of the cave is shallow, between 10 and 30 m. We have used this cave site to perform a sensitivity test for both gravimetric and geoelectic methods above the cave. Additionally, geoelectic mapping has been used to assess the thickness of the cave sediments in one of the chambers. Our results show a clear signal in the Bouguer anomaly, which can only be explained by a combined model of the void space and the sediment filling. Geoelectric results are less clear, but support the gravimetry.

Optimization research of structural parameters in non-pillar sublevel caving method with large structural parameters

NASA Astrophysics Data System (ADS)

Han, Wencheng; Zhou, Renjie; Liu, Xianfeng; Sun, Dongdong

2018-03-01

The non-pillar sublevel caving method with large structural parameters used in Mao Gong Iron Mine is of high rate of dilution and loss, and the ore recovery rate is less than 50%. Aiming at this problem, this paper analyzes the influence mechanism of the caving step on the mining index by means of the matching relationship between the shape of caved ore body and the drawn-out ore body, then through the physical simulation experiment in laboratory, the mining index such as the volume of pure ore drawing, ore recovery ratio and rock mixing ratio are studied under different caving step. The results show that the mining index under caving step of two row of blast hole is better than that under caving step of one row of blast hole. The research has guided significance for production of the mine.

The microbiology of Lascaux Cave.

PubMed

Bastian, F; Jurado, V; Nováková, A; Alabouvette, C; Saiz-Jimenez, C

2010-03-01

Lascaux Cave (Montignac, France) contains paintings from the Upper Paleolithic period. Shortly after its discovery in 1940, the cave was seriously disturbed by major destructive interventions. In 1963, the cave was closed due to algal growth on the walls. In 2001, the ceiling, walls and sediments were colonized by the fungus Fusarium solani. Later, black stains, probably of fungal origin, appeared on the walls. Biocide treatments, including quaternary ammonium derivatives, were extensively applied for a few years, and have been in use again since January 2008. The microbial communities in Lascaux Cave were shown to be composed of human-pathogenic bacteria and entomopathogenic fungi, the former as a result of the biocide selection. The data show that fungi play an important role in the cave, and arthropods contribute to the dispersion of conidia. A careful study on the fungal ecology is needed in order to complete the cave food web and to control the black stains threatening the Paleolithic paintings.

A synopsis of centipedes in Brazilian caves: hidden species diversity that needs conservation (Myriapoda, Chilopoda)

PubMed Central

Chagas-Jr, Amazonas; Bichuette, Maria Elina

2018-01-01

Abstract This study revises centipede fauna found in Brazilian caves, focusing on troglomorphic taxa and emphasizing conservation status. We present 563 centipede specimens from 274 caves across eleven Brazilian states. Of these, 22 records were derived from existing literature and 252 are newly collected. Specimens represent four orders, ten families, 18 genera, and 47 morphospecies. Together, the cave records represent 21 % of Brazil’s centipede fauna. Scolopendromorpha was the most representative order (41 %), followed by Geophilomorpha (26 %), Scutigeromorpha (23 %), and Lithobiomorpha (10 %). Six species were found only in caves, with four considered troglobitic. The distribution of Cryptops iporangensis, the first Brazilian troglobitic centipede species to be discovered, was expanded to other three caves. Cryptops spelaeoraptor and Cryptops iporangensis are two troglobitic species considered Vulnerable and Endangered, respectively, according to the IUCN Red List. Main threats to Brazilian caves are mining, hydroelectric projects, water pollution, and unregulated tourism. PMID:29674871

Semisupervised learning using Bayesian interpretation: application to LS-SVM.

PubMed

Adankon, Mathias M; Cheriet, Mohamed; Biem, Alain

2011-04-01

Bayesian reasoning provides an ideal basis for representing and manipulating uncertain knowledge, with the result that many interesting algorithms in machine learning are based on Bayesian inference. In this paper, we use the Bayesian approach with one and two levels of inference to model the semisupervised learning problem and give its application to the successful kernel classifier support vector machine (SVM) and its variant least-squares SVM (LS-SVM). Taking advantage of Bayesian interpretation of LS-SVM, we develop a semisupervised learning algorithm for Bayesian LS-SVM using our approach based on two levels of inference. Experimental results on both artificial and real pattern recognition problems show the utility of our method.

A Framework for Aligning Instructional Design Strategies with Affordances of CAVE Immersive Virtual Reality Systems

ERIC Educational Resources Information Center

Ritz, Leah T.; Buss, Alan R.

2016-01-01

Increasing availability of immersive virtual reality (IVR) systems, such as the Cave Automatic Virtual Environment (CAVE) and head-mounted displays, for use in education contexts is providing new opportunities and challenges for instructional designers. By highlighting the affordances of IVR specific to the CAVE, the authors emphasize the…

Alternative Fuels Data Center: Mammoth Cave National Park Uses Only

Science.gov Websites

Alternative Fuel Vehicles Mammoth Cave National Park Uses Only Alternative Fuel Vehicles to someone by E-mail Share Alternative Fuels Data Center: Mammoth Cave National Park Uses Only Alternative Fuel Vehicles on Facebook Tweet about Alternative Fuels Data Center: Mammoth Cave National Park Uses

Comparison between cimetidine and Caved-S in the treatment of gastric ulceration, and subsequent maintenance therapy.

PubMed Central

Morgan, A G; McAdam, W A; Pacsoo, C; Darnborough, A

1982-01-01

One hundred patients with benign gastric ulceration were treated in a single-blind, endoscopically controlled trial to assess the relative efficacy of cimetidine (1 g daily) and Caved-S (six tablets daily). Ulcer healing was assessed after six weeks' treatment, and, if incomplete, after a further six weeks. There was no significant difference between the two drug regimens (approximately 63% at six weeks and 91% at 12 weeks). If an ulcer remains unhealed after 10 weeks' treatment the patient should undergo surgery. There was no difference in the relief of day pain between the two drug regimens but cimetidine was more effective over the first two weeks of treatment relieving night pain, than was Caved-S (p less than 0 . 02). After ulcer healing, drug dosage was reduced (cimetidine to 400 mg at night and Caved-S to two tablets twice daily). So far, 56 patients, 28 in each group, have completed the first year's maintenance treatment, and there have been four ulcer recurrences in each group (14%). PMID:7042486

Defense applications of the CAVE (CAVE automatic virtual environment)

NASA Astrophysics Data System (ADS)

Isabelle, Scott K.; Gilkey, Robert H.; Kenyon, Robert V.; Valentino, George; Flach, John M.; Spenny, Curtis H.; Anderson, Timothy R.

1997-07-01

The CAVE is a multi-person, room-sized, high-resolution, 3D video and auditory environment, which can be used to present very immersive virtual environment experiences. This paper describes the CAVE technology and the capability of the CAVE system as originally developed at the Electronics Visualization Laboratory of the University of Illinois- Chicago and as more recently implemented by Wright State University (WSU) in the Armstrong Laboratory at Wright- Patterson Air Force Base (WPAFB). One planned use of the WSU/WPAFB CAVE is research addressing the appropriate design of display and control interfaces for controlling uninhabited aerial vehicles. The WSU/WPAFB CAVE has a number of features that make it well-suited to this work: (1) 360 degrees surround, plus floor, high resolution visual displays, (2) virtual spatialized audio, (3) the ability to integrate real and virtual objects, and (4) rapid and flexible reconfiguration. However, even though the CAVE is likely to have broad utility for military applications, it does have certain limitations that may make it less well- suited to applications that require 'natural' haptic feedback, vestibular stimulation, or an ability to interact with close detailed objects.

CaveMan Enterprise version 1.0 Software Validation and Verification.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, David

The U.S. Department of Energy Strategic Petroleum Reserve stores crude oil in caverns solution-mined in salt domes along the Gulf Coast of Louisiana and Texas. The CaveMan software program has been used since the late 1990s as one tool to analyze pressure mea- surements monitored at each cavern. The purpose of this monitoring is to catch potential cavern integrity issues as soon as possible. The CaveMan software was written in Microsoft Visual Basic, and embedded in a Microsoft Excel workbook; this method of running the CaveMan software is no longer sustainable. As such, a new version called CaveMan Enter- prisemore » has been developed. CaveMan Enterprise version 1.0 does not have any changes to the CaveMan numerical models. CaveMan Enterprise represents, instead, a change from desktop-managed work- books to an enterprise framework, moving data management into coordinated databases and porting the numerical modeling codes into the Python programming language. This document provides a report of the code validation and verification testing.« less

Rock fall simulation at Timpanogos Cave National Monument, American Fork Canyon, Utah, USA

USGS Publications Warehouse

Harp, E.L.; Dart, R.L.; Reichenbach, P.

2011-01-01

Rock fall from limestone cliffs at Timpanogos Cave National Monument in American Fork Canyon east of Provo, Utah, is a common occurrence. The cave is located in limestone cliffs high on the southern side of the canyon. One fatality in 1933 led to the construction of rock fall shelters at the cave entrance and exit in 1976. Numerous rock fall incidents, including a near miss in 2000 in the vicinity of the trail below the cave exit, have led to a decision to extend the shelter at the cave exit to protect visitors from these ongoing rock fall events initiating from cliffs immediately above the cave exit. Three-dimensional rock fall simulations from sources at the top of these cliffs have provided data from which to assess the spatial frequencies and velocities of rock falls from the cliffs and to constrain the design of protective measures to reduce the rock fall hazard. Results from the rock fall simulations are consistent with the spatial patterns of rock fall impacts that have been observed at the cave exit site. ?? 2011 Springer-Verlag.

Rock fall simulation at Timpanogos Cave National Monument, American Fork Canyon, Utah, USA

USGS Publications Warehouse

Harp, Edwin L.; Dart, Richard L.; Reichenbach, Paola

2011-01-01

Rock fall from limestone cliffs at Timpanogos Cave National Monument in American Fork Canyon east of Provo, Utah, is a common occurrence. The cave is located in limestone cliffs high on the southern side of the canyon. One fatality in 1933 led to the construction of rock fall shelters at the cave entrance and exit in 1976. Numerous rock fall incidents, including a near miss in 2000 in the vicinity of the trail below the cave exit, have led to a decision to extend the shelter at the cave exit to protect visitors from these ongoing rock fall events initiating from cliffs immediately above the cave exit. Three-dimensional rock fall simulations from sources at the top of these cliffs have provided data from which to assess the spatial frequencies and velocities of rock falls from the cliffs and to constrain the design of protective measures to reduce the rock fall hazard. Results from the rock fall simulations are consistent with the spatial patterns of rock fall impacts that have been observed at the cave exit site.

High endemism at cave entrances: a case study of spiders of the genus Uthina

PubMed Central

Yao, Zhiyuan; Dong, Tingting; Zheng, Guo; Fu, Jinzhong; Li, Shuqiang

2016-01-01

Endemism, which is typically high on islands and in caves, has rarely been studied in the cave entrance ecotone. We investigated the endemism of the spider genus Uthina at cave entrances. Totally 212 spiders were sampled from 46 localities, from Seychelles across Southeast Asia to Fiji. They mostly occur at cave entrances but occasionally appear at various epigean environments. Phylogenetic analysis of DNA sequence data from COI and 28S genes suggested that Uthina was grouped into 13 well-supported clades. We used three methods, the Bayesian Poisson Tree Processes (bPTP) model, the Bayesian Phylogenetics and Phylogeography (BPP) method, and the general mixed Yule coalescent (GMYC) model, to investigate species boundaries. Both bPTP and BPP identified the 13 clades as 13 separate species, while GMYC identified 19 species. Furthermore, our results revealed high endemism at cave entrances. Of the 13 provisional species, twelve (one known and eleven new) are endemic to one or a cluster of caves, and all of them occurred only at cave entrances except for one population of one species. The only widely distributed species, U. luzonica, mostly occurred in epigean environments while three populations were found at cave entrances. Additionally, eleven new species of the genus are described. PMID:27775081

Response of ice caves to weather extremes in the southeastern Alps, Europe

NASA Astrophysics Data System (ADS)

Colucci, R. R.; Fontana, D.; Forte, E.; Potleca, M.; Guglielmin, M.

2016-05-01

High altitude karstic environments often preserve permanent ice deposits within caves, representing the lesser-known portion of the cryosphere. Despite being not so widespread and easily reachable as mountain glaciers and ice caps, ice caves preserve much information about past environmental changes and climatic evolution. We selected 1111 ice caves from the existing cave inventory, predominantly but not exclusively located in the periglacial domain where permafrost is not dominant (i.e., with mean annual air temperature < 3 °C but not in a permafrost environment). The influence of climate and topography on ice cave distribution is also investigated. In order to assess the thickness and the inner structure of the deposits, we selected two exemplary ice caves in the Canin massif (Julian Alps) performing several multifrequency GPR surveys. A strong influence of global and local climate change in the evolution of the ice deposits has been particularly highlighted in the dynamic ice cave type, especially in regard to the role of weather extremes. The natural response of ice caves to a warming climate could lead to a fast reduction of such ice masses. The increased occurrence of weather extremes, especially warmer and more intense precipitation caused by higher mean 0 °C-isotherms, could in fact be crucial in the future mass balance evolution of such permanent ice deposits.

‘Neanderthal bone flutes’: simply products of Ice Age spotted hyena scavenging activities on cave bear cubs in European cave bear dens

PubMed Central

Diedrich, Cajus G.

2015-01-01

Punctured extinct cave bear femora were misidentified in southeastern Europe (Hungary/Slovenia) as ‘Palaeolithic bone flutes’ and the ‘oldest Neanderthal instruments’. These are not instruments, nor human made, but products of the most important cave bear scavengers of Europe, hyenas. Late Middle to Late Pleistocene (Mousterian to Gravettian) Ice Age spotted hyenas of Europe occupied mainly cave entrances as dens (communal/cub raising den types), but went deeper for scavenging into cave bear dens, or used in a few cases branches/diagonal shafts (i.e. prey storage den type). In most of those dens, about 20% of adult to 80% of bear cub remains have large carnivore damage. Hyenas left bones in repeating similar tooth mark and crush damage stages, demonstrating a butchering/bone cracking strategy. The femora of subadult cave bears are intermediate in damage patterns, compared to the adult ones, which were fully crushed to pieces. Hyenas produced round–oval puncture marks in cub femora only by the bone-crushing premolar teeth of both upper and lower jaw. The punctures/tooth impact marks are often present on both sides of the shaft of cave bear cub femora and are simply a result of non-breakage of the slightly calcified shaft compacta. All stages of femur puncturing to crushing are demonstrated herein, especially on a large cave bear population from a German cave bear den. PMID:26064624

Morphological and genetic identification and isotopic study of the hair of a cave lion (Panthera spelaea Goldfuss, 1810) from the Malyi Anyui River (Chukotka, Russia)

NASA Astrophysics Data System (ADS)

Chernova, O. F.; Kirillova, I. V.; Shapiro, B.; Shidlovskiy, F. K.; Soares, A. E. R.; Levchenko, V. A.; Bertuch, F.

2016-06-01

We present the first detailed analyses of the preserved hair of a cave lion (Panthera spelaea Goldfuss, 1810). The hair was found in association with a skeleton that was recovered recently from perennially frozen Pleistocene sediments in the lower reaches of the Malyi Anyui River (Chukotka, Russia). We extract mitochondrial DNA from the hair to confirm its taxonomic identity, and perform detailed morphological analyses of the color and structure of the hair using light optical microscopy and SEM. In addition, we compare the cave lion hair to hair taken from the back and mane of an African lion. We find that cave lion hair is similar but not identical to that of the present-day lion. In addition to slightly different coloration, cave lions had a very thick and dense undercoat comprising closed and compressed wavy downy hair with a medulla. In addition, while the microstructures of the medulla and cortex of cave lion hair are similar in extinct and living lions, the cuticular scales of cave lion hair are higher than those in living lions, suggesting that cave lion hair is stronger and more robust than that of living lions. We hypothesize that the differences between cave lion hair and present-day lion hair may be due to adaptations of cave lions to the harsh climatic and environmental conditions of the Pleistocene Ice Ages.

Envitonmental monitoring and radiation protection in Škocjan Caves, Slovenia

NASA Astrophysics Data System (ADS)

Debevec Gerjeviè, V.; Jovanovič, P.

2012-04-01

Škocjan Caves were listed as UNESCO World Heritage Sites in 1986, due to their exceptional significance for cultural and natural heritage. Park Škocjan Caves is located in South Eastern part of Slovenia. It was established with aim of conserving and protecting exceptional geomorphological, geological and hydrological outstanding features, rare and endangered plant and animal species, paleontological and archaeological sites, ethnological and architectural characteristics and cultural landscape and for the purpose of ensuring opportunities for suitable development, by the National Assembly of the Republic of Slovenia in 1996. Park Škocjan Caves established monitoring that includes caves microclimate parameters: humidity, CO2, wind flow and radon concentration and daughter products. The approach in managing the working place with natural background radiation is complex. Monitoring of Radon has been functioning for more than ten years now. Presentation will show the dynamic observed in the different parts of the caves, related to radon daughter products and other microclimatic data. Relation of background radiation to carrying capacity will be explained. Implementing the Slovene legislation in the field of radiation protection, we are obligated to perform special measurements in the caves and also having our guides and workers in the caves regularly examined according to established procedure. The medical exams are performed at Institution of Occupational Safety, Ljubljana in order to monitor the influence of Radon to the workers in the cave. The equivalent dose for each employed person is also established on regular basis and it is part of medical survey of workers in the caves. A system of education of the staff working in the caves in the field of radiation protection will be presented as well.

Feeding habits of amphipods (Crustacea: Malacostraca) from shallow soft bottom communities: Comparison between marine caves and open habitats

NASA Astrophysics Data System (ADS)

Navarro-Barranco, Carlos; Tierno-de-Figueroa, José Manuel; Guerra-García, José Manuel; Sánchez-Tocino, Luis; García-Gómez, José Carlos

2013-04-01

Marine caves are environments of great interest since the organisms that inhabit them are forced to develop specific adaptations to high constraint conditions. Because of some of these particular conditions, such as light absence or oligotrophy, it can be expected that feeding strategies into caves differ from that present outside them. Nevertheless, no studies have been done to compare the trophic structure of marine caves and open habitats, at least for amphipod communities, considering their importance both inside and outside of the caves. In this study, the diet of the dominant amphipod species living on shallow sediments, both inside and outside of six marine caves in western Mediterranean, was characterized. Thereby, the gut content of 17 amphipod species was studied, being this study the first attempt to establish the feeding habit of most of these species. Analysis of digestive contents of the species showed that amphipod diet is less diverse in sediments than in other environments, such as algae and seagrasses. No herbivorous species were found in the sediment and carnivorous amphipods showed a little variety of prey, feeding mainly on crustaceans. Differences in the trophic structure were also found between marine caves and open habitats sediments: while outside the caves detritivorous was the dominant group (both in number of species and number of individuals), amphipods mainly play the role of carnivorous inside the caves. No detritivorous species were found into the caves, where carnivorous represents almost 60% of amphipods species and more than 80% of amphipod individuals. This pattern obtained in amphipods differ from the general trend observed in marine cave organisms, for which a generalist diet, such as omnivory, usually is an advantage in these oligotrophic conditions. The possible causes of this pattern are discussed.

Geological constraints on cave development in the plateau-gorge karst of South China (Wulong, Chongqing)

NASA Astrophysics Data System (ADS)

Szczygieł, Jacek; Golicz, Mateusz; Hercman, Helena; Lynch, Erin

2018-03-01

The Houping Tiankeng cluster is a part of the South China Karst UNESCO World Natural Heritage Site. Within the distinctive Wulong plateau-gorge karst, > 200 km of cave passages have been documented to date. This paper focuses on detailed tectonic and morphological research on the Luo Shui Kong cave, enriched with U-series dating of speleothems and complemented by morphometric analysis of the San Wang Dong and Er Wang Dong caves. All of these caves exhibit three regional levels of cave development: 1) 1040-1020 m a.s.l.; 2) 900-840 m a.s.l.; and 3) 740-660 m a.s.l. The Houping Tiankeng area is a carbonate rock sequence several hundred meters thick, overlain by the less soluble Lower Ordovician strata, limiting recharge points to faults exposing underlying easily soluble formations. This leads to the domination of concentrated, high-volume inflow and thus results in caves of large volume in the plateau-gorge karst. Shafts connecting the surface with cave passages located underneath formed along faults, changing the hydrogeological pattern through karst water capture and remodeling of existing conduits, albeit mainly by increasing their overall dimensions rather than by deepening them. The most favorable structures for cave-level development are two sets of joints conjugated with gently inclined bedding. Since these joints are characterized by a small vertical extent, downward development is limited. Hence, most of the passages are wide but not deep canyons and typical of a water-table cave pattern. Places where the fault plane is eroded from the surface and where, at the same time, an underneath cave chamber ceiling expands upwards are particularly predisposed to the formation of a tiankeng.

Monitoring of Radon in Tourist Part of Skocjan Caves

NASA Astrophysics Data System (ADS)

Debevec Gerjevic, Vanja; Jovanovic, Peter

2010-05-01

Due to their exceptional significance for cultural and natural heritage, the Škocjan Caves were entered on UNESCO's list of natural and cultural world heritage sites in 1986. Park Škocjan Caves is located in South Eastern part of Slovenia. It was established with aim of conserving and protecting exceptional geomorphological, geological and hydrological outstanding features, rare and endangered plant and animal species, paleontological and archaeological sites, ethnological and architectural characteristics and cultural landscape and for the purpose of ensuring opportunities for suitable development, by the National Assembly of the Republic of Slovenia in 1996. Park Škocjan Caves established monitoring that includes caves microclimate parameters: humidity, CO2, wind flow and radon concentration and daughter products. The approach in managing the working place with natural background radiation is complex. Monitoring of Radon has been functioning for more than ten years now. Presentation will show the yearly dynamic observed in the different parts of the caves, related to radon daughter products and other microclimatic data, beside the most convenient measuring technique. Implementing the Slovene legislation in the field of radiation protection, we are obligated to perform special measurements in the caves and also having our guides and workers in the caves regularly examined according to established procedure. The medical exams are performed at Institution of Occupational Safety, Ljubljana in order to monitor the influence of Radon to the workers in the cave. The equivalent dose for each employed person is also established on regular basis and it is part of medical survey of workers in the caves. The survey will be described along with education of the staff working in the caves in the field of radiation protection. An overview of Slovene legislation with practical example on implementation will be demonstrated in the case of Škocjan Caves where the managing authority considers the monitoring of Radon as one of the tools for adaptive management.

Monitoring of cave air temperature and humidity in the Niedźwiedzia Cave system (Sudetes, Poland) - a key to understanding tourists activity impact to cave environment

NASA Astrophysics Data System (ADS)

Gasiorowski, M.; Hercman, H.

2012-04-01

The Niedźwiedzia Cave is located in Śnieżnik Massif (the Easter Sudetes, SW Poland) at 800 m a.s.l. The length of known passages is ~3000 m and denivelation is 69 m. The system is composed of 3 levels of passages and chambers. It is a show cave with ~80,000 visitors every year. In 2010 we started monitoring program of cave air temperature and humidity, drip rate, stable isotopes and Uranium and Polonium content in water in selected sites inside the cave and in its vicinity. Changes in dropping rate in upper level are well correlated with precipitation. However, a response of dripping to rainfall depends on former precipitation frequency and intensity - during the humid period the dripping reacts immediately and after long dry period dripping responses with two-weeks delay. There is not so direct correlation between precipitation and dripping in lower level of the system. Air temperature inside the cave is almost stable in lower level (mean annual ~5.3 °C, and annual variation up to 0.7 °C) and more dynamic in the middle level (mean annual ~6.4 °C, and mean annual amplitude up to 4 °C). Daily and weekly measured changes of cave air temperature demonstrate extremely well correlation with number of visitors. In show cave passages (the middle level of the system) temperature increase 0.1-0.2 °C during every day when the cave is open for tourists and such changes is not observed during days without visitors and in lower level of the system closed for tourists. But even short visits of 3-4 cavers are recorded by temperature sensors exposed in the lower level (~0.02 °C increase). It proves very high sensitivity of cave environment to human activity. This study is funded by the National Science Centre and Higher Education grant no. N N306 131038.

The use of water marks mapping to understand flood overflow events inside karstic cavities: Cueva Fría and Cueva Rosa (Asturias, NW Spain)

NASA Astrophysics Data System (ADS)

González Lemos, Saúl; Stoll, Heather M.

2014-05-01

Several karst systems in Asturias (NW Spain) present evidence of fluvial deposits cemented in speleothems that may provide good chronology of past flood events inside the caves. This flood record is under research in two karstic caves of this region, Cueva Fría and Cueva Rosa, which have in common the presence of a perennial stream inside the cave and a low gradient of the cave passage. Immediately after a flood overflow event, water marks, foam and detritus are visible at different heights on the cave walls and correspond to heights of bottlenecks in overflow drainage through the cave passage. Flood events also deposit sand and gravel on terraces on the cave wall and move large volumes of sand in the cave bed. We have noted that detrital particles (like sand or silt particles) are preserved as inclusions inside the stalagmites and that their abundance inside coeval stalagmites decreases as altitude and distance from the perennial stream increase, supporting its fluvial affinity. However, not all the stalagmites that contain detrital particles are located close to the perennial streams. In this work, we have mapped the water marks preserved in the cave walls to reconstruct water levels associated to flood overflow events of different magnitude. We have found that water mark correlation along the cave passage is very useful to define the hydrological behaviour and flood model of the cave during these extreme events. The water mark mapping and correlation have been also useful to prove that during periods of high rainfall, the movement of the sand-bars inside the cave can cover partially or completely active stalagmites, facilitating the cementation process and trapping abundant detrital material inside the stalagmite carbonate. 14C and U/Th dating of the stalagmites can provide a chronology for the detrital rich layers, so that the abundance of fluvial material in the stalagmites can reveal periods of enhanced vs. reduced flooding in the cave over the past several thousand years (Holocene).

Sources and transport of microbial tetraether membrane lipids in Karst Systems

NASA Astrophysics Data System (ADS)

Jex, C.; Blyth, A. J.; McDonald, J.; Woltering, M.; Khan, S.; Baker, A.

2014-12-01

Speleothems preserve organic biomarkers, proxies for surface climate. Microbial-derived lipids, specifically glycerol dialkyl glycerol tetraetheral (GDGT) lipids have been identified in cave deposits and shown to correlate well with surface air temperature using the archaea-derived isoprenoid '(i)GDGT' index of TEX86 and the bacteria derived branched '(b)GDGT' index of MBT/CBT of modern speleothems [1]. Two competing sources for GDGTs in karst systems have been suggested: 1) A soil derived microbial signal dominated by bGDGTs; and 2) An in situ signal dominated by iGDGTs, representative of archaea existing within the cave or overlying bedrock [2]. These findings are yet to be thoroughly tested by characterising the seasonal nature of GDGTs in caves to establish the source and transport pathways within these complex fractured rock systems. Here, we address this and present the results of a yearlong monitoring campaign of GDGTs within two contrasting cave sites from the Yarrangobilly Caves in Kosciuszko national park, SE Australia. The caves are located at a high altitude, semi-arid site. Harriewood cave is dominated by discrete infiltration events throughout the year. Above the cave there are thin soils consisting of loose shallow scree, steep slopes and sparse shrub vegetation. The surface above Jillabenan is characterised by thick red clays of moderate to no slope and Eucalypt dominated forest. As such, these caves provide ideal test sites to characterise the variability in GDGT signals that may be a result of non-temperature related factors, including varying inputs (groundwater vs. in situ growth) or site-specific hydrological conditions. We present data obtained from within the cave: drip waters and in situ collection of GDGTs formed on filter papers left inside the cave throughout the year, and externally sourced signals from soils and their leachates. We also identify key differences in soil pH and cave air temperatures that are best predicted by using cave specific GDGT calibrations of [1]. [1] Blyth et al. 2013. Calibrating the glycerol dialkyl glycerol tetraether temperature signal in speleothems. Geochim Cosmochim Ac. 109, 312-328. [2] Blyth et al. 2014. Contrasting distributions of glycerol dialkyl glycerol tetraethers (GDGTs) in speleothems and associated soils, Org Geochem, 69, 1-10.

Forensic Fluid Dynamics and the Indian Spring (1991) cave collapse problem

NASA Astrophysics Data System (ADS)

Nof, D.

2013-05-01

The collapse of the Indian spring cave (Florida) in 1991 was unique because it occurred while cave divers were in the cave. For the most part, the submerged cave is large enough to accommodate a passing truck so the cave divers were not in touch with its walls and it is hard to imagine why would it naturally collapse just when the divers were in it. Recently, Nof and Paldor (2010) resolved this apparent paradox by suggesting that resonance in the air pockets in the cavern, created by breathing (open circuit) divers, may have contributed to the collapse. In this scenario, divers present in the cavern during the dive may have (unknowingly) caused the collapse through the pressurized air/gas that they release with each breath. When the breathing period of the diver(s) matches the natural oscillations period of the "cave oscillator", the ensuing resonance causes the air pressure in the pockets to increase uncontrollably. Here, we place the above theory on a more solid ground. To do so, we first extended the resonance theory from our original two-pockets, symmetrical U-tube model (with two identical branches that were not specifically identified within the cave system) to a one (identified) pocket in the cavern and a very broad basin (identified, of course) that serves as the other branch of the U-tube. Our methodology is to apply familiar fluid dynamics principles to the situation that occurred in the cave. We did so, step-by-step, on the basis of our interviews with four out of the five surviving cave-divers. Namely, we dissected their testimonies to arrive at a physically plausible scenario determined on basis of a fluid dynamics application to the natural flow in the cave and the flow induced by the compressed air released by the divers as well as the collapsed mud. We found that the oscillation period was larger than what we earlier calculated (still relevant to the case, nevertheless), and that, in contrast to what most cave divers believe, there was a temporary flow blocking during the collapse but no total flow reversal within the cave. Observed swirling in the basin during the collapse is attributed to a dipole flow corresponding to an inflow and outflow from the cave.

Detrital cave sediments record Late Quaternary hydrologic and climatic variability in northwestern Florida, USA

NASA Astrophysics Data System (ADS)

Winkler, Tyler S.; van Hengstum, Peter J.; Horgan, Meghan C.; Donnelly, Jeffrey P.; Reibenspies, Joseph H.

2016-04-01

Detrital sediment in Florida's (USA) submerged cave systems may preserve records of regional climate and hydrologic variability. However, the basic sedimentology, mineralogy, stratigraphic variability, and emplacement history of the successions in Florida's submerged caves remains poorly understood. Here we present stratigraphic, mineralogical, and elemental data on sediment cores from two phreatic cave systems in northwestern Florida (USA), on the Dougherty Karst Plain: Hole in the Wall Cave (HITW) and Twin Cave. Water flowing through these caves is subsurface flow in the Apalachicola River drainage basin, and the caves are located just downstream from Jackson Blue (1st magnitude spring, > 2.8 m3 s- 1 discharge). Sedimentation in these caves is dominated by three primary sedimentary styles: (i) ferromanganese deposits dominate the basal recovered stratigraphy, which pass upsection into (ii) poorly sorted carbonate sediment, and finally into (iii) fine-grained organic matter (gyttja) deposits. Resolving the emplacement history of the lower stratigraphic units was hampered by a lack of suitable material for radiocarbon dating, but the upper organic-rich deposits have a punctuated depositional history beginning in the earliest Holocene. For example, gyttja primarily accumulated in HITW and Twin Caves from ~ 5500 to 3500 cal yr. BP, which coincides with regional evidence for water-table rise of the Upper Floridian Aquifer associated with relative sea-level rise in the Gulf of Mexico, and evidence for invigorated drainage through the Apalachicola River drainage basin. Gyttja sediments were also deposited in one of the caves during the Bølling/Allerød climate oscillation. Biologically, these results indicate that some Floridian aquatic cave (stygobitic) ecosystems presently receive minimal organic matter supply in comparison to prehistoric intervals. The pre-Holocene poorly sorted carbonate sediment contains abundant invertebrate fossils, and likely documents a period of enhanced limestone dissolution and cave formation (speleogenesis) during lower paleo water levels. Further work is still required to (a) determine whether precipitation of the ferromanganese deposits is inorganically or biologically mediated, (b) temporally constrain the emplacement history of the primary sedimentary styles, and (c) determine the full geographic extent of these sedimentary signals. However, these preliminary observations suggest that sedimentation in the inland underwater caves of northwestern Florida is related to Quaternary-scale hydrographic variability in the Apalachicola River drainage basin in response to broader ocean and atmospheric forcing.

Hydraulics of Reka-Timavo system, Classical Karst (Carso), Slovenia-Italy

NASA Astrophysics Data System (ADS)

Gabrovsek, Franci; Kaufmann, Georg; Peric, Borut

2016-04-01

In tectonically active areas, karst systems continuously adapt to the relatively rapid changes of the structural and boundary conditions. The flow pathways in such systems are characterised by high variability of channel cross-sections and breakdowns, which restrict the flow and cause high fluctuations of groundwater level, particularly if the recharge variations are high. One of the world's most prominent karst systems with such characteristics is the Kras/Carso plateau (Classical Karst), which extends between SW Slovenia and NE Italy. The ground water dynamics is mainly influenced by the allogenic input of Reka river which sinks at the Škocjanske jame (Škocjan caves) and emerges about 40 km north-west at the coast of Adria near Duino in springs of Timavo. The ratio between highest and lowest flow of Reka reaches 1700 with the maximum measured discharge 305 m3/s, and minimum 0.18 m3/s. This work is based on the long-term continuous monitoring of basic physical parameters of underground flow within six active caves of the Reka-Timavo system. Using stage, temperature and specific electric conductivity hydrographs, following questions were addressed: How do different signals (flood pulse, temperature, SEP) propagate through the system? How does the known geometry relate to the recorded hydrographs in caves? Can we infer on the structure of unknown parts of the system from the recorded hydrographs ? Where are the restrictions causing floods in different parts of the system? The data analysis includes heuristic and statistical analysis of the hydrographs and optimisation based hydraulic modelling. The response to recharge events is vigorous; high flow variability causes extreme stage variations along the whole observed system, with more than 100 m difference between the base and highest water levels at rising and recession rates reaching almost 10 m/h. By analysing large recharge events, we show that high floods in the two most upstream caves (Škocjanske jame and Kačna jama) are controlled by the same restriction downwards from the second one (Kačna jama). We furthermore relate stage observation in Kačna jama to its known geometry and relate stage and temperature signal in the lower part of the system to storage in the mostly unknown overflow galleries between the Kačna jama and the cave that follows it (Jama 1 v Kanjaducah). Temperature and conductivity data were used to calculate transit times between different points of the system at various hydrological conditions. Finally, we parametrise the system and apply the US EPA SWMM model to simulate the response to recorded flood events. The best fit was achieved by addition of overflow channels in the lower part of the system.

Semi-Supervised Multi-View Learning for Gene Network Reconstruction

PubMed Central

Ceci, Michelangelo; Pio, Gianvito; Kuzmanovski, Vladimir; Džeroski, Sašo

2015-01-01

The task of gene regulatory network reconstruction from high-throughput data is receiving increasing attention in recent years. As a consequence, many inference methods for solving this task have been proposed in the literature. It has been recently observed, however, that no single inference method performs optimally across all datasets. It has also been shown that the integration of predictions from multiple inference methods is more robust and shows high performance across diverse datasets. Inspired by this research, in this paper, we propose a machine learning solution which learns to combine predictions from multiple inference methods. While this approach adds additional complexity to the inference process, we expect it would also carry substantial benefits. These would come from the automatic adaptation to patterns on the outputs of individual inference methods, so that it is possible to identify regulatory interactions more reliably when these patterns occur. This article demonstrates the benefits (in terms of accuracy of the reconstructed networks) of the proposed method, which exploits an iterative, semi-supervised ensemble-based algorithm. The algorithm learns to combine the interactions predicted by many different inference methods in the multi-view learning setting. The empirical evaluation of the proposed algorithm on a prokaryotic model organism (E. coli) and on a eukaryotic model organism (S. cerevisiae) clearly shows improved performance over the state of the art methods. The results indicate that gene regulatory network reconstruction for the real datasets is more difficult for S. cerevisiae than for E. coli. The software, all the datasets used in the experiments and all the results are available for download at the following link: http://figshare.com/articles/Semi_supervised_Multi_View_Learning_for_Gene_Network_Reconstruction/1604827. PMID:26641091

Entropy-Based Search Algorithm for Experimental Design

NASA Astrophysics Data System (ADS)

Malakar, N. K.; Knuth, K. H.

2011-03-01

The scientific method relies on the iterated processes of inference and inquiry. The inference phase consists of selecting the most probable models based on the available data; whereas the inquiry phase consists of using what is known about the models to select the most relevant experiment. Optimizing inquiry involves searching the parameterized space of experiments to select the experiment that promises, on average, to be maximally informative. In the case where it is important to learn about each of the model parameters, the relevance of an experiment is quantified by Shannon entropy of the distribution of experimental outcomes predicted by a probable set of models. If the set of potential experiments is described by many parameters, we must search this high-dimensional entropy space. Brute force search methods will be slow and computationally expensive. We present an entropy-based search algorithm, called nested entropy sampling, to select the most informative experiment for efficient experimental design. This algorithm is inspired by Skilling's nested sampling algorithm used in inference and borrows the concept of a rising threshold while a set of experiment samples are maintained. We demonstrate that this algorithm not only selects highly relevant experiments, but also is more efficient than brute force search. Such entropic search techniques promise to greatly benefit autonomous experimental design.

MULTINEST: an efficient and robust Bayesian inference tool for cosmology and particle physics

NASA Astrophysics Data System (ADS)

Feroz, F.; Hobson, M. P.; Bridges, M.

2009-10-01

We present further development and the first public release of our multimodal nested sampling algorithm, called MULTINEST. This Bayesian inference tool calculates the evidence, with an associated error estimate, and produces posterior samples from distributions that may contain multiple modes and pronounced (curving) degeneracies in high dimensions. The developments presented here lead to further substantial improvements in sampling efficiency and robustness, as compared to the original algorithm presented in Feroz & Hobson, which itself significantly outperformed existing Markov chain Monte Carlo techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MULTINEST algorithm are demonstrated by application to two toy problems and to a cosmological inference problem focusing on the extension of the vanilla Λ cold dark matter model to include spatial curvature and a varying equation of state for dark energy. The MULTINEST software, which is fully parallelized using MPI and includes an interface to COSMOMC, is available at http://www.mrao.cam.ac.uk/software/multinest/. It will also be released as part of the SUPERBAYES package, for the analysis of supersymmetric theories of particle physics, at http://www.superbayes.org.

Identifying Source Mixing and Examining Water Chemistry Variations: The Carroll Cave - Toronto Springs System

USDA-ARS?s Scientific Manuscript database

Located in the Missouri Ozarks, Carroll Cave is a dendritic stream cave system, formed in Ordivician Gasconade dolomite. In 2002, a new survey effort was launched under the auspices of the Carroll Cave Conservancy to provide a comprehensive map of the system. Since that time, 29.89 km of estimated p...

A review of factors affecting cave climates for hibernating bats in temperate North America

Treesearch

Roger W. Perry

2013-01-01

The fungal pathogen Geomyces destructans, which causes white-nose syndrome in bats, thrives in the cold and moist conditions found in caves where bats hibernate. To aid managers and researchers address this disease, an updated and accessible review of cave hibernacula and cave microclimates is presented. To maximize energy savings and reduce...

76 FR 1629 - Public Land Order No. 7757; Withdrawal of National Forest System Land for the Big Ice Cave; Montana

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-11

... United States Forest Service to protect the Big Ice Cave, its subterranean water supply, and Federal... to protect the Big Ice Cave, its subterranean water supply, and Federal improvements. The Big Ice... protect the Big Ice Cave, its subterranean water supply, and Federal improvements: Custer National Forest...

