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Over recent years, a growing number of case studies have highlighted the relevance of fluid inclusion (FI) isotope analysis on speleothem calcite for the reconstruction of rainfall isotope variation back in time. Multiple studies documented FI isotope results consistent with projected local meteoric water line values, demonstrating that FI isotope analysis can provide unique and quantitative paleohydrological data. Several other studies have shown that FI isotope data can be compromised due to diagenetic effects, or (petrography-controlled) analytical artefacts. Such diagenetic or analytical artefacts typically have a detrimental impact on the accuracy of isotope equilibrium-based cave temperatures calculated from paired oxygen isotope values of FI water and host calcite.Here, we will highlight some recent FI isotope records, discuss current views on the recognition of FI isotopic artefacts, and provide guidelines for the interpretation of FI isotope data as a paleo-rainfall proxy, with particular focus on direct comparison to novel TEX86 paleotemperatures that can be derived from the same speleothem calcite.

The fluctuating climatic conditions of the Saharo-Arabian desert belt are increasingly important for both palaeoclimatic and palaeoanthropological debates. Currently, Saharo-Arabia acts as a vast biogeographic barrier between the Afrotropical and Palaearctic realms. On orbital timescales, northward incursions of the African (ASM) and Indian (ISM) Summer Monsoons activated fluvio-lacustrine systems and led to the formation of grassland habitats. The formation of these habitats has been considered a crucial factor in Homo sapiens dispersals into the Saharo-Arabian deserts and beyond. The so-called “northern route” favours a terrestrial dispersal through green palaeohydrological corridors. However, a maritime “southern route” during the sea-level low-stand of Glacial Termination-II (T-II) has also been proposed. The precise phasing between the onset of wetter conditions and rising sea-levels may thus be a crucial factor for testing these alternative hypotheses. Here, we present a precisely dated high-resolution (

The Saharo-Arabian desert is part of the largest near-continuous chain of drylands stretching from north-western Africa to the northern China. This harsh and often hyper-arid belt acts as a transition zone separating major biogeographic realms, including the Palearctic, Afrotropics and Indomalayan. This aridity is thought responsible for the creation of unique geographic endemism between Africa and Eurasia. However, there are no direct hydroclimate records from the Arabian hyper-arid interior before the mid-Pleistocene, leaving the terrestrial hydroclimate and the role of Arabia as a biogeographic crossroads or barrier largely unknown.We use desert speleothems preserved from the northern Arabian interior to identify past humid phases over the last 8 million years. These are particularly useful terrestrial climate archives as they act as underground rain gauges, requiring a minimum of ~300 mm a-1 precipitation, pedogenesis and vegetation cover to form. Moreover, they can be accurately and precisely dated and are subsequently a valuable tool in identifying past large-scale hydrological and vegetation changes in ancient drylands. Our data reveal evidence of multiple ‘windows of opportunity’ of climate amelioration, allowing biogeographic exchange and dispersals to occur across the Arabian hyper-arid zone. Further, the novel analyses of the isotopic composition (d18O and d2H) of speleothem fluid inclusion waters, representing ‘fossil rainwater’, reveal the diminishing influence of tropical rain-belt precipitation in Arabia across Earth’s transition from a largely ‘ice-free’ northern hemisphere to an ‘ice-age’ world. The extent of Arabian aridity may thus be important in controlling biogeographic dispersals through the Arabian corridor, becoming increasingly less favourable through time. This is supported by fossil evidence which suggest that exchange between biogeographic regions across the Old World Savannah Biome were favoured in the Late Miocene, but became increasingly latitudinally fragmented from the Pliocene onwards. These results have significant implications for understanding the drivers of dryland aridity in non-polar deserts globally.