Application and research of block caving in Pulang copper mine

NASA Astrophysics Data System (ADS)

Ge, Qifa; Fan, Wenlu; Zhu, Weigen; Chen, Xiaowei

2018-01-01

The application of block caving in mines shows significant advantages in large scale, low cost and high efficiency, thus block caving is worth promoting in the mines that meets the requirement of natural caving. Due to large scale of production and low ore grade in Pulang copper mine in China, comprehensive analysis and research were conducted on rock mechanics, mining sequence, undercutting and stability of bottom structure in terms of raising mine benefit and maximizing the recovery mineral resources. Finally this study summarizes that block caving is completely suitable for Pulang copper mine.

Microbiological and environmental issues in show caves.

PubMed

Saiz-Jimenez, Cesareo

2012-07-01

Cultural tourism expanded in the last half of the twentieth century, and the interest of visitors has come to include caves containing archaeological remains. Some show caves attracted mass tourism, and economical interests prevailed over conservation, which led to a deterioration of the subterranean environment and the rock art. The presence and the role of microorganisms in caves is a topic that is often ignored in cave management. Knowledge of the colonisation patterns, the dispersion mechanisms, and the effect on human health and, when present, over rock art paintings of these microorganisms is of the utmost importance. In this review the most recent advances in the study of microorganisms in caves are presented, together with the environmental implications of the findings.

Transcriptional network inference from functional similarity and expression data: a global supervised approach.

PubMed

Ambroise, Jérôme; Robert, Annie; Macq, Benoit; Gala, Jean-Luc

2012-01-06

An important challenge in system biology is the inference of biological networks from postgenomic data. Among these biological networks, a gene transcriptional regulatory network focuses on interactions existing between transcription factors (TFs) and and their corresponding target genes. A large number of reverse engineering algorithms were proposed to infer such networks from gene expression profiles, but most current methods have relatively low predictive performances. In this paper, we introduce the novel TNIFSED method (Transcriptional Network Inference from Functional Similarity and Expression Data), that infers a transcriptional network from the integration of correlations and partial correlations of gene expression profiles and gene functional similarities through a supervised classifier. In the current work, TNIFSED was applied to predict the transcriptional network in Escherichia coli and in Saccharomyces cerevisiae, using datasets of 445 and 170 affymetrix arrays, respectively. Using the area under the curve of the receiver operating characteristics and the F-measure as indicators, we showed the predictive performance of TNIFSED to be better than unsupervised state-of-the-art methods. TNIFSED performed slightly worse than the supervised SIRENE algorithm for the target genes identification of the TF having a wide range of yet identified target genes but better for TF having only few identified target genes. Our results indicate that TNIFSED is complementary to the SIRENE algorithm, and particularly suitable to discover target genes of "orphan" TFs.

On the palaeobiology of the extinct cave bear Ursus spelaeus ROSENMÜLLER. Insights from stable isotope analysis

NASA Astrophysics Data System (ADS)

Grandal-D'Anglade, Aurora; Pérez-Rama, Marta; Fernández-Mosquera, Daniel

2010-05-01

Isotopic signatures (δ13C, δ15N) of bone collagen are used more and more to obtain the paleobiological data of fossil species. By means of these signatures, for example, the diet type of an extint species may be inferred. Also, the climate in which this species developed may greatly influence on the isotopic signature of its bone collagen. This influence is firstly produced in the initial material of the trophic chain but also may produce variations due to physiological changes caused by climatic changes in the species involved in this trophic chain. The cave bear (Ursus spelaeus ROSENMÜLLER) is a species of broad distribution in the European Pleistocene sites that has been studied from the isotopic point of view, trying to establish its diet type. For the moment, the results vary: though in most cases the isotopic values indicate a preferably herbivore diet type, differences exist between sites of different geographic zones and chronologies. Taking into account that climate influences on the cave bear's physiology through the physiological mechanism of hibernation, it is expected that in bears that lived in different climatic phases, the isotopic signatures will be also different. During hibernation a recycling of nitrogenised compounds is produced for protein synthesis, including bone collagen, so it is expected that the isotopic signature, at least of Nitrogen, will be altered with respect to the synthesized collagen when the bear is active and feeds normally. However, it is difficult to establish up to what extent the isotopic signatures due to hibernation or diet are overlapped. To study the physiological effect of hibernation on isotopic signatures we have selected bone remains of cave bears from populations whose chronologies correspond to different climatic moments, and in different ontogenetic stages, coming from Galician caves (NW of the Iberian Peninsula). Adult individuals show different isotopic signatures depending on their chronology. Juvenile individuals show differences originated by the effect of a greater or less contribution of maternal milk in their diets. Finally, the neonate individuals or still in foetal stage show isotopic values that directly reflect their mother's physiology in the hibernation, during which foetal development is produced. Interestingly, all the individuals of this age class present similar isotopic values in spite of belonging to populations with different values in the adults. This indicates, on one hand, that there exists a physiological effect on the isotopic signals produced by hibernation, effect that is similar in all the studied populations, and on the other, that this physiological effect of hibernation only appears in adult individuals of populations corresponding to cold moments, in which the hibernation period is longer. According to the results, we suggest the use of isotopic values of adult cave bears as climatic proxy for European Pleistocene sites. This work is part of the Ph.D. Thesis of M.P.R. and is a contribution to the research project BTE-CGL-2006-08996 of the Education and Science Ministry of Spain.

Knowledge requirements for automated inference of medical textbook markup.

PubMed Central

Berrios, D. C.; Kehler, A.; Fagan, L. M.

1999-01-01

Indexing medical text in journals or textbooks requires a tremendous amount of resources. We tested two algorithms for automatically indexing nouns, noun-modifiers, and noun phrases, and inferring selected binary relations between UMLS concepts in a textbook of infectious disease. Sixty-six percent of nouns and noun-modifiers and 81% of noun phrases were correctly matched to UMLS concepts. Semantic relations were identified with 100% specificity and 94% sensitivity. For some medical sub-domains, these algorithms could permit expeditious generation of more complex indexing. PMID:10566445

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

PubMed

Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

2017-03-15

Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone

PubMed Central

Gerhard, Felipe; Kispersky, Tilman; Gutierrez, Gabrielle J.; Marder, Eve; Kramer, Mark; Eden, Uri

2013-01-01

Identifying the structure and dynamics of synaptic interactions between neurons is the first step to understanding neural network dynamics. The presence of synaptic connections is traditionally inferred through the use of targeted stimulation and paired recordings or by post-hoc histology. More recently, causal network inference algorithms have been proposed to deduce connectivity directly from electrophysiological signals, such as extracellularly recorded spiking activity. Usually, these algorithms have not been validated on a neurophysiological data set for which the actual circuitry is known. Recent work has shown that traditional network inference algorithms based on linear models typically fail to identify the correct coupling of a small central pattern generating circuit in the stomatogastric ganglion of the crab Cancer borealis. In this work, we show that point process models of observed spike trains can guide inference of relative connectivity estimates that match the known physiological connectivity of the central pattern generator up to a choice of threshold. We elucidate the necessary steps to derive faithful connectivity estimates from a model that incorporates the spike train nature of the data. We then apply the model to measure changes in the effective connectivity pattern in response to two pharmacological interventions, which affect both intrinsic neural dynamics and synaptic transmission. Our results provide the first successful application of a network inference algorithm to a circuit for which the actual physiological synapses between neurons are known. The point process methodology presented here generalizes well to larger networks and can describe the statistics of neural populations. In general we show that advanced statistical models allow for the characterization of effective network structure, deciphering underlying network dynamics and estimating information-processing capabilities. PMID:23874181

The evolution of cave systems from the surface to subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loucks, R.G.; Handford, C.R.

1996-01-01

Many carbonate reservoirs are the result of cave-forming processes. The origin and recognition of fractures, breccias, and sediment fills associated with paleocaves were determined through the study of modern and paleocaves systems. Cave formation and destruction are the products of near-surface processes. Near-surface processes include solutional excavation, clastic and chemical sedimentation, and collapse of cave walls and ceilings. Cave sediment is derived from inside and/or outside the system. Depositional mechanisms include suspension, tractional, mass-flow and rock-fall. Collapse of ceilings and walls from chaotic breakdown breccias. These piles can be tens of meters thick and contain large voids and variable amountsmore » of matrix. Cave-roof crackle breccia forms from stress-and tension-related fractures in cave-roof strata. As the cave-bearing strata subside into the subsurface, mechanical compaction increases and restructures the existing breccias and remaining cavities. Fracture porosity increases and breccia and vug porosity decreases. Large cavities collapse forming burial chaotic breakdown breccias. Differentially compacted strata over the collapsed chamber fracture and form burial cave-roof crackle breccias. Continued burial leads to more extensive mechanical compaction causing previously formed clasts to fracture and pack closer together. The resulting product is a rebrecciated chaotic breakdown breccia composed predominantly of small clasts. Rebrecciated blocks are often overprinted by crackling. Subsurface paleocave systems commonly have a complex history with several episodes of fracturing and brecciation. The resulting collapsed-paleocave reservoir targets are not single collapsed passages of tens of feet across, but are homogenized collapsed-cave systems hundreds to several thousand feet across.« less

The evolution of cave systems from the surface to subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loucks, R.G.; Handford, C.R.

1996-12-31

Many carbonate reservoirs are the result of cave-forming processes. The origin and recognition of fractures, breccias, and sediment fills associated with paleocaves were determined through the study of modern and paleocaves systems. Cave formation and destruction are the products of near-surface processes. Near-surface processes include solutional excavation, clastic and chemical sedimentation, and collapse of cave walls and ceilings. Cave sediment is derived from inside and/or outside the system. Depositional mechanisms include suspension, tractional, mass-flow and rock-fall. Collapse of ceilings and walls from chaotic breakdown breccias. These piles can be tens of meters thick and contain large voids and variable amountsmore » of matrix. Cave-roof crackle breccia forms from stress-and tension-related fractures in cave-roof strata. As the cave-bearing strata subside into the subsurface, mechanical compaction increases and restructures the existing breccias and remaining cavities. Fracture porosity increases and breccia and vug porosity decreases. Large cavities collapse forming burial chaotic breakdown breccias. Differentially compacted strata over the collapsed chamber fracture and form burial cave-roof crackle breccias. Continued burial leads to more extensive mechanical compaction causing previously formed clasts to fracture and pack closer together. The resulting product is a rebrecciated chaotic breakdown breccia composed predominantly of small clasts. Rebrecciated blocks are often overprinted by crackling. Subsurface paleocave systems commonly have a complex history with several episodes of fracturing and brecciation. The resulting collapsed-paleocave reservoir targets are not single collapsed passages of tens of feet across, but are homogenized collapsed-cave systems hundreds to several thousand feet across.« less

Does the Cave Environment Reduce Functional Diversity?

PubMed Central

Fernandes, Camile Sorbo; Batalha, Marco Antonio; Bichuette, Maria Elina

2016-01-01

Caves are not colonised by all taxa present in the surface species pool, due to absence of light and the tendency to food limitation when compared to surface communities. Under strong species sorting during colonisation and later by the restrictive environmental filter, traits that are not adaptive in subterranean habitats may be filtered out. We tested whether cave communities were assembled by the restrictive regime propitiated by permanent darkness or by competitive exclusion due to resource scarcity. When compared to surface communities, the restrictive subterranean regime would lead to lower functional diversity and phenotypic clustering inside the caves, and the opposite should be expected in the case of competitive exclusion. Using isopods (Oniscidea) as model taxa, we measured several niche descriptors of taxa from surface and cave habitats, used a multivariate measure of functional diversity, and compared their widths. We found phenotypic overdispersion and higher functional diversity in cave taxa when compared to surface taxa. On the one hand, the dry climate outside of caves hampered the survival of several taxa and their ecological strategies, not viable under severe desiccation risk, culminating in the clustering of functional traits. In contrast, this restriction does not occur inside of caves, where isopods find favourable conditions under lower predation pressures and more amenable environmental parameters that allow occupation and subsequent diversification. Our results showed that, at least for some taxa, caves may not be such a harsh environment as previously thought. The high functional diversity we found inside caves adds an additional reason for the conservation of these sensitive environments. PMID:27003837

Pisgah Lava Cave Communication Test: Science Case Study for the Networked Constellations Initiative

NASA Technical Reports Server (NTRS)

Belov, K.; Ellison, D.; Fraeman, A.

2017-01-01

As part of the science case study for the Networked Constellations initiative, a team of JPL scientists explore the possibility of a mission to study the lava caves on Mars. Natural caves on Mars and the Moon present a unique opportunity to learn about the planetary geology and to provide a shelter for human explorers. Due to power and communication challenges, a network of assets has significant advantages over a single asset sent inside a cave. However, communication between the assets and the data downlink present significant difficulties due to the presence of rough walls, boulders, and other obstacles with unknown dielectric constant inside a typical cave, disturbing the propagation of the radio waves. A detailed study is needed to establish the limitations of the current communication technologies and to develop requirements for the new communication technology applicable to the cave environment. On May 4 of 2017, Konstantin Belov, Doug Ellison, and Abby Fraeman visited a lava cave in Pisgah, CA. The purpose of the visit was to build a 3D map of the cave, which could be used to create a model of radio wave propagation, and to conduct a series of communication tests using off-the-shelf equipment to verify the in-cave communication challenges. This experiment should be considered as a simple 'proof of concept' and is the subject of this report.

From Cave Walls to Clay Images

ERIC Educational Resources Information Center

Stone, Julie

2004-01-01

About 15,000 BC, the bison and other animals roamed the land and cave people, in their spare time, found colorful, chalky rocks with which to play. Over the course of time, they found that the chalky rocks would rub off on the cave walls, thus cave paintings and the pursuit of art was born. This article describes one fourth-grade classroom's…

Summit firn caves, mount rainier, washington.

PubMed

Kiver, E P; Mumma, M D

1971-07-23

Heat and steam from the crater fumaroles have melted over 5700 feet (1737 meters) of cave passage in the ice-filled east crater of Mount Rainier. The caves are in approximate balance with the present geothermal heat release. Future changes in the thermal activity of the summit cone will cause corresponding changes in cave passage dimensions, location, and ceiling and wall ablation features.

A high-precision chronological model for the decorated Upper Paleolithic cave of Chauvet-Pont d'Arc, Ardèche, France.

PubMed

Quiles, Anita; Valladas, Hélène; Bocherens, Hervé; Delqué-Količ, Emmanuelle; Kaltnecker, Evelyne; van der Plicht, Johannes; Delannoy, Jean-Jacques; Feruglio, Valérie; Fritz, Carole; Monney, Julien; Philippe, Michel; Tosello, Gilles; Clottes, Jean; Geneste, Jean-Michel

2016-04-26

Radiocarbon dates for the ancient drawings in the Chauvet-Pont d'Arc Cave revealed ages much older than expected. These early ages and nature of this Paleolithic art make this United Nations Educational, Scientific and Cultural Organization (UNESCO) site indisputably unique. A large, multidisciplinary dating program has recently mapped the anthropological evolution associated with the cave. More than 350 dates (by (14)C, U-Th, TL and (36)Cl) were obtained over the last 15 y. They include 259 radiocarbon dates, mainly related to the rock art and human activity in the cave. We present here more than 80 previously unpublished dates. All of the dates were integrated into a high-precision Bayesian model based on archaeological evidence to securely reconstruct the complete history of the Chauvet-Pont d'Arc Cave on an absolute timescale. It shows that there were two distinct periods of human activity in the cave, one from 37 to 33,500 y ago, and the other from 31 to 28,000 y ago. Cave bears also took refuge in the cave until 33,000 y ago.

A high-precision chronological model for the decorated Upper Paleolithic cave of Chauvet-Pont d’Arc, Ardèche, France

PubMed Central

Quiles, Anita; Valladas, Hélène; Bocherens, Hervé; Delqué-Količ, Emmanuelle; Kaltnecker, Evelyne; van der Plicht, Johannes; Delannoy, Jean-Jacques; Feruglio, Valérie; Fritz, Carole; Monney, Julien; Philippe, Michel; Tosello, Gilles; Clottes, Jean; Geneste, Jean-Michel

2016-01-01

Radiocarbon dates for the ancient drawings in the Chauvet-Pont d’Arc Cave revealed ages much older than expected. These early ages and nature of this Paleolithic art make this United Nations Educational, Scientific and Cultural Organization (UNESCO) site indisputably unique. A large, multidisciplinary dating program has recently mapped the anthropological evolution associated with the cave. More than 350 dates (by 14C, U-Th, TL and 36Cl) were obtained over the last 15 y. They include 259 radiocarbon dates, mainly related to the rock art and human activity in the cave. We present here more than 80 previously unpublished dates. All of the dates were integrated into a high-precision Bayesian model based on archaeological evidence to securely reconstruct the complete history of the Chauvet-Pont d’Arc Cave on an absolute timescale. It shows that there were two distinct periods of human activity in the cave, one from 37 to 33,500 y ago, and the other from 31 to 28,000 y ago. Cave bears also took refuge in the cave until 33,000 y ago. PMID:27071106

Vision-mediated interaction with the Nottingham caves

NASA Astrophysics Data System (ADS)

Ghali, Ahmed; Bayomi, Sahar; Green, Jonathan; Pridmore, Tony; Benford, Steve

2003-05-01

The English city of Nottingham is widely known for its rich history and compelling folklore. A key attraction is the extensive system of caves to be found beneath Nottingham Castle. Regular guided tours are made of the Nottingham caves, during which castle staff tell stories and explain historical events to small groups of visitors while pointing out relevant cave locations and features. The work reported here is part of a project aimed at enhancing the experience of cave visitors, and providing flexible storytelling tools to their guides, by developing machine vision systems capable of identifying specific actions of guides and/or visitors and triggering audio and/or video presentations as a result. Attention is currently focused on triggering audio material by directing the beam of a standard domestic flashlight towards features of interest on the cave wall. Cameras attached to the walls or roof provide image sequences within which torch light and cave features are detected and their relative positions estimated. When a target feature is illuminated the corresponding audio response is generated. We describe the architecture of the system, its implementation within the caves and the results of initial evaluations carried out with castle guides and members of the public.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

PubMed

Helaers, Raphaël; Milinkovitch, Michel C

2010-07-15

The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

PubMed Central

2010-01-01

Background The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Results Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. Conclusions The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org. PMID:20633263

Spatiotemporal analysis of air conditions as a tool for the environmental management of a show cave (Cueva del Agua, Spain)

NASA Astrophysics Data System (ADS)

Fernandez-Cortes, A.; Calaforra, J. M.; Sanchez-Martos, F.

We recorded the air temperature and carbon dioxide concentration within the Cueva del Agua, a cave in Spain, under natural conditions prior to the cave being opened to tourists. Geostatistical tools are useful techniques for characterizing microclimate parameters with the aim of adopting measures to ensure the conservation and sound environmental management of tourist caves. We modelled the spatial distribution of these microclimatic parameters over an annual cycle using iterative residual kriging, revealing the stratification of air related to the cave's topography. Replenishment of the cave air is activated by convective circulation that accompanies the development of inversions in the thermal gradient of the air. Comparison of the spatial distribution of each microclimatic parameter over time enables us to characterize the exchange of air between the cave interior and the outside, as well as identify potential areas that could be opened to tourists and determine suitable visiting schedules.

Collapse of caves at shallow depth in Gaziantep city center, Turkey: a case study

NASA Astrophysics Data System (ADS)

Canakci, Hanifi

2007-12-01

This paper focuses on an investigation of the possible causes for the collapse of limestone caves in Gaziantep, Turkey. The city contains a lot of man-made caves, at a shallow depth, of various width and length. These caves were mainly excavated to provide work or storage space. As the city has been growing fast with increased population, many structures were constructed over these caves. Recently, two caves collapsed and five houses were damaged. These caves are all made of limestone and it was observed after the collapse that the limestone was saturated with water due to sewer pipe leakage and surface water. Tests were carried out on the limestone and it was determined that the compressive strength of limestone decreases by about 50% and the tensile strength decreased by about 80% when saturated with water. It was concluded that the reduced strength of the limestone combined with additional loads due to the factors mentioned above seem to be the main reason for these collapses.

Isotopic evidence for omnivory among European cave bears: Late Pleistocene Ursus spelaeus from the Peştera cu Oase, Romania

PubMed Central

Richards, Michael P.; Pacher, Martina; Stiller, Mathias; Quilès, Jérôme; Hofreiter, Michael; Constantin, Silviu; Zilhão, João; Trinkaus, Erik

2008-01-01

Previous bone collagen carbon and nitrogen isotopic studies of Late Pleistocene European cave bears (Ursus spelaeus) have shown that these bears frequently had low nitrogen isotope values, similar to those of herbivores and indicating either unusual physiology related to hibernation or a herbivorous diet. Isotopic analysis of animal bone from the Peştera cu Oase (Cave with Bones), Romania, shows that most of its cave bears had higher nitrogen isotope values than the associated herbivores and were, therefore, omnivorous. The Oase bears are securely identified as cave bears by both their morphology and DNA sequences. Although many cave bear populations may have behaved like herbivores, the Oase isotopic data demonstrate that cave bears were capable of altering their diets to become omnivores or even carnivores. These data therefore broaden the dietary profile of U. spelaeus and raise questions about the nature of the carnivore guild in Pleistocene Europe. PMID:18187577

Tamarugite in the Steam-Condensate Alteration Paragenesis in Diana Cave (SW Romania)

NASA Astrophysics Data System (ADS)

Puscas, C. M.; Onac, B. P.; Effenberger, H. S.; Povară, I.

2012-12-01

The double-salt hydrate tamarugite [NaAl(SO4)2 6H2O] is an uncommon mineral in the cave environment, forming as a result of chemical reactions between water and bedrock only under very specific conditions. The Diana Cave hosts a unique tamarugite occurrence, the first one to be reported from a typical karst environment. The cave is located within the limits of Băile Herculane township in the Cerna Mountains, SW Romania. It consists of a 14 m long, westward-oriented single passage, developed along the Diana Fault. In 1974 a concrete-clad mine gallery was created to channel the thermal water (Diana 1+2 Spring) flowing through the cave to a pumping station. The spring's chemical and physical parameters fluctuated through time, averaging 51.98° C, discharge of 0.96 Ls-1, pH of 7.46, 5768.66 ppm TDS, 9303 μScm-1 conductivity, 5.02 salinity. The major chemical components of the thermo-mineral water in Diana Cave are, Na+ (1392.57 ppm), K+ (58.55 ppm), Ca2+ (725.16 ppm), Mg2+ (10.78 ppm), Cl- (3376.83 ppm), and SO42- (92.27 ppm), and H2S (24.05 ppm), with traces of Si, Fe2+, Br+, I-, and Li+. The general air circulation pattern within the cave is fairly simple: cold air from the outside sweeps into the cave along the floor, heats up at the contact with the thermo-mineral water, ascends, and exists the cave along the ceiling. At the contact with the cold walls of the Diana Cave, the hot steam condenses and gives rise to a rich and exotic sulfate-mineral paragenesis (including halotrichite-series minerals, gypsum, bassanite, anhydrite, epsomite, alunite, halite, native sulfur, etc.). The most exotic minerals precipitate at or below the contact between the Tithonic - Neocomian limestone and the overlaying Cretaceous shaly limestone, as a result of steam-condensate alteration. Minerogenetic mechanisms responsible for the peculiar sulfate mineral assemblage in Diana Cave are evaporation, oxidation, hydrolysis, double exchange reactions, and deposition from vapours or possibly aerosols. This highly aggressive alteration of the carbonate rock (known as sulfuric acid speleogenesis) extends from the ceiling of the cave downward to, or slightly below, the water table and is responsible for further enlargement of cave passages. Given the availability of SO42-, gypsum replacement crusts form in the subaerial part of the cave, as well as thin gypsum rafts at the water surface. The presence of tamarugite indicates sufficiently strong acid conditions in the steam-condensate film to dissolve clay minerals, releasing Na+ and Al3+ into the geochemical system. Conditions conducive to tamarugite precipitation in carbonate caves seem to be the presence of: 1) thermo-mineral water, which through surface evaporation and condensation on the cold cave walls causes steam-condensate alteration processes, 2) sulfuric acid, and 3) a constant source of Al3+ and Na+. Such conditions are seldom fulfilled in any ordinary limestone caves. The bedrock geology and the particular tectonics and hydrogeology of the Băile Herculane area seem to be the essential prerequisites, not only for the development of hypogene karst, but also for producing an outstanding cave mineral assemblage.

Theory of mind broad and narrow: reasoning about social exchange engages ToM areas, precautionary reasoning does not.

PubMed

Ermer, Elsa; Guerin, Scott A; Cosmides, Leda; Tooby, John; Miller, Michael B

2006-01-01

Baron-Cohen (1995) proposed that the theory of mind (ToM) inference system evolved to promote strategic social interaction. Social exchange--a form of co-operation for mutual benefit--involves strategic social interaction and requires ToM inferences about the contents of other individuals' mental states, especially their desires, goals, and intentions. There are behavioral and neuropsychological dissociations between reasoning about social exchange and reasoning about equivalent problems tapping other, more general content domains. It has therefore been proposed that social exchange behavior is regulated by social contract algorithms: a domain-specific inference system that is functionally specialized for reasoning about social exchange. We report an fMRI study using the Wason selection task that provides further support for this hypothesis. Precautionary rules share so many properties with social exchange rules--they are conditional, deontic, and involve subjective utilities--that most reasoning theories claim they are processed by the same neurocomputational machinery. Nevertheless, neuroimaging shows that reasoning about social exchange activates brain areas not activated by reasoning about precautionary rules, and vice versa. As predicted, neural correlates of ToM (anterior and posterior temporal cortex) were activated when subjects interpreted social exchange rules, but not precautionary rules (where ToM inferences are unnecessary). We argue that the interaction between ToM and social contract algorithms can be reciprocal: social contract algorithms requires ToM inferences, but their functional logic also allows ToM inferences to be made. By considering interactions between ToM in the narrower sense (belief-desire reasoning) and all the social inference systems that create the logic of human social interaction--ones that enable as well as use inferences about the content of mental states--a broader conception of ToM may emerge: a computational model embodying a Theory of Human Nature (ToHN).

Edge-directed inference for microaneurysms detection in digital fundus images

NASA Astrophysics Data System (ADS)

Huang, Ke; Yan, Michelle; Aviyente, Selin

2007-03-01

Microaneurysms (MAs) detection is a critical step in diabetic retinopathy screening, since MAs are the earliest visible warning of potential future problems. A variety of algorithms have been proposed for MAs detection in mass screening. Different methods have been proposed for MAs detection. The core technology for most of existing methods is based on a directional mathematical morphological operation called "Top-Hat" filter that requires multiple filtering operations at each pixel. Background structure, uneven illumination and noise often cause confusion between MAs and some non-MA structures and limits the applicability of the filter. In this paper, a novel detection framework based on edge directed inference is proposed for MAs detection. The candidate MA regions are first delineated from the edge map of a fundus image. Features measuring shape, brightness and contrast are extracted for each candidate MA region to better exclude false detection from true MAs. Algorithmic analysis and empirical evaluation reveal that the proposed edge directed inference outperforms the "Top-Hat" based algorithm in both detection accuracy and computational speed.

An experimental phylogeny to benchmark ancestral sequence reconstruction

PubMed Central

Randall, Ryan N.; Radford, Caelan E.; Roof, Kelsey A.; Natarajan, Divya K.; Gaucher, Eric A.

2016-01-01

Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as ‘modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

Evolution of arched roofs in salt caves: Role of gravity-induced stress and relative air humidity and temperature changes (Zagros Mts., Iran)

NASA Astrophysics Data System (ADS)

Bruthans, Jiri; Filippi, Michal; Zare, Mohammad

2016-04-01

In salt caves in the halite karst in SE Iran the disintegration of rock salt into individual grains can be observed. Highly disintegrated blocks and individual grains form a major volume of debris in many caves on islands in the Persian Gulf. Larger cave rooms have often perfectly arched roof. The perfect geometry of rooms and interlocking of salt grains indicate that evolution of room cross-sections in these caves is controlled by feedback between gravity-induced stress and rock salt disintegration in similar way as in evolution of sandstone landforms (Bruthans et al. 2014). Those portions of rock salt, which are under compressional stress, disintegrate much slower than portions under tensile stress. Important question is the kind of weathering mechanism responsible for intergranular disintegration of rock salt. The relationship between disintegration, its rate and cave climate was studied. Clearly the fastest disintegration rate was found in caves with strong air circulation (i.e, short caves with large cross-sections, open on both ends). Temperature and air humidity changes are considerable in these caves. On the other hand the disintegration is very slow in the inner parts of long caves with slow air circulation or caves with one entrance. The best example of such caves is the inner part of 3N Cave on Namakdan salt diapir with nearly no air circulation and stable temperature and humidity, where disintegration of rock salt into grains is missing. Strong effect of cave climate on disintegration rate can be explained by deliquescence properties of halite. Halite is absorbing air moisture forming NaCl solution if relative humidity (RH) exceeds 75 % (at 20-30 oC). In the Persian Gulf region the RH of the air is passing the 75 % threshold in case of 91% days (Qeshm Island, years 2002-2005), while in mountainous areas in mainland this threshold is less commonly reached. In most of nights (91 %) in Persian Gulf the air with RH >75 % is entering the salt caves and air moisture is wetting the dry rock and slightly diluting the percolating brine in ceiling of the caves, which is otherwise just saturated with respect to halite. During days the RH is <75% and brine partly dries up and precipitates halite. By repeating the cycle of dissolution and precipitation of halite and possibly also by temperature changes the rock salt is disintegrated into interlocked salt grains, whose behavior is then strongly controlled by gravity-induced stress. Research was funded by the Czech Science Foundation (GA CR No. 16-19459S). Reference: Bruthans J, Soukup J., Vaculíková J., Filippi M., Schweigstillova J., Mayo A.L., Masin D., Kletetschka G.,Rihosek J. (2014): Sandstone landforms shaped by negative feedback between stress and erosion. Nature Geoscience 7(8): 597-601.

Light from dark: A relictual troglobite reveals a broader ancestral distribution for kimulid harvestmen (Opiliones: Laniatores: Kimulidae) in South America

PubMed Central

Ceccarelli, F. Sara; Monte, Bruno G. O.; Proud, Daniel N.; DaSilva, Márcio Bernardino; Bichuette, Maria E.

2017-01-01

A new troglobitic harvestman, Relictopiolus galadriel gen. nov et sp. nov., is described from Olhos d’Água cave, Itacarambi, Minas Gerais State, Brazil. Morphological characters, including male genitalia and exomorphology, suggest that this species belongs to the family Kimulidae, and it appears to share the greatest similarities with Tegipiolus pachypus. Bayesian inference analyses of a molecular dataset strongly support the inclusion of this species in Kimulidae and confirm the hypothesized sister-group relationship between R. galadriel and T. pachypus. A time calibrated phylogeny indicates that these sister-taxa diverged from a common ancestor approximately 40 Mya, during the Paleogene. The current range of Kimulidae illustrates a remarkable disjunct distribution, and leads us to hypothesize that the ancestral distribution of Kimulidae was once much more widespread across eastern Brazil. This may be attributed to the Eocene radiation associated with the warming (and humidifying) events in the Cenozoic when the best conditions for evergreen tropical vegetation in South America were established and followed by the extinction of kimulid epigean populations together with the retraction of rain forests during the Oligocene to Miocene cooling. The discovery of this relictual troglobite indicates that the Olhos d’Água cave was a stable refugium for this ancient lineage of kimulids and acted as a "museum" of biodiversity. Our findings, considered collectively with the diverse troglofauna of the Olhos d’Água cave, highlight it as one of the most important hotspots of troglobite diversity and endemism in the Neotropics. Given the ecological stresses on this habitat, the cavernicolous fauna are at risk of extinction and we emphasize the urgent need for appropriate conservation actions. Finally, we propose the transfer of Acanthominua, Euminua, Euminuoides and Pseudominua from Kimulidae to Zalmoxidae, resulting in two new synonymies and 13 new combinations. PMID:29190302

Light from dark: A relictual troglobite reveals a broader ancestral distribution for kimulid harvestmen (Opiliones: Laniatores: Kimulidae) in South America.

PubMed

Pérez-González, Abel; Ceccarelli, F Sara; Monte, Bruno G O; Proud, Daniel N; DaSilva, Márcio Bernardino; Bichuette, Maria E

2017-01-01

A new troglobitic harvestman, Relictopiolus galadriel gen. nov et sp. nov., is described from Olhos d'Água cave, Itacarambi, Minas Gerais State, Brazil. Morphological characters, including male genitalia and exomorphology, suggest that this species belongs to the family Kimulidae, and it appears to share the greatest similarities with Tegipiolus pachypus. Bayesian inference analyses of a molecular dataset strongly support the inclusion of this species in Kimulidae and confirm the hypothesized sister-group relationship between R. galadriel and T. pachypus. A time calibrated phylogeny indicates that these sister-taxa diverged from a common ancestor approximately 40 Mya, during the Paleogene. The current range of Kimulidae illustrates a remarkable disjunct distribution, and leads us to hypothesize that the ancestral distribution of Kimulidae was once much more widespread across eastern Brazil. This may be attributed to the Eocene radiation associated with the warming (and humidifying) events in the Cenozoic when the best conditions for evergreen tropical vegetation in South America were established and followed by the extinction of kimulid epigean populations together with the retraction of rain forests during the Oligocene to Miocene cooling. The discovery of this relictual troglobite indicates that the Olhos d'Água cave was a stable refugium for this ancient lineage of kimulids and acted as a "museum" of biodiversity. Our findings, considered collectively with the diverse troglofauna of the Olhos d'Água cave, highlight it as one of the most important hotspots of troglobite diversity and endemism in the Neotropics. Given the ecological stresses on this habitat, the cavernicolous fauna are at risk of extinction and we emphasize the urgent need for appropriate conservation actions. Finally, we propose the transfer of Acanthominua, Euminua, Euminuoides and Pseudominua from Kimulidae to Zalmoxidae, resulting in two new synonymies and 13 new combinations.

Climatic variability during the penultimate interglacial (MIS 7) and glacial (MIS 6) periods recorded in a speleothem from Kanaan cave, Lebanon (Central Levant)

NASA Astrophysics Data System (ADS)

Nehme, Carole; Verheyden, Sophie; Breitenbach, Sebastian F. M.; Gillikin, David P.; Verheyden, Anouk; Cheng, Hai; Edwards, Laurence; Hellstrom, John; Noble, Stephen R.; Farrant, Andrew R.; Sahy, Diana; Goovaerts, Thomas; Salem, Ghada; Claeys, Philippe

2017-04-01

Little is known about terrestrial climate dynamics of the Levant during the penultimate interglacial-glacial period. A well-dated stalagmite ( 194 to 154 ka) from Kanaan cave, located near the Mediterranean in Lebanon, is examined for its petrography, growth history, and stable isotope geochemistry to answer the climate instability pattern of the glacial MIS 6 and possible wet phases. A highly resolved continental climate record from the northern Levant has been recovered from this precisely U-Th-dated speleothem, spanning the late penultimate interglacial (equivalent of the MIS 7) to the mid-penultimate glacial period ( MIS 6). The stalagmite grew slowly and discontinuously with an unstable isotopic pattern from 194 and at least up to 178 ka. Subsequently, the stalagmite ceased growing from 169.5 to 163.1 ka (interpolated ages) with a hiatus of ca. 6.24 ka according to the model age. However, low δ 18O and δ 13C values indicate generally cold, but overall more humid climate compared to the last glacial (MIS 3). Higher growth rates during the mid-penultimate glacial period ( 163-154 ka) are most probably linked to increased water recharge in the vadose zone. A short More distinct layering in the upper section compared to the basal part of the stalagmite suggests stronger seasonality from 163 ka to 154 ka. Negative oxygen and carbon isotope excursions were found at ˜155.5 ka, ˜156 ka, between ˜159.6 and ˜160.1 ka and at ˜162.6 ka. The inferred Kanaan cave humid intervals during the mid-penultimate period follow variations of pollen records in the Eastern and Western Mediterranean basins and correlate well with the synthetic Greenland records and East Asian Summer Monsoon Interstadials, indicating short warm/wet periods similar to the D-O events during MIS 4-3 in the Eastern Mediterranean region.

iNJclust: Iterative Neighbor-Joining Tree Clustering Framework for Inferring Population Structure.

PubMed

Limpiti, Tulaya; Amornbunchornvej, Chainarong; Intarapanich, Apichart; Assawamakin, Anunchai; Tongsima, Sissades

2014-01-01

Understanding genetic differences among populations is one of the most important issues in population genetics. Genetic variations, e.g., single nucleotide polymorphisms, are used to characterize commonality and difference of individuals from various populations. This paper presents an efficient graph-based clustering framework which operates iteratively on the Neighbor-Joining (NJ) tree called the iNJclust algorithm. The framework uses well-known genetic measurements, namely the allele-sharing distance, the neighbor-joining tree, and the fixation index. The behavior of the fixation index is utilized in the algorithm's stopping criterion. The algorithm provides an estimated number of populations, individual assignments, and relationships between populations as outputs. The clustering result is reported in the form of a binary tree, whose terminal nodes represent the final inferred populations and the tree structure preserves the genetic relationships among them. The clustering performance and the robustness of the proposed algorithm are tested extensively using simulated and real data sets from bovine, sheep, and human populations. The result indicates that the number of populations within each data set is reasonably estimated, the individual assignment is robust, and the structure of the inferred population tree corresponds to the intrinsic relationships among populations within the data.

Isotopic variability of cave bears (δ15N, δ13C) across Europe during MIS 3

NASA Astrophysics Data System (ADS)

Krajcarz, Magdalena; Pacher, Martina; Krajcarz, Maciej T.; Laughlan, Lana; Rabeder, Gernot; Sabol, Martin; Wojtal, Piotr; Bocherens, Hervé

2016-01-01

Collagen, the organic fraction of bone, records the isotopic parameters of consumed food for carbon (δ13C) and nitrogen (δ15N). This relationship of isotopic signature between diet and tissue is an important tool for the study of dietary preferences of modern and fossil animal species. Since the first information on the isotopic signature of cave bear was reported, numerous data from Europe have become available. The goal of this work is to track the geographical variation of cave bear collagen isotopic values in Europe during Marine Isotopic Stage 3 (about 60,000-25,000 yr BP). In this study the results of new δ13C and δ15N isotopic analyses of cave bear collagen from four Central-Eastern European sites are presented, as well as a review of all published isotopic data for cave bears of the same period. The main conclusion is a lack of geographical East-West pattern in the variations of δ13C and δ15N values of cave bear collagen. Moreover, no relationship was found between cave bear taxonomy and isotopic composition. The cave bears from Central-Eastern Europe exhibit δ13C and δ15N values near the average of the range of Central, Western and Southern European cave bears. Despite the fact that most cave bear sites follow an altitudinal gradient, separate groups of sites exhibit shift in absolute values of δ13C, what disturbs an altitude-related isotopic pattern. The most distinct groups are: high Alpine sites situated over 1500 m a.s.l. - in terms of δ13C; and two Romanian sites Peştera cu Oase and Urşilor - in case of δ15N. Although the cave bear isotopic signature is driven by altitude, the altitudinal adjustment of isotopic data is not enough to explain the isotopic dissimilarity of these cave bears. The unusually high δ15N signature of mentioned Romanian sites is an isolated case in Europe. Cave bears from relatively closely situated Central-Eastern European sites and other Romanian sites are more similar to Western European than to Romanian populations in terms of isotopic composition, and probably ecology.

Using stable isotopes of carbon to investigate the seasonal variation of carbon transfer in a northwestern Arkansas cave

USGS Publications Warehouse

Knierim, Katherine J.; Pollock, Erik; Hays, Phillip D.; Khojasteh, Jam

2015-01-01

Stable-isotope analyses are valuable in karst settings, where characterizing biogeochemical cycling of carbon along groundwater flow paths is critical for understanding and protecting sensitive cave and karst water resources. This study quantified the seasonal changes in concentration and isotopic composition (δ13C) of aqueous and gaseous carbon species—dissolved inorganic carbon (DIC) and gaseous carbon dioxide (CO2)—to characterize sources and transfer of these species along a karst flow path, with emphasis on a cave environment. Gas and water samples were collected from the soil and a cave in northwestern Arkansas approximately once a month for one year to characterize carbon cycling along a conceptual groundwater flow path. In the soil, as the DIC concentration increased, the isotopic composition of the DIC became relatively lighter, indicating an organic carbon source for a component of the DIC and corroborating soil DIC as a proxy for soil respiration. In the cave, a positive correlation between DIC and surface temperature was due to increased soil respiration as the organic carbon signal from the soil was transferred to the cave environment via the aqueous phase. CO2 concentration was lowest in the cave during colder months and increased exponentially with increasing surface temperature, presumably due to higher rates of soil respiration during warmer periods and changing ventilation patterns between the surface and cave atmosphere. Isotopic disequilibrium between CO2 and DIC in the cave was greatest when CO2 concentration was changing during November/ December and March/April, presumably due to the rapid addition or removal of gaseous CO2. The isotopic disequilibrium between DIC and CO2 provided evidence that cave CO2 was a mixture of carbon from several sources, which was mostly constrained by mixture between atmospheric CO2 and soil CO2. The concentration and isotopic composition of gaseous and aqueous carbon species were controlled by month-to-month variations in temperature and precipitation and provided insight into the sources of carbon in the cave. Stable carbon isotope ratios provided an effective tool to explore carbon transfer from the soil zone and into the cave, identify carbon sources in the cave, and investigate how seasonality affected the transfer of carbon in a shallow karst system.

Geochemical Investigation of Source Water to Cave Springs, Great Basin National Park, White Pine County, Nevada

USGS Publications Warehouse

Prudic, David E.; Glancy, Patrick A.

2009-01-01

Cave Springs supply the water for the Lehman Caves Visitor Center at Great Basin National Park, which is about 60 miles east of Ely, Nevada, in White Pine County. The source of water to the springs was investigated to evaluate the potential depletion caused by ground-water pumping in areas east of the park and to consider means to protect the supply from contamination. Cave Springs are a collection of several small springs that discharge from alluvial and glacial deposits near the contact between quartzite and granite. Four of the largest springs are diverted into a water-collection system for the park. Water from Cave Springs had more dissolved strontium, calcium, and bicarbonate, and a heavier value of carbon-13 than water from Marmot Spring at the contact between quartzite and granite near Baker Creek campground indicating that limestone had dissolved into water at Cave Springs prior to discharging. The source of the limestone at Cave Springs was determined to be rounded gravels from a pit near Baker, Nevada, which was placed around the springs during the reconstruction of the water-collection system in 1996. Isotopic compositions of water at Cave Springs and Marmot Spring indicate that the source of water to these springs primarily is from winter precipitation. Mixing of water at Cave Springs between alluvial and glacial deposits along Lehman Creek and water from quartzite is unlikely because deuterium and oxygen-18 values from a spring discharging from the alluvial and glacial deposits near upper Lehman Creek campground were heavier than the deuterium and oxygen-18 values from Cave Springs. Additionally, the estimated mean age of water determined from chlorofluorocarbon concentrations indicates water discharging from the spring near upper Lehman Creek campground is younger than that discharging from either Cave Springs or Marmot Spring. The source of water at Cave Springs is from quartzite and water discharges from the springs on the upstream side of the contact between quartzite and granite where the alluvial and glacial deposits are thin. Consequently, the potential for depletion of discharge at Cave Springs from ground-water pumping in Snake Valley east of the park is less than if the source of water was from alluvial and glacial deposits or carbonate rocks, which would be more directly connected to downstream pumping sites in Snake Valley.

76 FR 42654 - Endangered and Threatened Wildlife and Plants; Petition To List Grand Canyon Cave Pseudoscorpion

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-19

... posterior eyes, and fewer setae (stiff bristles present on the body) on its upper dorsal section (Muchmore...) reported that most of the caves surveyed were dry and dusty with low relative humidity, and that most of...'s hydrologist, the Cave of the Domes is considered to be a dry cave with no discharge or pools, but...

Some new cave diving exploration results from Croatian karst area

NASA Astrophysics Data System (ADS)

Garasic, Davor; Garasic, Mladen

2017-04-01

In the recent years, several international cave diving expeditions took place in the Dinaric karst of Croatia. The objectives were conducting a new research of previously known karstic springs and also exploring new ones. The deepest karst cave in Croatia filled with water is Crveno jezero (lake) near Imotski town, with water depth of 281 meters and total cave depth of 528 meters. Volume of water in this cave is about 16 millions m3. Diving expeditions were held in 1997 and 1998.The deepest karst spring in the Dinaric karst of Croatia is Vrelo of Una River (with max discharge about 100 m3/s), where divers measured depth of -248 meters. Explorations were made in 2007 and 2016. Sinac spring in Pla\\vsko Polje has been dived to the depth of -203 meters. Cave diving was done in 1984, 1999, 2003, 2007 - 2016. Furthermore, very popular springs of the river Kupa (-155 m) in Gorski Kotar (explored since1995 till 2015), river Gacka (-105 in depth, 1150m in length) in Lika, explored from 1992 to 2016, river Cetina (-110 m in depth, 1300 m in length), cave diving explored from 2000 to 2016 in the Dalmatinska Zagora, Rumin Veliki spring (- 150 m in depth) in the Sinjska Krajina (explored and dived in 2006 and 2010), than rivers Krnjeza and Krupa in Ravni kotari with diving depths of over 100 meters (in 2004 and 2005) and so on. Along the Adriatic coast in Croatia there are many deep and long submarine springs (vrulje), ie. caves under seawater springs. called - vruljas for example Vrulja Zecica with over 900 meters ine length and Vrulja Modrič with completely flooded cave channels that extend over 2300 meters in length. Cave diving was conducted from 2010 to 2016. Vrulja Dubci is also worth mentioning (dived and explored in 2000), 161 meters deep and so on. Tectonic activity plays a dominant role in the creation and function of these caves. Geological, hydrogeological and lithostratigraphic conditions are also very important in speleogenesis of these caves in Croatian karst system.

Engineering geologic conditions at the sinkhole entrance to Logan Cave, Benton County, Arkansas

USGS Publications Warehouse

Schulz, William H.; McKenna, Jonathan P.

2004-01-01

Logan Cave, located in Benton County, Arkansas, is inhabited by several endangered and threatened species. The cave and surrounding area was designated a National Wildlife Refuge under the control of the U.S. Fish and Wildlife Service (USFWS) in 1989. Cave researchers access the cave through a steep-sided sinkhole entrance, which also is one of the two access points used by endangered bats. There is evidence of instability of one of the entrance slopes that has raised concerns that the entrance could close if slope failure was to occur. At the request of USFWS, we performed an engineering geologic investigation of the sinkhole to evaluate stability of this slope, which is comprised of soil, and other mechanisms of sediment transport into the cave entrance. The investigation included engineering geologic mapping, sampling and laboratory testing of subsurface geologic materials, and slope-stability analysis. We found that the sinkhole slope that extends into the entrance of the cave is comprised of sandy and gravelly soil to the depths explored (6.4 meters). This soil likely was deposited as alluvium within a previous, larger sinkhole. Based on properties of the alluvium, geometry of the slope, and results of finite-element slope-stability analyses, we conclude that the slope is marginally stable. Future failures of the slope probably would be relatively thin and small, thus several would be required to completely close the cave entrance. However, sediment is accumulating within the cave entrance due to foot traffic of those accessing the cave, surface-water erosion and transport, and shallow slope failures from the other sinkhole slopes. We conclude that the entrance will be closed by sediment in the future, similar to another entrance that we identified that completely closed in the past. Several measures could be taken to reduce the potential for closure of the cave entrance, including periodic sediment removal, installation of materials that reduce erosion by foot traffic and surface water, construction of a sediment-retention wall, and excavation of the soil slope. Any measures taken must be carefully planned and executed so that they have no impact on organisms within the cave.

Sequence of mammalian fossils, including hominoid teeth, from the Bubing Basin caves, South China.

PubMed

Wang, Wei; Potts, Richard; Baoyin, Yuan; Huang, Weiwen; Cheng, Hai; Edwards, R Lawrence; Ditchfield, Peter

2007-04-01

A Plio-Pleistocene to Holocene faunal sequence has been recovered from four carefully excavated caves in the Bubing Basin, adjacent to the larger Bose Basin of South China. The caves vary in elevation; we suggest that the higher caves were formed and filled with sediments prior to the lower caves. The highest deposits, which are from Mohui Cave, contain hominoid teeth and other fossilized remains of mammalian taxa most similar to late Pliocene and early Pleistocene faunas. Wuyun Cave ( approximately 50m lower in elevation than Mohui) contains a late middle Pleistocene fauna, which is supported by U-series age constraints from 350 to 200ka. Lower Pubu Cave ( approximately 23m below Wuyun) is assigned to the late Pleistocene, while the Cunkong Cave (the lowest, approximately 2m lower elevation than Lower Pubu) preserves a Holocene fauna. The four faunal assemblages indicate species-level changes in Ailuropoda, Stegodon, and Sus, the appearance of Elephas, the local disappearance of Stegodon, and the migration of Equus hemionus to South China. These initial results of our work call into question the continued value of the Stegodon/Ailuropoda Fauna, a category long used to characterize the Pleistocene faunas of South China. Excavation of karstic caves of varying elevation within the basins of South China holds promise for defining local sequences of mammalian fossils that can be used to investigate faunal variations related to climate change, biogeographic events, and evolutionary change over the past two million years. Stable isotopic analysis of a small sample of mammalian teeth from Bubing Basin caves is consistent with 100% C(3) vegetation in the Bubing/Bose region, with certain delta(13)C values consistent with a canopied woodland or forest. A preliminary assessment of the hominoid teeth indicates the presence of diverse molar and premolar morphologies including dental remains of Gigantopithecus blacki and a sample with similarities to the teeth reported from Longgupo.

Changes in the inhabitation of the Biśnik Cave during the Pleistocene

NASA Astrophysics Data System (ADS)

Cyrek, Krzysztof; Sudoł, Magdalena

2010-01-01

The Biśnik Cave lies on the left western slope of the Wodąca Valley, which is part of the Niegownice-Smoleń hills, situated in the central part of the Kraków-Częstochowa Upland. The cave consists of several chambers joined by corridors, and a number of entrances. Interdisciplinary research (archaeology, sedimentology, geomorphology and paleozoology) carried out since 1992 has dealt with the exploration of the following elements of the cave system: the main chamber, side shelter, side chamber and the area underneath the overhang. The Biśnik Cave is currently the oldest cave site in Poland with a well-preserved cross-section of sediments formed in separate stages of climatic changes, starting with the period preceding the Odra Glaciation to the Holocene. The oldest traces of settlement of Palaeolithic man go as far back as over 400,000 years ago. The most interesting mid-Palaeolithic sequence of the cave inhabitation comprises 17 cultural levels preserved in the form of stone and bone artefacts' concentrations, hearth remains and fragments of animal bones of post-consumption character. The attempts to date separate levels using the uranium-thorium dating method, electronic paramagnetic resonance and thermoluminescence method are very relevant. Scientific value of the Biśnik Cave turns it into a sample mid-Palaeolithic site in this part of Europe. A three-dimensional localisation of all finds made it possible to prepare a detailed map of the artefacts' distribution in the consecutive sedimentary layers. This, in turn, enabled the reconstruction of changes of the cave inhabitation by man. The correlation of those changes with the description of climatic conditions in the period of formation of sedimentary layers helped link the cave inhabitation methods with natural conditions dominating the area of the Biśnik Cave at that time.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

PubMed

Weyrich, Laura S; Duchene, Sebastian; Soubrier, Julien; Arriola, Luis; Llamas, Bastien; Breen, James; Morris, Alan G; Alt, Kurt W; Caramelli, David; Dresely, Veit; Farrell, Milly; Farrer, Andrew G; Francken, Michael; Gully, Neville; Haak, Wolfgang; Hardy, Karen; Harvati, Katerina; Held, Petra; Holmes, Edward C; Kaidonis, John; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Semal, Patrick; Soltysiak, Arkadiusz; Townsend, Grant; Usai, Donatella; Wahl, Joachim; Huson, Daniel H; Dobney, Keith; Cooper, Alan

2017-04-20

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

The Atmosphere of Crystal Cave: Understanding Sources and Sinks of Trace Gases

NASA Astrophysics Data System (ADS)

Jarnot, A. W.; Hughes, S.; Blake, D. R.

2016-12-01

The atmospheric chemistry of cave systems has not been previously studied in depth; however, cave systems are prime locations to study potential sources and sinks for trace gas pollutants. Relatively constant temperatures, humidity, minimal air flow, and lack of sunlight create a stable environment that allows for biogeochemical processes to go on uninterrupted for extended periods of time. Carbonyl sulfide (OCS) is one of the main contributors to air pollution globally, but many OCS sinks are not fully understood. A preliminary analysis of cave air from Crystal Cave in Sequoia National Park yielded OCS concentrations of 35.2 ± 0.7 pptv, approximately 16 times lower than the average concentration of 568 ± 8 pptv measured outside of the cave. In addition, the concentrations of several other trace gases such as alpha-pinene and methyl bromide were found to be abnormally low (10.5 ± 0.3 pptv inside and 387 ± 8 pptv for alpha-pinene, and 387 ± 8 pptv inside and 11.1 ± 0.4 pptv outside for methyl bromide). The cave air was found to be well-mixed as the concentrations of long lived halocarbons such as CFC-12 were similar inside and outside of the cave (545 ± 5 pptv and 538 ± 4 pptv, respectively). This indicates that there may be one or more factors causing the cave to act a sink for several trace gas species. Further sampling and analysis of the atmosphere in the cave is required to draw any concrete conclusions about the unique environment presented here. The information gathered will help elucidate mechanisms for trace gas degradation, which could yield information about global trace gas budgets and their effect on global air quality.

Repeated and Time-Correlated Morphological Convergence in Cave-Dwelling Harvestmen (Opiliones, Laniatores) from Montane Western North America

PubMed Central

Derkarabetian, Shahan; Steinmann, David B.; Hedin, Marshal

2010-01-01

Background Many cave-dwelling animal species display similar morphologies (troglomorphism) that have evolved convergent within and among lineages under the similar selective pressures imposed by cave habitats. Here we study such ecomorphological evolution in cave-dwelling Sclerobuninae harvestmen (Opiliones) from the western United States, providing general insights into morphological homoplasy, rates of morphological change, and the temporal context of cave evolution. Methodology/Principal Findings We gathered DNA sequence data from three independent gene regions, and combined these data with Bayesian hypothesis testing, morphometrics analysis, study of penis morphology, and relaxed molecular clock analyses. Using multivariate morphometric analysis, we find that phylogenetically unrelated taxa have convergently evolved troglomorphism; alternative phylogenetic hypotheses involving less morphological convergence are not supported by Bayesian hypothesis testing. In one instance, this morphology is found in specimens from a high-elevation stony debris habitat, suggesting that troglomorphism can evolve in non-cave habitats. We discovered a strong positive relationship between troglomorphy index and relative divergence time, making it possible to predict taxon age from morphology. Most of our time estimates for the origin of highly-troglomorphic cave forms predate the Pleistocene. Conclusions/Significance While several regions in the eastern and central United States are well-known hotspots for cave evolution, few modern phylogenetic studies have addressed the evolution of cave-obligate species in the western United States. Our integrative studies reveal the recurrent evolution of troglomorphism in a perhaps unexpected geographic region, at surprisingly deep time depths, and in sometimes surprising habitats. Because some newly discovered troglomorphic populations represent undescribed species, our findings stress the need for further biological exploration, integrative systematic research, and conservation efforts in western US cave habitats. PMID:20479884

Source to sink characterization of dissolved organic matter in a tropical karst system

NASA Astrophysics Data System (ADS)

Lechleitner, Franziska; Lang, Susan Q.; McIntyre, Cameron; Baldini, James U. L.; Dittmar, Thorsten; Eglinton, Timothy I.

2016-04-01

Karst systems are widespread surface features present on all continents. They are characterized by complex hydrology with a multitude of possible flow regimes, from diffuse seepage through the host rock to fracture flow in larger conduits. As stalagmite proxy records are important indicators of past terrestrial climate conditions, detailed understanding of the biogeochemistry of cave systems and their relationships to the overlying karst network is crucial. Microbial communities that drive the carbon cycle in caves are nourished by dissolved organic matter (DOM) carried with water into the cave system. Water samples from the Yok Balum cave in Belize were collected for DOM analysis, including soil waters, drip waters and pool waters from inside the cave. Additionally, DOM extracts from a stalagmite from the same cave were analysed to examine DOM signatures and test their applicability for reconstruction of environmental conditions. Ultrahigh-resolution mass spectrometry (via the ESI-FT-ICR-MS technique) yielded detailed molecular fingerprints on DOM from these samples. Several thousand molecular formulae of DOM compounds were identified. In addition, radiocarbon analyses were performed on the DOM samples to gain information on karst turnover times. A principal component analysis of the molecular data revealed a clear gradient between soil waters and cave waters, as soil waters were enriched in highly unsaturated oxygen-rich compounds (typical for vascular plants), which were much less abundant in drip waters. Conversely, peptides, which can originate from bacterial processes, were present only in the drip waters. Our data clearly show connectivity between the cave and overlaying soils, and reworking of DOM by the cave bacterial community. Furthermore, we found molecular evidence for the selective removal of vascular plant-derived DOM in the caves, possibly due to abiotic interactions with minerals.

Palaeoclimate signal recorded by stable isotopes in cave ice: a modeling approach

NASA Astrophysics Data System (ADS)

Perşoiu, A.; Bojar, A.-V.

2012-04-01

Ice accumulations in caves preserve a large variety of geochemical information as candidate proxies for both past climate and environmental changes, one of the most significant being the stable isotopic composition of the ice. A series of recent studies have targeted oxygen and hydrogen stable isotopes in cave ice as proxies for past air temperatures, but the results are far from being as straightforward as they are in high latitude and altitude glaciers and ice caps. The main problems emerging from these studies are related to the mechanisms of cave ice formation (i.e., freezing of water) and post-formation processes (melting and refreezing), which both alter the original isotopic signal in water. Different methods have been put forward to solve these issues and a fair understanding of the present-day link between stable isotopes in precipitation and cave ice exists now. However, the main issues still lays unsolved: 1) is it possible to extend this link to older ice and thus reconstruct past changes in air temperature?; 2) to what extent are ice dynamics processes modifying the original climatic signal and 3) what is the best method to be used in extracting a climatic signal from stable isotopes in cave ice? To respond to these questions, we have conducted a modeling experiment, in which a theoretical cave ice stable isotope record was constructed using present-day observations on stable isotope behavior in cave ice and ice dynamics, and different methods (presently used for both polar and cave glaciers), were used to reconstruct the original, known, isotopic values. Our results show that it is possible to remove the effects of ice melting and refreezing on stable isotope composition of cave ice, and thus reconstruct the original isotopic signal, and further the climatic one.

A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus

PubMed Central

Stahl, Bethany A.; Gross, Joshua B.; Speiser, Daniel I.; Oakley, Todd H.; Patel, Nipam H.; Gould, Douglas B.; Protas, Meredith E.

2015-01-01

Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment. PMID:26462237

Identifying Seizure Onset Zone From the Causal Connectivity Inferred Using Directed Information

NASA Astrophysics Data System (ADS)

Malladi, Rakesh; Kalamangalam, Giridhar; Tandon, Nitin; Aazhang, Behnaam

2016-10-01

In this paper, we developed a model-based and a data-driven estimator for directed information (DI) to infer the causal connectivity graph between electrocorticographic (ECoG) signals recorded from brain and to identify the seizure onset zone (SOZ) in epileptic patients. Directed information, an information theoretic quantity, is a general metric to infer causal connectivity between time-series and is not restricted to a particular class of models unlike the popular metrics based on Granger causality or transfer entropy. The proposed estimators are shown to be almost surely convergent. Causal connectivity between ECoG electrodes in five epileptic patients is inferred using the proposed DI estimators, after validating their performance on simulated data. We then proposed a model-based and a data-driven SOZ identification algorithm to identify SOZ from the causal connectivity inferred using model-based and data-driven DI estimators respectively. The data-driven SOZ identification outperforms the model-based SOZ identification algorithm when benchmarked against visual analysis by neurologist, the current clinical gold standard. The causal connectivity analysis presented here is the first step towards developing novel non-surgical treatments for epilepsy.

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model

PubMed Central

Jensen, Greg; Muñoz, Fabian; Alkan, Yelda; Ferrera, Vincent P.; Terrace, Herbert S.

2015-01-01

Transitive inference (the ability to infer that B > D given that B > C and C > D) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q-learning, an established reward-prediction error (RPE) model. Of these, only Q-learning failed to respond above chance during critical test trials. Betasort’s success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models. PMID:26407227

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model.

PubMed

Jensen, Greg; Muñoz, Fabian; Alkan, Yelda; Ferrera, Vincent P; Terrace, Herbert S

2015-01-01

Transitive inference (the ability to infer that B > D given that B > C and C > D) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q-learning, an established reward-prediction error (RPE) model. Of these, only Q-learning failed to respond above chance during critical test trials. Betasort's success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models.

The view from the Lincoln Cave: mid- to late Pleistocene fossil deposits from Sterkfontein hominid site, South Africa.

PubMed

Reynolds, S C; Clarke, R J; Kuman, K A

2007-09-01

The Lincoln-Fault cave system lies adjacent to the Sterkfontein Cave system in the Cradle of Humankind World Heritage Site, Gauteng Province, South Africa. Lincoln Cave contains a mid- to late Pleistocene fossiliferous deposit which has been dated using uranium series methods to between 252,600+/-35,600 and 115,300+/-7,700 years old. Although speleologists presumed that there was no connection between the Lincoln Cave and Sterkfontein Cave systems, results of excavations conducted in 1997 suggest a link between the deposits. Detailed comparisons of artifacts, fauna, hominid material, and a statistical correspondence analysis (CA) of the macromammalian fauna in the deposits strongly support this hypothesis. The recovery of Early Acheulean-type artifacts from the Lincoln Cave suggests that older artifacts eroded out of Sterkfontein Member 5 West and were redeposited into the younger Lincoln Cave deposits. The close physical proximity of these deposits, and the nature of the material recovered from them, indicates that the material was probably redeposited via a link between the two cave systems. Although faunal mixing is present, it is possible to say that large carnivorans become more scarce at Sterkfontein during the mid- to late Pleistocene, while small canids and felids appear to become more abundant, indicating that large and small carnivorans probably varied their use of the site through time. This may also reflect an increasing presence of humans in the Sterkfontein area during the mid- to late Pleistocene.

The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanus

PubMed Central

Bradic, Martina; Teotónio, Henrique; Borowsky, Richard L.

2013-01-01

Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment. PMID:23927992

Convergent Evolution of Unique Morphological Adaptations to a Subterranean Environment in Cave Millipedes (Diplopoda)

PubMed Central

Golovatch, Sergei; Wesener, Thomas; Tian, Mingyi

2017-01-01

Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life. PMID:28178274

Convergent Evolution of Unique Morphological Adaptations to a Subterranean Environment in Cave Millipedes (Diplopoda).

PubMed

Liu, Weixin; Golovatch, Sergei; Wesener, Thomas; Tian, Mingyi

2017-01-01

Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life.

Helium Isotopes and Noble Gas Abundances of Cave Dripping Water in Three Caves in East Asia

NASA Astrophysics Data System (ADS)

Chen, A. T.; Shen, C. C.; Tan, M.; Li, T.; Uemura, R.; Asami, R.

2015-12-01

Paleo-temperature recorded in nature archives is a critical parameter to understand climate change in the past. With advantages of unique inert chemical characteristics and sensitive solubilities with temperature, dissolved noble gases in speleothem inclusion water were recently proposed to retrieve terrestrial temperature history. In order to accurately apply this newly-developed speleothem noble gas temperature (NGT) as a reliable proxy, a fundamental issue about behaviors of noble gases in the karst should be first clarified. In this study, we measured noble gas contents in air and dripping water to evaluate any ratio deviation between noble gases. Cave dripping water samples was collected from three selected caves, Shihua Cave in northern China, Furong Cave in southwestern, and Gyukusen Cave in an island located in the western Pacific. For these caves are characterized by a thorough mixing and long-term storage of waters in a karst aquifer by the absence of seasonal oxygen isotope shifts. Ratios of dripping water noble gases are statistically insignificant from air data. Helium isotopic ratios in the dripping water samples match air value. The results indicate that elemental and isotopic signatures of noble gases from air can be frankly preserved in the epikarst and support the fidelity of NGT techniques.

Is radon emission in caves causing deletions in satellite DNA sequences of cave-dwelling crickets?

PubMed

Allegrucci, Giuliana; Sbordoni, Valerio; Cesaroni, Donatella

2015-01-01

The most stable isotope of radon, 222Rn, represents the major source of natural radioactivity in confined environments such as mines, caves and houses. In this study, we explored the possible radon-related effects on the genome of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae) sampled in caves with different concentrations of radon. We analyzed specimens from ten populations belonging to two genetically closely related species, D. geniculata and D. laetitiae, and explored the possible association between the radioactivity dose and the level of genetic polymorphism in a specific family of satellite DNA (pDo500 satDNA). Radon concentration in the analyzed caves ranged from 221 to 26,000 Bq/m3. Specimens coming from caves with the highest radon concentration showed also the highest variability estimates in both species, and the increased sequence heterogeneity at pDo500 satDNA level can be explained as an effect of the mutation pressure induced by radon in cave. We discovered a specific category of nuclear DNA, the highly repetitive satellite DNA, where the effects of the exposure at high levels of radon-related ionizing radiation are detectable, suggesting that the satDNA sequences might be a valuable tool to disclose harmful effects also in other organisms exposed to high levels of radon concentration.

Human utilization of subsurface extraterrestrial environments.

PubMed

Boston, P J; Frederick, R D; Welch, S M; Werker, J; Meyer, T R; Sprungman, B; Hildreth-Werker, V; Thompson, S L; Murphy, D L

2003-06-01

Caves have been used in the ancient past as shelter or habitat by many organisms (including humans). Since antiquity, humans have explored caves for the minerals they contain and sometimes for ceremonial purposes. Over the past century, caves have become the target of increasing exploration, scientific research, and recreation. The use of caves on extraterrestrial bodies for human habitation has been suggested by several investigators. Lunar lava tube bases received early attention because lava tubes were clearly visible in lunar images from the Apollo Era. More recently, Mars Observer Camera data has shown us clear evidence of large tubes visible in a number of volcanic regions on Mars. The budding field of cave geomicrobiology has direct application to questions about subsurface life on other planets. Caves contain many unusual organisms making their living from unlikely materials like manganese, iron, and sulfur. This makes caves and other subsurface habitats prime targets for astrobiological missions to Mars and possibly other bodies. We present the results of a completed Phase I and on-going Phase II NASA Institute for Advanced Concepts (NIAC) study that intensively examines the possibilities of using extraterrestrial caves as both a resource for human explorers and as a highly promising scientific target for both robotic and future human missions to Mars and beyond.

Instrumenting caves to collect hydrologic and geochemical data: case study from James Cave, Virginia

USGS Publications Warehouse

Schreiber, Madeline E.; Schwartz, Benjamin F.; Orndorff, William; Doctor, Daniel H.; Eagle, Sarah D.; Gerst, Jonathan D.

2015-01-01

Karst aquifers are productive groundwater systems, supplying approximately 25 % of the world’s drinking water. Sustainable use of this critical water supply requires information about rates of recharge to karst aquifers. The overall goal of this project is to collect long-term, high-resolution hydrologic and geochemical datasets at James Cave, Virginia, to evaluate the quantity and quality of recharge to the karst system. To achieve this goal, the cave has been instrumented for continuous (10-min interval) measurement of the (1) temperature and rate of precipitation; (2) temperature, specific conductance, and rate of epikarst dripwater; (3) temperature of the cave air; and (4) temperature, conductivity, and discharge of the cave stream. Instrumentation has also been installed to collect both composite and grab samples of precipitation, soil water, the cave stream, and dripwater for geochemical analysis. This chapter provides detailed information about the instrumentation, data processing, and data management; shows examples of collected datasets; and discusses recommendations for other researchers interested in hydrologic and geochemical monitoring of cave systems. Results from the research, briefly described here and discussed in more detail in other publications, document a strong seasonality of the start of the recharge season, the extent of the recharge season, and the geochemistry of recharge.

A comparison of algorithms for inference and learning in probabilistic graphical models.

PubMed

Frey, Brendan J; Jojic, Nebojsa

2005-09-01

Research into methods for reasoning under uncertainty is currently one of the most exciting areas of artificial intelligence, largely because it has recently become possible to record, store, and process large amounts of data. While impressive achievements have been made in pattern classification problems such as handwritten character recognition, face detection, speaker identification, and prediction of gene function, it is even more exciting that researchers are on the verge of introducing systems that can perform large-scale combinatorial analyses of data, decomposing the data into interacting components. For example, computational methods for automatic scene analysis are now emerging in the computer vision community. These methods decompose an input image into its constituent objects, lighting conditions, motion patterns, etc. Two of the main challenges are finding effective representations and models in specific applications and finding efficient algorithms for inference and learning in these models. In this paper, we advocate the use of graph-based probability models and their associated inference and learning algorithms. We review exact techniques and various approximate, computationally efficient techniques, including iterated conditional modes, the expectation maximization (EM) algorithm, Gibbs sampling, the mean field method, variational techniques, structured variational techniques and the sum-product algorithm ("loopy" belief propagation). We describe how each technique can be applied in a vision model of multiple, occluding objects and contrast the behaviors and performances of the techniques using a unifying cost function, free energy.

Probabilistic inference using linear Gaussian importance sampling for hybrid Bayesian networks

NASA Astrophysics Data System (ADS)

Sun, Wei; Chang, K. C.

2005-05-01

Probabilistic inference for Bayesian networks is in general NP-hard using either exact algorithms or approximate methods. However, for very complex networks, only the approximate methods such as stochastic sampling could be used to provide a solution given any time constraint. There are several simulation methods currently available. They include logic sampling (the first proposed stochastic method for Bayesian networks, the likelihood weighting algorithm) the most commonly used simulation method because of its simplicity and efficiency, the Markov blanket scoring method, and the importance sampling algorithm. In this paper, we first briefly review and compare these available simulation methods, then we propose an improved importance sampling algorithm called linear Gaussian importance sampling algorithm for general hybrid model (LGIS). LGIS is aimed for hybrid Bayesian networks consisting of both discrete and continuous random variables with arbitrary distributions. It uses linear function and Gaussian additive noise to approximate the true conditional probability distribution for continuous variable given both its parents and evidence in a Bayesian network. One of the most important features of the newly developed method is that it can adaptively learn the optimal important function from the previous samples. We test the inference performance of LGIS using a 16-node linear Gaussian model and a 6-node general hybrid model. The performance comparison with other well-known methods such as Junction tree (JT) and likelihood weighting (LW) shows that LGIS-GHM is very promising.

Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time.

PubMed

Orlando, Ludovic; Bonjean, Dominique; Bocherens, Herve; Thenot, Aurelie; Argant, Alain; Otte, Marcel; Hänni, Catherine

2002-11-01

The cave bear spread from Western Europe to the Near East during the Riss glaciation (250 KYA) before becoming extinct approximately 12 KYA. During that period, the climatic conditions were highly dynamic, oscillating between glacial and temperate episodes. Such events have constrained the geographic repartition of species, the movements of populations and shaped their genetic diversity. We retrieved and analyzed ancient DNA from 21 samples from five European caves ranging from 40 to 130 KYA. Combined with available data, our data set accounts for a total of 41 sequences of cave bear, coming from 18 European caves. We distinguish four haplogroups at the level of the mitochondrial DNA control region. The large population size of cave bear could account for the maintenance of such polymorphism. Extensive gene flow seems to have connected European populations because two haplogroups cover wide geographic areas. Furthermore, the extensive sampling of the deposits of the Scladina cave located in Belgium allowed us to correlate changes in climatic conditions with the intrapopulational genetic diversity over 90 KY.

A Bat's-Eye View of Holocene Climate Change in the Southwest: Resolving Ambiguities in Cave Isotopic Records

NASA Astrophysics Data System (ADS)

Cole, J. E.; Truebe, S. A.; Harrington, M. D.; Woodhead, J. D.; Overpeck, J. T.; Hlohowskyj, S.; Henderson, G. M.

2015-12-01

In dry environments, speleothems provide an outstanding archive of information on past climate change, particularly since lakes are typically absent or intermittent. Speleothem stable isotopes are widely used for climate reconstruction, but the isotope-climate relationship is complex in arid-region precipitation, and within-cave processes further complicate climate interpretations. Our isotope results from 3 southeastern Arizona caves, spanning the past 3.5-12 kyr, collectively indicate a weakening monsoon from 7kyr to present. These records exhibit substantial multidecadal-multicentury variability that is sometimes shared, and sometimes independent among caves. Strategies to overcome ambiguities in isotope records include long-term monitoring of cave dripwaters, multi-site comparisons, and multiproxy measurements. Monthly dripwater measurements from two caves spanning several years highlight substantial seasonal biases that create distinct differences in the climate sensitivity of individual cave records. These biases can lead to lack of correlation between records, but also creates opportunities for seasonally specific moisture reconstructions. New preliminary analyses suggest that elemental data can help to unravel the multivariate signal contained in speleothem oxygen isotope records.

The Astrobiology of the Subsurface: Caves and Rock Fracture Habitats on Earth, Mars and Beyond

NASA Technical Reports Server (NTRS)

Boston, Penelope J.

2017-01-01

The Astrobiology of the Subsurface: Exploring Cave Habitats on Earth, Mars and Beyond. We are using the spectacular underground landscapes of Earth caves as models for the subsurfaces of other planets. Caves have been detected on the Moon and Mars and are strongly suspected for other bodies in the Solar System including some of the ice covered Ocean Worlds that orbit gas giant planets. The caves we explore and study include many extreme conditions of relevance to planetary astrobiology exploration including high and low temperatures, gas atmospheres poisonous to humans but where exotic microbes can fluorish, highly acidic or salty fluids, heavy metals, and high background radiation levels. Some cave microorganisms eat their way through bedrock, some live in battery acid conditions, some produce unusual biominerals and rare cave formations, and many produce compounds of potential pharmaceutical and industrial significance. We study these unique lifeforms and the physical and chemical biosignatures that they leave behind. Such traces can be used to provide a Field Guide to Unknown Organisms for developing life detection space missions.

Potential collapse due to geological structures influence in Seropan Cave, Gunung Kidul, Yogyakarta, Indonesia

NASA Astrophysics Data System (ADS)

Nugroho, B.; Pranantya, P. A.; Witjahjati, R.; Rofinus

2018-01-01

This study aims to estimate the potential collapse in the Seropan cave, based on the existing geological structure conditions in the cave. This is very necessary because in the Seropan cave will be built Microhydro installation for power plants. The electricity will be used to raise the underground river water in the cave to a barren soil surface, which can be used for surface irrigation. The method used is analysis the quality of rock mass along the cave. Analysis of rock mass quality using Geomechanical Classification or Rock Mass Rating (RMR), to determine the magnitude of the effect of geological structure on rock mass stability. The research path is divided into several sections and quality analysis is performed on each section. The results show that the influence of geological structure is very large and along the cave where the research there are several places that have the potential to collapse, so need to get serious attention in handling it. Nevertheless, the construction of this Microhydro installation can still be carried out by making a reinforcement on potentially collapsing parts

An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree

PubMed Central

2016-01-01

Motivation: Gene tree represents the evolutionary history of gene lineages that originate from multiple related populations. Under the multispecies coalescent model, lineages may coalesce outside the species (population) boundary. Given a species tree (with branch lengths), the gene tree probability is the probability of observing a specific gene tree topology under the multispecies coalescent model. There are two existing algorithms for computing the exact gene tree probability. The first algorithm is due to Degnan and Salter, where they enumerate all the so-called coalescent histories for the given species tree and the gene tree topology. Their algorithm runs in exponential time in the number of gene lineages in general. The second algorithm is the STELLS algorithm (2012), which is usually faster but also runs in exponential time in almost all the cases. Results: In this article, we present a new algorithm, called CompactCH, for computing the exact gene tree probability. This new algorithm is based on the notion of compact coalescent histories: multiple coalescent histories are represented by a single compact coalescent history. The key advantage of our new algorithm is that it runs in polynomial time in the number of gene lineages if the number of populations is fixed to be a constant. The new algorithm is more efficient than the STELLS algorithm both in theory and in practice when the number of populations is small and there are multiple gene lineages from each population. As an application, we show that CompactCH can be applied in the inference of population tree (i.e. the population divergence history) from population haplotypes. Simulation results show that the CompactCH algorithm enables efficient and accurate inference of population trees with much more haplotypes than a previous approach. Availability: The CompactCH algorithm is implemented in the STELLS software package, which is available for download at http://www.engr.uconn.edu/ywu/STELLS.html. Contact: ywu@engr.uconn.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307621

Object/rule integration in CLIPS. [C Language Integrated Production System

NASA Technical Reports Server (NTRS)

Donnell, Brian L.

1993-01-01

This paper gives a brief overview of the C Language Integrated Production System (CLIPS) with a focus on the object-oriented features. The advantages of an object data representation over the traditional working memory element (WME), i.e., facts, are discussed, and the implementation of the Rete inference algorithm in CLIPS is presented in detail. A few methods for achieving pattern-matching on objects with the current inference engine are given, and finally, the paper examines the modifications necessary to the Rete algorithm to allow direct object pattern-matching.

NIFTY - Numerical Information Field Theory. A versatile PYTHON library for signal inference

NASA Astrophysics Data System (ADS)

Selig, M.; Bell, M. R.; Junklewitz, H.; Oppermann, N.; Reinecke, M.; Greiner, M.; Pachajoa, C.; Enßlin, T. A.

2013-06-01

NIFTy (Numerical Information Field Theory) is a software package designed to enable the development of signal inference algorithms that operate regardless of the underlying spatial grid and its resolution. Its object-oriented framework is written in Python, although it accesses libraries written in Cython, C++, and C for efficiency. NIFTy offers a toolkit that abstracts discretized representations of continuous spaces, fields in these spaces, and operators acting on fields into classes. Thereby, the correct normalization of operations on fields is taken care of automatically without concerning the user. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTy permits its user to rapidly prototype algorithms in 1D, and then apply the developed code in higher-dimensional settings of real world problems. The set of spaces on which NIFTy operates comprises point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those. The functionality and diversity of the package is demonstrated by a Wiener filter code example that successfully runs without modification regardless of the space on which the inference problem is defined. NIFTy homepage http://www.mpa-garching.mpg.de/ift/nifty/; Excerpts of this paper are part of the NIFTy source code and documentation.

Technical devices of powered roof support for the top coal caving as automation objects

NASA Astrophysics Data System (ADS)

Nikitenko, M. S.; Kizilov, S. A.; Nikolaev, P. I.; Kuznetsov, I. S.

2018-05-01

In the paper technical devices for the top coal caving as automation objects in the composition of the longwall mining complex (LTCC) are considered. The proposed concept for automation of the top coal caving process allows caving efficiency to be ensured, coal dilution to be prevented, conveyor overloading to be prevented, the shearer service personnel to be unloaded, the influence of the “human factor” to be reduced.