The global development and modern distribution of arid zones in subtropical regions (drylands) are likely associated with the global cooling marking the dawn of the Quaternary (~2.6 Ma). This coincides with global shifts in ocean circulation patterns, the intensification of the Walker-Hadley circulation, declining atmospheric CO2, the initiation of glacial–interglacial cycles and the intensification of Northern Hemisphere glaciation, the combination of which has led to the current global distribution of non-polar deserts at ~30° latitude. Although modern drylands represent Earth’s largest terrestrial biome, covering ~46% of global land surfaces and supporting a global population of ~3 billion people, it is currently unclear how drylands will change under future climate change scenarios. Speleothems, preserved in arid-zone caves, are particularly useful terrestrial climate archives as they act as underground rain gauges, which require a minimum of ~300 mm a-1 precipitation, pedogenesis and vegetation cover to form. Moreover, they can be accurately and precisely dated and are subsequently a valuable tool in identifying past large-scale hydrological and vegetation changes in ancient drylands. Here, we present new data from speleothems during past ‘warm periods’ from the Arabian hyper-arid zone. We apply a novel technique of extracting speleothem fluid inclusions waters to reconstruct the isotopic composition (d18O and d2H) of ‘fossil rainwater’ preserved in the speleothem fabric pristinely over millions of years. Speleothem evidence suggests that during the last 7 million years, the Sahara-Arabian desert experienced numerous intermittent humid phases, typically occurring with periods of low global ice-volume and warmer global temperatures. We further explore tropical push-pull mechanisms driving heating of the deep tropics and subsequent expansion of the tropical zone and synchronicity of humid phases regionally. These results have significant implications for understanding the drivers of dryland aridity in non-polar deserts globally.

The Murray Darling Basin contains 40% of Australia’s farms and is subject to multi-year droughts that put severe pressure on southeast Australia’s freshwater resources. Yet the long-term frequency, timing and potential severity of these droughts is unknown, as there are few high-resolution paleoclimate records from the basin that extend past the instrumental era. In this study, we investigate the potential of stalagmites from Careys Cave, Wee Jasper, in the Murray-Darling Basin to record past droughts. We use a multiproxy approach of stalagmite stable isotopes, trace element data, and climate reanalysis. We show that (a) stalagmite δ18O at this site likely records either local or regional precipitation amount and (b) stalagmite δ18O shows reasonable coherence with decadal-scale wet and dry changes in regional rainfall over the last 150 years, including the Federation Drought (1895–1902). Therefore, stalagmites from Wee Jasper can be used to draw regional inferences about past rainfall and have potential to extend the record of past droughts in the Murray Darling Basin beyond the limits of historical data. Extracting such a record will enable a better understanding of the causes of multi-year droughts in the region and consequently better planning, mitigation, and resilience in the basin.

Rationale Since their introduction more than a decade ago, isotope ratio infrared spectroscopy (IRIS) systems have rapidly become the standard for oxygen (δ18O) and hydrogen (δ2H) isotope analysis of water samples. An important disadvantage of IRIS systems is the well-documented sample-to-sample memory effect, which requires each sample to be analyzed multiple times before the desired accuracy is reached, lengthening analysis times and driving up the costs of analyses. Methods We present an adapted set-up and calculation protocol for fully automated analysis of water samples using a Picarro L2140-i cavity ring-down spectroscopy instrument. The adaptation removes memory effects by use of a continuously moisturized nitrogen carrier gas. Water samples of 0.5 μL are measured on top of the water vapor background, after which isotope ratios are calculated by subtraction of the background from the sample peaks. Results With this new technique, single injections of water samples have internal precisions (1σ) below 0.05‰ for δ18O values and 0.1‰ for δ2H values, regardless of the isotope ratio of the previous sample. Precision is worse, however, when the isotope difference between the sample and background water is too large (i.e., exceeding approximately 9‰ for δ18O values and 70‰ for δ2H values). Isotope ratios show negligible drift across the four weeks within which the experiments were performed. The single-injection 1σ precision for 17O excess (Δ′17O) determined with this method is 60 per meg. Conclusions Our experiments demonstrate that by removing sample-to-sample memory effects with a moisturized carrier gas, the time for measurement of δ18O and δ2H values using an IRIS system can be reduced markedly without compromising the analytical precision and accuracy. Thorough replication is needed to achieve sufficiently low uncertainties for Δ′17O., Rapid Communications in Mass Spectrometry, 35 (8), ISSN:1097-0231, ISSN:0951-4198