Late quaternary brown bear (Ursidae: Ursus cf. arctos) from a cave in the Huachuca Mountains, Arizona

Treesearch

Nicholas J. Czaplewski; Steve Willsey

2013-01-01

In 2008, Steve Willsey discovered the fragmentary cranium of a bear loose on the floor of a cave at about 2270 m elevation near the crest of the Huachuca Mountains. In 2009, we revisited the cave to examine the specimen with the intention of identifying the species. We photographed and measured the main pieces and left them in the cave. The skull is from an adult,...

Late quaternary regional geoarchaeology of Southeast Alaska Karst: A progress report

USGS Publications Warehouse

Dixon, E.J.; Heaton, T.H.; Fifield, T.E.; Hamilton, T.D.; Putnam, D.E.; Grady, F.

1997-01-01

Karst systems, sea caves, and rock shelters within the coastal temperate rain forest of Alaska's Alexander Archipelago preserve important records of regional archaeology, sea level history, glacial and climatic history, and vertebrate paleontology. Two 14C AMS dates on human bone discovered in a remote cave (49-PET-408) on Prince of Wales Island document the oldest reliably dated human in Alaska to ca. 9800 B.P. A series of 14C AMS dates from cave deposits span the past 40,000 years and provide the first evidence of Pleistocene faunas from the northwest coast of North America. Other discoveries include sea caves and marine beach deposits elevated above modern sea level, extensive solution caves, and mammalian remains of species previously undocumented within the region. Records of human activity, including cave art, artifacts, and habitation sites may provide new insights into the early human colonization of the Americas. ??1997 John Wiley & Sons, Inc.

Effect of soil-rock system on speleothems weathering in Bailong Cave, Yunnan Province, China*

PubMed Central

Wang, Jing; Song, Lin-hua

2005-01-01

Bailong Cave with its well-developed Middle Triassic calcareous dolomite’s system was opened as a show cave for visitors in 1988. The speleothem scenery has been strongly weathered as white powder on the outer layers. Study of the cave winds, permeability of soil-rock system and the chemical compositions of the dripping water indicated: (1) The cave dimension structure distinctively affects the cave winds, which were stronger at narrow places. (2) Based on the different soil grain size distribution, clay was the highest in composition in the soil. The response sense of dripping water to the rainwater percolation was slow. The density of joints and other openings in dolomite make the dolomite as mesh seepage body forming piles of thin and high columns and stalactites. (3) Study of 9 dripping water samples by HYDROWIN computer program showed that the major mineral in the water was dolomite. PMID:15682505

Vibrational spectroscopy of synthetic archerite (K,NH4)HPO4- and in comparison with the natural cave mineral

NASA Astrophysics Data System (ADS)

Frost, Ray L.; Xi, Yunfei; Palmer, Sara J.; Tan, Keqin; Millar, Graeme J.

2012-03-01

In order to mimic the formation of archerite in cave minerals, the mineral analogue has been synthesised. The cave mineral is formed by the reaction of the chemicals in bat guano with calcite substrates. X-ray diffraction proves that the synthesised archerite analogue was pure and more pure than the natural cave mineral. The vibrational spectra of the synthesised mineral are compared with that of the natural cave mineral from the Murra-el-elevyn Cave, Eucla, Western Australia. Raman and infrared bands are assigned to HPO4-, OH and NH stretching and bending vibrations. The Raman band at 917 cm-1 is assigned to the HOP stretching vibration of HPO4- units. Bands in the 1200-1800 cm-1 region are associated with NH4+ bending modes. Vibrational spectroscopy enables the molecular structure of archerite analogue to be analysed.

DIVERSITY OF THE TYPE 1 INTRON-ITS REGION OF THE 18S rRNA GENE IN PSEUDOGYMNOASCUS SPECIES FROM THE RED HILLS OF KANSAS.

PubMed

Chen, Xi; Crupper, Scott S

2016-09-01

Gypsum caves found throughout the Red Hills of Kansas have the state's most diverse and largest population of cave-roosting bats. White-nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans, which threatens all temperate bat species, has not been previously detected in the gypsum caves as this disease moves westward from the eastern United States. Cave soil was obtained from the gypsum caves, and using the polymerase chain reaction, a 624-nucleotide DNA fragment specific to the Type 1 intron-internal transcribed spacer region of the 18S rRNA gene from Pseudogymnoascus species was amplified. Subsequent cloning and DNA sequencing indicated P. destructans DNA was present, along with 26 uncharacterized Pseudogymnoascus DNA variants. However, no evidence of WNS was observed in bat populations residing in these caves.

Reduced opsin gene expression in a cave-dwelling fish

PubMed Central

Tobler, Michael; Coleman, Seth W.; Perkins, Brian D.; Rosenthal, Gil G.

2010-01-01

Regressive evolution of structures associated with vision in cave-dwelling organisms is the focus of intense research. Most work has focused on differences between extreme visual phenotypes: sighted, surface animals and their completely blind, cave-dwelling counterparts. We suggest that troglodytic systems, comprising multiple populations that vary along a gradient of visual function, may prove critical in understanding the mechanisms underlying initial regression in visual pathways. Gene expression assays of natural and laboratory-reared populations of the Atlantic molly (Poecilia mexicana) revealed reduced opsin expression in cave-dwelling populations compared with surface-dwelling conspecifics. Our results suggest that the reduction in opsin expression in cave-dwelling populations is not phenotypically plastic but reflects a hardwired system not rescued by exposure to light during retinal ontogeny. Changes in opsin gene expression may consequently represent a first evolutionary step in the regression of eyes in cave organisms. PMID:19740890

Effect of soil-rock system on speleothems weathering in Bailong Cave, Yunnan Province, China.

PubMed

Wang, Jing; Song, Lin-Hua

2005-03-01

Bailong Cave with its well-developed Middle Triassic calcareous dolomite's system was opened as a show cave for visitors in 1988. The speleothem scenery has been strongly weathered as white powder on the outer layers. Study of the cave winds, permeability of soil-rock system and the chemical compositions of the dripping water indicated: (1) The cave dimension structure distinctively affects the cave winds, which were stronger at narrow places. (2) Based on the different soil grain size distribution, clay was the highest in composition in the soil. The response sense of dripping water to the rainwater percolation was slow. The density of joints and other openings in dolomite make the dolomite as mesh seepage body forming piles of thin and high columns and stalactites. (3) Study of 9 dripping water samples by HYDROWIN computer program showed that the major mineral in the water was dolomite.

U-series dating of Paleolithic art in 11 caves in Spain.

PubMed

Pike, A W G; Hoffmann, D L; García-Diez, M; Pettitt, P B; Alcolea, J; De Balbín, R; González-Sainz, C; de las Heras, C; Lasheras, J A; Montes, R; Zilhão, J

2012-06-15

Paleolithic cave art is an exceptional archive of early human symbolic behavior, but because obtaining reliable dates has been difficult, its chronology is still poorly understood after more than a century of study. We present uranium-series disequilibrium dates of calcite deposits overlying or underlying art found in 11 caves, including the United Nations Educational, Scientific, and Cultural Organization (UNESCO) World Heritage sites of Altamira, El Castillo, and Tito Bustillo, Spain. The results demonstrate that the tradition of decorating caves extends back at least to the Early Aurignacian period, with minimum ages of 40.8 thousand years for a red disk, 37.3 thousand years for a hand stencil, and 35.6 thousand years for a claviform-like symbol. These minimum ages reveal either that cave art was a part of the cultural repertoire of the first anatomically modern humans in Europe or that perhaps Neandertals also engaged in painting caves.

Founder effects initiated rapid species radiation in Hawaiian cave planthoppers

PubMed Central

Wessel, Andreas; Hoch, Hannelore; Asche, Manfred; von Rintelen, Thomas; Stelbrink, Björn; Heck, Volker; Stone, Fred D.; Howarth, Francis G.

2013-01-01

The Hawaiian Islands provide the venue of one of nature’s grand experiments in evolution. Here, we present morphological, behavioral, genetic, and geologic data from a young subterranean insect lineage in lava tube caves on Hawai‘i Island. The Oliarus polyphemus species complex has the potential to become a model for studying rapid speciation by stochastic events. All species in this lineage live in extremely similar environments but show strong differentiation in behavioral and morphometric characters, which are random with respect to cave age and geographic distribution. Our observation that phenotypic variability within populations decreases with increasing cave age challenges traditional views on founder effects. Furthermore, these cave populations are natural replicates that can be used to test the contradictory hypotheses. Moreover, Hawaiian cave planthoppers exhibit one of the highest speciation rates among animals and, thus, radically shift our perception on the evolutionary potential of obligate cavernicoles. PMID:23696661

Theoretical study of the ionospheric plasma cave in the equatorial ionization anomaly region

NASA Astrophysics Data System (ADS)

Chen, Yu-Tsung; Lin, C. H.; Chen, C. H.; Liu, J. Y.; Huba, J. D.; Chang, L. C.; Liu, H.-L.; Lin, J. T.; Rajesh, P. K.

2014-12-01

This paper investigates the physical mechanism of an unusual equatorial electron density structure, plasma cave, located underneath the equatorial ionization anomaly by using theoretical simulations. The simulation results provide important new understanding of the dynamics of the equatorial ionosphere. It has been suggested previously that unusual E>⇀×B>⇀ drifts might be responsible for the observed plasma cave structure, but model simulations in this paper suggest that the more likely cause is latitudinal meridional neutral wind variations. The neutral winds are featured by two divergent wind regions at off-equator latitudes and a convergent wind region around the magnetic equator, resulting in plasma divergences and convergence, respectively, to form the plasma caves structure. The tidal-decomposition analysis further suggests that the cave related meridional neutral winds and the intensity of plasma cave are highly associated with the migrating terdiurnal tidal component of the neutral winds.

Implementation of the Iterative Proportion Fitting Algorithm for Geostatistical Facies Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Yupeng, E-mail: yupeng@ualberta.ca; Deutsch, Clayton V.

2012-06-15

In geostatistics, most stochastic algorithm for simulation of categorical variables such as facies or rock types require a conditional probability distribution. The multivariate probability distribution of all the grouped locations including the unsampled location permits calculation of the conditional probability directly based on its definition. In this article, the iterative proportion fitting (IPF) algorithm is implemented to infer this multivariate probability. Using the IPF algorithm, the multivariate probability is obtained by iterative modification to an initial estimated multivariate probability using lower order bivariate probabilities as constraints. The imposed bivariate marginal probabilities are inferred from profiles along drill holes or wells.more » In the IPF process, a sparse matrix is used to calculate the marginal probabilities from the multivariate probability, which makes the iterative fitting more tractable and practical. This algorithm can be extended to higher order marginal probability constraints as used in multiple point statistics. The theoretical framework is developed and illustrated with estimation and simulation example.« less

User's guide to the Fault Inferring Nonlinear Detection System (FINDS) computer program

NASA Technical Reports Server (NTRS)

Caglayan, A. K.; Godiwala, P. M.; Satz, H. S.

1988-01-01

Described are the operation and internal structure of the computer program FINDS (Fault Inferring Nonlinear Detection System). The FINDS algorithm is designed to provide reliable estimates for aircraft position, velocity, attitude, and horizontal winds to be used for guidance and control laws in the presence of possible failures in the avionics sensors. The FINDS algorithm was developed with the use of a digital simulation of a commercial transport aircraft and tested with flight recorded data. The algorithm was then modified to meet the size constraints and real-time execution requirements on a flight computer. For the real-time operation, a multi-rate implementation of the FINDS algorithm has been partitioned to execute on a dual parallel processor configuration: one based on the translational dynamics and the other on the rotational kinematics. The report presents an overview of the FINDS algorithm, the implemented equations, the flow charts for the key subprograms, the input and output files, program variable indexing convention, subprogram descriptions, and the common block descriptions used in the program.

Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.

PubMed

Berens, Philipp; Freeman, Jeremy; Deneux, Thomas; Chenkov, Nikolay; McColgan, Thomas; Speiser, Artur; Macke, Jakob H; Turaga, Srinivas C; Mineault, Patrick; Rupprecht, Peter; Gerhard, Stephan; Friedrich, Rainer W; Friedrich, Johannes; Paninski, Liam; Pachitariu, Marius; Harris, Kenneth D; Bolte, Ben; Machado, Timothy A; Ringach, Dario; Stone, Jasmine; Rogerson, Luke E; Sofroniew, Nicolas J; Reimer, Jacob; Froudarakis, Emmanouil; Euler, Thomas; Román Rosón, Miroslav; Theis, Lucas; Tolias, Andreas S; Bethge, Matthias

2018-05-01

In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing. We present ten of the submitted algorithms which show improved performance compared to previously evaluated methods. Interestingly, the top-performing algorithms are based on a wide range of principles from deep neural networks to generative models, yet provide highly correlated estimates of the neural activity. The competition shows that benchmark challenges can drive algorithmic developments in neuroscience.

Continuous multichannel monitoring of cave air carbon dioxide using a pumped non-dispersive infrared analyser

NASA Astrophysics Data System (ADS)

Mattey, D.

2012-04-01

The concentration of CO2 in cave air is one of the main controls on the rate of degassing of dripwater and on the kinetics of calcite precipitation forming speleothem deposits. Measurements of cave air CO2reveal great complexity in the spatial distribution among interconnected cave chambers and temporal changes on synoptic to seasonal time scales. The rock of Gibraltar hosts a large number of caves distributed over a 300 meter range in altitude and monthly sampling and analysis of air and water combined with continuous logging of temperature, humidity and drip discharge rates since 2004 reveals the importance of density-driven seasonal ventilation which drives large-scale advection of CO2-rich air though the cave systems. Since 2008 we have deployed automatic CO2 monitoring systems that regularly sample cave air from up to 8 locations distributed laterally and vertically in St Michaels Cave located near the top of the rock at 275m asl and Ragged Staff Cave located in the heart of the rock near sea level. The logging system is controlled by a Campbell Scientific CR1000 programmable datalogger which controls an 8 port manifold connected to sampling lines leading to different parts of the cave over a distance of up to 250 meters. The manifold is pumped at a rate of 5l per minute drawing air through 6mm or 8mm id polythene tubing via a 1m Nafion loop to reduce humidity to local ambient conditions. The outlet of the primary pump leads to an open split which is sampled by a second low flow pump which delivers air at 100ml/minute to a Licor 820 CO2 analyser. The software selects the port to be sampled, flushes the line for 2 minutes and CO2 analysed as a set of 5 measurements averaged over 10 second intervals. The system then switches to the next port and when complete shuts down to conserve power after using 20 watts over a 30 minute period of analysis. In the absence of local mains power (eg from the show cave lighting system) two 12v car batteries will power the system for analysis at 4h intervals for about 1 month. Two logging systems sampling cave air from 13 locations over a vertical range of 275m have run continuously for up to 5 years and return a very detailed picture of cave ventilation patterns and their responses to local weather and seasonal change.

An ancient example of fluvial cave sediment derived from dust (eolian silt) infiltration

NASA Astrophysics Data System (ADS)

Evans, J. E.

2011-12-01

Silt-rich grain size distributions are geologically rare and typically eolian. Such sediments (and lithified equivalents) are called dust/dustites in a general case, or loess/loessite in the special case of eolian silts derived from glacial deposits. In both cases, silt-rich deposits require a source area of silt-sized materials, transport mechanisms (prevailing winds of sufficient energy) and one or more depositional mechanisms (such as trapping in the lee of topographic obstacles or adhesion to surfaces with moisture or vegetation). This study evaluates a third type of silt-rich geological deposit, paleo-cave sediments derived from mixtures of dust (eolian silt) and karst breccias. Cave sediments can be autochthonous (speleothems), parautochthonous (karst breccias), and allochthonous (such as fluvial cave sediments). The provenance of fluvial cave sediments is the landscape overlying the cave-karst system, and they are introduced to the cave-karst system by flood events. The Mississippian Leadville Limestone (SW Colorado) was subject to karst processes following Late Mississippian eustatic sea-level fall. These processes included formation of phreatic tubes, tower karst (kegelkarst), solution valleys (poljes), sinkholes (dolines), solution-enhanced joints (grikes), surficial flutes (rillenkarren), solution pans (kamenitzas), and breakout domes containing mosaic and crackle breccias. Flowstone, dripstone, and cave pearls are interbedded with karst breccias and fluvial cave sediments in the Leadville Limestone. The overlying Pennsylvanian Molas Formation is an eolian siltstone (dustite) with sediment sources from the peri-Gondwanan and Grenville rocks of eastern North America. Evidence that the fluvial cave sediments in the Leadville Limestone are derived from this dustite include compositional and textural matches, especially grain size distribution trends vertically downward from the former landscape surface. These grain size trends indicate infiltration of the dustite into the underlying cave-karst system. There is a significant amount of evidence that the resedimentation process was episodic. Some individual phreatic tubes have complex infill history of up to eight events (successive debrites or inundites interbedded with speleothems). Some individual vertical grikes have complex infill histories of as many as six laminated or massive jointites with weakly developed paleosols superimposed on these individual deposits. Late Cenozoic cave sediments are increasingly utilized as archives of geologic change. The role of dust (eolian silt), including its inherited compositional and textural properties from a distant source area, land-atmosphere transfer processes, and resedimentation processes on the land surface overlying the cave-karst system, remain promising areas for research.

Comparative analysis on the selection of number of clusters in community detection

NASA Astrophysics Data System (ADS)

Kawamoto, Tatsuro; Kabashima, Yoshiyuki

2018-02-01

We conduct a comparative analysis on various estimates of the number of clusters in community detection. An exhaustive comparison requires testing of all possible combinations of frameworks, algorithms, and assessment criteria. In this paper we focus on the framework based on a stochastic block model, and investigate the performance of greedy algorithms, statistical inference, and spectral methods. For the assessment criteria, we consider modularity, map equation, Bethe free energy, prediction errors, and isolated eigenvalues. From the analysis, the tendency of overfit and underfit that the assessment criteria and algorithms have becomes apparent. In addition, we propose that the alluvial diagram is a suitable tool to visualize statistical inference results and can be useful to determine the number of clusters.

Learning Extended Finite State Machines

NASA Technical Reports Server (NTRS)

Cassel, Sofia; Howar, Falk; Jonsson, Bengt; Steffen, Bernhard

2014-01-01

We present an active learning algorithm for inferring extended finite state machines (EFSM)s, combining data flow and control behavior. Key to our learning technique is a novel learning model based on so-called tree queries. The learning algorithm uses the tree queries to infer symbolic data constraints on parameters, e.g., sequence numbers, time stamps, identifiers, or even simple arithmetic. We describe sufficient conditions for the properties that the symbolic constraints provided by a tree query in general must have to be usable in our learning model. We have evaluated our algorithm in a black-box scenario, where tree queries are realized through (black-box) testing. Our case studies include connection establishment in TCP and a priority queue from the Java Class Library.

Estimation of tool wear length in finish milling using a fuzzy inference algorithm

NASA Astrophysics Data System (ADS)

Ko, Tae Jo; Cho, Dong Woo

1993-10-01

The geometric accuracy and surface roughness are mainly affected by the flank wear at the minor cutting edge in finish machining. A fuzzy estimator obtained by a fuzzy inference algorithm with a max-min composition rule to evaluate the minor flank wear length in finish milling is introduced. The features sensitive to minor flank wear are extracted from the dispersion analysis of a time series AR model of the feed directional acceleration of the spindle housing. Linguistic rules for fuzzy estimation are constructed using these features, and then fuzzy inferences are carried out with test data sets under various cutting conditions. The proposed system turns out to be effective for estimating minor flank wear length, and its mean error is less than 12%.

Thirty year ecosystem trajectories in a submerged marine cave under changing pressure regime.

PubMed

Montefalcone, Monica; De Falco, Giada; Nepote, Ettore; Canessa, Martina; Bertolino, Marco; Bavestrello, Giorgio; Morri, Carla; Bianchi, Carlo Nike

2018-06-01

Marine caves are unique and vulnerable habitats exhibiting high biodiversity and heterogeneity, but threatened by multiple global and local disturbances. Marine caves, although widely distributed along the Mediterranean coast, suffer for the lack of quantitative data on their structure and function, which hinder their conservation status assessment. Thanks to the availability of a nearly 30-year-long series of data (1986-2013), we evaluated ecosystem change in the Bergeggi marine cave (Ligurian Sea, NW Mediterranean), a cave with a complex shape and high habitat heterogeneity. Non-taxonomic descriptors were adopted, namely growth forms (GF) and trophic guilds (TG), which are informative about ecosystem structure and functioning, respectively. The cave experienced a general trend of change during the last three decades, mainly due to the decline in the cover of sessile organisms (especially 3-dimensional forms) matched by an increase of turf and sediment, thus causing the structural and functional homogenization of the cave community. While change before 2004 had been attributed to climatic factors (especially to the summer heat waves of 1999 and 2003), the most important rate of change was observed between 2009 and 2013, coinciding with recent major beach nourishments and the extension of the neighbouring Vado Ligure harbour, thus providing evidences on the importance of local disturbances deriving from coastal interventions. Monitoring the status of cave ecosystems is urgently needed, and the use of effective indicators, such as the specific traits here adopted (morphology and feeding strategy), could provide effective tools to assist marine cave conservation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distinction between epigenic and hypogenic maze caves

NASA Astrophysics Data System (ADS)

Palmer, Arthur N.

2011-11-01

Certain caves formed by dissolution of bedrock have maze patterns composed of closed loops in which many intersecting fractures or pores have enlarged simultaneously. Their origin can be epigenic (by shallow circulation of meteoric groundwater) or hypogenic (by rising groundwater or production of deep-seated solutional aggressiveness). Epigenic mazes form by diffuse infiltration through a permeable insoluble caprock or by floodwater supplied by sinking streams. Most hypogenic caves involve deep sources of aggressiveness. Transverse hypogenic cave origin is a recently proposed concept in which groundwater of mainly meteoric origin rises across strata in the distal portions of large flow systems, to form mazes in soluble rock sandwiched between permeable but insoluble strata. The distinction between maze types is debated and is usually based on examination of diagnostic cave features and relation of caves to their regional setting. In this paper, the principles of mass transfer are applied to clarify the limits of each model, to show how cave origin is related to groundwater discharge, dissolution rate, and time. The results show that diffuse infiltration and floodwater can each form maze caves at geologically feasible rates (typically within 500 ka). Transverse hypogenic mazes in limestone, to enlarge significantly within 1 Ma, require an unusually high permeability of the non-carbonate beds (generally ≥ 10-4 cm/s), large discharge, and calcite saturation no greater than 90%, which is rare in deep diffuse flow in sedimentary rocks. Deep sources of aggressiveness are usually required. The origin of caves by transverse hypogenic flow is much more favorable in evaporite rocks than in carbonate rocks.

Population trends of Rhinolophus affinis during the breeding and non-breeding season roosting at the Kota Gelanggi limestone complex, Pahang

NASA Astrophysics Data System (ADS)

Sia, Ting Jin; Zubaid, Akbar; Foo, Ng Yong

2015-09-01

Monitoring population trends of bats in caves is difficult but is very important for their conservation. Their vulnerability to decline cannot be taken lightly and must be monitored for future management purposes especially in places open to the public. No studies have been done on bats roosting in caves at Kota Gelanggi and there are very few published studies of cave-dwelling bats in Malaysia. To fill this gap, a study on monitoring the population trends of Rhinolophus affinis was carried out in two caves namely, Gua Kepala Gajah and Gua Tongkat. This study was conducted from October 2013 until December 2014. The population size was estimated by direct visual counts and photographic methods during the day. The bats were caught by using mists net and harp traps. The reproductive condition of both female and male individuals was examined. The mean estimated population size for R. affinis in Gua Kepala Gajah was 221 individuals and 464 in Gua Tongkat. The population size of R. affinis showed an obvious decline during the breeding season and increased gradually after that for both caves. Pregnant R. affinis were found in April 2014 and lactating in June 2014 in both caves. It is important to know the breeding and non-breeding season of bats in both caves and their roosting behaviour in order to protect the bats from human disturbance as these caves are open to the public. The findings will enable the TEKAM management to come out with a proper conservation and management plan for protecting the bat fauna in these caves.

76 FR 19129 - Excavations (Design of Cave-in Protection Systems); Extension of the Office of Management and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-06

... paragraphs require employers to use protective systems to prevent cave-ins during excavation work; these... work, thereby assuring employees of maximum protection against cave-ins. II. Special Issues for Comment...

Paleo-watertable definition using cave ferromanganese stromatolites and associated cave-wall notches (Sierra de Arnero, Spain)

NASA Astrophysics Data System (ADS)

Rossi, Carlos; Villalaín, Juan J.; Lozano, Rafael P.; Hellstrom, John

2016-05-01

The steeply-dipping-dolostone-hosted caves of the Sierra de Arnero (N Spain) contain low-gradient relict canyons with up to ten mapped levels of ferromanganese stromatolites and associated wall notches over a vertical range of 85 m, the highest occurring 460 m above base level. Despite a plausible speleogenetic contribution by pyrite oxidation, and the irregular cave-wall mesomorphologies suggestive of hypogenic speleogenesis, the Arnero relict caves are dominantly epigenic, as indicated by the conduit pattern and the abundant allogenic sediments. Allogenic input declined over time due to a piracy-related decrease in the drainage area of allogenic streams, explaining the large size of the relict Arnero caves relative to the limited present-day outcrop area of the karstified carbonates. Allogenic-sediment input also explains the observed change from watertable canyons to phreatic conduits in the paleo-downstream direction. Stromatolites and notches arguably formed in cave-stream passages at the watertable. The best-defined paleo-watertables show an overall slope of 1.7°, consistent with the present-day relief of the watertable, with higher-slope segments caused by barriers related to sulfide mineralization. The formation of watertable stromatolites favored wall notching by the combined effect of enhanced acidity by Mn-Fe oxidation and shielding of cave floors against erosion. Abrasive bedload further contributed to notch formation by promoting lateral mechanical erosion and protecting passage floors. The irregular wallrock erosional forms of Arnero caves are related partly to paragenesis and partly to the porous nature of the host dolostones, which favored irregular dissolution near passage walls, generating friable halos. Subsequent mechanical erosion contributed to generate spongework patterns. The dolostone porosity also contributes to explain the paradox that virtually all Arnero caves are developed in dolostone despite being less soluble than adjacent limestone. U-series dating of carbonate speleothems and paleomagnetic data from ferromanganese stromatolites and clastic sediments indicate that the paleo-watertables recorded 320 m above the present-day watertable formed during the Matuyama Chron but prior to 1.5 Ma, implying long-term base-level-lowering rates from 125 to 213 m/Ma. To our knowledge, this is the first attempt of paleomagnetic dating of cave ferromanganese stromatolites. These deposits are excellent geomagnetic recorders and offer a direct way to delineate and date paleo-watertables, especially in caves developed in dolostone.

Radon Dose Determination for Cave Guides in Czech Republic

NASA Astrophysics Data System (ADS)

Thinova, Lenka; Rovenska, Katerina

2008-08-01

According to recommended approach there are six (from total of twelve) open-to-public caves in Czech Republic, reaching near to an effective lung-dose of 6mSv/year. A conservative approach for estimating the potential effective lung-dose in caves (or underground) is based on two season's measurements, using solid state alpha track detector (Kodak in plastic diffusion chamber). The obtained dataset is converted into an annual effective dose, in agreement with the ICRP65 recommendation, using the "cave factor" 1.5. The value of "cave factor" which depends on the spectrum of aerosol particles, or on the proportional representation of the unattached/attached ratio (6.5 : 93.5 for residential places, 13.6 : 86.4 for caves due to lower concentration of free aerosols) and on the equilibrium factor. Thus conversion factor is 1.5 times higher in comparison with ICRP 65. Is this correct? Because a more precisely determined dose value would have a significant impact on radon remedies, or on restricting the time workers stay underground, a series of measurement was initiated in 2003 with the aim to specify input data, computation and errors in effective dose assessment in each one of the evaluated caves separately. The enhancement of personal dosimetry for underground work places includes a study of the given questions, from the following points of view in each cave: continual radon measurement; regular measurements of radon and its daughters to estimate the equilibrium factor and the presence of free 218Po; regular indoor air flow measurements to study the location of the radon supply and its transfer among individual areas of the cave; natural radioactive element content evaluation in subsoil and in water inside/outside, a study of the radon sources in the cave; determination of the free fraction from continual unattached and attached fraction measurement (grid and filter); thoron measurement. Air flow measurements provide very interesting information about the origin of "radon pockets" with very high radon concentration, and enable study of the location of the radon supply and its transfer among individual areas of the cave. Most of the results show the equilibrium factor around F = 0.2-0.7 and the unattached fraction around 2%-30%. One of the most important question remains: how accurately was the unattached fraction measured? Part of this project was to verify the influence of etched track detector position in the cave.

Climatic control on the growth of gigantic gypsum crystals within hypogenic caves (Naica mine, Mexico)?

NASA Astrophysics Data System (ADS)

Garofalo, Paolo S.; Fricker, Mattias B.; Günther, Detlef; Forti, Paolo; Mercuri, Anna-Maria; Loreti, Mara; Capaccioni, Bruno

2010-01-01

Three hypogenic caves within the Naica mine of Mexico ( Cueva de los Cristales — CLC, Ojo de la Reina — OR, and Cueva de las Velas — CLV) host spectacular gypsum crystals up to 11 m in length. These caves are close to another shallow cave of the area ( Cueva de las Espadas — CLE), with which they cover a 160 m-deep vertical section of the local drainage basin. Similar to other hypogenic caves, all these caves lack a direct connection with the land surface and should be unrelated with climate. A record of multi-technique fluid inclusion data and pollen spectra from cave and mine gypsum indicates surprisingly that climatic changes occurring at Naica could have controlled fluid composition in these caves, and hence crystal growth. Microthermometry and LA-ICP-Mass Spectrometry of fluid inclusions indicate that the shallow, chemically peculiar, saline fluid (up to 7.7 eq. wt.%NaCl) of CLE could have formed from evaporation, during a dry and hot climatic period. The fluid of the deep caves was instead of low salinity (˜ 3.5 eq. wt.% NaCl) and chemically homogeneous, and was poorly affected by evaporation. We propose that mixing of these two fluids, generated at different depths of the Naica drainage basin, determined the stable supersaturation conditions for the gigantic gypsum crystals to grow. Fluid mixing was controlled by the hydraulic communication between CLE and the other deep caves, and must have taken place during cycles of warm-dry and fresh-wet climatic periods, which are known to have occurred in the region. Pollen grains from a 35 ka-old gypsum crystal of CLC corresponds to a fairly homogenous catchment basin made of a mixed broadleaf wet forest, which suggests precipitation during a fresh-wet climatic period and confirms our interpretation of the fluid inclusion data. The unusual combination of geological and geochemical factors of Naica suggests that other hypogenic caves found elsewhere may not host similar crystals. However, this work shows that fluid inclusions and pollen spectra represent a useful tool for cave studies in general, and if used in future studies might be essential to unravel the mechanisms of hypogenic deposition.

Hypogenic speleogenesis in quartzite: The case of Corona 'e Sa Craba Cave (SW Sardinia, Italy)

NASA Astrophysics Data System (ADS)

Sauro, Francesco; De Waele, Jo; Onac, Bogdan P.; Galli, Ermanno; Dublyansky, Yuri; Baldoni, Eleonora; Sanna, Laura

2014-04-01

The paper presents a detailed study demonstrating the hypogenic origin of the Corona 'e Sa Craba quartzite cave in SW Sardinia (Italy). Although the quartzite host-rock of this cave derived from silicification of Cambrian dolostones and dissolution of carbonate remnants could have had a role in the speleogenesis, detailed morphologic and petrographic investigation revealed clear evidence of quartz dissolution without signs of mechanical erosion by running waters. Thin section microscopy and scanning electron microscope (SEM) images show pervasive dissolution morphologies, such as pits and notches on quartz crystals causing the deep arenization of the cave walls, suggesting that the dissolution of quartz had a primary role in the formation of the void. The study of secondary cave minerals and the sulfur isotopic composition of sulfates and sulfides, coupled with data on fluid inclusions, allowed reconstruction of the peculiar speleogenetic history of this hypogenic hydrothermal quartzite cave. The cave formed by reduced hydrothermal fluids, probably under basic-neutral pH in phreatic conditions. The presence of abundant cations of Ba2 + in reduced Cl-rich fluids enhanced the quartz dissolution rate, allowing the formation of the voids in deep settings. During the Late Oligocene uplift of the area, the hydrothermal fluids in the cave reached oxygen-rich conditions, thus a minerogenetic phase started with the deposition of barite when the temperature of the fluid was ≤ 50 °C. The presence of cinnabar crusts in the lower part of the cave walls and on the boulders suggests a later volcanic phase with Hg-rich vapors ascending from below. Other minerals such as alunite, basaluminite, gypsum and halloysite (typical of an acid sulfate alteration environment), and phosphates were formed in a final, much more recent stage. The δ34S values of the cave sulfate minerals indicate that S is derived from the remobilization of original Precambrian Pb-Zn Mississippi Valley Type ores. These last two stages did not significantly affect the morphology of the cave. The Corona 'e Sa Craba appears to be the world's first example of a hypogenic cave in quartzite where the speleogenetic mechanisms have been studied and reconstructed in detail, using a variety of modern methods. This study confirms that dissolution of quartz by thermal alkaline fluids at depth can produce large dissolutional voids in the apparently poorly soluble quartzite rocks.

Fast Inference with Min-Sum Matrix Product.

PubMed

Felzenszwalb, Pedro F; McAuley, Julian J

2011-12-01

The MAP inference problem in many graphical models can be solved efficiently using a fast algorithm for computing min-sum products of n × n matrices. The class of models in question includes cyclic and skip-chain models that arise in many applications. Although the worst-case complexity of the min-sum product operation is not known to be much better than O(n(3)), an O(n(2.5)) expected time algorithm was recently given, subject to some constraints on the input matrices. In this paper, we give an algorithm that runs in O(n(2) log n) expected time, assuming that the entries in the input matrices are independent samples from a uniform distribution. We also show that two variants of our algorithm are quite fast for inputs that arise in several applications. This leads to significant performance gains over previous methods in applications within computer vision and natural language processing.

Probabilistic cosmological mass mapping from weak lensing shear

DOE PAGES

Schneider, M. D.; Ng, K. Y.; Dawson, W. A.; ...

2017-04-10

Here, we infer gravitational lensing shear and convergence fields from galaxy ellipticity catalogs under a spatial process prior for the lensing potential. We demonstrate the performance of our algorithm with simulated Gaussian-distributed cosmological lensing shear maps and a reconstruction of the mass distribution of the merging galaxy cluster Abell 781 using galaxy ellipticities measured with the Deep Lens Survey. Given interim posterior samples of lensing shear or convergence fields on the sky, we describe an algorithm to infer cosmological parameters via lens field marginalization. In the most general formulation of our algorithm we make no assumptions about weak shear ormore » Gaussian-distributed shape noise or shears. Because we require solutions and matrix determinants of a linear system of dimension that scales with the number of galaxies, we expect our algorithm to require parallel high-performance computing resources for application to ongoing wide field lensing surveys.« less

Probabilistic Cosmological Mass Mapping from Weak Lensing Shear

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schneider, M. D.; Dawson, W. A.; Ng, K. Y.

2017-04-10

We infer gravitational lensing shear and convergence fields from galaxy ellipticity catalogs under a spatial process prior for the lensing potential. We demonstrate the performance of our algorithm with simulated Gaussian-distributed cosmological lensing shear maps and a reconstruction of the mass distribution of the merging galaxy cluster Abell 781 using galaxy ellipticities measured with the Deep Lens Survey. Given interim posterior samples of lensing shear or convergence fields on the sky, we describe an algorithm to infer cosmological parameters via lens field marginalization. In the most general formulation of our algorithm we make no assumptions about weak shear or Gaussian-distributedmore » shape noise or shears. Because we require solutions and matrix determinants of a linear system of dimension that scales with the number of galaxies, we expect our algorithm to require parallel high-performance computing resources for application to ongoing wide field lensing surveys.« less

Measuring radon concentrations and estimating dose in tourist caves.

PubMed

Martín Sánchez, A; de la Torre Pérez, J; Ruano Sánchez, A B; Naranjo Correa, F L

2015-11-01

Caves and mines are considered to be places of especial risk of exposure to (222)Rn. This is particularly important for guides and workers, but also for visitors. In the Extremadura region (Spain), there are two cave systems in which there are workers carrying out their normal everyday tasks. In one, visits have been reduced to maintain the conditions of temperature and humidity. The other comprises several caves frequently visited by school groups. The caves were radiologically characterised in order to estimate the dose received by workers or possible hazards for visitors. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Southwest Caves Reveal New Forms of Life

USGS Publications Warehouse

Wynne, J. Judson; Drost, Charles

2009-01-01

Caves in northern Arizona and western New Mexico are being researched and inventoried by scientists with the U.S. Geological Survey and cooperating agencies. Southwestern caves have been little studied, and scientists are now finding that these lightless and nutrient-poor natural systems are home to life forms found nowhere else on Earth. This research has identified unique communities of arthropods (insects, arachnids, and crustaceans) that include 3 new genera, or groups of species, and at least 15 new species - some only known to exist in a single cave. This exciting research is yielding information that will be used by resource managers to better understand and protect fragile and important Southwestern cave ecosystems.

Using Stan for Item Response Theory Models

ERIC Educational Resources Information Center

Ames, Allison J.; Au, Chi Hang

2018-01-01

Stan is a flexible probabilistic programming language providing full Bayesian inference through Hamiltonian Monte Carlo algorithms. The benefits of Hamiltonian Monte Carlo include improved efficiency and faster inference, when compared to other MCMC software implementations. Users can interface with Stan through a variety of computing…

Causal Inference and Explaining Away in a Spiking Network

PubMed Central

Moreno-Bote, Rubén; Drugowitsch, Jan

2015-01-01

While the brain uses spiking neurons for communication, theoretical research on brain computations has mostly focused on non-spiking networks. The nature of spike-based algorithms that achieve complex computations, such as object probabilistic inference, is largely unknown. Here we demonstrate that a family of high-dimensional quadratic optimization problems with non-negativity constraints can be solved exactly and efficiently by a network of spiking neurons. The network naturally imposes the non-negativity of causal contributions that is fundamental to causal inference, and uses simple operations, such as linear synapses with realistic time constants, and neural spike generation and reset non-linearities. The network infers the set of most likely causes from an observation using explaining away, which is dynamically implemented by spike-based, tuned inhibition. The algorithm performs remarkably well even when the network intrinsically generates variable spike trains, the timing of spikes is scrambled by external sources of noise, or the network is mistuned. This type of network might underlie tasks such as odor identification and classification. PMID:26621426

Causal Inference and Explaining Away in a Spiking Network.

PubMed

Moreno-Bote, Rubén; Drugowitsch, Jan

2015-12-01

While the brain uses spiking neurons for communication, theoretical research on brain computations has mostly focused on non-spiking networks. The nature of spike-based algorithms that achieve complex computations, such as object probabilistic inference, is largely unknown. Here we demonstrate that a family of high-dimensional quadratic optimization problems with non-negativity constraints can be solved exactly and efficiently by a network of spiking neurons. The network naturally imposes the non-negativity of causal contributions that is fundamental to causal inference, and uses simple operations, such as linear synapses with realistic time constants, and neural spike generation and reset non-linearities. The network infers the set of most likely causes from an observation using explaining away, which is dynamically implemented by spike-based, tuned inhibition. The algorithm performs remarkably well even when the network intrinsically generates variable spike trains, the timing of spikes is scrambled by external sources of noise, or the network is mistuned. This type of network might underlie tasks such as odor identification and classification.

The tardigrade fauna of Australian marine caves: with descriptions of nine new species of Arthrotardigrada.

PubMed

Jørgensen, Aslak; Boesgaard, Tom M; Møbjerg, Nadja; Kristensen, Reinhardt M

2014-05-28

Marine caves are known to support a rich macrofauna; however, few studies have focused on meiofauna. Marine cave meiofaunal tardigrades have been reported from Japan and the Mediterranean Sea and a preliminary list of species including a redescription of Actinarctus neretinus Grimaldi de Zio, D'Addabbo Gallo, Morone De Lucia, Vaccarella and Grimaldi, 1982 was reported from Fish Rock Cave and Jim's Cave on the coast of Australia. This study is the fourth in a series describing the unique meiofauna in two Australian submarine caves located off the coast of New South Wales, describing nine new species.        Only 67 tardigrades were collected from the two caves, yet these contained a high diversity of at least 16 different species which are quite different in the two caves. The fauna includes nine arthrotardigrade genera: Actinarctus, Batillipes, Dipodarctus, Halechiniscus, Raiarctus, Styraconyx, Tanarctus, Tholoarctus, and Wingstrandarctus. This fauna is different from that reported for the high energy beaches along the East Coast of Australia.        We describe nine new species comprising a single batillipedid and eight halechiniscids: Batillipes solitarius nov. sp., Dipodarctus australiensis nov. sp., Dipodarctus susannae nov. sp., Raiarctus jesperi nov. sp., Raiarctus katrinae nov. sp., Tanarctus hirsutospinosus nov. sp., Tholoarctus oleseni nov. sp., Wingstrandarctus stinae nov. sp. and Wingstrandarctus unsculptus nov. sp.

Unexpected diversity of sandflies (Diptera: Psychodidae) in tourist caves in Northern Thailand.

PubMed

Sukantamala, Jedsada; Sing, Kong-Wah; Jaturas, Narong; Polseela, Raxsina; Wilson, John-James

2017-11-01

Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity. DNA barcodes have been used for the identification of sandflies in Thailand. We collected sandflies using CDC light trap from four tourist caves in Northern Thailand. Female sandflies were provisionally sorted into 13 morphospecies and 19 unidentified specimens. DNA was extracted from the thorax and legs of sandflies and the DNA barcode region of cytochrome c oxidase I mtDNA amplified and sequenced. The specimens were sorted into 22 molecular operational taxonomic units (MOTU) based on the 145 DNA barcodes, which is significantly more than the morphospecies. Several of the taxa thought to be present in multiple caves, based on morphospecies sorting, split into cave-specific MOTU which likely represent cryptic species. Several MOTU reported in an earlier study from Wihan Cave, Thailand, were also found in these caves. This supports the use of DNA barcodes to investigate species diversity of sandflies and their useful role in surveillance of sandflies in Thailand.

3D Volume and Morphology of Perennial Cave Ice and Related Geomorphological Models at Scăriloara Ice Cave, Romania, from Structure from Motion, Ground Penetrating Radar and Total Station Surveys

NASA Astrophysics Data System (ADS)

Hubbard, J.; Onac, B. P.; Kruse, S.; Forray, F. L.

2017-12-01

Research at Scăriloara Ice Cave has proceeded for over 150 years, primarily driven by the presence and paleoclimatic importance of the large perennial ice block and various ice speleothems located within its galleries. Previous observations of the ice block led to rudimentary volume estimates of 70,000 to 120,000 cubic meters (m3), prospectively placing it as one of the world's largest cave ice deposits. The cave morphology and the surface of the ice block are now recreated in a total station survey-validated 3D model, produced using Structure from Motion (SfM) software. With the total station survey and the novel use of ArcGIS tools, the SfM validation process is drastically simplified to produce a scaled, georeferenced, and photo-texturized 3D model of the cave environment with a root-mean-square error (RMSE) of 0.24 m. Furthermore, ground penetrating radar data was collected and spatially oriented with the total station survey to recreate the ice block basal surface and was combined with the SfM model to create a model of the ice block itself. The resulting ice block model has a volume of over 118,000 m3 with an uncertainty of 9.5%, with additional volumes left un-surveyed. The varying elevation of the ice block basal surface model reflect specific features of the cave roof, such as areas of enlargement, shafts, and potential joints, which offer further validation and inform theories on cave and ice genesis. Specifically, a large depression area was identified as a potential area of initial ice growth. Finally, an ice thickness map was produced that will aid in the designing of future ice coring projects. This methodology presents a powerful means to observe and accurately characterize and measure cave and cave ice morphologies with ease and affordability. Results further establish the significance of Scăriloara's ice block to paleoclimate research, provide insights into cave and ice block genesis, and aid future study design.

PATTERNS OF ENDEMISM OF THE EASTERN NORTH AMERICAN CAVE FAUNA

EPA Science Inventory

Over 250 species of obligate terrestrial cave-dwelling animals (troglobionts) are known from single caves in the eastern United States. We investigate their geographic distribution, especially in relation to other troglobionts. We relate these patterns to taxonomic group, oppor...

Coupling cosmogenic dating and magnetostratigraphy to constrain the chronological evolution of peri-Mediterranean karsts during the Messinian and the Pliocene: Example of Ardèche Valley, Southern France

NASA Astrophysics Data System (ADS)

Tassy, Aurélie; Mocochain, Ludovic; Bellier, Olivier; Braucher, Régis; Gattacceca, Jérôme; Bourlès, Didier

2013-05-01

The Ardèche River entrenches a deep canyon in the Saint Remèze plateau from Vallon-Pont-d'Arc to its confluence with the Rhône. This plateau is part of the Ardèche Cretaceous limestone plateau located at the edge of the Mid Rhône valley. It is characterized by dense multi-level cave systems, such as Saint-Marcel Cave (50 km of mapped passages) and Chauvet Cave, famous for its paleolithic paintings. Until now, and despite the absence of absolute dating, stepping of the Saint Remèze cave levels has been interpreted as the result of the Messinian salinity crisis. To clarify this interpretation, fluvial sediments of cave systems have been absolutely dated, while cave sediments have been demonstrated to be ideal for "burial dating" based on the different radioactive decay rates of the in situ-produced cosmogenic nuclides 10Be and 26Al. Combined with magnetostratigraphy and constrained by the Lower Ardèche base-level curve, this contribution provides an absolute dating for each cave level. The obtained results are consistent with the stepping per ascensum model of both surface landforms and caves for the Messinian-Pliocene eustatic cycle. Finally, this study provides evidence for a rise of the Ardèche river level to 40 m above the Pliocene abandonment surface. The second active period of the Chauvet Cave is evidenced between 2.96 and 2.18 Ma (cave filling). An absolute dating for the Pliocene abandonment surface between 1.94 and 1.77 Ma is also obtained, which brings new understandings to the geodynamic evolution of the area. The Lower Ardèche has been uplifted after the Pliocene, with a rate of 0.03 mm/year since 1.77 Ma.

The CAVE (TM) automatic virtual environment: Characteristics and applications

NASA Technical Reports Server (NTRS)

Kenyon, Robert V.

1995-01-01

Virtual reality may best be defined as the wide-field presentation of computer-generated, multi-sensory information that tracks a user in real time. In addition to the more well-known modes of virtual reality -- head-mounted displays and boom-mounted displays -- the Electronic Visualization Laboratory at the University of Illinois at Chicago recently introduced a third mode: a room constructed from large screens on which the graphics are projected on to three walls and the floor. The CAVE is a multi-person, room sized, high resolution, 3D video and audio environment. Graphics are rear projected in stereo onto three walls and the floor, and viewed with stereo glasses. As a viewer wearing a location sensor moves within its display boundaries, the correct perspective and stereo projections of the environment are updated, and the image moves with and surrounds the viewer. The other viewers in the CAVE are like passengers in a bus, along for the ride. 'CAVE,' the name selected for the virtual reality theater, is both a recursive acronym (Cave Automatic Virtual Environment) and a reference to 'The Simile of the Cave' found in Plato's 'Republic,' in which the philosopher explores the ideas of perception, reality, and illusion. Plato used the analogy of a person facing the back of a cave alive with shadows that are his/her only basis for ideas of what real objects are. Rather than having evolved from video games or flight simulation, the CAVE has its motivation rooted in scientific visualization and the SIGGRAPH 92 Showcase effort. The CAVE was designed to be a useful tool for scientific visualization. The Showcase event was an experiment; the Showcase chair and committee advocated an environment for computational scientists to interactively present their research at a major professional conference in a one-to-many format on high-end workstations attached to large projection screens. The CAVE was developed as a 'virtual reality theater' with scientific content and projection that met the criteria of Showcase.

Application of spectral decomposition of ²²²Rn activity concentration signal series measured in Niedźwiedzia Cave to identification of mechanisms responsible for different time-period variations.

PubMed

Przylibski, Tadeusz Andrzej; Wyłomańska, Agnieszka; Zimroz, Radosław; Fijałkowska-Lichwa, Lidia

2015-10-01

The authors present an application of spectral decomposition of (222)Rn activity concentration signal series as a mathematical tool used for distinguishing processes determining temporal changes of radon concentration in cave air. The authors demonstrate that decomposition of monitored signal such as (222)Rn activity concentration in cave air facilitates characterizing the processes affecting changes in the measured concentration of this gas. Thanks to this, one can better correlate and characterize the influence of various processes on radon behaviour in cave air. Distinguishing and characterising these processes enables the understanding of radon behaviour in cave environment and it may also enable and facilitate using radon as a precursor of geodynamic phenomena in the lithosphere. Thanks to the conducted analyses, the authors confirmed the unquestionable influence of convective air exchange between the cave and the atmosphere on seasonal and short-term (diurnal) changes in (222)Rn activity concentration in cave air. Thanks to the applied methodology of signal analysis and decomposition, the authors also identified a third process affecting (222)Rn activity concentration changes in cave air. This is a deterministic process causing changes in radon concentration, with a distribution different from the Gaussian one. The authors consider these changes to be the effect of turbulent air movements caused by the movement of visitors in caves. This movement is heterogeneous in terms of the number of visitors per group and the number of groups visiting a cave per day and per year. Such a process perfectly elucidates the observed character of the registered changes in (222)Rn activity concentration in one of the decomposed components of the analysed signal. The obtained results encourage further research into precise relationships between the registered (222)Rn activity concentration changes and factors causing them, as well as into using radon as a precursor of geodynamic phenomena in the lithosphere. Copyright © 2015 Elsevier Ltd. All rights reserved.

Estimation of deep infiltration in unsaturated limestone environments using cave lidar and drip count data

NASA Astrophysics Data System (ADS)

Mahmud, K.; Mariethoz, G.; Baker, A.; Treble, P. C.; Markowska, M.; McGuire, E.

2016-01-01

Limestone aeolianites constitute karstic aquifers covering much of the western and southern Australian coastal fringe. They are a key groundwater resource for a range of industries such as winery and tourism, and provide important ecosystem services such as habitat for stygofauna. Moreover, recharge estimation is important for understanding the water cycle, for contaminant transport, for water management, and for stalagmite-based paleoclimate reconstructions. Caves offer a natural inception point to observe both the long-term groundwater recharge and the preferential movement of water through the unsaturated zone of such limestone. With the availability of automated drip rate logging systems and remote sensing techniques, it is now possible to deploy the combination of these methods for larger-scale studies of infiltration processes within a cave. In this study, we utilize a spatial survey of automated cave drip monitoring in two large chambers of Golgotha Cave, south-western Western Australia (SWWA), with the aim of better understanding infiltration water movement and the relationship between infiltration, stalactite morphology, and unsaturated zone recharge. By applying morphological analysis of ceiling features from Terrestrial LiDAR (T-LiDAR) data, coupled with drip time series and climate data from 2012 to 2014, we demonstrate the nature of the relationships between infiltration through fractures in the limestone and unsaturated zone recharge. Similarities between drip rate time series are interpreted in terms of flow patterns, cave chamber morphology, and lithology. Moreover, we develop a new technique to estimate recharge in large-scale caves, engaging flow classification to determine the cave ceiling area covered by each flow category and drip data for the entire observation period, to calculate the total volume of cave discharge. This new technique can be applied to other cave sites to identify highly focussed areas of recharge and can help to better estimate the total recharge volume.

Estimation of deep infiltration in unsaturated limestone environments using cave LiDAR and drip count data

NASA Astrophysics Data System (ADS)

Mahmud, K.; Mariethoz, G.; Baker, A.; Treble, P. C.; Markowska, M.; McGuire, E.

2015-09-01

Limestone aeolianites constitute karstic aquifers covering much of the western and southern Australian coastal fringe. They are a key groundwater resource for a range of industries such as winery and tourism, and provide important ecosystem services such as habitat for stygofauna. Moreover, recharge estimation is important for understanding the water cycle, for contaminant transport, for water management and for stalagmite-based paleoclimate reconstructions. Caves offer a natural inception point to observe both the long-term groundwater recharge and the preferential movement of water through the unsaturated zone of such limestone. With the availability of automated drip rate logging systems and remote sensing techniques, it is now possible to deploy the combination of these methods for larger scale studies of infiltration processes within a cave. In this study, we utilize a spatial survey of automated cave drip monitoring in two large chambers of the Golgotha Cave, South-West Western Australia (SWWA), with the aim of better understanding infiltration water movement and the relationship between infiltration, stalactite morphology and unsaturated zone recharge. By applying morphological analysis of ceiling features from Terrestrial LiDAR (T-LiDAR) data, coupled with drip time series and climate data from 2012-2014, we demonstrate the nature of the relationships between infiltration through fractures in the limestone and unsaturated zone recharge. Similarities between drip-rate time series are interpreted in terms of flow patterns, cave chamber morphology and lithology. Moreover, we develop a new technique to estimate recharge in large scale caves, engaging flow classification to determine the cave ceiling area covered by each flow category and drip data for the entire observation period, to calculate the total volume of cave discharge. This new technique can be applied to other cave sites to identify highly focused areas of recharge and can help to better estimate the total recharge volume.

Luminescent microbanding in speleothems: High-resolution chronology and paleoclimate

NASA Astrophysics Data System (ADS)

Shopov, Y. Y.; Ford, D. C.; Schwarcz, H. P.

1994-05-01

When illuminated by ultraviolet light, many calcite speleothems (stalagmites, stalactites, flowstones) display luminescence caused by the presence of organic (humic) substances occluded in the calcite. The amplitude of luminescence varies in a banded pattern parallel to growth layering. Through 14C and thermal ionization mass spectrometry uranium-series dating, we show that cyclical oscillations in the luminescence have periodicities ranging from a few days to ≥105 yr. A well-defined annual cycle is present in many vadose-zone speleothems and can be used to define the chronology of short-term events. This cycle is probably a response to hydrological events in the recharge to the cave. Longer term oscillations are inferred to be controlled by climate, through its effect on organic activity in the overlying soil.

Boosting Bayesian parameter inference of stochastic differential equation models with methods from statistical physics

NASA Astrophysics Data System (ADS)

Albert, Carlo; Ulzega, Simone; Stoop, Ruedi

2016-04-01

Measured time-series of both precipitation and runoff are known to exhibit highly non-trivial statistical properties. For making reliable probabilistic predictions in hydrology, it is therefore desirable to have stochastic models with output distributions that share these properties. When parameters of such models have to be inferred from data, we also need to quantify the associated parametric uncertainty. For non-trivial stochastic models, however, this latter step is typically very demanding, both conceptually and numerically, and always never done in hydrology. Here, we demonstrate that methods developed in statistical physics make a large class of stochastic differential equation (SDE) models amenable to a full-fledged Bayesian parameter inference. For concreteness we demonstrate these methods by means of a simple yet non-trivial toy SDE model. We consider a natural catchment that can be described by a linear reservoir, at the scale of observation. All the neglected processes are assumed to happen at much shorter time-scales and are therefore modeled with a Gaussian white noise term, the standard deviation of which is assumed to scale linearly with the system state (water volume in the catchment). Even for constant input, the outputs of this simple non-linear SDE model show a wealth of desirable statistical properties, such as fat-tailed distributions and long-range correlations. Standard algorithms for Bayesian inference fail, for models of this kind, because their likelihood functions are extremely high-dimensional intractable integrals over all possible model realizations. The use of Kalman filters is illegitimate due to the non-linearity of the model. Particle filters could be used but become increasingly inefficient with growing number of data points. Hamiltonian Monte Carlo algorithms allow us to translate this inference problem to the problem of simulating the dynamics of a statistical mechanics system and give us access to most sophisticated methods that have been developed in the statistical physics community over the last few decades. We demonstrate that such methods, along with automated differentiation algorithms, allow us to perform a full-fledged Bayesian inference, for a large class of SDE models, in a highly efficient and largely automatized manner. Furthermore, our algorithm is highly parallelizable. For our toy model, discretized with a few hundred points, a full Bayesian inference can be performed in a matter of seconds on a standard PC.

A Low-cost data-logging platform for long-term field sensor deployment in caves

NASA Astrophysics Data System (ADS)

Cruz, M. A.; Myre, J. M.; Covington, M. D.

2014-12-01

Active karst systems are notoriously inhospitable environments for humans and equipment. Caves require equipment to cope with high humidity, high velocity flows, submersion, sediment loads, and harassment from local fauna. Equipment taken into caves is often considered "consumable" due to the extreme nature of cave environments and the difficulty of transport. Further, because many interesting monitoring locations within caves can be considered remote, it is ideal for electronic monitoring platforms to require minimal maintenance of parts and power supplies. To partially address the challenge of scientifically monitoring such environments, we have developed an arduino based platform for environmental monitoring of cave systems. The arduino is a general purpose open source microcontroller that is easily programmed with only a basic knowledge of the C programming language. The arduino is capable of controlling digital and analog electronics in a modular fashion. Using this capability, we have created a platform for monitoring CO2 levels in cave systems that costs one-tenth of a comparable commercial system while using a fraction of the power. The modular nature of the arduino system allows the incorporation of additional environmental sensors in the future.

Genomic sequencing of Pleistocene cave bears

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noonan, James P.; Hofreiter, Michael; Smith, Doug

2005-04-01

Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome,more » the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.« less

Study of the environmental variables affecting the natural preservation of the Altamira Cave paintings located at Santillana del Mar, Spain

NASA Astrophysics Data System (ADS)

Quindos, L. S.; Bonet, A.; Diaz-Caneja, N.; Fernandez, P. L.; Gutierrez, I.; Solana, J. R.; Soto, J.; Villar, E.

A study was carried out over a period of more than two years of the seasonal variations shown by the different variables that determine the microclimatic and chromatic characteristics of the Altamira Cave, Spain, under natural conditions, i.e. in the absence of visitors to the cave. The Altamira Cave contains 16,000-year-old prehistoric paintings and as such is a priceless legacy from the distant past. Temperatures of the air, floors and roofs, air humidity, and CO 2 concentrations of the different chambers of the cave were measured. Flow rate and chemical composition of the waters flowing into the paintings chamber were also analyzed. A chromatic characterization of the paintings, determining the psychrometric coordinates of the colour, lightness, chroma and hue, was made. This study has not only enabled presentation of the state of conservation of the famous polychrome roof of the Paintings Chamber, but has also supplied a reference point for later studies. Future experiments could be made with various controlled regimes of visitors to the cave in order to establish suitable criteria for the best possible preservation of the cave paintings.

Gene Regulatory Network Inferences Using a Maximum-Relevance and Maximum-Significance Strategy

PubMed Central

Liu, Wei; Zhu, Wen; Liao, Bo; Chen, Xiangtao

2016-01-01

Recovering gene regulatory networks from expression data is a challenging problem in systems biology that provides valuable information on the regulatory mechanisms of cells. A number of algorithms based on computational models are currently used to recover network topology. However, most of these algorithms have limitations. For example, many models tend to be complicated because of the “large p, small n” problem. In this paper, we propose a novel regulatory network inference method called the maximum-relevance and maximum-significance network (MRMSn) method, which converts the problem of recovering networks into a problem of how to select the regulator genes for each gene. To solve the latter problem, we present an algorithm that is based on information theory and selects the regulator genes for a specific gene by maximizing the relevance and significance. A first-order incremental search algorithm is used to search for regulator genes. Eventually, a strict constraint is adopted to adjust all of the regulatory relationships according to the obtained regulator genes and thus obtain the complete network structure. We performed our method on five different datasets and compared our method to five state-of-the-art methods for network inference based on information theory. The results confirm the effectiveness of our method. PMID:27829000

Morphology and evolution of sulphuric acid caves in South Italy

NASA Astrophysics Data System (ADS)

D'Angeli, Ilenia M.; De Waele, Jo; Galdenzi, Sandro; Madonia, Giuliana; Parise, Mario; Vattano, Marco

2016-04-01

Sulphuric acid speleogenesis (SAS) related to the upwelling of acid water enriched in H2S and CO2 represents an unusual way of cave development. Since meteoric infiltration waters are not necessarily involved in speleogenesis, caves can form without the typical associated karst expressions (i.e. dolines) at the surface. The main mechanism of sulphuric acid dissolution is the oxidation of H2S (Jones et al., 2015) which can be amplified by bacterial mediation (Engel et al., 2004). In these conditions, carbonate dissolution associated with gypsum replacement, is generally believed to be faster than the normal epigenic one (De Waele et al., 2016). In Italy several SAS caves have been identified, but only few systems have been studied in detail: Frasassi and Acquasanta Terme (Marche)(Galdenzi et al., 2010), Monte Cucco (Umbria) (Galdenzi & Menichetti, 1995), and Montecchio (Tuscany) (Piccini et al., 2015). Other preliminary studies have been carried out in Calabria (Galdenzi, 2007) and Sicily (De Waele et al., 2016). Several less studied SAS cave systems located in South Italy, and in particular in Apulia (Santa Cesarea Terme), Sicily (Acqua Fitusa, Acqua Mintina) and Calabria (Mt. Sellaro and Cassano allo Ionio) have been selected in the framework of a PhD thesis on SAS caves and their speleogenesis. Using both limestone tablet weight loss (Galdenzi et al., 2012) and micro erosion meter (MEM) (Furlani et al., 2010) methods the dissolution rate above and under water in the caves will be quantified. Geomorphological observations, landscape analysis using GIS tools, and the analysis of gypsum and other secondary minerals (alunite and jarosite) (stable isotopes and dating) will help to reconstruct the speleogenetic stages of cave formation. Preliminary microbiological analysis will determine the microbial diversity and ecology in the biofilms. References Engel S.A., Stern L.A., Bennett P.C., 2004 - Microbial contributions to cave formation: New insight into sulfuric acid speleogenesis. Geology, 32: 369-372. De Waele J., Audra P., Madonia G., Vattano M., Plan L., D'Angeli I.M., Bigot J.-Y., Nobécourt J.-C., 2016 - Sulfuric acid speleogenesis (SAS) close to the water table: examples from southern France, Austria, and Sicily. Geomorphology, 253: 452-467. Furlani S., Cucchi F., Odorico R., 2010 - A new method to study micro-topographical changes in the intertidal zone: one year of TMEM measurements on a limestone removable slab (RRS). Z. Geomorph., 54(2): 137-151. Galdenzi S., 1997 - Initial geological observations in caves bordering the Sibari plain (southern Italy). J. Cave Karst Stud., 59: 81-86. Galdenzi S., 2012 - Corrosion of limestone tablets in sulfidic ground-water: measurements and speleogenetic implications. Int. J. Spel., 41(2): 149-159. Galdenzi S., Menichetti M., 1995 - Occurrence of hypogenic caves in a karst region: examples from central Italy. Environmental Geology, 26: 39-47. Galdenzi S., Cocchioni F., Filipponi G., Selvaggio R., Scuri S., Morichetti L., Cocchioni M., 2010 - The sulfidic thermal caves of Acquasanta Terme (central Italy). J. Cave Karst Stud. 72(1): 43-58. Jones, D.S., Polerecky, L., Galdenzi, S., Dempsey, B.A., Macalady, J.L., 2015 - Fate of sulfide in the Frasassi cave system and implications for sulfuric acid speleogenesis. Chemical Geology, 410: 21-27.

THE MID-LATITUDE BIODIVERSITY RIDGE IN TERRESTRIAL CAVE FAUNA

EPA Science Inventory

The world's obligate cave-dwelling fauna holds considerable promise for biogeographic analysis because it represents a large number of independent evolutionary experiments in isolation in caves and adaptation to subterranean life. We focus on seven north temperate regions of at l...

An experimental study on Sokkuram Cave Temple dome's indoor environment using a miniature model in winter season

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kong, S.H.; Chung, K.S.; Park, J.S.

1999-07-01

Currently, there are many researches on the analysis of indoor environment in Sokkuram Cave Temple. However, there is not enough researches about an experimental study on the dome's indoor environment in Sokkuram Cave Temple using a miniature model. The purpose of this investigation is to measure and analyze characteristics of indoor environment such as relative humidity, dry bulb temperature and air velocity in the miniature model of Sokkuram Cave dome during winter season.

Network Inference via the Time-Varying Graphical Lasso

PubMed Central

Hallac, David; Park, Youngsuk; Boyd, Stephen; Leskovec, Jure

2018-01-01

Many important problems can be modeled as a system of interconnected entities, where each entity is recording time-dependent observations or measurements. In order to spot trends, detect anomalies, and interpret the temporal dynamics of such data, it is essential to understand the relationships between the different entities and how these relationships evolve over time. In this paper, we introduce the time-varying graphical lasso (TVGL), a method of inferring time-varying networks from raw time series data. We cast the problem in terms of estimating a sparse time-varying inverse covariance matrix, which reveals a dynamic network of interdependencies between the entities. Since dynamic network inference is a computationally expensive task, we derive a scalable message-passing algorithm based on the Alternating Direction Method of Multipliers (ADMM) to solve this problem in an efficient way. We also discuss several extensions, including a streaming algorithm to update the model and incorporate new observations in real time. Finally, we evaluate our TVGL algorithm on both real and synthetic datasets, obtaining interpretable results and outperforming state-of-the-art baselines in terms of both accuracy and scalability. PMID:29770256

DOE Office of Scientific and Technical Information (OSTI.GOV)

Na, Man Gyun; Oh, Seungrohk

A neuro-fuzzy inference system combined with the wavelet denoising, principal component analysis (PCA), and sequential probability ratio test (SPRT) methods has been developed to monitor the relevant sensor using the information of other sensors. The parameters of the neuro-fuzzy inference system that estimates the relevant sensor signal are optimized by a genetic algorithm and a least-squares algorithm. The wavelet denoising technique was applied to remove noise components in input signals into the neuro-fuzzy system. By reducing the dimension of an input space into the neuro-fuzzy system without losing a significant amount of information, the PCA was used to reduce themore » time necessary to train the neuro-fuzzy system, simplify the structure of the neuro-fuzzy inference system, and also, make easy the selection of the input signals into the neuro-fuzzy system. By using the residual signals between the estimated signals and the measured signals, the SPRT is applied to detect whether the sensors are degraded or not. The proposed sensor-monitoring algorithm was verified through applications to the pressurizer water level, the pressurizer pressure, and the hot-leg temperature sensors in pressurized water reactors.« less

Fast algorithms for computing phylogenetic divergence time.

PubMed

Crosby, Ralph W; Williams, Tiffani L

2017-12-06

The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. For example a study of 349 primate taxa was estimated to require over 9 months of processing time. In this work, we present a new algorithm, AncestralAge, that significantly improves the performance of the divergence time process. As part of AncestralAge, we demonstrate a new method for the computation of phylogenetic likelihood and our experiments show a 90% improvement in likelihood computation time on the aforementioned dataset of 349 primates taxa with over 60,000 DNA base pairs. Additionally, we show that our new method for the computation of the Bayesian prior on node ages reduces the running time for this computation on the 349 taxa dataset by 99%. Through the use of these new algorithms we open up the ability to perform divergence time inference on large phylogenetic studies.

Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona.

PubMed

Ikner, Luisa A; Toomey, Rickard S; Nolan, Ginger; Neilson, Julia W; Pryor, Barry M; Maier, Raina M

2007-01-01

Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year-1) and compared to samples taken from areas designated as having medium (30-40 visitors year-1) and low (2-3 visitors year-1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations.

Determination of Sinkholes with Different Geophysical Techniques; A Case Study in Yarımburgaz, Küçükçekmece Lake NW Istanbul, Turkey

NASA Astrophysics Data System (ADS)

Karabulut, Savas; Cengiz Cinku, Mualla; Tezel, Okan; Dedecan, Hasan; Oygo, Azat

2016-04-01

The Yarımburgaz cave which is located in the city of Istanbul, NW Turkey plays an important host to the first human culture and preserve significant archaeological and paleontological resources. The cave was formed as a result of a subterranean stream erosion on the limestones of the Eocene Kırklareli formation. It has been reported that a double cave with upper and lower entrance chambers exist, although no geophysical research was conducted to detect the cave's trunk passages and the extend of the sediment fill inside the cave. The aim of this study was to test the preferred order for detection the response to different geophysical methods applied on the cave. We therefore carried out an a series of geophysical study to determine the size, position, and depth of sinkholes inside the caves. Integrated methodological approaches including multichannel analysis of surface wave (MASW) 2- microtremor array method, 3-single station microtremor measurements, 4- electrical tomography (ET) measuruments and 5-microgravity imaging showed that the geophysical response was succesfully applied. Based upon the flow-chart we concluded that the microgravity survey should be applied as a first step to detect the air-filled void and the geometry of the cave. The electric tomography method was well applied showing high resistivity values across the voids. The surface wave method showed that the low-velocity zones are detected in various locations of the cave. In addition we the results of MASW and ReMi methods showed clearly the density variation in the lateral direction. Fundamental frequency value above void decraese according the properties of geological units in lateral directional, especially when they are engineering rock like limestone.

Methane concentration and isotopic composition (δ13C-CH4) in the Nerja Cave system (South Spain)

NASA Astrophysics Data System (ADS)

Vadillo, Iñaki; Etiope, Giuseppe; Benavente, José; Ojeda, Lucia; Liñán, Cristina; Carrasco, Francisco

2016-04-01

Air in underground caves often has methane (CH4) concentrations below the atmospheric level, due to methanotrophic or other unkown CH4 consuming processes. Caves are thus considered a potential sink for atmospheric methane. If globally important, this underground CH4 oxidation should be taken into account in the atmospheric methane budget, in addition to the known soil methanotrophy and tropospheric/stratospheric sinks. A large set of data is however necessary to understand how and how much methane from external atmospheric air is consumed in the caves. While methane concentration data are available for several caves worldwide, its isotopic composition and variations in space and time are poorly documented. We measured methane concentration and stable C isotope composition (δ13C) in the Nerja cave (Southern Spain) air during two surveys in March and April 2015. CH4 concentration decreases progressively from the more external cave rooms, with atmospheric levels of 1.9 ppmv, to the more internal and isolated rooms down to 0.5 ppmv. δ13C increases correspondingly from -47 ‰ to -41 ‰ (VPDB). CH4 is systematically 13C-enriched (δ13C > -45) in areas of the cave where the concentration is below 1.4 ppmv. This combination of concentration decrease and 13C-enrichment towards the more internal and isolated zones of the cave confirms the importance of CH4 oxidation, likely driven by methanotrophic bacteria. Further data, including stable H isotope composition of sub-atmospheric CH4 concentrations, CO2 and microbial analyses, shall be acquired over time to assess the actual role of methanotrophic bacteria and seasonal controls in the CH4 consumption process.

Retreat and extinction of the Late Pleistocene cave bear ( Ursus spelaeus sensu lato)

NASA Astrophysics Data System (ADS)

Baca, Mateusz; Popović, Danijela; Stefaniak, Krzysztof; Marciszak, Adrian; Urbanowski, Mikołaj; Nadachowski, Adam; Mackiewicz, Paweł

2016-12-01

The cave bear ( Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 14C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100-24,300 cal. years BP. The time is only slightly earlier, i.e. 27,000-26,100 cal. years BP, when young dates without associated collagen data are excluded. The demise of cave bear falls within the coldest phase of the last glacial period, Greenland Stadial 3. This finding and the significant decrease in the cave bear records with cooling indicate that the drastic climatic changes were responsible for its extinction. Climate deterioration lowered vegetation productivity, on which the cave bear strongly depended as a strict herbivore. The distribution of the last cave bear records in Europe suggests that this animal was vanishing by fragmentation into subpopulations occupying small habitats. One of them was the Kraków-Częstochowa Upland in Poland, where we discovered the latest record of the cave bear and also two other, younger than 25,000 14C years BP. The relatively long survival of this bear in karst regions may result from suitable microclimate and continuous access to water provided by deep aquifers, indicating a refugial role of such regions in the Pleistocene for many species.

Retreat and extinction of the Late Pleistocene cave bear (Ursus spelaeus sensu lato).

PubMed

Baca, Mateusz; Popović, Danijela; Stefaniak, Krzysztof; Marciszak, Adrian; Urbanowski, Mikołaj; Nadachowski, Adam; Mackiewicz, Paweł

2016-12-01

The cave bear (Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 14 C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100-24,300 cal. years BP. The time is only slightly earlier, i.e. 27,000-26,100 cal. years BP, when young dates without associated collagen data are excluded. The demise of cave bear falls within the coldest phase of the last glacial period, Greenland Stadial 3. This finding and the significant decrease in the cave bear records with cooling indicate that the drastic climatic changes were responsible for its extinction. Climate deterioration lowered vegetation productivity, on which the cave bear strongly depended as a strict herbivore. The distribution of the last cave bear records in Europe suggests that this animal was vanishing by fragmentation into subpopulations occupying small habitats. One of them was the Kraków-Częstochowa Upland in Poland, where we discovered the latest record of the cave bear and also two other, younger than 25,000 14 C years BP. The relatively long survival of this bear in karst regions may result from suitable microclimate and continuous access to water provided by deep aquifers, indicating a refugial role of such regions in the Pleistocene for many species.

Dissolved organic matter in the unsaturated zone: the view from the cave

NASA Astrophysics Data System (ADS)

Baker, A.; Duan, W.; Rutlidge, H.; McDonough, L.; Oudone, P.; Meredith, K.; Andersen, M. S.; O'Carroll, D. M.; Coleborn, K.; Treble, P. C.

2017-12-01

Soil organic matter content is typically a few percent of the total soil composition. Diffuse recharge can mobilise some of this soil-derived organic matter. While soil pore water dissolved organic matter (DOM) concentrations are up to 100 ppm, the resulting groundwater dissolved organic matter concentration is typically less than 2ppm. Dissolved organic matter transported from the soil can be both biodegraded and sorbed to minerals, and the relative importance of these two processes in the unsaturated zone is poorly understood. Caves in karstified limestone uniquely provide direct access to water percolating from the soil to the groundwater. Cave percolation waters can be analysed for their DOM concentration and character. This provides insights into the extent and type of biological and chemical processing of DOM during transport from the soil to the groundwater. We determine the concentration and characteristics of DOM in cave percolation waters using liquid chromatography (LC-OCD) and optical spectrophotometry (fluorescence and absorbance). We sample DOM from multiple caves in SE Australia (Cathedral Cave, Wellington; South Glory and Harrie Wood Caves, Yarrangobilly), permitting comparison of unsaturated zone DOM properties at different depths (up to 30m below land surface) and different climate zones (montane and temperate). We use caves with long-term hydrological monitoring programs so that DOM in waters of contrasting residence times can be compared. Additionally, we compare these cave percolation water DOM characteristics to those from local and regional groundwater, sampled from nearby wells. Our results will help improve our understanding of how DOM is processed from soil to groundwater, and is also relevant to speleothem scientists interested in using organic matter preserved in speleothems as a paleoclimate or paleoenvironmental proxy.

Marine Caves of the Mediterranean Sea: A Sponge Biodiversity Reservoir within a Biodiversity Hotspot

PubMed Central

Gerovasileiou, Vasilis; Voultsiadou, Eleni

2012-01-01

Marine caves are widely acknowledged for their unique biodiversity and constitute a typical feature of the Mediterranean coastline. Herein an attempt was made to evaluate the ecological significance of this particular ecosystem in the Mediterranean Sea, which is considered a biodiversity hotspot. This was accomplished by using Porifera, which dominate the rocky sublittoral substrata, as a reference group in a meta-analytical approach, combining primary research data from the Aegean Sea (eastern Mediterranean) with data derived from the literature. In total 311 species from all poriferan classes were recorded, representing 45.7% of the Mediterranean Porifera. Demospongiae and Homoscleromorpha are highly represented in marine caves at the family (88%), generic (70%), and species level (47.5%), the latter being the most favored group along with Dictyoceratida and Lithistida. Several rare and cave-exclusive species were reported from only one or few caves, indicating the fragmentation and peculiarity of this unique ecosystem. Species richness and phylogenetic diversity varied among Mediterranean areas; the former was positively correlated with research effort, being higher in the northern Mediterranean, while the latter was generally higher in caves than in the overall sponge assemblages of each area. Resemblance analysis among areas revealed that cavernicolous sponge assemblages followed a pattern quite similar to that of the overall Mediterranean assemblages. The same pattern was exhibited by the zoogeographic affinities of cave sponges: species with Atlanto-Mediterranean distribution and Mediterranean endemics prevailed (more than 40% each), 70% of them having warm-water affinities, since most caves were studied in shallow waters. According to our findings, Mediterranean marine caves appear to be important sponge biodiversity reservoirs of high representativeness and great scientific interest, deserving further detailed study and protection. PMID:22808070

A Low-Power Sensor Network for Long Duration Monitoring in Deep Caves

NASA Astrophysics Data System (ADS)

Silva, A.; Johnson, I.; Bick, T.; Winclechter, C.; Jorgensen, A. M.; Teare, S. W.; Arechiga, R. O.

2010-12-01

Monitoring deep and inaccessible caves is important and challenging for a variety of reasons. It is of interest to study caves environments for understanding cave ecosystems, and human impact on the ecosystems. Caves may also hold clues to past climate changes. Cave instrumentation must however carry out its job with minimal human intervention and without disturbing the fragile environment. This requires unobtrusive and autonomous instrumentation. Earth-bound caves can also serve as analogs for caves on other planets and act as testbeds for autonomous sensor networks. Here we report on a project to design and implement a low-power, ad-hoc, wireless sensor network for monitoring caves and similar environments. The implemented network is composed of individual nodes which consist of a sensor, processing unit, memory, transceiver and a power source. Data collected at these nodes is transmitted through a wireless ZigBee network to a central data collection point from which the researcher may transfer collected data to a laptop for further analysis. The project accomplished a node design with a physical footprint of 2 inches long by 3 inches wide. The design is based on the EZMSP430-RF2480, a Zigbee hardware base offered by Texas Instruments. Five functioning nodes have been constructed at very low cost and tested. Due to the use of an external analog-to-digital converter the design was able to achieve a 16-bit resolution. The operational time achieved by the prototype was calculated to be approximately 80 days of autonomous operation while sampling once per minute. Each node is able to support and record data from up to four different sensors.

Stratigraphy, U-Th chronology, and paleoenvironments at Gladysvale Cave: insights into the climatic control of South African hominin-bearing cave deposits.

PubMed

Pickering, Robyn; Hancox, Phillip J; Lee-Thorp, Julia A; Grün, Rainer; Mortimer, Graham E; McCulloch, Malcolm; Berger, Lee R

2007-11-01

Gladysvale Cave is one of the few Plio-Pleistocene hominin-bearing cave sites in South Africa that contains a well-stratified cave fill with clastic sediments interspersed with flowstones. The clastic sediments can be divided into units based on the presence of intercalated flowstones, forming flowstone bounded units (FBU). Ten MC-ICP-MS uranium-series dates on several flowstone horizons in the Gladysvale Internal Deposit fan indicate deposition from the late mid-Pleistocene ( approximately 570 ka) to Holocene ( approximately 7 ka) during limited periods of higher effective moisture. Clastic sedimentation occurred during the interceding, presumably more arid, periods. This sequence is not consistent with earlier models for South African caves that simply assumed interglacial sedimentation and glacial erosion. (13)C/(12)C data suggest that flowstone tended to form during periods with higher proportions of C(3) plants in the local vegetation, while clastic sediments reflect higher proportions of C(4) grasses, although this is not always the case. We argue that flowstones are precipitated during periods of higher effective precipitation and restricted cave entrances, while clastic sediments accumulated during periods with more open vegetation. The sedimentary fill of the fossiliferous deposits are, therefore, highly episodic in nature, with large periods of time unlikely to be represented. This has serious implications for the other hominin-bearing caves close by, as these deposits are likely to be similarly episodic. This is especially pertinent when addressing extinction events and reconstructions of paleoenvironments, as large periods of time may be unrecorded. The Gladysvale Cave fill sediments may serve as a climatically forced chronostratigraphic model for these less well-stratified and well-dated Plio-Pleistocene sites.

Carbon dioxide, ground air and carbon cycling in Gibraltar karst

NASA Astrophysics Data System (ADS)

Mattey, D. P.; Atkinson, T. C.; Barker, J. A.; Fisher, R.; Latin, J.-P.; Durrell, R.; Ainsworth, M.

2016-07-01

We put forward a general conceptual model of CO2 behaviour in the vadose zone of karst aquifers, based on physical principles of air flow through porous media and caves, combined with a geochemical interpretation of cave monitoring data. This 'Gibraltar model' links fluxes of water, air and carbon through the soil with the porosity of the vadose zone, the circulation of ground air and the ventilation of caves. Gibraltar hosts many natural caves whose locations span the full length and vertical range of the Rock. We report results of an 8-year monitoring study of carbon in soil organic matter and bedrock carbonate, dissolved inorganic carbon in vadose waters, and gaseous CO2 in soil, cave and ground air. Results show that the regime of cave air CO2 results from the interaction of cave ventilation with a reservoir of CO2-enriched ground air held within the smaller voids of the bedrock. The pCO2 of ground air, and of vadose waters that have been in close contact with it, are determined by multiple factors that include recharge patterns, vegetation productivity and root respiration, and conversion of organic matter to CO2 within the soil, the epikarst and the whole vadose zone. Mathematical modelling and field observations show that ground air is subject to a density-driven circulation that reverses seasonally, as the difference between surface and underground temperatures reverses in sign. The Gibraltar model suggests that cave air pCO2 is not directly related to CO2 generated in the soil or the epikarstic zone, as is often assumed. Ground air CO2 formed by the decay of organic matter (OM) washed down into the deeper unsaturated zone is an important additional source of pCO2. In Gibraltar the addition of OM-derived CO2 is the dominant control on the pCO2 of ground air and the Ca-hardness of waters within the deep vadose zone. The seasonal regime of CO2 in cave air depends on the position of a cave in relation to the density-driven ground air circulation pattern which is itself determined by the topography, as well as by the high-permeability conduits for air movement provided by caves themselves. In the steep topography of Gibraltar, caves in the lower part of the Rock act as outflow conduits for descending ground air in summer, and so have higher pCO2 in that season. Caves in the upper Rock have high pCO2 in winter, when they act as outflow conduits for rising currents of CO2-enriched ground air. Understanding seasonal flows of ground air in the vadose zone, together with the origins and seasonal regimes of CO2 in cave air underpins robust interpretation of speleothem-based climate proxy records.

Tamarugite from Diana Cave (SW Romania) -first true karst occurrence

NASA Astrophysics Data System (ADS)

Pušcaš, C. M.; Onac, B. P.; Effenberger, H. S.; Povarǎ, I.

2012-04-01

Diana Cave is located within the town limits of Baile Herculane (SW Romania) and develops as a 14 m long, westward oriented, unique passage guided by the Diana fault [1]. At the far end of the cave, the thermo-mineral Diana Spring wells forth. In the early 1970s a mine gallery that intersected the cave was created to drain the water into a pumping station and the original cave passage was somewhat altered and reinforced with concrete. Today the concrete and the silty limestone cave walls are heavily corroded by H2SO4 outgassing from the hot water (ca. 50°C) and display abundant gypsum crusts, soggy aggregates of native S, and a variety of more exotic sulfates. Among them, a mineral that has been previously identified in caves only in connection to volcanic activity, either as thermal springs or fumaroles [2]: tamarugite [NaAl(SO4)26H2O]. It was [3] that first mentioned the occurrence of this Na and Al sulfate in Diana Cave, our research aiming to give a detailed description of this mineral, its paragenesis, and mechanisms of precipitation. Recently, tamarugite has also been identified in a sulfuric acid cave from Greece [4]. Along with powder X-ray diffractions coupled with Rietveld refinement, scanning electron microscope, and electron probe micro-analysis, δ18O and δ34S compositions of the sulfate mineral as well as precipitates from the water were analyzed to identify and better constrain the genesis of this rare sulfate. Regrettably, the crystal size of our specimens is inappropriate for identification by means of single crystal X-ray diffraction. Physical and chemical parameters of Diana Spring were as well measured on several occasions. Geochemical analysis suggests that the minute, white tamarugite flakes precipitated in Diana Cave as a result of the interactions between the thermo-mineral water or water vapor and the original limestone bedrock and concrete that blankets the mine gallery. [1] Povara, I., Diaconu, G., Goran, C. (1972). Observations préliminaires sur les grottes influencées par les eaux thermo-minérales de la zone Baile-Herculane. Trav. Inst. Speol. "Emile Racovitza", XI, 355-365. [2] Rodgers, K.A., Hamlin, K.A., Browne, P.R.L., Campbell, K.A., Martin, R. (2000). The steam condensate alteration mineralogy of Ruatapu cave, Orakei Korako geothermal field, Taupo Volcanic Zone, New Zealand. Mineralogical magazine, 64(1), 125-142. [3] Onac, B.P., Sumrall, J., Tama?¸ T., Povara, I., Kerns, J., Dârmiceanu, V., Vere?¸ D., Lascu, C. (2009). The relationship between cave minerals and H2S-rich thermal waters along the Cerna Valley (SW Romania). Acta Carsologica, 38(1), 27-39. [4] Lazaridis G, Melfos, V, Papadopoulou L (2011). The first cave occurrence of orpiment (As2S3) from the sulfuric acid caves of Aghia Paraskevi (Kassandra Peninsula, N. Greece). International Journal of Speleology, 40(2): 133-139.

Basaltic caves at Craters of the Moon National Monument and Preserve as analogs for Mars

NASA Astrophysics Data System (ADS)

Hinman, N. W.; Richardson, C. D.; McHenry, L.; Scott, J. R.

2010-12-01

Basaltic caves and lava tubes offer stable physicochemical conditions for formation of secondary minerals. Such features, putatively observed on Mars, intercept groundwater to weather country rock, leading to formation of secondary minerals. Further, caves are stable environments to search for evidence of past life, as they could offer protection from the oxidizing martian atmosphere. Searching for signs of life in a cave that could protect bio/organic compounds would preclude the need for risky drilling on Mars. Craters of the Moon National Monument (COM) offers an opportunity to study caves in Holocene iron-rich basalt flows to characterize secondary mineral deposits and search for organic compounds associated with secondary minerals; COM basalts are a good analog for martian basalts because of their high iron but other elements are higher at COM than on Mars. The Blue Dragon flow (~2.1 ka) contains the majority of the accessible caves and lava tubes. Two types of secondary mineral deposits were observed in these caves: ceiling coatings and crack or floor precipitates. Hematite, silica, and calcite comprise ceiling coatings. The crack and floor precipitates are white, efflorescent deposits in cavities along cave walls and ceilings or in localized mounds on cave floors. The secondary minerals in crack and floor precipitates are mainly thenardite and mirabilite with some minor concentrations of trona and/or burkeite. Organic compounds were found associated with the efflorescent deposits. Formation of the deposits is likely due to chemical leaching of basalt by meteoritic water. To test this, fluids collected from the ceiling and walls of the caves were analyzed. Solutions were modeled with the geochemical code, PHREEQC. The model tracked composition as water evaporated. Selected minerals were allowed to precipitate as they became oversaturated. Among the first minerals to become oversaturated were quartz and calcite, which are observed in ceiling deposits. Iron minerals were not included as no iron was detected in solution. Results compared well with evaporation of solutions generated by simulating chemical weathering of minerals found in the basalt; this approach allowed iron minerals to precipitate during evaporation because minerals in the basalt contained iron. The minerals modeled upon evaporation included the minerals observed in the actual deposits - hematite, calcite, and quartz. Na-minerals neared saturation in simulations but were normally not saturated, leaving open the question of their origin. One possible explanation for the presence of Na-minerals could be seasonal ice formation in the caves followed by sublimation, leaving more concentrated solutions behind than were sampled here. A seasonal model for mineral deposition in caves could be relevant to deposits in martian caves. While the formation mechanism for the secondary minerals at COM is not completely understood, the presence of secondary minerals that harbor organic compounds in a cave environment that may be analogous to Mar has implications for where to search for signs of martian life.

Hydrological responses of the Chihuahua Desert of Mexico to possible Heinrich Stadials: A study inferred from geochemistry and stable isotopes of lacustrine sediments

NASA Astrophysics Data System (ADS)

Quiroz-Jiménez, J. D.; Roy, P. D.; Lozano-SantaCruz, R.; López Balbiaux, N.; Girón-García, P.

2016-12-01

The Heinrich Stadials (H6-H1) were cooler intervals of different duration characterized by massive discharge of icebergs from the Laurentide Ice Sheet mainly through the Hudson Straight into the Atlantic Ocean. In this paper, we present a proxy record to infer hydrological responses of the Chihuahua Desert of Mexico to all the Heinrich Stadials (HS) from element ratios, CO3 abundance, and oxygen and carbon isotope compositions of lacustrine calcite of the sediments deposited between depths of 560-78 cm ( 66-8 ka) of a new core collected from the Santiaguillo Basin. Sediments deposited during different HS were identified by radiocarbon dating up to 27.3 ka, extrapolation of an average sediment rate and tuning the CO3 abundance record with insolation in rest of the sequence, and oxygen isotope composition of authigenic CO3. Proxies suggest that hydroclimate of the Chihuahua Desert of Mexico responded differently to different HS. The overall runoff and hence precipitation remained below average during H6, H4, H2 and H1. Both of them were above average during H5 and H3. Similarly, runoff during H4 showed the least variability and it was the most variable during H5. Except for H2, negative excursions in δ18O values suggest cooler conditions during all other HS. In general, dissolved HCO3- was mainly sourced from the atmospheric CO2 during arid intervals. Both the lake productivity and atmospheric CO2 influenced the carbon isotope composition of dissolved HCO3- during humid intervals. During the H2, δ13C values indicate dominant influence of lacustrine productivity. Similar to Chihuahua Desert of Mexico, speleothem records from Fort Stanton and Cave of the Bells (Asmerom et al., 2010; Wagner et al., 2010) showed that hydroclimate of southwest USA also experienced millennial-scale variability and some intervals were more homogeneous compared to others. We did not observe concurrency in proxy records of the Chihuahua Desert of Mexico and southwest USA. Instead, we observed a possible hemispheric link between hydroclimate of the Chihuahua Desert of Mexico and the East Asian Monsoon. Characterized by millennial-scale fluctuations, tendencies of runoff into the Santiaguillo Basin and intensity of the East Asian Monsoon inferred from speleothems from the Hulu Cave of China (Wang et al., 2001) across the six HS were similar.

76 FR 26982 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-10

.... Specifically, it addresses the flooding source Licking River (Cave Run Lake). DATES: Comments are to be... Incorporated Areas,'' addressed the flooding source Licking River (Cave Run Lake). That table contained... River (Cave Run Lake)....... At the Buck Creek None +765 City of Frenchburg, confluence. Unincorporated...

Status and Natural History of Emballonura Semicaudata Rotensis on Aguiguan, Mariana Islands

USGS Publications Warehouse

Wiles, Gary J.; O'Shea, Thomas J.; Worthington, David J.; Esselstyn, Jacob A.; Valdez, Ernest W.

2011-01-01

Pacific sheath-tailed bats (Emballonura semicaudata rotensis) in the Mariana Islands declined greatly in abundance and distribution during the 20th century. The small island of Aguiguan now supports the only persisting population. We studied abundance and natural history of this population from 1995–2008. There was a likely population increase during the study, with 359–466 (minimum and maximum) bats counted at caves in 2008. Bats roosted only in caves, primarily those of relatively larger size. Bats were detected in only seven of 95 caves; three caves were always occupied when surveyed. One cave consistently had the largest colony ( ± SD = 333 ± 33.6 in 2008). Others held 1–64 bats. Cave environments showed no complexities in temperature or humidity. Preliminary observations indicate a litter size of one and the possibility of birthing timed to coincide with the transitional period leading into the rainy season (June–July). We review potential threats to E. s. rotensis on Aguiguan and make suggestions for conservation.

The Astrobiology of the Subsurface: Exploring Cave Habitats on Earth, Mars and Beyond

NASA Technical Reports Server (NTRS)

Boston, Penelope Jane

2016-01-01

We are using the spectacular underground landscapes of Earth caves as models for the subsurfaces of other planets. Caves have been detected on the Moon and Mars and are strongly suspected for other bodies in the Solar System including some of the ice covered Ocean Worlds that orbit gas giant planets. The caves we explore and study include many extreme conditions of relevance to planetary astrobiology exploration including high and low temperatures, gas atmospheres poisonous to humans but where exotic microbes can flourish, highly acidic or salty fluids, heavy metals, and high background radiation levels. Some cave microorganisms eat their way through bedrock, some live in battery acid conditions, some produce unusual biominerals and rare cave formations, and many produce compounds of potential pharmaceutical and industrial significance. We study these unique lifeforms and the physical and chemical biosignatures that they leave behind. Such traces can be used to provide a "Field Guide to Unknown Organisms" for developing life detection space missions.

X-ray analysis of aerosol samples from a therapeutic cave

NASA Astrophysics Data System (ADS)

Alföldy, B.; Török, Sz.; Kocsonya, A.; Szőkefalvi-Nagy, Z.; Balla, Md. I.

2001-04-01

Cave therapy is an efficient therapeutic method to cure asthma, the exact healing effect, however, is not clarified, yet. This study is motivated by the basic assumption that aerosols do play the key role in the cave therapy. This study is based on measurements of single aerosol particles originating from a therapeutic cave of Budapest, Hungary (Szemlőhegyi cave). Aerosol particles have been collected in the regions arranged for the therapeutic treatment. Samples were further analysed for chemical and morphological aspects, determining the particle size distribution and classifying them according to elemental composition. Three particle classes have been detected based on major element concentration: alumino-silicate, quartz and calcium carbonate. Calcium ions have well-known physiological influence: anti-spastic, anti-inflammation and excretion reducing effects. Inflammation, accompanying spasm and extreme excretion production cause the smothering stigma, the so-called asthma. Therefore it could be assumed that calcium ions present in high concentration in the cave's atmosphere is the major cause of the healing effect.

Identification of montgomeryite mineral [Ca4MgAl4(PO4)6·(OH)4·12H2O] found in the Jenolan Caves—Australia

NASA Astrophysics Data System (ADS)

Frost, Ray L.; Xi, Yunfei; Palmer, Sara J.; Pogson, Ross E.

In this paper, we report on many phosphate containing natural minerals found in the Jenolan Caves - Australia. Such minerals are formed by the reaction of bat guano and clays from the caves. Among these cave minerals is the montgomeryite mineral [Ca4MgAl4(PO4)6·(OH)4·12H2O]. The presence of montgomeryite in deposits of the Jenolan Caves - Australia has been identified by X-ray diffraction (XRD). Raman spectroscopy complimented with infrared spectroscopy has been used to characterise the crystal structure of montgomeryite. The Raman spectrum of a standard montgomeryite mineral is identical to that of the Jenolan Caves sample. Bands are assigned to H2PO4-, OH and NH stretching vibrations. By using a combination of XRD and Raman spectroscopy, the existence of montgomeryite in the Jenolan Caves - Australia has been proven. A mechanism for the formation of montgomeryite is proposed.

Wireless and Low-Weight Technologies: Advanced Medical Assistance During a Cave Rescue: A Case Report.

PubMed

Petrucci, Emiliano; Pizzi, Barbara; Scimia, Paolo; Conti, Giuseppe; Di Carlo, Stefano; Santini, Antonella; Fusco, Pierfrancesco

2018-06-01

Trauma care in cave rescue is a unique situation that requires an advanced and organized approach with medical and technical assistance because of the extreme environmental conditions and logistical factors. In caving accidents, the most common injuries involve lower limbs. We describe an advanced medical rescue performed by the Italian Corpo Nazionale del Soccorso Alpino e Speleologico, in which extended focused assessment with sonography for trauma and an ultrasound-guided adductor canal block were performed on a patient with a knee distortion directly in the cave. The rescue team inside the cave shared data on patient monitoring and the ultrasound scanning in real time with rescuers at the entrance, using a video conference powered by the new Ermes system. The use of handheld, battery-powered, low-weight, multiparametric monitors, ultrasound machines, and digital data transmission systems could ensure complete medical assistance in harsh environmental conditions such as those found in a cave. Copyright © 2018 Wilderness Medical Society. Published by Elsevier Inc. All rights reserved.

An overview of the Mediterranean cave-dwelling horny sponges (Porifera, Demospongiae)

PubMed Central

Manconi, Renata; Cadeddu, Barbara; Ledda, Fabio; Pronzato, Roberto

2013-01-01

Abstract The present synthesis focuses on the so called ‘horny sponges’ recorded from marine caves of the Mediterranean Sea. The main aim is to provide a list of all recorded species, diagnostic keys to their identification up to family and genus level, and exhaustive, formally uniform descriptions at the species level contributing to sharing of information on the faunistics and taxonomy of Mediterranean cave-dwelling species, including habitat preferences. The majority of species was recorded in 105 Mediterranean marine caves hosting four orders of horny sponges belonging to 9 families, 19 genera and 40 species. Species endemic to the Mediterranean Sea harboured in marine caves are 14 with an endemicity value of 35%. For each species morphological descriptions are supported by illustrations both original and from the literature, including the diagnostic traits of the skeleton by light and scanning electron microscopy giving further characterization at the specific level. A detailed map together with a list of all caves harbouring horny sponges is also provided with geographic coordinates. PMID:23794833

Meteoric phreatic speleothems and the development of cave stratigraphy: An example from Tounj Cave, Dinarides, Croatia

NASA Astrophysics Data System (ADS)

Babić, Ljubomir; Lacković, Damir; HorvatinČIĆ, Nada

Speleothems occurring in some caves of the carbonate Dinarides line all channel surfaces, and have been deposited from meteoric waters under phreatic conditions. Such phreatic speleothemic deposition modifies common experience (l) that meteoric phreatic conditions cause dissolutional widening of cave voids, and (2) that speleothems imply vadose conditions. The phreatic speleothems described here postdate an early polygenetic evolution of the cave voids, and predate the last, vadose stage. They were likely produced during the late/postglacial warming period, when dissolved carbonate was amply supplied, and when there was much water available for saturation of underground voids. Phreatic speleothems may be used as a tool for time correlation of internal deposits, both within one cave and within a karst region. They indicate an important stage in the history of the ground-water regime of an area. In general, phreatic speleothems help in better understanding of the development of subterranean voids and related karst/palaeokarst.

Stability numerical analysis of soil cave in karst area to drawdown of underground water level

NASA Astrophysics Data System (ADS)

Mo, Yizheng; Xiao, Rencheng; Deng, Zongwei

2018-05-01

With the underground water level falling, the reliable estimates of the stability and deformation characteristics of soil caves in karst region area are required for analysis used for engineering design. Aimed at this goal, combined with practical engineering and field geotechnical test, detail analysis on vertical maximum displacement of top, vertical maximum displacement of surface, maximum principal stress and maximum shear stress were conducted by finite element software, with an emphasis on two varying factors: the size and the depth of soil cave. The calculations on the soil cave show that, its stability of soil cave is affected by both the size and depth, and only when extending a certain limit, the collapse occurred along with the falling of underground water; Additionally, its maximum shear stress is in arch toes, and its deformation curve trend of maximum displacement is similar to the maximum shear stress, which further verified that the collapse of soil cave was mainly due to shear-failure.

Permutation inference for the general linear model

PubMed Central

Winkler, Anderson M.; Ridgway, Gerard R.; Webster, Matthew A.; Smith, Stephen M.; Nichols, Thomas E.

2014-01-01

Permutation methods can provide exact control of false positives and allow the use of non-standard statistics, making only weak assumptions about the data. With the availability of fast and inexpensive computing, their main limitation would be some lack of flexibility to work with arbitrary experimental designs. In this paper we report on results on approximate permutation methods that are more flexible with respect to the experimental design and nuisance variables, and conduct detailed simulations to identify the best method for settings that are typical for imaging research scenarios. We present a generic framework for permutation inference for complex general linear models (glms) when the errors are exchangeable and/or have a symmetric distribution, and show that, even in the presence of nuisance effects, these permutation inferences are powerful while providing excellent control of false positives in a wide range of common and relevant imaging research scenarios. We also demonstrate how the inference on glm parameters, originally intended for independent data, can be used in certain special but useful cases in which independence is violated. Detailed examples of common neuroimaging applications are provided, as well as a complete algorithm – the “randomise” algorithm – for permutation inference with the glm. PMID:24530839

Bayesian microsaccade detection

PubMed Central

Mihali, Andra; van Opheusden, Bas; Ma, Wei Ji

2017-01-01

Microsaccades are high-velocity fixational eye movements, with special roles in perception and cognition. The default microsaccade detection method is to determine when the smoothed eye velocity exceeds a threshold. We have developed a new method, Bayesian microsaccade detection (BMD), which performs inference based on a simple statistical model of eye positions. In this model, a hidden state variable changes between drift and microsaccade states at random times. The eye position is a biased random walk with different velocity distributions for each state. BMD generates samples from the posterior probability distribution over the eye state time series given the eye position time series. Applied to simulated data, BMD recovers the “true” microsaccades with fewer errors than alternative algorithms, especially at high noise. Applied to EyeLink eye tracker data, BMD detects almost all the microsaccades detected by the default method, but also apparent microsaccades embedded in high noise—although these can also be interpreted as false positives. Next we apply the algorithms to data collected with a Dual Purkinje Image eye tracker, whose higher precision justifies defining the inferred microsaccades as ground truth. When we add artificial measurement noise, the inferences of all algorithms degrade; however, at noise levels comparable to EyeLink data, BMD recovers the “true” microsaccades with 54% fewer errors than the default algorithm. Though unsuitable for online detection, BMD has other advantages: It returns probabilities rather than binary judgments, and it can be straightforwardly adapted as the generative model is refined. We make our algorithm available as a software package. PMID:28114483

CaSPIAN: A Causal Compressive Sensing Algorithm for Discovering Directed Interactions in Gene Networks

PubMed Central

Emad, Amin; Milenkovic, Olgica

2014-01-01

We introduce a novel algorithm for inference of causal gene interactions, termed CaSPIAN (Causal Subspace Pursuit for Inference and Analysis of Networks), which is based on coupling compressive sensing and Granger causality techniques. The core of the approach is to discover sparse linear dependencies between shifted time series of gene expressions using a sequential list-version of the subspace pursuit reconstruction algorithm and to estimate the direction of gene interactions via Granger-type elimination. The method is conceptually simple and computationally efficient, and it allows for dealing with noisy measurements. Its performance as a stand-alone platform without biological side-information was tested on simulated networks, on the synthetic IRMA network in Saccharomyces cerevisiae, and on data pertaining to the human HeLa cell network and the SOS network in E. coli. The results produced by CaSPIAN are compared to the results of several related algorithms, demonstrating significant improvements in inference accuracy of documented interactions. These findings highlight the importance of Granger causality techniques for reducing the number of false-positives, as well as the influence of noise and sampling period on the accuracy of the estimates. In addition, the performance of the method was tested in conjunction with biological side information of the form of sparse “scaffold networks”, to which new edges were added using available RNA-seq or microarray data. These biological priors aid in increasing the sensitivity and precision of the algorithm in the small sample regime. PMID:24622336

Karst show caves - how DTN technology as used in space assists automatic environmental monitoring and tourist protection - experiment in Postojna cave

NASA Astrophysics Data System (ADS)

Gabrovšek, F.; Grašič, B.; Božnar, M. Z.; Mlakar, P.; Udén, M.; Davies, E.

2013-10-01

The paper presents an experiment demonstrating a novel and successful application of Delay- and Disruption-Tolerant Networking (DTN) technology for automatic data transfer in a karst cave Early Warning and Measuring System. The experiment took place inside the Postojna Cave in Slovenia, which is open to tourists. Several automatic meteorological measuring stations are set up inside the cave, as an adjunct to the surveillance infrastructure; the regular data transfer provided by the DTN technology allows the surveillance system to take on the role of an Early Warning System (EWS). One of the stations is set up alongside the railway tracks, which allows the tourist to travel inside the cave by train. The experiment was carried out by placing a DTN "data mule" (a DTN-enabled computer with WiFi connection) on the train and by upgrading the meteorological station with a DTN-enabled WiFi transmission system. When the data mule is in the wireless drive-by mode, it collects measurement data from the station over a period of several seconds as the train passes the stationary equipment, and delivers data at the final train station by the cave entrance. This paper describes an overview of the experimental equipment and organisation allowing the use of a DTN system for data collection and an EWS inside karst caves where there is a regular traffic of tourists and researchers.

Karst show caves - how DTN technology as used in space assists automatic environmental monitoring and tourist protection - experiment in Postojna Cave

NASA Astrophysics Data System (ADS)

Gabrovšek, F.; Grašič, B.; Božnar, M. Z.; Mlakar, P.; Udén, M.; Davies, E.

2014-02-01

The paper presents an experiment demonstrating a novel and successful application of delay- and disruption-tolerant networking (DTN) technology for automatic data transfer in a karst cave early warning and measuring system. The experiment took place inside the Postojna Cave in Slovenia, which is open to tourists. Several automatic meteorological measuring stations are set up inside the cave, as an adjunct to the surveillance infrastructure; the regular data transfer provided by the DTN technology allows the surveillance system to take on the role of an early warning system (EWS). One of the stations is set up alongside the railway tracks, which allows the tourist to travel inside the cave by train. The experiment was carried out by placing a DTN "data mule" (a DTN-enabled computer with WiFi connection) on the train and by upgrading the meteorological station with a DTN-enabled WiFi transmission system. When the data mule is in the wireless drive-by mode, it collects measurement data from the station over a period of several seconds as the train without stopping passes the stationary equipment, and delivers data at the final train station by the cave entrance. This paper describes an overview of the experimental equipment and organization allowing the use of a DTN system for data collection and an EWS inside karst caves where there is regular traffic of tourists and researchers.

Regressive Evolution in the Mexican Cave Tetra, Astyanax mexicanus

PubMed Central

Protas, Meredith; Conrad, Melissa; Gross, Joshua B.; Tabin, Clifford; Borowsky, Richard

2007-01-01

Summary Cave adapted animals generally have reduced pigmentation and eyes, but the evolutionary forces driving the reductions are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes; “As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse” [1]. We studied the genetic basis of this phenomenon in the Mexican cave tetra, Astyanax mexicanus, by mapping the quantitative trait loci (QTL) determining differences in eye/lens sizes and melanophore number between cave and surface fish. In addition, we mapped QTL for the putatively constructive traits of jaw size, tooth number, and numbers of taste buds. The data suggest that eyes and pigmentation regressed through different mechanisms. Cave alleles at each eye/lens QTL we detected caused size reductions. This uniform negative polarity is consistent with evolution by natural selection and inconsistent with evolution by drift. In contrast, QTL polarities for melanophore number were mixed, consistent with evolution by genetic drift or indirect selection through pleiotropy. Past arguments against a role for selection in regression of cave fish eyes cited the insignificant cost of their development [2, 3], but we argue that the energetic cost of their maintenance is sufficiently high for eyes to be detrimental in the cave environment. Regression, a ubiquitous aspect of all evolutionary change, can be caused either by selection or genetic drift/pleiotropy. PMID:17306543

Investigation of tracking systems properties in CAVE-type virtual reality systems

NASA Astrophysics Data System (ADS)

Szymaniak, Magda; Mazikowski, Adam; Meironke, Michał

2017-08-01

In recent years, many scientific and industrial centers in the world developed a virtual reality systems or laboratories. One of the most advanced solutions are Immersive 3D Visualization Lab (I3DVL), a CAVE-type (Cave Automatic Virtual Environment) laboratory. It contains two CAVE-type installations: six-screen installation arranged in a form of a cube, and four-screen installation, a simplified version of the previous one. The user feeling of "immersion" and interaction with virtual world depend on many factors, in particular on the accuracy of the tracking system of the user. In this paper properties of the tracking systems applied in I3DVL was investigated. For analysis two parameters were selected: the accuracy of the tracking system and the range of detection of markers by the tracking system in space of the CAVE. Measurements of system accuracy were performed for six-screen installation, equipped with four tracking cameras for three axes: X, Y, Z. Rotation around the Y axis was also analyzed. Measured tracking system shows good linear and rotating accuracy. The biggest issue was the range of the monitoring of markers inside the CAVE. It turned out, that the tracking system lose sight of the markers in the corners of the installation. For comparison, for a simplified version of CAVE (four-screen installation), equipped with eight tracking cameras, this problem was not occur. Obtained results will allow for improvement of cave quality.

The Jettencave, Southern Harz Mountains, Germany: Geophysical observations and a structural model of a shallow cave in gypsum/anhydrite-bearing rocks

NASA Astrophysics Data System (ADS)

Kaufmann, Georg; Romanov, Douchko

2017-12-01

Gypsum and anhydrite are soluble rocks, where fissures and bedding partings can be enlarged with time by the dissolution of the mineral species through water. The selective enlargement results in sub-surface voids acting as preferential flow path for the drainage of the rock. With time, larger cavities develop, and a network of cave passages can evolve. If the enlarged cave voids are not too deep under the surface, geophysical measurements can be used to detect, identify and trace these structures. We have used gravity measurements (GRAV), electrical resistivity imaging (ERI), self-potential measurements (SP), electrical conductivity measurements (EC), and ground-penetrating radar (GPR) above the cave Jettenhöhle, a cave located in the southern Harz Mountains in Germany. The Jettencave is developed in the Hauptanhydrit formation of the Permian Zechstein sequence, characterised by large breakdown rooms and an exposed water table. The overburden of the cave is only around 10-15 m, and dolomitic rocks are located in close vicinity. We present results from our geophysical surveys in vicinity of the cave. We are able to identify the cave geometry from GRAV, ERI, and GPR measurements, which distinguish the local lithology of the Permian Zechstein rocks in the area. From the ERI and EC measurements, we derive information on the void volume in the soluble rocks. We finally present a three-dimensional structural model of the Jettencave and its surroundings, based on our geophysical results and the hydrological interpretation.

Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods

PubMed Central

Cocco, Simona; Leibler, Stanislas; Monasson, Rémi

2009-01-01

Complexity of neural systems often makes impracticable explicit measurements of all interactions between their constituents. Inverse statistical physics approaches, which infer effective couplings between neurons from their spiking activity, have been so far hindered by their computational complexity. Here, we present 2 complementary, computationally efficient inverse algorithms based on the Ising and “leaky integrate-and-fire” models. We apply those algorithms to reanalyze multielectrode recordings in the salamander retina in darkness and under random visual stimulus. We find strong positive couplings between nearby ganglion cells common to both stimuli, whereas long-range couplings appear under random stimulus only. The uncertainty on the inferred couplings due to limitations in the recordings (duration, small area covered on the retina) is discussed. Our methods will allow real-time evaluation of couplings for large assemblies of neurons. PMID:19666487

Early Pliocene Hiatus in Sand Output by the Colorado River: Evidence From Marine Deposits in the Salton Trough, Southern California

NASA Astrophysics Data System (ADS)

Dorsey, R. J.; Bykerk-Kauffman, A.

2015-12-01

Early Pliocene deposits in the western Salton Trough preserve a high-fidelity record of sediment dispersal into the marine realm during initiation and early evolution of the Colorado River (CR). Grain-size fractionation, sediment routing, and transport dynamics of the early CR delta are recorded in sediments of the Fish Creek - Vallecito basin, which was located ~100 km south of Yuma along the transform plate boundary at 5 Ma. Early Pliocene delivery of CR sand to the basin took place in two distinct pulses: (1) deposition of sandy turbidites (Wind Caves Mbr of the Latrania Fm) in a restricted submarine canyon at Split Mt Gorge between ~5.3 and 5.1 Ma; and (2) progradation of a thick, widespread, coarsening-up deltaic sequence of marine mudstone, sandstone, and coquinas (Deguynos Fm) between ~4.8 and 4.2 Ma. Estimated flux of CR sediment during Wind Caves deposition was weak (~3-5 Mt/yr) compared to the long-term average (172±64 Mt/yr). The two pulses of CR sand input are separated by the Coyote Clay (CC, ~5.1-4.8 Ma), a regionally correlable, greenish-yellow-weathering marine claystone unit at the base of the Deguynos Fm. CC gradationally overlies Wind Caves turbidites in the area of the paleocanyon. In contrast, in the Coyote Mts 15-23 km to the south and SE, CC rests on coarse-grained locally-derived late Miocene sedimentary rocks, Alverson volcanics, and metamorphic basement rock along a regional unconformity. Identical claystone facies occur in the NW Indio Hills (restores to Yuma at the mouth of the CR at 5 Ma), and Sierra Cucapa in Mexico (~200 km south of Yuma at 5 Ma). Marine localities outside of the Wind Caves paleocanyon experienced slow to negligible sedimentation along a rugged rocky shoreline until abrupt arrival of CR-derived clay. CC accumulated in a sand-starved, pro-delta marine setting (Winker, 1987) over an inferred N-S distance of ~200 km. We therefore reject an alternate hypothesis that CC accumulated on the muddy slope of the prograding CR delta (Cloos, 2014). The CC records a pronounced 200-300 Kyr hiatus in delivery of sand from the CR to the basin at ca. 5 Ma that requires a regional explanation. The hiatus could have been caused by (1) global sea-level rise, (2) accelerated basin subsidence, or (3) tectonic damming and ponding of the lower CR by fault-related bedrock uplift in the Chocolate Mts.

Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data

PubMed Central

Bandaru, Pradeep; Bansal, Mukesh

2011-01-01

Abstract We present a step towards the metabolome-wide computational inference of cellular metabolic reaction networks from metabolic profiling data, such as mass spectrometry. The reconstruction is based on identification of irreducible statistical interactions among the metabolite activities using the ARACNE reverse-engineering algorithm and on constraining possible metabolic transformations to satisfy the conservation of mass. The resulting algorithms are validated on synthetic data from an abridged computational model of Escherichia coli metabolism. Precision rates upwards of 50% are routinely observed for identification of full metabolic reactions, and recalls upwards of 20% are also seen. PMID:21314454

Inferring Boolean network states from partial information

PubMed Central

2013-01-01

Networks of molecular interactions regulate key processes in living cells. Therefore, understanding their functionality is a high priority in advancing biological knowledge. Boolean networks are often used to describe cellular networks mathematically and are fitted to experimental datasets. The fitting often results in ambiguities since the interpretation of the measurements is not straightforward and since the data contain noise. In order to facilitate a more reliable mapping between datasets and Boolean networks, we develop an algorithm that infers network trajectories from a dataset distorted by noise. We analyze our algorithm theoretically and demonstrate its accuracy using simulation and microarray expression data. PMID:24006954

Carbon monoxide mixing ratio inference from gas filter radiometer data

NASA Technical Reports Server (NTRS)

Wallio, H. A.; Reichle, H. G., Jr.; Casas, J. C.; Saylor, M. S.; Gormsen, B. B.

1983-01-01

A new algorithm has been developed which permits, for the first time, real time data reduction of nadir measurements taken with a gas filter correlation radiometer to determine tropospheric carbon monoxide concentrations. The algorithm significantly reduces the complexity of the equations to be solved while providing accuracy comparable to line-by-line calculations. The method is based on a regression analysis technique using a truncated power series representation of the primary instrument output signals to infer directly a weighted average of trace gas concentration. The results produced by a microcomputer-based implementation of this technique are compared with those produced by the more rigorous line-by-line methods. This algorithm has been used in the reduction of Measurement of Air Pollution from Satellites, Shuttle, and aircraft data.

A 3D Cloud-Construction Algorithm for the EarthCARE Satellite Mission

NASA Technical Reports Server (NTRS)

Barker, H. W.; Jerg, M. P.; Wehr, T.; Kato, S.; Donovan, D. P.; Hogan, R. J.

2011-01-01

This article presents and assesses an algorithm that constructs 3D distributions of cloud from passive satellite imagery and collocated 2D nadir profiles of cloud properties inferred synergistically from lidar, cloud radar and imager data.

36 CFR 290.4 - Confidentiality of cave location information.

Code of Federal Regulations, 2010 CFR

2010-07-01

... AGRICULTURE CAVE RESOURCES MANAGEMENT § 290.4 Confidentiality of cave location information. (a) Information... determines that disclosure will further the purposes of the Act and will not create a substantial risk of... Federal or State governmental agencies, bona fide educational or research institutes, or individuals or...

36 CFR 290.4 - Confidentiality of cave location information.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 2 2012-07-01 2012-07-01 false Confidentiality of cave location information. 290.4 Section 290.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... organizations assisting the land management agencies with cave management activities. To request confidential...

36 CFR 290.4 - Confidentiality of cave location information.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Confidentiality of cave location information. 290.4 Section 290.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... organizations assisting the land management agencies with cave management activities. To request confidential...

36 CFR 290.4 - Confidentiality of cave location information.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 2 2014-07-01 2014-07-01 false Confidentiality of cave location information. 290.4 Section 290.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... organizations assisting the land management agencies with cave management activities. To request confidential...

36 CFR 290.4 - Confidentiality of cave location information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Confidentiality of cave location information. 290.4 Section 290.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... organizations assisting the land management agencies with cave management activities. To request confidential...

Radon Dose Determination for Cave Guides in Czech Republic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thinova, Lenka; Rovenska, Katerina

2008-08-07

According to recommended approach there are six (from total of twelve) open-to-public caves in Czech Republic, reaching near to an effective lung-dose of 6mSv/year. A conservative approach for estimating the potential effective lung-dose in caves (or underground) is based on two season's measurements, using solid state alpha track detector (Kodak in plastic diffusion chamber). The obtained dataset is converted into an annual effective dose, in agreement with the ICRP65 recommendation, using the 'cave factor' 1.5. The value of 'cave factor' which depends on the spectrum of aerosol particles, or on the proportional representation of the unattached/attached ratio (6.5 : 93.5more » for residential places, 13.6 : 86.4 for caves due to lower concentration of free aerosols) and on the equilibrium factor. Thus conversion factor is 1.5 times higher in comparison with ICRP 65. Is this correct? Because a more precisely determined dose value would have a significant impact on radon remedies, or on restricting the time workers stay underground, a series of measurement was initiated in 2003 with the aim to specify input data, computation and errors in effective dose assessment in each one of the evaluated caves separately. The enhancement of personal dosimetry for underground work places includes a study of the given questions, from the following points of view in each cave: continual radon measurement; regular measurements of radon and its daughters to estimate the equilibrium factor and the presence of free {sup 218}Po; regular indoor air flow measurements to study the location of the radon supply and its transfer among individual areas of the cave; natural radioactive element content evaluation in subsoil and in water inside/outside, a study of the radon sources in the cave; determination of the free fraction from continual unattached and attached fraction measurement (grid and filter); thoron measurement. Air flow measurements provide very interesting information about the origin of 'radon pockets' with very high radon concentration, and enable study of the location of the radon supply and its transfer among individual areas of the cave. Most of the results show the equilibrium factor around F = 0.2-0.7 and the unattached fraction around 2%-30%. One of the most important question remains: how accurately was the unattached fraction measured? Part of this project was to verify the influence of etched track detector position in the cave.« less

Contribution of stable isotopes (C,N,S) in collagen of late Pleistocene large mammal trophic ecology and landscape use: a case study in Goyet and Scladina cave (30-40,000 years BP)

NASA Astrophysics Data System (ADS)

Bocherens, Hervé; Germonpré, Mietje

2010-05-01

Two Belgian caves yielded very rich large mammal associations dating around 30 to 40,000 years ago: Goyet and Scladina cave (layer 1A). These sites are only 5 km apart but the cave entrances open on different valleys, in a quite diverse landscape ranging between open, unprotected uplands, steep cliffs and sheltered sun-exposed gorges, with the larger Meuse valley nearby. This mosaic scenery permitted during the Last Glacial a rich diversity of fossil flora and fauna. The faunal association includes a large diversity of taxa including Aurochs Bos primigenius, steppe bison Bison priscus, reindeer Rangifer tarandus, giant deer Megaloceros giganteus, horse Equus ferus, woolly rhinoceros Coelodonta antiquitatis, woolly mammoth Mammuthus primigenius, cave bear Ursus spelaeus, brown bear Ursus arctos, wolf Canis lupus, cave lion Panthera leo spelaea, and cave hyaena Crocuta crocuta spelaea. All the 90 studied bones and teeth yielded collagen with excellent collagen preservation, allowing reliable investigations of carbon, nitrogen and sulfur isotopic biogeochemistry. The combination of three different isotopic tracers allows to deciphering the effects of food selection and landscape use by different herbivorous and carnivorous taxa. This is the first study to include sulfur isotopic signatures in the study of late Quaternary large mammal palaeobiology. This new tracer yields evidence on mobility and differences in pasture areas, as different geological bedrock may exhibit various sulfur isotopic signatures that will pass on the herbivores and further on their predators. Using this feature in addition to the trophic information provided by carbon and nitrogen isotopic signatures, it appears that for some species present in both sites, such as horse and woolly rhinoceros, the individuals found in each site probably did not use the same pasture areas. This seems to also the case for the overwhelmingly vegetarian cave bears. In addition, individuals from the same species found in one site sometimes exhibit clear isotopic differences in the three isotopic tracers that suggest different pasture grounds as well, and therefore the possibility of different herds in the vicinity of the cave site. In the case of cave hyeanas, the isotopic signatures of individuals from both caves are not significantly different and suggest that these predators obtained their prey from a large territory including the pasture grounds of herbivores from both caves. In addition, direct radiocarbon dating of some of the studied collagen allows to investigating possible chronological trends. This study shows how new isotopic tracers can provide invaluable information on late Quaternary large mammal palaeobiology.

Construction of regulatory networks using expression time-series data of a genotyped population.

PubMed

Yeung, Ka Yee; Dombek, Kenneth M; Lo, Kenneth; Mittler, John E; Zhu, Jun; Schadt, Eric E; Bumgarner, Roger E; Raftery, Adrian E

2011-11-29

The inference of regulatory and biochemical networks from large-scale genomics data is a basic problem in molecular biology. The goal is to generate testable hypotheses of gene-to-gene influences and subsequently to design bench experiments to confirm these network predictions. Coexpression of genes in large-scale gene-expression data implies coregulation and potential gene-gene interactions, but provide little information about the direction of influences. Here, we use both time-series data and genetics data to infer directionality of edges in regulatory networks: time-series data contain information about the chronological order of regulatory events and genetics data allow us to map DNA variations to variations at the RNA level. We generate microarray data measuring time-dependent gene-expression levels in 95 genotyped yeast segregants subjected to a drug perturbation. We develop a Bayesian model averaging regression algorithm that incorporates external information from diverse data types to infer regulatory networks from the time-series and genetics data. Our algorithm is capable of generating feedback loops. We show that our inferred network recovers existing and novel regulatory relationships. Following network construction, we generate independent microarray data on selected deletion mutants to prospectively test network predictions. We demonstrate the potential of our network to discover de novo transcription-factor binding sites. Applying our construction method to previously published data demonstrates that our method is competitive with leading network construction algorithms in the literature.

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

NASA Technical Reports Server (NTRS)

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Visual recognition and inference using dynamic overcomplete sparse learning.

PubMed

Murray, Joseph F; Kreutz-Delgado, Kenneth

2007-09-01

We present a hierarchical architecture and learning algorithm for visual recognition and other visual inference tasks such as imagination, reconstruction of occluded images, and expectation-driven segmentation. Using properties of biological vision for guidance, we posit a stochastic generative world model and from it develop a simplified world model (SWM) based on a tractable variational approximation that is designed to enforce sparse coding. Recent developments in computational methods for learning overcomplete representations (Lewicki & Sejnowski, 2000; Teh, Welling, Osindero, & Hinton, 2003) suggest that overcompleteness can be useful for visual tasks, and we use an overcomplete dictionary learning algorithm (Kreutz-Delgado, et al., 2003) as a preprocessing stage to produce accurate, sparse codings of images. Inference is performed by constructing a dynamic multilayer network with feedforward, feedback, and lateral connections, which is trained to approximate the SWM. Learning is done with a variant of the back-propagation-through-time algorithm, which encourages convergence to desired states within a fixed number of iterations. Vision tasks require large networks, and to make learning efficient, we take advantage of the sparsity of each layer to update only a small subset of elements in a large weight matrix at each iteration. Experiments on a set of rotated objects demonstrate various types of visual inference and show that increasing the degree of overcompleteness improves recognition performance in difficult scenes with occluded objects in clutter.

Guanophilic fungi in three caves of southwestern Puerto Rico

USDA-ARS?s Scientific Manuscript database

Fifty species of guanophilic (bat guano-loving) fungi were isolated from field-collected samples within three caves in south-western Puerto Rico; most were mitosporic fungi (23 species). The caves studied were Cueva La Tuna (Cabo Rojo), Cueva de Malano (Sistema de Los Chorros, San Germán), and Cuev...

Caves: A Course of Study.

ERIC Educational Resources Information Center

Phillips, Jan

Middle school students from The College School, a private school in Webster Groves (Missouri) have completed a class called "Caves and Crystallography." A thematic approach was used in the course in which students and teachers read books telling how caves were formed, saw movies which explained the delicate balance of life underground,…

Fungal outbreak in a show cave.

PubMed

Jurado, V; Porca, E; Cuezva, S; Fernandez-Cortes, A; Sanchez-Moral, S; Saiz-Jimenez, C

2010-08-01

Castañar de Ibor Cave (Spain) was discovered in 1967 and declared a Natural Monument in 1997. In 2003 the cave was opened to public visits. Despite of extensive control, on 26 August 2008 the cave walls and sediments appeared colonized by long, white fungal mycelia. This event was the result of an accidental input of detritus on the afternoon of 24 August 2008. We report here a fungal outbreak initiated by Mucor circinelloides and Fusarium solani and the methods used to control it. 2010 Elsevier B.V. All rights reserved.

Cryptotephra from the 74 ka BP Toba super-eruption in the Billa Surgam caves, southern India

NASA Astrophysics Data System (ADS)

Lane, Christine; Haslam, Michael; Petraglia, Michael; Ditchfield, Peter; Smith, Victoria; Korisettar, Ravi

2011-07-01

The ˜74 ka BP Youngest Toba Tuff (YTT), from the largest known Quaternary volcanic eruption, has been found for the first time as a non-visible ( crypto-) tephra layer within the Billa Surgam caves, southern India. The occurrence of the YTT layer in Charnel House Cave provides the first calendrical age estimate for this much debated Pleistocene faunal sequence and demonstrates the first successful application of cryptotephrochronology within a cave sequence. The YTT layer lies ˜50 cm below a major sedimentological change, which is related to global cooling around the MIS 5 to MIS 4 transition. Using this isochronous event layer the Billa Surgam Cave record can be directly correlated with other archaeological sites in peninsular India and palaeoenvironmental archives across southern Asia.

Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave

USGS Publications Warehouse

Azua-Bustos, A.; Gonzalez-Silva, C.; Mancilla, R.A.; Salas, L.; Palma, R.E.; Wynne, J.J.; McKay, C.P.; Vicuna, R.

2009-01-01

Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert. ?? Springer Science + Business Media, LLC 2009.

Modeling of luminance distribution in CAVE-type virtual reality systems

NASA Astrophysics Data System (ADS)

Meironke, Michał; Mazikowski, Adam

2017-08-01

At present, one of the most advanced virtual reality systems are CAVE-type (Cave Automatic Virtual Environment) installations. Such systems are usually consisted of four, five or six projection screens and in case of six screens arranged in form of a cube. Providing the user with a high level of immersion feeling in such systems is largely dependent of optical properties of the system. The modeling of physical phenomena plays nowadays a huge role in the most fields of science and technology. It allows to simulate work of device without a need to make any changes in the physical constructions. In this paper distribution of luminance in CAVE-type virtual reality systems were modelled. Calculations were performed for the model of 6-walled CAVE-type installation, based on Immersive 3D Visualization Laboratory, situated at the Faculty of Electronics, Telecommunications and Informatics at the Gdańsk University of Technology. Tests have been carried out for two different scattering distribution of the screen material in order to check how these characteristicinfluence on the luminance distribution of the whole CAVE. The basis assumption and simplification of modeled CAVE-type installation and results were presented. The brief discussion about the results and usefulness of developed model were also carried out.

Preliminary Genetic Analysis Supports Cave Populations as Targets for Conservation in the Endemic Endangered Puerto Rican Boa (Boidae: Epicrates inornatus)

PubMed Central

Revell, Liam J.

2013-01-01

The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas. PMID:23691110

Preliminary genetic analysis supports cave populations as targets for conservation in the endemic endangered Puerto Rican boa (Boidae: Epicrates inornatus).

PubMed

Puente-Rolón, Alberto R; Reynolds, R Graham; Revell, Liam J

2013-01-01

The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas.

Raman spectroscopy of stercorite H(NH 4)Na(PO 4)·4H 2O--A cave mineral from Petrogale Cave, Madura, Eucla, Western Australia

NASA Astrophysics Data System (ADS)

Frost, Ray L.; Palmer, Sara J.

2011-09-01

Raman spectroscopy complimented with infrared spectroscopy has been used to characterise the mineral stercorite H(NH 4)Na(PO 4)·4H 2O. The mineral stercorite originated from the Petrogale Cave, Madura, Eucla, Western Australia. This cave is one of many caves in the Nullarbor Plain in the South of Western Australia. These caves have been in existence for eons of time and have been dated at more than 550 million years old. The mineral is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm -1 defines the presence of phosphate in the mineral. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm -1. Raman spectroscopy shows the mineral is based upon the phosphate anion and not the hydrogen phosphate anion. Raman and infrared bands are found and assigned to PO 43-, H 2O, OH and NH stretching vibrations. The detection of stercorite by Raman spectroscopy shows that the mineral can be readily determined; as such the application of a portable Raman spectrometer in a 'cave' situation enables the detection of minerals, some of which may remain to be identified.

Life on the edge: hydrogen sulfide and the fish communities of a Mexican cave and surrounding waters.

PubMed

Tobler, Michael; Schlupp, Ingo; Heubel, Katja U; Riesch, Rüdiger; de León, Francisco J García; Giere, Olav; Plath, Martin

2006-12-01

Most eucaryotic organisms classified as living in an extreme habitat are invertebrates. Here we report of a fish living in a Mexican cave (Cueva del Azufre) that is rich in highly toxic H(2)S. We compared the water chemistry and fish communities of the cave and several nearby surface streams. Our study revealed high concentrations of H(2)S in the cave and its outflow (El Azufre). The concentrations of H(2)S reach more than 300 muM inside the cave, which are acutely toxic for most fishes. In both sulfidic habitats, the diversity of fishes was heavily reduced, and Poecilia mexicana was the dominant species indicating that the presence of H(2)S has an all-or-none effect, permitting only few species to survive in sulfidic habitats. Compared to habitats without H(2)S, P. mexicana from the cave and the outflow have a significantly lower body condition. Although there are microhabitats with varying concentrations of H(2)S within the cave, we could not find a higher fish density in areas with lower concentrations of H(2)S. We discuss that P. mexicana is one of the few extremophile vertebrates. Our study supports the idea that extreme habitats lead to an impoverished species diversity.

Energy expenditure in caving.

PubMed

Antoni, Giorgia; Marini, Elisabetta; Curreli, Nicoletta; Tuveri, Valerio; Comandini, Ornella; Cabras, Stefano; Gabba, Silvia; Madeddu, Clelia; Crisafulli, Antonio; Rinaldi, Andrea C

2017-01-01

The aim of this study was to determine the energy expenditure of a group of cavers of both genders and different ages and experience during a 10 hour subterranean exploration, using portable metabolimeters. The impact of caving activity on body composition and hydration were also assessed through bioelectrical impedance, and nutritional habits of cavers surveyed. During cave activity, measured total energy expenditure (TEE) was in the range 225-287 kcal/h for women-men (MET = 4.1), respectively; subjects had an energy intake from food in the range 1000-1200 kcal, thus inadequate to restore lost calories. Bayesian statistical analysis estimated the effect of predictive variables on TEE, revealing that experienced subjects had a 5% lower TEE than the less skilled ones and that women required a comparatively larger energy expenditure than men to perform the same task. BIVA (bioelectrical impedance vector analysis) showed that subjects were within the range of normal hydration before and after cave activity, but bioelectrical changes indicated a reduction of extracellular water in men, which might result in hypo-osmolal dehydration in the case of prolonged underground exercise. All these facts should be considered when planning cave explorations, preparing training programs for subjects practising caving, and optimizing a diet for cavers. Further, information gathered through this study could be of value to reduce accidents in caves related to increase in fatigue.

Comparison of Bacterial Diversity in Azorean and Hawai’ian Lava Cave Microbial Mats

PubMed Central

MARSHALL HATHAWAY, JENNIFER J.; GARCIA, MATTHEW G.; BALASCH, MONICA MOYA; SPILDE, MICHAEL N.; STONE, FRED D.; DAPKEVICIUS, MARIA DE LURDES N. E.; AMORIM, ISABEL R.; GABRIEL, ROSALINA; BORGES, PAULO A. V.; NORTHUP, DIANA E.

2015-01-01

Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai’i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai’ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai’ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography. PMID:26924866

Hypogenic origin, geologic controls and functional organization of a giant cave system in Precambrian carbonates, Brazil

NASA Astrophysics Data System (ADS)

Klimchouk, Alexander; Auler, Augusto S.; Bezerra, Francisco H. R.; Cazarin, Caroline L.; Balsamo, Fabrizio; Dublyansky, Yuri

2016-01-01

This study is focused on speleogenesis of the Toca da Boa Vista (TBV) and Toca da Barriguda (TBR), the longest caves in South America occurring in the Neoproterozoic Salitre Formation in the São Francisco Craton, NE Brazil. We employ a multidisciplinary approach integrating detailed speleomorphogenetic, lithostratigraphic and geological structure studies in order to reveal the origin of the caves, their functional organization and geologic controls on their development. The caves developed in deep-seated confined conditions by rising flow. The overall fields of passages of TBV and TBR caves represent a speleogenetically exploited large NE-SW-trending fracture corridor associated with a major thrust. This corridor vertically extends across the Salitre Formation allowing the rise of deep fluids. In the overall ascending flow system, the formation of the cave pattern was controlled by a system of sub-parallel anticlines and troughs with NNE-SSW dominant orientation, and by vertical and lateral heterogeneities in fracture distribution. Three cave-stratigraphic stories reflect the actual hydrostratigraphy during the main phase of speleogenesis. Cavities at different stories are distinct in morphology and functioning. The gross tree-dimensional pattern of the system is effectively organized to conduct rising flow in deep-seated confined conditions. Cavities in the lower story developed as recharge components to the system. A laterally extensive conduit network in the middle story formed because the vertical flow from numerous recharge points has been redirected laterally along the highly conductive unit, occurring below the major seal - a scarcely fractured unit. Rift-like and shaft-like conduits in the upper story developed along fracture-controlled outflow paths, breaching the integrity of the major seal, and served as outlets for the cave system. The cave system represents a series of vertically organized, functionally largely independent clusters of cavities developed within individual ascending flow cells. Lateral integration of clusters occurred due to hydrodynamic interaction between the flow cells in course of speleogenetic evolution and change of boundary conditions. The main speleogenetic phase, during which the gross cave pattern has been established and the caves acquired most of their volume, was likely related to rise of deep fluids at about 520 Ma or associated with rifting and the Pangea break-up in Triassic-Cretaceous. This study highlights the importance of speleogenetic studies for interpreting porosity and permeability features in carbonate reservoirs.

Seasonal variations of cave conditions and drip water stable isotopes from a monitoring study of Raccoon Mountain Caverns, Tennessee, and its implications in interpreting speleothem record

NASA Astrophysics Data System (ADS)

Holtzclaw, C. L.; Gordon, R. D.; Feng, W.; Allard, J.

2015-12-01

A two-year monitoring study at Raccoon Mountain Caverns near Chattanooga, Tennessee was carried out in an attempt to establish quantitative relationships between climate signals and drip water stable isotopes for interpreting speleothem paleoclimate records from the cave. Eight field trips were made from Jan. 2014 to Jun. 2015, during which cave meteorological conditions (RH, temperature and cave air CO2 concentration) and drip rate were measured for 5 sites inside the cave. 63 cave drip and pool water samples were collected and analyzed for oxygen and hydrogen isotope compositions (δ18O and δD values). Cave air temperature varied throughout the study period, the temporal variations ranged at different sites from 2 to 8.4 °C (the greatest variation was observed at sites that are closer to the entrance or surface). These are significantly less than outside temperatures range of 24 °C, but more than observed in other monitored caves. Elevated cave-air CO2 concentration (3200 ppm) and slow drip rate during the summer indicated slowed or stalled growth of calcite. The overall range of δ18O values were -7.1‰ to -4.5‰. A δD vs δ18O diagram yields a slope of 6.1, which falls within the normal range of 6-8 for local Meteoric Water Line. The value is slightly above Global Meteoric Water Line, indicating lack of evaporative effect. Throughout the study period, the δ18O values varied from 0.6 ‰ at some sites to 1.9‰ at others. The largest changes were likely due to the close proximity of collection sites to the surface precipitation. Spatially, for samples collected at each cave trip, different sites displayed variations of δ18O values from 0‰ to 1.7‰. The difference could be attributed to different type of drip sites with varying types of flow paths rainwater takes to the drip sites. The significant seasonal shift of drip water δ18O values and growth conditions indicate importance of consideration of seasonality in interpreting speleothem δ18O record from this cave.

Radon, radionuclides and the Cretaceous Folkestone Sands - gamma spectroscopy and geochemical analysis of silver sands and associated deposits in the SE of England.

NASA Astrophysics Data System (ADS)

Gillmore, Gavin; Al-Rafai, Yousef; Flowers, Alan

2017-04-01

Radon concentrations in a historic sand mine in Surrey, UK (Reigate Caves), have been measured by both real-time and time-averaged methods over a number of years. These mines are not identified as being in a 'Radon Affected Area' as defined by Public Health England, although concentrations show a summer level of 640 Bqm3 +-44 Bqm3. Average radon concentrations (September 2013 to January 2014) in Reigate caves were above the UK 200 Bqm3 domestic Action Level, above the UK domestic Target Level (of 100 Bqm3) but below the current workplace Action Level of 400 Bqm3. By way of a comparison radon has also been measured in nearby Dorking (South Street Caves). These enigmatic caves were not mined for sand for glass manufacture as Reigate Caves were and there is speculation on why the caves were created. Both are visited by tourists on a semi-regular basis. Dorking caves have a different morphology with radon concentrations in Autumn 2016 of up to 1940 +/- 230 Bqm3. The caves in Reigate are situated along Tunnel Road. These mines were also used as air raid shelters and wine stores. They consist of an East and West system and an older cave (Barons cave) which may have a medieval origin. As the Western Caves are now a shooting range our work has been carried out in the Eastern section at Reigate. Where Dorking is concerned the shops and houses in the town have extensive interconnected cellars and galleries cut into these sands. The caves probably date from the 17th century but were used quite extensively for wine storage in the 19th century due to their constant 140C air temperatures. Real-time measurements were taken with a Durridge Rad7 with time-averaged CR39 SSNTDs being placed throughout the cave systems to assess radon distribution and compare results with the real-time detector. Both caves contain marine shallow-water deposited locking (having tensile and compressive strength) silica sands of the Cretaceous Lower Greensand Group, Folkestone Formation, with little cement holding the grains together (typical porosity being around 30%). Microscope analysis shows that this material contains mostly angular to sub-angular quartz grains, some with undulose extinction under cross-polarised light. This suggests a metamorphic origin for the quartz. There are also some relatively rare rock fragments present. These silver sands are a mixture of fine to medium grain sizes (0.10 to 0.5 mm) with small proportions of finer and coarser grades and are in the order of 30 - 36 metres thick at Reigate. These beds show lateral and vertical variability in their grain size, mineralogy and geochemical make up such as iron oxide content and are heavily faulted in places. In view of these radon results, in order to determine whether these levels are supported or unsupported, samples were collected and subjected to laboratory-based Gamma spectrometry. This indicated the presence of U235 (186keV) and Pb212 (238keV) in sands from these caves. We will shortly be in a position to also report in-situ gamma spectrometry and ICPMS analysis of samples taken from these beds.

Comparison of Spring and Cave Drip Water in Westcave Preserve, Central Texas May Reveal Epikarst CO2 Degassing

NASA Astrophysics Data System (ADS)

Carlson, P.; Banner, J. L.; Casteel, R. C.; Breecker, D.

2013-12-01

The cave at Westcave Preserve, in central Texas, is a unique location to study karst processes due to its low, nearly atmospheric cave-air CO2 levels and seasonally variable temperature. The source of water that drips into the cave, however, has not been constrained, limiting interpretation of climate proxies in the cave. It is possible that a nearby spring and the cave drip-waters share a common source. Alternatively, the drip-waters could represent precipitation that has infiltrated the host rock. These hypotheses should be tested using Sr isotope ratios and/or other tracers. If they do share a common source, analysis of dissolved inorganic carbon (DIC) concentration , δ13CDIC, and cation concentrations of the two waters could provide insight into epikarst processes such as CO2 degassing and prior calcite precipitation (PCP) that are otherwise difficult to constrain. Westcave Preserve includes outcrops of the Hensell Sand, the Cow Creek Limestone, and the Hammett Shale, with a small cave at the contact between the Cow Creek and Hammett formations. The overlying Hensell Sand contains water that emerges at the surface as a spring near the cave. Water also drips directly into the cave, forming speleothems. Previous research has established that although δ18O values of rainfall in the area vary seasonally, between -10.5 and 1.1‰ with a weighted mean of -6.5‰ (VSMOW), the drip-water varies only between -4.7 and -4.3‰ with a weighted mean of -4.5‰ (Feng et al., in review). This suggests a large well-mixed reservoir above the cave. The soils above the cave have high CO2 of up to 17,500 ppmv, but because the cave is shallow with multiple large openings, cave CO2 levels are near-atmospheric (Casteel and Banner, in review). This creates a steep CO2 gradient between the soil and the cave air. The spring water DIC is nearly in carbon-isotope equilibrium with the soil CO2, suggesting that soil respiration, here controlled by C3 plants, is the primary source of CO2 for this reservoir. The drip water δ13CDIC is higher than the spring water (-10.3‰ versus -13.0‰). Although the spring water has higher DIC concentration than the drip water, with mean values of 128 mg/L C versus 113 mg/L C, respectively, preliminary data suggest that for some drips, the drip water DIC concentrations and δ13CDIC may vary with spring DIC values. We propose that if the spring and the drip water prove to be derived from the same source, the differences in DIC and δ13CDIC between spring and drip water are due to epikarst CO2 degassing as the water percolates down the CO2 gradient toward the cave ceiling. If the spring represents the source of the drip water, the calculated δ13 value of degassed CO2 is -33.3‰, assuming no PCP. PCP may occur, leading to a δ13C of degassed CO2 lower than calculated, but would result in a decrease or no change in δ13CDIC and therefore does not explain the observed difference between spring water and drip water.

Marginal Consistency: Upper-Bounding Partition Functions over Commutative Semirings.

PubMed

Werner, Tomás

2015-07-01

Many inference tasks in pattern recognition and artificial intelligence lead to partition functions in which addition and multiplication are abstract binary operations forming a commutative semiring. By generalizing max-sum diffusion (one of convergent message passing algorithms for approximate MAP inference in graphical models), we propose an iterative algorithm to upper bound such partition functions over commutative semirings. The iteration of the algorithm is remarkably simple: change any two factors of the partition function such that their product remains the same and their overlapping marginals become equal. In many commutative semirings, repeating this iteration for different pairs of factors converges to a fixed point when the overlapping marginals of every pair of factors coincide. We call this state marginal consistency. During that, an upper bound on the partition function monotonically decreases. This abstract algorithm unifies several existing algorithms, including max-sum diffusion and basic constraint propagation (or local consistency) algorithms in constraint programming. We further construct a hierarchy of marginal consistencies of increasingly higher levels and show than any such level can be enforced by adding identity factors of higher arity (order). Finally, we discuss instances of the framework for several semirings, including the distributive lattice and the max-sum and sum-product semirings.

Near Surface Geophysical Methods Applied to the Rising Star Cave System

NASA Astrophysics Data System (ADS)

Webb, S. J.; Naidoo, M.; Elliott, M. C.; Kruger, A.; Roberts, E.; Dirks, P.

2017-12-01

The Rising Star Cave system is located approximately 40 km northwest of Johannesburg in the Malmani dolomites (Chuniespoort group,Transvaal Supergroup). The cave system is extensive with 4 km of mapped passages and chambers. The Dinaledi chamber, host to the Homo Naledi fossils, is reached by following a tortuous route with squeezes as small as 20 cm. The chamber is located 30 m below surface and 80 m from the entrance. The enigmatic find of fossils from at least 15 individual hominins, without the presence of other species, led to the idea of deliberate burial. The present access route is difficult and it is unclear how early hominins were able to navigate it, prompting the suggestion of an undiscovered entrance. We are using near surface geophysical methods to investigate possible connections between the surface and the caves. Using a Geometrics Cs-vapor Walkmag, we collected preliminary ground magnetic intensity measurements over a region 300 m x 200 m, using 1 m station spacing and 10 m line spacing. The average magnetic variation along line is 200 nT. We also collected over 100 susceptibility measurements on outcropping lithologies, surface soil and cave sediments using a SM-30 susceptibility meter. The surface soil was one to two orders of magnitude higher than surrounding lithologies (average = 1.5 x 10-3 SI) and the cave sediment samples were slightly higher (average = 3.07 x 10-3 SI). We were able to collect GPR data (GSSI SIR-3000, 400 MHz) in selected spots on the cave floor with the goal of locating the cave floor beneath the sediments. Dolomites usually have low magnetic susceptibilities, but erosion products of the nearby magnetic Hospital Hill or Rooihoogte shales may have been transported into or onto the cave system. This is a likely cause of the magnetic anomalies and larger amplitude anomalies may indicate an accumulation of sediments, extending to depth. These anomalies will be further investigated using gravity to determine if there are previously unknown connections between the surface and the cave system.

Hydrological characterization of cave drip waters in a porous limestone: Golgotha Cave, Western Australia

NASA Astrophysics Data System (ADS)

Mahmud, Kashif; Mariethoz, Gregoire; Baker, Andy; Treble, Pauline C.

2018-02-01

Cave drip water response to surface meteorological conditions is complex due to the heterogeneity of water movement in the karst unsaturated zone. Previous studies have focused on the monitoring of fractured rock limestones that have little or no primary porosity. In this study, we aim to further understand infiltration water hydrology in the Tamala Limestone of SW Australia, which is Quaternary aeolianite with primary porosity. We build on our previous studies of the Golgotha Cave system and utilize the existing spatial survey of 29 automated cave drip loggers and a lidar-based flow classification scheme, conducted in the two main chambers of this cave. We find that a daily sampling frequency at our cave site optimizes the capture of drip variability with the least possible sampling artifacts. With the optimum sampling frequency, most of the drip sites show persistent autocorrelation for at least a month, typically much longer, indicating ample storage of water feeding all stalactites investigated. Drip discharge histograms are highly variable, showing sometimes multimodal distributions. Histogram skewness is shown to relate to the wetter-than-average 2013 hydrological year and modality is affected by seasonality. The hydrological classification scheme with respect to mean discharge and the flow variation can distinguish between groundwater flow types in limestones with primary porosity, and the technique could be used to characterize different karst flow paths when high-frequency automated drip logger data are available. We observe little difference in the coefficient of variation (COV) between flow classification types, probably reflecting the ample storage due to the dominance of primary porosity at this cave site. Moreover, we do not find any relationship between drip variability and discharge within similar flow type. Finally, a combination of multidimensional scaling (MDS) and clustering by k means is used to classify similar drip types based on time series analysis. This clustering reveals four unique drip regimes which agree with previous flow type classification for this site. It highlights a spatial homogeneity in drip types in one cave chamber, and spatial heterogeneity in the other, which is in agreement with our understanding of cave chamber morphology and lithology.

Biogeography, phylogeny, and morphological evolution of central Texas cave and spring salamanders

PubMed Central

2013-01-01

Background Subterranean faunal radiations can result in complex patterns of morphological divergence involving both convergent or parallel phenotypic evolution and cryptic species diversity. Salamanders of the genus Eurycea in central Texas provide a particularly challenging example with respect to phylogeny reconstruction, biogeography and taxonomy. These predominantly aquatic species inhabit karst limestone aquifers and spring outflows, and exhibit a wide range of morphological and genetic variation. We extensively sampled spring and cave populations of six Eurycea species within this group (eastern Blepsimolge clade), to reconstruct their phylogenetic and biogeographic history using mtDNA and examine patterns and origins of cave- and surface-associated morphological variation. Results Genetic divergence is generally low, and many populations share ancestral haplotypes and/or show evidence of introgression. This pattern likely indicates a recent radiation coupled with a complex history of intermittent connections within the aquatic karst system. Cave populations that exhibit the most extreme troglobitic morphologies show no or very low divergence from surface populations and are geographically interspersed among them, suggesting multiple instances of rapid, parallel phenotypic evolution. Morphological variation is diffuse among cave populations; this is in contrast to surface populations, which form a tight cluster in morphospace. Unexpectedly, our analyses reveal two distinct and previously unrecognized morphological groups encompassing multiple species that are not correlated with spring or cave habitat, phylogeny or geography, and may be due to developmental plasticity. Conclusions The evolutionary history of this group of spring- and cave-dwelling salamanders reflects patterns of intermittent isolation and gene flow influenced by complex hydrogeologic dynamics that are characteristic of karst regions. Shallow genetic divergences among several species, evidence of genetic exchange, and nested relationships across morphologically disparate cave and spring forms suggests that cave invasion was recent and many troglobitic morphologies arose independently. These patterns are consistent with an adaptive-shift hypothesis of divergence, which has been proposed to explain diversification in other karst fauna. While cave and surface forms often do not appear to be genetically isolated, morphological diversity within and among populations may be maintained by developmental plasticity, selection, or a combination thereof. PMID:24044519

Reconstructing water level in Hoyo Negro, Quintana Roo, Mexico, implications for early Paleoamerican and faunal access

NASA Astrophysics Data System (ADS)

Collins, S. V.; Reinhardt, E. G.; Rissolo, D.; Chatters, J. C.; Nava Blank, A.; Luna Erreguerena, P.

2015-09-01

The skeletal remains of a Paleoamerican (Naia; HN5/48) and extinct megafauna were found at -40 to -43 mbsl in a submerged dissolution chamber named Hoyo Negro (HN) in the Sac Actun Cave System, Yucatan Peninsula, Mexico. The human remains were dated to between 12 and 13 Ka, making these remains the oldest securely dated in the Yucatan. Twelve sediment cores were used to reconstruct the Holocene flooding history of the now phreatic cave passages and cenotes (Ich Balam, Oasis) that connect to HN. Four facies were found: 1. bat guano and Seed (SF), 2. lime Mud (MF), 3. Calcite Rafts (CRF) and 4. Organic Matter/Calcite Rafts (OM/CRF) which were defined by their lithologic characteristics and ostracod, foraminifera and testate amoebae content. Basal radiocarbon ages (AMS) of aquatic sediments (SF) combined with cave bottom and ceiling height profiles determined the history of flooding in HN and when access was restricted for human and animal entry. Our results show that the bottom of HN was flooded at least by 9850 cal yr BP but likely earlier. We also found, that the pit became inaccessible for human and animal entry at ≈8100 cal yr BP, when water reaching the cave ceiling effectively prevented entry. Water level continued to rise between ≈6000 and 8100 cal yr BP, filling the cave passages and entry points to HN (Cenotes Ich Balam and Oasis). Analysis of cave facies revealed that both Holocene sea-level rise and cave ceiling height determined the configuration of airways and the deposition of floating and bat derived OM (guano and seeds). Calcite rafts, which form on the water surface, are also dependent on the presence of airways but can also form in isolated air domes in the cave ceiling that affect their loci of deposition on the cave bottom. These results indicated that aquatic cave sedimentation is transient in time and space, necessitating extraction of multiple cores to determine a limit after which flooding occurred.

Evaluating the Carrying Capacity in The Škocjan Caves, Slovenia

NASA Astrophysics Data System (ADS)

Debevec Gerjevic, V.

2009-04-01

Park Škocjanske jame, Slovenija is a multidesignation site, located in south western part of Slovenia. In 1986 the Škocjanske jame - Škocjan Caves were listed in UNESCO world heritage list, in 1996 the Government of Republic Slovenia established the Regional Park Škocjanske jame, Slovenija. In 1999 the underground course of The Reka River in Škocjan Caves was designated a Ramsar site as first underground wetland of international importance. The park lies within three locations Natura 2000. In 2004 Park Škocjanske jame became a MAB locality as The Karst Biosphere Reserve. The tourist activity was already developed in the early 19th century. Today's research projects are focused on quality of caves microclimate, in order to enable the cave to remain as pristine as possible due to tourism and on the other hand to provide safe environment for people who work in the caves, and on quality of the water that flows from buffer zone to the underground world an then to the sea in Italy. The tourist activity increased during the past years. With the aim of nature conservation and protection the management plan was developed and special programme of monitoring started in order to detect changes in the environment due to the anthropogenic impact. In the park we consider the estimation of the carrying capacity as a key element for preparation of proper management guidelines for the tourism development in site. The caves system is rich in several halls and tunnels and distinguishes the caves for its variety of dimensions. There are several limitations of the visits and number of visitors. They merely depend on spatial characteristic of the caves and its surroundings and on human resources of the experts stuff that is in charge of guiding tourists groups to the caves. There is no simple formula that could be used for evaluation of capacity on general, but detailed studies of several locations and suitable description of parameters could give us an idea of proposing the limiting numbers. Physical and actual capacities will be discussed and a model of preparation of social capacity will be provided.

Discovering time-lagged rules from microarray data using gene profile classifiers

PubMed Central

2011-01-01

Background Gene regulatory networks have an essential role in every process of life. In this regard, the amount of genome-wide time series data is becoming increasingly available, providing the opportunity to discover the time-delayed gene regulatory networks that govern the majority of these molecular processes. Results This paper aims at reconstructing gene regulatory networks from multiple genome-wide microarray time series datasets. In this sense, a new model-free algorithm called GRNCOP2 (Gene Regulatory Network inference by Combinatorial OPtimization 2), which is a significant evolution of the GRNCOP algorithm, was developed using combinatorial optimization of gene profile classifiers. The method is capable of inferring potential time-delay relationships with any span of time between genes from various time series datasets given as input. The proposed algorithm was applied to time series data composed of twenty yeast genes that are highly relevant for the cell-cycle study, and the results were compared against several related approaches. The outcomes have shown that GRNCOP2 outperforms the contrasted methods in terms of the proposed metrics, and that the results are consistent with previous biological knowledge. Additionally, a genome-wide study on multiple publicly available time series data was performed. In this case, the experimentation has exhibited the soundness and scalability of the new method which inferred highly-related statistically-significant gene associations. Conclusions A novel method for inferring time-delayed gene regulatory networks from genome-wide time series datasets is proposed in this paper. The method was carefully validated with several publicly available data sets. The results have demonstrated that the algorithm constitutes a usable model-free approach capable of predicting meaningful relationships between genes, revealing the time-trends of gene regulation. PMID:21524308

Single nucleotide polymorphism coverage and inference of N-acetyltransferase-2 acetylator phenotypes in wordwide population groups.

PubMed

Suarez-Kurtz, Guilherme; Fuchshuber-Moraes, Mateus; Struchiner, Claudio J; Parra, Esteban J

2016-08-01

Several algorithms have been proposed to reduce the genotyping effort and cost, while retaining the accuracy of N-acetyltransferase-2 (NAT2) phenotype prediction. Data from the 1000 Genomes (1KG) project and an admixed cohort of Black Brazilians were used to assess the accuracy of NAT2 phenotype prediction using algorithms based on paired single nucleotide polymorphisms (SNPs) (rs1041983 and rs1801280) or a tag SNP (rs1495741). NAT2 haplotypes comprising SNPs rs1801279, rs1041983, rs1801280, rs1799929, rs1799930, rs1208 and rs1799931 were assigned according to the arylamine N-acetyltransferases database. Contingency tables were used to visualize the agreement between the NAT2 acetylator phenotypes on the basis of these haplotypes versus phenotypes inferred by the prediction algorithms. The paired and tag SNP algorithms provided more than 96% agreement with the 7-SNP derived phenotypes in Europeans, East Asians, South Asians and Admixed Americans, but discordance of phenotype prediction occurred in 30.2 and 24.8% 1KG Africans and in 14.4 and 18.6% Black Brazilians, respectively. Paired SNP panel misclassification occurs in carriers of NATs haplotypes *13A (282T alone), *12B (282T and 803G), *6B (590A alone) and *14A (191A alone), whereas haplotype *14, defined by the 191A allele, is the major culprit of misclassification by the tag allele. Both the paired SNP and the tag SNP algorithms may be used, with economy of scale, to infer NAT2 acetylator phenotypes, including the ultra-slow phenotype, in European, East Asian, South Asian and American populations represented in the 1KG cohort. Both algorithms, however, perform poorly in populations of predominant African descent, including admixed African-Americans, African Caribbeans and Black Brazilians.

Denoising, deconvolving, and decomposing photon observations. Derivation of the D3PO algorithm

NASA Astrophysics Data System (ADS)

Selig, Marco; Enßlin, Torsten A.

2015-02-01

The analysis of astronomical images is a non-trivial task. The D3PO algorithm addresses the inference problem of denoising, deconvolving, and decomposing photon observations. Its primary goal is the simultaneous but individual reconstruction of the diffuse and point-like photon flux given a single photon count image, where the fluxes are superimposed. In order to discriminate between these morphologically different signal components, a probabilistic algorithm is derived in the language of information field theory based on a hierarchical Bayesian parameter model. The signal inference exploits prior information on the spatial correlation structure of the diffuse component and the brightness distribution of the spatially uncorrelated point-like sources. A maximum a posteriori solution and a solution minimizing the Gibbs free energy of the inference problem using variational Bayesian methods are discussed. Since the derivation of the solution is not dependent on the underlying position space, the implementation of the D3PO algorithm uses the nifty package to ensure applicability to various spatial grids and at any resolution. The fidelity of the algorithm is validated by the analysis of simulated data, including a realistic high energy photon count image showing a 32 × 32 arcmin2 observation with a spatial resolution of 0.1 arcmin. In all tests the D3PO algorithm successfully denoised, deconvolved, and decomposed the data into a diffuse and a point-like signal estimate for the respective photon flux components. A copy of the code is available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/574/A74

A Coalitional Game for Distributed Inference in Sensor Networks With Dependent Observations

NASA Astrophysics Data System (ADS)

He, Hao; Varshney, Pramod K.

2016-04-01

We consider the problem of collaborative inference in a sensor network with heterogeneous and statistically dependent sensor observations. Each sensor aims to maximize its inference performance by forming a coalition with other sensors and sharing information within the coalition. It is proved that the inference performance is a nondecreasing function of the coalition size. However, in an energy constrained network, the energy consumption of inter-sensor communication also increases with increasing coalition size, which discourages the formation of the grand coalition (the set of all sensors). In this paper, the formation of non-overlapping coalitions with statistically dependent sensors is investigated under a specific communication constraint. We apply a game theoretical approach to fully explore and utilize the information contained in the spatial dependence among sensors to maximize individual sensor performance. Before formulating the distributed inference problem as a coalition formation game, we first quantify the gain and loss in forming a coalition by introducing the concepts of diversity gain and redundancy loss for both estimation and detection problems. These definitions, enabled by the statistical theory of copulas, allow us to characterize the influence of statistical dependence among sensor observations on inference performance. An iterative algorithm based on merge-and-split operations is proposed for the solution and the stability of the proposed algorithm is analyzed. Numerical results are provided to demonstrate the superiority of our proposed game theoretical approach.

Radon in Ingleborough / Clapham Cave, North Yorkshire, UK.

NASA Astrophysics Data System (ADS)

Gillmore, Gavin

2015-04-01

Atmospheric radon concentration was measured at Ingleborough Cave, North Yorkshire during the summer of 2004, and the autumn / winter of 2004/5. Significantly, Ingleborough Cave forms part of a larger system which includes the world famous Gaping Gill pothole. This plunges 105 m (334 ft), contains the tallest unbroken waterfall in England and one of the largest known underground chambers in the UK. Measurements were taken to assess the effects of seasonal and spatial variation, elevation and ventilation on radon concentration in Ingleborough. In this study personal dose exposures for three groups of cave user were identified, and the performance of a variety of radon detection systems evaluated. Summer radon concentrations inside the cave peaked at around 7,000 Bq m-3, although average concentrations were less than 5,000 Bq m-3. During the winter measurement period, average concentrations were around 100 Bq m-3, and a winter / summer ration therefore of 47,4. The average annual radon concentration exceeded the legislative limitations for the workplace of 400 Bq m-3 due in part to a failed fan in the ventilation system. When the fan was running we noted an 80% reduction in radon concentrations although reliability of the fan was problematic due to extensive but relatively rare flooding of the cave system. The radon dose experienced by cave workers and guides in this study exceeded the Ionisation Radiation Regulations limit of 5 mSv/annum, and highlighted that for health and safety reasons the ventilation system should be fully operational during the high radon concentration summer months. Keywords: Radon, Cave, Ingleborough, Detection methods

Mimogonellus dreybrodti sp. n., a new cave-inhabiting Osoriinae from Laos (Coleoptera: Staphylinidae).

PubMed

Yin, Zi-Wei; Steiner, Helmut

2017-10-17

A new osoriine species, Mimogonellus dreybrodti Yin & Steiner, sp. n., collected from a cave in Houaphanh Province, Laos, is described and illustrated. This represents the third Mimogonellus species in Asia, and the first in the genus known to inhabit a cave environment.

Resource Documentation and Recharge Area Delineation of a Large Fluvial Karst System: Carroll Cave, Missouri

USDA-ARS?s Scientific Manuscript database

Located along Wet Glaize Creek in the central Missouri Ozarks, Toronto Spring is a distributary spring system where surface stream flow mixes with flow from the Carroll Cave system. Following recharge area delineations for Thunder River and Confusion Creek in Carroll Cave, flow from these rivers wa...

36 CFR 7.36 - Mammoth Cave National Park.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Mammoth Cave National Park. 7.36 Section 7.36 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.36 Mammoth Cave National Park. (a) Fishing—(1...

36 CFR 7.36 - Mammoth Cave National Park.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Mammoth Cave National Park. 7.36 Section 7.36 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.36 Mammoth Cave National Park. (a) Fishing—(1...

36 CFR 7.36 - Mammoth Cave National Park.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Mammoth Cave National Park. 7.36 Section 7.36 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.36 Mammoth Cave National Park. (a) Fishing—(1...

36 CFR 7.36 - Mammoth Cave National Park.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Mammoth Cave National Park. 7.36 Section 7.36 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.36 Mammoth Cave National Park. (a) Fishing—(1...

36 CFR 7.36 - Mammoth Cave National Park.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Mammoth Cave National Park. 7.36 Section 7.36 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.36 Mammoth Cave National Park. (a) Fishing—(1...

DNA analysis of fecal bacteria to augment an epikarst dye trace study at Crump's Cave, Kentucky

USDA-ARS?s Scientific Manuscript database

A rainfall simulation experiment was performed to investigate the transport behavior of fecal-derived bacteria through shallow karst soils and through the epikarst. The experiment was conducted at Cave Springs Cavern located just south of Mammoth Cave National Park on the Sinkhole Plain of South Cen...

Population connectivity of endangered Ozark big-eared bats (Corynorhinus townsendii ingens)

USGS Publications Warehouse

Lee, Dana N.; Stark, Richard C.; Puckette, William L.; Hamilton, Meredith J.; Leslie, David M.; Van Den Bussche, Ronald A.

2015-01-01

The endangered Ozark big-eared bat (Corynorhinus townsendii ingens) is restricted to eastern Oklahoma and western and north-central Arkansas, where populations may be susceptible to losses of genetic variation due to patchy distribution of colonies and potentially small effective population sizes. We used mitochondrial D-loop DNA sequences and 15 nuclear microsatellite loci to determine population connectivity among Ozark big-eared bat caves. Assessment of 7 caves revealed a haplotype not detected in a previous study (2002–2003) and gene flow among colonies in eastern Oklahoma. Our data suggest genetic mixing of individuals, which may be occurring at nearby swarming sites in the autumn. Further evidence of limited gene flow between caves in Oklahoma with a cave in Arkansas highlights the importance of including samples from geographically widespread caves to fully understand gene flow in this subspecies. It appears autumn swarming sites and winter hibernacula play an important role in providing opportunities for mating; therefore, we suggest protection of these sites, maternity caves, and surrounding habitat to facilitate gene flow among populations of Ozark big-eared bats.

The importance of selection in the evolution of blindness in cavefish.

PubMed

Cartwright, Reed A; Schwartz, Rachel S; Merry, Alexandra L; Howell, Megan M

2017-02-07

Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. We estimate that the selection coefficient for blindness would need to be at least 0.005 (and maybe as high as 0.5) for blindness to evolve in the model cave-organism, Astyanax mexicanus. Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development.

A New Methodology for Open Pit Slope Design in Karst-Prone Ground Conditions Based on Integrated Stochastic-Limit Equilibrium Analysis

NASA Astrophysics Data System (ADS)

Zhang, Ke; Cao, Ping; Ma, Guowei; Fan, Wenchen; Meng, Jingjing; Li, Kaihui

2016-07-01

Using the Chengmenshan Copper Mine as a case study, a new methodology for open pit slope design in karst-prone ground conditions is presented based on integrated stochastic-limit equilibrium analysis. The numerical modeling and optimization design procedure contain a collection of drill core data, karst cave stochastic model generation, SLIDE simulation and bisection method optimization. Borehole investigations are performed, and the statistical result shows that the length of the karst cave fits a negative exponential distribution model, but the length of carbonatite does not exactly follow any standard distribution. The inverse transform method and acceptance-rejection method are used to reproduce the length of the karst cave and carbonatite, respectively. A code for karst cave stochastic model generation, named KCSMG, is developed. The stability of the rock slope with the karst cave stochastic model is analyzed by combining the KCSMG code and the SLIDE program. This approach is then applied to study the effect of the karst cave on the stability of the open pit slope, and a procedure to optimize the open pit slope angle is presented.

The future of the CAVE

NASA Astrophysics Data System (ADS)

Defanti, Thomas A.; Acevedo, Daniel; Ainsworth, Richard A.; Brown, Maxine D.; Cutchin, Steven; Dawe, Gregory; Doerr, Kai-Uwe; Johnson, Andrew; Knox, Chris; Kooima, Robert; Kuester, Falko; Leigh, Jason; Long, Lance; Otto, Peter; Petrovic, Vid; Ponto, Kevin; Prudhomme, Andrew; Rao, Ramesh; Renambot, Luc; Sandin, Daniel J.; Schulze, Jurgen P.; Smarr, Larry; Srinivasan, Madhu; Weber, Philip; Wickham, Gregory

2011-03-01

The CAVE, a walk-in virtual reality environment typically consisting of 4-6 3 m-by-3 m sides of a room made of rear-projected screens, was first conceived and built in 1991. In the nearly two decades since its conception, the supporting technology has improved so that current CAVEs are much brighter, at much higher resolution, and have dramatically improved graphics performance. However, rear-projection-based CAVEs typically must be housed in a 10 m-by-10 m-by-10 m room (allowing space behind the screen walls for the projectors), which limits their deployment to large spaces. The CAVE of the future will be made of tessellated panel displays, eliminating the projection distance, but the implementation of such displays is challenging. Early multi-tile, panel-based, virtual-reality displays have been designed, prototyped, and built for the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia by researchers at the University of California, San Diego, and the University of Illinois at Chicago. New means of image generation and control are considered key contributions to the future viability of the CAVE as a virtual-reality device.

Graph rigidity, cyclic belief propagation, and point pattern matching.

PubMed

McAuley, Julian J; Caetano, Tibério S; Barbosa, Marconi S

2008-11-01

A recent paper [1] proposed a provably optimal polynomial time method for performing near-isometric point pattern matching by means of exact probabilistic inference in a chordal graphical model. Its fundamental result is that the chordal graph in question is shown to be globally rigid, implying that exact inference provides the same matching solution as exact inference in a complete graphical model. This implies that the algorithm is optimal when there is no noise in the point patterns. In this paper, we present a new graph that is also globally rigid but has an advantage over the graph proposed in [1]: Its maximal clique size is smaller, rendering inference significantly more efficient. However, this graph is not chordal, and thus, standard Junction Tree algorithms cannot be directly applied. Nevertheless, we show that loopy belief propagation in such a graph converges to the optimal solution. This allows us to retain the optimality guarantee in the noiseless case, while substantially reducing both memory requirements and processing time. Our experimental results show that the accuracy of the proposed solution is indistinguishable from that in [1] when there is noise in the point patterns.

Shear wave prediction using committee fuzzy model constrained by lithofacies, Zagros basin, SW Iran

NASA Astrophysics Data System (ADS)

Shiroodi, Sadjad Kazem; Ghafoori, Mohammad; Ansari, Hamid Reza; Lashkaripour, Golamreza; Ghanadian, Mostafa

2017-02-01

The main purpose of this study is to introduce the geological controlling factors in improving an intelligence-based model to estimate shear wave velocity from seismic attributes. The proposed method includes three main steps in the framework of geological events in a complex sedimentary succession located in the Persian Gulf. First, the best attributes were selected from extracted seismic data. Second, these attributes were transformed into shear wave velocity using fuzzy inference systems (FIS) such as Sugeno's fuzzy inference (SFIS), adaptive neuro-fuzzy inference (ANFIS) and optimized fuzzy inference (OFIS). Finally, a committee fuzzy machine (CFM) based on bat-inspired algorithm (BA) optimization was applied to combine previous predictions into an enhanced solution. In order to show the geological effect on improving the prediction, the main classes of predominate lithofacies in the reservoir of interest including shale, sand, and carbonate were selected and then the proposed algorithm was performed with and without lithofacies constraint. The results showed a good agreement between real and predicted shear wave velocity in the lithofacies-based model compared to the model without lithofacies especially in sand and carbonate.

Further constraints on the Chauvet cave artwork elaboration.

PubMed

Sadier, Benjamin; Delannoy, Jean-Jacques; Benedetti, Lucilla; Bourlès, Didier L; Jaillet, Stéphane; Geneste, Jean-Michel; Lebatard, Anne-Elisabeth; Arnold, Maurice

2012-05-22

Since its discovery, the Chauvet cave elaborate artwork called into question our understanding of Palaeolithic art evolution and challenged traditional chronological benchmarks [Valladas H et al. (2001) Nature 413:419-479]. Chronological approaches revealing human presences in the cavity during the Aurignacian and the Gravettian are indeed still debated on the basis of stylistic criteria [Pettitt P (2008) J Hum Evol 55:908-917]. The presented (36)Cl Cosmic Ray Exposure ages demonstrate that the cliff overhanging the Chauvet cave has collapsed several times since 29 ka until the sealing of the cavity entrance prohibited access to the cave at least 21 ka ago. Remarkably agreeing with the radiocarbon dates of the human and animal occupancy, this study confirms that the Chauvet cave paintings are the oldest and the most elaborate ever discovered, challenging our current knowledge of human cognitive evolution.

Further constraints on the Chauvet cave artwork elaboration

NASA Astrophysics Data System (ADS)

Sadier, Benjamin; Delannoy, Jean-Jacques; Benedetti, Lucilla; Bourlès, Didier L.; Jaillet, Stéphane; Geneste, Jean-Michel; Lebatard, Anne-Elisabeth; Arnold, Maurice

2012-05-01

Since its discovery, the Chauvet cave elaborate artwork called into question our understanding of Palaeolithic art evolution and challenged traditional chronological benchmarks [Valladas H et al. (2001) Nature 413:419-479]. Chronological approaches revealing human presences in the cavity during the Aurignacian and the Gravettian are indeed still debated on the basis of stylistic criteria [Pettitt P (2008) J Hum Evol 55:908-917]. The presented 36Cl Cosmic Ray Exposure ages demonstrate that the cliff overhanging the Chauvet cave has collapsed several times since 29 ka until the sealing of the cavity entrance prohibited access to the cave at least 21 ka ago. Remarkably agreeing with the radiocarbon dates of the human and animal occupancy, this study confirms that the Chauvet cave paintings are the oldest and the most elaborate ever discovered, challenging our current knowledge of human cognitive evolution.

Evaluation of a new neutron energy spectrum unfolding code based on an Adaptive Neuro-Fuzzy Inference System (ANFIS).

PubMed

Hosseini, Seyed Abolfazl; Esmaili Paeen Afrakoti, Iman

2018-01-17

The purpose of the present study was to reconstruct the energy spectrum of a poly-energetic neutron source using an algorithm developed based on an Adaptive Neuro-Fuzzy Inference System (ANFIS). ANFIS is a kind of artificial neural network based on the Takagi-Sugeno fuzzy inference system. The ANFIS algorithm uses the advantages of both fuzzy inference systems and artificial neural networks to improve the effectiveness of algorithms in various applications such as modeling, control and classification. The neutron pulse height distributions used as input data in the training procedure for the ANFIS algorithm were obtained from the simulations performed by MCNPX-ESUT computational code (MCNPX-Energy engineering of Sharif University of Technology). Taking into account the normalization condition of each energy spectrum, 4300 neutron energy spectra were generated randomly. (The value in each bin was generated randomly, and finally a normalization of each generated energy spectrum was performed). The randomly generated neutron energy spectra were considered as output data of the developed ANFIS computational code in the training step. To calculate the neutron energy spectrum using conventional methods, an inverse problem with an approximately singular response matrix (with the determinant of the matrix close to zero) should be solved. The solution of the inverse problem using the conventional methods unfold neutron energy spectrum with low accuracy. Application of the iterative algorithms in the solution of such a problem, or utilizing the intelligent algorithms (in which there is no need to solve the problem), is usually preferred for unfolding of the energy spectrum. Therefore, the main reason for development of intelligent algorithms like ANFIS for unfolding of neutron energy spectra is to avoid solving the inverse problem. In the present study, the unfolded neutron energy spectra of 252Cf and 241Am-9Be neutron sources using the developed computational code were found to have excellent agreement with the reference data. Also, the unfolded energy spectra of the neutron sources as obtained using ANFIS were more accurate than the results reported from calculations performed using artificial neural networks in previously published papers. © The Author(s) 2018. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Exact solutions for species tree inference from discordant gene trees.

PubMed

Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

2013-10-01

Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions.

Palaeohydrology of a 3D-maze cave (Hermannshöhle, Lower Austria)

NASA Astrophysics Data System (ADS)

Schober, Andrea; Plan, Lukas

2013-04-01

The 4.4 km-long Hermannshöhle (located in Kirchberg/Wechsel, Lower Austria) is one of the largest caves in the Lower Austroalpine Unit. It is developed in an isolated block of carbonate marble, taking up only 140 x 160 m of ground area and 73 m of elevation difference. The cave is unusual in two respects: (a) its dense network of corridors is arranged in a three-dimensional maze and (b) the most outstanding macro- and micromorphologic features were caused by paragenesis. Speleothems are abundant throughout the cave comprising flowstones, dripstones, helictites, popcorn, calcite rafts, a shield, and moonmilk. Even though most passages are canyon-shaped, the cave shows exclusively phreatic features. Sediment fills are abundant as well, mostly covering the floor of passages to an unknown depth, containing mainly allochthonous material, i.e. schists and gneisses. Besides some vadose dripwater the cave is dry today. A conspicuous feature is the lack of a single water path and instead a maze with multiple flow paths formed. Another interesting feature is that one part of the cave developed below the nearby Ramsbach brook but is still dry. There are small ponors reported from the Ramsbach brook (which were observed during river regulation) indicating an actively draining karst system, which is not yet explored. The aim of this study was to enlighten the palaeohydrology of this cave using morphological and sedimentological observations as well as U/Th dating of speleothems. First results show that the palaeo-environment and the hydrologic setting of the Hermannshöhle were drastically different from today. Undersaturated water sourced from nearby non-karstic gneisses and schists gave rise to well-developed contact karst features. Surprisingly the palaeo flow direction deduced from indicators like scallops and sediment structures was opposite to the flow direction of the present nearby brooks (Rams- and Feistrizbach). Following pulses of clastic sediment input a distinct system of paragenetic canyons developed creating the unique maze character of the cave.

New Results on the Palaeobiology of Bears on the Swabian Alb (Chronology, Isotopic Geochemistry and Palaeogenetics)

NASA Astrophysics Data System (ADS)

Muenzel, Susanne

2010-05-01

Paleogenetic investigations at three geographically close caves in the Ach Valley near Blaubeuren have revealed two different cave bear haplogroups. These two haplogroups correspond to Ursus spelaeus (haplogroup 1) and Ursus ingressus (haplogroup 4) (Rabeder & Hofreiter 2004, Die Höhle 55, 58-77). This genetic variability was first attested for Geißenklösterle and Sirgenstein cave, but the new genetic data attest them also for Hohle Fels. In all three caves Ursus ingressus replaced Ursus spelaeus around 28 000 B.P. The carbon and nitrogen isotopes of the two genetic types do not vary significantly, meaning that there is no dietary difference between them and Ursus spelaeus were in dietary competition with Ursus ingressus in the Ach valley. The radiocarbon dates suggested a sudden replacement (Hofreiter et al. 2007, Current Biology 17(4): R1-R3), which must have been accompanied by local extinction of the older cave bear, according to the dietary competition with the younger bear. The possible reasons for this replacement are not clear yet. Climatic changes are unlikely, since the faunal composition remains the same and the environmental data do not differ significantly. But we cannot exclude human impact on the cave bear population, since a cave bear vertebra with an embedded fragment of a flint projectile was recovered in the Gravettian layer AH IIcf dated to 27 830+150-140 B.P. and gives indisputable proof of the hunting of cave bears. Numerous cut marks proof an ongoing exploitation of this species. In this context, new radiocarbon dates and isotopic results on cave bears and coeval brown bears will help us to refine the possible scenarios of this complex evolutionary and ecological process. These results will be used to test hypotheses of competitive exclusion between the different bear species. This study will exemplify how combining evidence from different approaches can provide invaluable clues about palaeobiology of late Pleistocene large mammals such as fossil bears in Europe.

Predicting the Occurrence of Cave-Inhabiting Fauna Based on Features of the Earth Surface Environment.

PubMed

Christman, Mary C; Doctor, Daniel H; Niemiller, Matthew L; Weary, David J; Young, John A; Zigler, Kirk S; Culver, David C

2016-01-01

One of the most challenging fauna to study in situ is the obligate cave fauna because of the difficulty of sampling. Cave-limited species display patchy and restricted distributions, but it is often unclear whether the observed distribution is a sampling artifact or a true restriction in range. Further, the drivers of the distribution could be local environmental conditions, such as cave humidity, or they could be associated with surface features that are surrogates for cave conditions. If surface features can be used to predict the distribution of important cave taxa, then conservation management is more easily obtained. We examined the hypothesis that the presence of major faunal groups of cave obligate species could be predicted based on features of the earth surface. Georeferenced records of cave obligate amphipods, crayfish, fish, isopods, beetles, millipedes, pseudoscorpions, spiders, and springtails within the area of Appalachian Landscape Conservation Cooperative in the eastern United States (Illinois to Virginia and New York to Alabama) were assigned to 20 x 20 km grid cells. Habitat suitability for these faunal groups was modeled using logistic regression with twenty predictor variables within each grid cell, such as percent karst, soil features, temperature, precipitation, and elevation. Models successfully predicted the presence of a group greater than 65% of the time (mean = 88%) for the presence of single grid cell endemics, and for all faunal groups except pseudoscorpions. The most common predictor variables were latitude, percent karst, and the standard deviation of the Topographic Position Index (TPI), a measure of landscape rugosity within each grid cell. The overall success of these models points to a number of important connections between the surface and cave environments, and some of these, especially soil features and topographic variability, suggest new research directions. These models should prove to be useful tools in predicting the presence of species in understudied areas.

Carbon cycling in the mantled karst of the Ozark Plateaus, central United States

USGS Publications Warehouse

Knierim, Katherine J.; Pollock, Erik D.; Covington, Matthew D.; Hays, Phillip D.; Brye, Kristofor R.

2017-01-01

The nature of carbon (C) cycling in the unsaturated zone where groundwater is in contact with abundant gas-filled voids is poorly understood. The objective of this study was to trace inorganic-C cycling in a karst landscape using stable-C isotopes, with emphasis on a shallow groundwater flow path through the soil, to an underlying cave, and to the spring outlet of a cave stream in the Ozark Plateaus of northwestern Arkansas. Carbon dioxide (CO2) concentration and isotopic composition (δ13C-CO2) in gas and dissolved inorganic carbon (DIC) concentration and isotopic composition (δ13C-DIC) in water were measured in samples collected from two suction-cup soil samplers above the cave, three sites in the cave, and at the spring outlet of the cave stream. Soil-gas CO2 concentration (median 2,578 ppm) and δ13C-CO2 (median − 21.5‰) were seasonally variable, reflecting the effects of surface temperature changes on soil-CO2 production via respiration and organic-matter decomposition. Cave-air CO2 (median 1,026 ppm) was sourced from the soil zone and the surface atmosphere, with seasonally changing proportions of each source controlled by surface temperature-driven air density gradients. Soil-DIC concentration (median 1.7 mg L− 1) was lower and soil-δ13C-DIC (median − 19.5‰) was lighter compared to the cave (median 23.3 mg L− 1 and − 14.3‰, respectively) because carbonate-bedrock dissolution provided an inorganic source of C to the cave. Carbon species in the soil had a unique, light stable-C isotopic signature compared to the cave. Discrimination of soil-C sources to karst groundwater was achieved, which is critical for developing hydrologic budgets using environmental tracers such as C.

Predicting the Occurrence of Cave-Inhabiting Fauna Based on Features of the Earth Surface Environment

PubMed Central

Doctor, Daniel H.; Niemiller, Matthew L.; Weary, David J.; Young, John A.; Zigler, Kirk S.

2016-01-01

One of the most challenging fauna to study in situ is the obligate cave fauna because of the difficulty of sampling. Cave-limited species display patchy and restricted distributions, but it is often unclear whether the observed distribution is a sampling artifact or a true restriction in range. Further, the drivers of the distribution could be local environmental conditions, such as cave humidity, or they could be associated with surface features that are surrogates for cave conditions. If surface features can be used to predict the distribution of important cave taxa, then conservation management is more easily obtained. We examined the hypothesis that the presence of major faunal groups of cave obligate species could be predicted based on features of the earth surface. Georeferenced records of cave obligate amphipods, crayfish, fish, isopods, beetles, millipedes, pseudoscorpions, spiders, and springtails within the area of Appalachian Landscape Conservation Cooperative in the eastern United States (Illinois to Virginia and New York to Alabama) were assigned to 20 x 20 km grid cells. Habitat suitability for these faunal groups was modeled using logistic regression with twenty predictor variables within each grid cell, such as percent karst, soil features, temperature, precipitation, and elevation. Models successfully predicted the presence of a group greater than 65% of the time (mean = 88%) for the presence of single grid cell endemics, and for all faunal groups except pseudoscorpions. The most common predictor variables were latitude, percent karst, and the standard deviation of the Topographic Position Index (TPI), a measure of landscape rugosity within each grid cell. The overall success of these models points to a number of important connections between the surface and cave environments, and some of these, especially soil features and topographic variability, suggest new research directions. These models should prove to be useful tools in predicting the presence of species in understudied areas. PMID:27532611

Predicting the occurrence of cave-inhabiting fauna based on features of the earth surface environment

USGS Publications Warehouse

Christman, Mary C.; Doctor, Daniel H.; Niemiller, Matthew L.; Weary, David J.; Young, John A.; Zigler, Kirk S.; Culver, David C.

2016-01-01

One of the most challenging fauna to study in situ is the obligate cave fauna because of the difficulty of sampling. Cave-limited species display patchy and restricted distributions, but it is often unclear whether the observed distribution is a sampling artifact or a true restriction in range. Further, the drivers of the distribution could be local environmental conditions, such as cave humidity, or they could be associated with surface features that are surrogates for cave conditions. If surface features can be used to predict the distribution of important cave taxa, then conservation management is more easily obtained. We examined the hypothesis that the presence of major faunal groups of cave obligate species could be predicted based on features of the earth surface. Georeferenced records of cave obligate amphipods, crayfish, fish, isopods, beetles, millipedes, pseudoscorpions, spiders, and springtails within the area of Appalachian Landscape Conservation Cooperative in the eastern United States (Illinois to Virginia and New York to Alabama) were assigned to 20 x 20 km grid cells. Habitat suitability for these faunal groups was modeled using logistic regression with twenty predictor variables within each grid cell, such as percent karst, soil features, temperature, precipitation, and elevation. Models successfully predicted the presence of a group greater than 65% of the time (mean = 88%) for the presence of single grid cell endemics, and for all faunal groups except pseudoscorpions. The most common predictor variables were latitude, percent karst, and the standard deviation of the Topographic Position Index (TPI), a measure of landscape rugosity within each grid cell. The overall success of these models points to a number of important connections between the surface and cave environments, and some of these, especially soil features and topographic variability, suggest new research directions. These models should prove to be useful tools in predicting the presence of species in understudied areas.

Inference of Gene Regulatory Networks Using Bayesian Nonparametric Regression and Topology Information.

PubMed

Fan, Yue; Wang, Xiao; Peng, Qinke

2017-01-01

Gene regulatory networks (GRNs) play an important role in cellular systems and are important for understanding biological processes. Many algorithms have been developed to infer the GRNs. However, most algorithms only pay attention to the gene expression data but do not consider the topology information in their inference process, while incorporating this information can partially compensate for the lack of reliable expression data. Here we develop a Bayesian group lasso with spike and slab priors to perform gene selection and estimation for nonparametric models. B-spline basis functions are used to capture the nonlinear relationships flexibly and penalties are used to avoid overfitting. Further, we incorporate the topology information into the Bayesian method as a prior. We present the application of our method on DREAM3 and DREAM4 datasets and two real biological datasets. The results show that our method performs better than existing methods and the topology information prior can improve the result.

Localization of the lumbar discs using machine learning and exact probabilistic inference.

PubMed

Oktay, Ayse Betul; Akgul, Yusuf Sinan

2011-01-01

We propose a novel fully automatic approach to localize the lumbar intervertebral discs in MR images with PHOG based SVM and a probabilistic graphical model. At the local level, our method assigns a score to each pixel in target image that indicates whether it is a disc center or not. At the global level, we define a chain-like graphical model that represents the lumbar intervertebral discs and we use an exact inference algorithm to localize the discs. Our main contributions are the employment of the SVM with the PHOG based descriptor which is robust against variations of the discs and a graphical model that reflects the linear nature of the vertebral column. Our inference algorithm runs in polynomial time and produces globally optimal results. The developed system is validated on a real spine MRI dataset and the final localization results are favorable compared to the results reported in the literature.

Pesticide contamination of endangered gray bats and their food base in Boone County, Missouri, 1982

USGS Publications Warehouse

Clawson, R.L.; Clark, D.R.

1989-01-01

Gray bat guano from Devil's Icebox and Hunters Caves contained dieldrin at levels previously associated with gray bat mortality. Two of four gray bats found dead in Holton Cave had lethal brain concentrations of dieldrin. Twenty-five of 28 (86%) insect samples from bat foraging areas contained measurable dieldrin, heptachlor epoxide or both. Beetle samples were most heavily contaminated containing up to 2.2 ppm and 1.1 ppm heptachlor epoxide. The addition of Holton Cave brings to five the number of Missouri caves where gray bats have died of food chain pesticide poisoning.

Karst in Wadi Bani Khalid, Oman

NASA Astrophysics Data System (ADS)

Abdelaziz, Ramadan

2017-04-01

There are several important in Oman. The main aquifer is surficial aquifer and fractured rocks. In fact, the geology of Oman is complex whichmake the hydraulic continuity of bedrock is limited and formaing localized aquifers. caves in Oman are varying types and length, size and geographic formations. Many caves and valleys founded in Oman. Wadi Bani Khalid hosts complex network of fractured rock. Karst in Wadi Bani Kalid made upof Limestone(Calcium, which is dissolve in water.A rain water pass through the rock it is erode the rock and form caves. The cave located in Miqil. The karst was formed in Calcium Carbonate rocks.

Inferring phenomenological models of Markov processes from data

NASA Astrophysics Data System (ADS)

Rivera, Catalina; Nemenman, Ilya

Microscopically accurate modeling of stochastic dynamics of biochemical networks is hard due to the extremely high dimensionality of the state space of such networks. Here we propose an algorithm for inference of phenomenological, coarse-grained models of Markov processes describing the network dynamics directly from data, without the intermediate step of microscopically accurate modeling. The approach relies on the linear nature of the Chemical Master Equation and uses Bayesian Model Selection for identification of parsimonious models that fit the data. When applied to synthetic data from the Kinetic Proofreading process (KPR), a common mechanism used by cells for increasing specificity of molecular assembly, the algorithm successfully uncovers the known coarse-grained description of the process. This phenomenological description has been notice previously, but this time it is derived in an automated manner by the algorithm. James S. McDonnell Foundation Grant No. 220020321.

Meckel's cave access: anatomic study comparing the endoscopic transantral and endonasal approaches.

PubMed

Van Rompaey, Jason; Suruliraj, Anand; Carrau, Ricardo; Panizza, Benedict; Solares, C Arturo

2014-04-01

Recent advances in endonasal endoscopy have facilitated the surgical access to the lateral skull base including areas such as Meckel's cave. This approach has been well documented, however, few studies have outlined transantral specific access to Meckel's. A transantral approach provides a direct pathway to this region obviating the need for extensive endonasal and transsphenoidal resection. Our aim in this study is to compare the anatomical perspectives obtained in endonasal and transantral approaches. We prepared 14 cadaveric specimens with intravascular injections of colored latex. Eight cadavers underwent endoscopic endonasal transpterygoid approaches to Meckel's cave. Six additional specimens underwent an endoscopic transantral approach to the same region. Photographic evidence was obtained for review. 30 CT scans were analyzed to measure comparative distances to Meckel's cave for both approaches. The endoscopic approaches provided a direct access to the anterior and inferior portions of Meckel's cave. However, the transantral approach required shorter instrumentation, and did not require clearing of the endonasal corridor. This approach gave an anterior view of Meckel's cave making posterior dissection more difficult. A transantral approach to Meckel's cave provides access similar to the endonasal approach with minimal invasiveness. Some of the morbidity associated with extensive endonasal resection could possibly be avoided. Better understanding of the complex skull base anatomy, from different perspectives, helps to improve current endoscopic skull base surgery and to develop new alternatives, consequently, leading to improvements in safety and efficacy.

Energy expenditure in caving

PubMed Central

Antoni, Giorgia; Marini, Elisabetta; Curreli, Nicoletta; Tuveri, Valerio; Comandini, Ornella; Cabras, Stefano; Gabba, Silvia; Madeddu, Clelia; Crisafulli, Antonio

2017-01-01

The aim of this study was to determine the energy expenditure of a group of cavers of both genders and different ages and experience during a 10 hour subterranean exploration, using portable metabolimeters. The impact of caving activity on body composition and hydration were also assessed through bioelectrical impedance, and nutritional habits of cavers surveyed. During cave activity, measured total energy expenditure (TEE) was in the range 225–287 kcal/h for women-men (MET = 4.1), respectively; subjects had an energy intake from food in the range 1000–1200 kcal, thus inadequate to restore lost calories. Bayesian statistical analysis estimated the effect of predictive variables on TEE, revealing that experienced subjects had a 5% lower TEE than the less skilled ones and that women required a comparatively larger energy expenditure than men to perform the same task. BIVA (bioelectrical impedance vector analysis) showed that subjects were within the range of normal hydration before and after cave activity, but bioelectrical changes indicated a reduction of extracellular water in men, which might result in hypo-osmolal dehydration in the case of prolonged underground exercise. All these facts should be considered when planning cave explorations, preparing training programs for subjects practising caving, and optimizing a diet for cavers. Further, information gathered through this study could be of value to reduce accidents in caves related to increase in fatigue. PMID:28158208

Gradient Evolution of Body Colouration in Surface- and Cave-Dwelling Poecilia mexicana and the Role of Phenotype-Assortative Female Mate Choice

PubMed Central

Penshorn, Marina; Hamfler, Sybille; Herbert, Denise B.; Appel, Jessica; Meyer, Philipp; Slattery, Patrick; Charaf, Sarah; Wolf, Raoul; Völker, Johannes; Berger, Elisabeth A. M.; Dröge, Janis; Riesch, Rüdiger; Arias-Rodriguez, Lenin; Indy, Jeanne R.; Plath, Martin

2013-01-01

Ecological speciation assumes reproductive isolation to be the product of ecologically based divergent selection. Beside natural selection, sexual selection via phenotype-assortative mating is thought to promote reproductive isolation. Using the neotropical fish Poecilia mexicana from a system that has been described to undergo incipient ecological speciation in adjacent, but ecologically divergent habitats characterized by the presence or absence of toxic H2S and darkness in cave habitats, we demonstrate a gradual change in male body colouration along the gradient of light/darkness, including a reduction of ornaments that are under both inter- and intrasexual selection in surface populations. In dichotomous choice tests using video-animated stimuli, we found surface females to prefer males from their own population over the cave phenotype. However, female cave fish, observed on site via infrared techniques, preferred to associate with surface males rather than size-matched cave males, likely reflecting the female preference for better-nourished (in this case: surface) males. Hence, divergent selection on body colouration indeed translates into phenotype-assortative mating in the surface ecotype, by selecting against potential migrant males. Female cave fish, by contrast, do not have a preference for the resident male phenotype, identifying natural selection against migrants imposed by the cave environment as the major driver of the observed reproductive isolation. PMID:24175282

Microhabitat use, population densities, and size distributions of sulfur cave-dwelling Poecilia mexicana

PubMed Central

Bierbach, David; Riesch, Rüdiger; Schießl, Angela; Wigh, Adriana; Arias-Rodriguez, Lenin; Indy, Jeane Rimber; Klaus, Sebastian; Zimmer, Claudia; Plath, Martin

2014-01-01

The Cueva del Azufre in Tabasco, Mexico, is a nutrient-rich cave and its inhabitants need to cope with high levels of dissolved hydrogen sulfide and extreme hypoxia. One of the successful colonizers of this cave is the poeciliid fish Poecilia mexicana, which has received considerable attention as a model organism to examine evolutionary adaptations to extreme environmental conditions. Nonetheless, basic ecological data on the endemic cave molly population are still missing; here we aim to provide data on population densities, size class compositions and use of different microhabitats. We found high overall densities in the cave and highest densities at the middle part of the cave with more than 200 individuals per square meter. These sites have lower H2S concentrations compared to the inner parts where most large sulfide sources are located, but they are annually exposed to a religious harvesting ceremony of local Zoque people called La Pesca. We found a marked shift in size/age compositions towards an overabundance of smaller, juvenile fish at those sites. We discuss these findings in relation to several environmental gradients within the cave (i.e., differences in toxicity and lighting conditions), but we also tentatively argue that the annual fish harvest during a religious ceremony (La Pesca) locally diminishes competition (and possibly, cannibalism by large adults), which is followed by a phase of overcompensation of fish densities. PMID:25083351

Microhabitat use, population densities, and size distributions of sulfur cave-dwelling Poecilia mexicana.

PubMed

Jourdan, Jonas; Bierbach, David; Riesch, Rüdiger; Schießl, Angela; Wigh, Adriana; Arias-Rodriguez, Lenin; Indy, Jeane Rimber; Klaus, Sebastian; Zimmer, Claudia; Plath, Martin

2014-01-01

The Cueva del Azufre in Tabasco, Mexico, is a nutrient-rich cave and its inhabitants need to cope with high levels of dissolved hydrogen sulfide and extreme hypoxia. One of the successful colonizers of this cave is the poeciliid fish Poecilia mexicana, which has received considerable attention as a model organism to examine evolutionary adaptations to extreme environmental conditions. Nonetheless, basic ecological data on the endemic cave molly population are still missing; here we aim to provide data on population densities, size class compositions and use of different microhabitats. We found high overall densities in the cave and highest densities at the middle part of the cave with more than 200 individuals per square meter. These sites have lower H2S concentrations compared to the inner parts where most large sulfide sources are located, but they are annually exposed to a religious harvesting ceremony of local Zoque people called La Pesca. We found a marked shift in size/age compositions towards an overabundance of smaller, juvenile fish at those sites. We discuss these findings in relation to several environmental gradients within the cave (i.e., differences in toxicity and lighting conditions), but we also tentatively argue that the annual fish harvest during a religious ceremony (La Pesca) locally diminishes competition (and possibly, cannibalism by large adults), which is followed by a phase of overcompensation of fish densities.

Hurricane Impact on Seepage Water in Larga Cave, Puerto Rico

NASA Astrophysics Data System (ADS)

Vieten, Rolf; Warken, Sophie; Winter, Amos; Schröder-Ritzrau, Andrea; Scholz, Denis; Spötl, Christoph

2018-03-01

Hurricane-induced rainfall over Puerto Rico has characteristic δ18O values which are more negative than local rainfall events. Thus, hurricanes may be recorded in speleothems from Larga cave, Puerto Rico, as characteristic oxygen isotope excursions. Samples of 84 local rainfall events between 2012 and 2013 ranged from -6.2 to +0.3‰, whereas nine rainfall samples belonging to a rainband of hurricane Isaac (23-24 August 2012) ranged from -11.8 to -7.1‰. Cave monitoring covered the hurricane season of 2014 and investigated the impact of hurricane rainfall on drip water chemistry. δ18O values were measured in cumulative monthly rainwater samples above the cave. Inside the cave, δ18O values of instantaneous drip water samples were analyzed and drip rates were recorded at six drip sites. Most effective recharge appears to occur during the wet months (April-May and August-November). δ18O values of instantaneous drip water samples ranged from -3.5 to -2.4‰. In April 2014 and April 2015 some drip sites showed more negative δ18O values than the effective rainfall (-2.9‰), implying an influence of hurricane rainfall reaching the cave via stratified seepage flow months to years after the event. Speleothems from these drip sites in Larga cave have a high potential for paleotempestology studies.