Stromatolites represent some of the earliest evidence for life and are valuable geochemical archives for understanding the rise of oxygen on early Earth. Metal redox proxies in carbonates, such as stable uranium isotopes (238U/235U), are useful for assessing the oxidation state of ancient waterbodies, but may also be sensitive to local water chemistry and early sedimentary diagenesis. This requires the validation of such proxies in modern environments before applying them to ancient carbonates. Here we measure the U isotopic composition of modern stromatolites forming in Hamelin Pool in Shark Bay, Western Australia – a large hypersaline marine embayment and the largest modern example of stromatolite development globally. Actively-growing stromatolite tops from Shark Bay exhibited a narrow range of δ238U from -0.30 to -0.33‰, corresponding to an offset of ca. +0.1‰ from seawater. Such an offset has not been found in other biotic marine carbonates, which exhibit seawater-like δ238U (ca. -0.4‰), but is consistent with findings from carbonate co-precipitation experiments. One hypothesis for our measured +0.1‰ offset is the elevated Ca concentration of the hypersaline Shark Bay seawater relative to open seawater. This results in a greater proportion of dissolved U present as Ca2UO2(CO3)3, which is expected to be isotopically lighter than other U species and not incorporated during carbonate mineral formation. Higher δ238U up to +0.11‰ were measured in the deeper stromatolite laminae, consistent with the expected U isotope signatures for U reduction. Stromatolite radiocarbon ages show that the diagenetic modification of U occurs within ~1 ka and may be considered syndepositional on geological timescales. These results from the deeper stromatolite laminae support the application of a ca. -0.4‰ correction factor to the δ238U of stromatolites formed in oxic waterbodies, similar to other biotic carbonates. It is unclear whether the additional +0.1‰ offset found in stromatolite tops is particular to seawater chemistry of Shark Bay or a general feature of microbial carbonate precipitation. This warrants investigation of the δ238U proxy in other modern environments where stromatolites proliferate.

In the context of human evolution and dispersal in Africa, it is important to understand past climate conditions and changes as possible drivers of these processes. One of the most recent climatic events was the end of the African Humid Period (AHP) at around 5 ka BP. This was marked by a decrease in precipitation following a long wet-phase in northern and eastern Africa, which caused many lakes to decrease in size or even desiccate. Although the termination of the AHP is well known, the timing and rate of the transition from wet to dry conditions is still heavily debated. To investigate the termination of the AHP at a high temporal resolution (subdecadal and subannual), fossil stromatolites and Etheria elliptica shells from paleo-shorelines in the Chew Bahir Basin, southern Ethiopia, were collected. Today, Lake Chew Bahir is a deltaic swamp, however in past pluvials a large lake was present that likely overflowed and connected to other basins similar to other amplifier lakes in the East African Rift System. Radiocarbon dating, oxygen and carbon stable isotope analyses, trace element analyses and petrographic mapping of stromatolite laminae structure were conducted. A strong correlation between δ18O and δ13C shows that paleo-lake Chew Bahir likely experienced highly evaporative conditions and indicate an endorheic state of the basin in times of stromatolite growth at 7.1, 5.8, 4.7 and 4.6 ka BP. Furthermore, our findings suggest highly fluctuating environmental conditions during these times and demonstrate that the transition to drier conditions was not a strictly linear trend. In summary, the stromatolites and Etheria elliptica shells are an excellent environmental archive due to their high temporal resolution, precise dating (± 30 yrs) and an indication of the paleo-lake water depth. These types of records provide insights to past changes in freshwater availability, the variability of which would have had large consequences for humans living in the region.

Dryland regions are generally projected to become drier under future climate change scenarios. Understanding the long-term natural variability of dryland regions via paleo-reconstructions is therefore highly desirable. The δ18O of two coeval modern speleothems from Cathedral Cave, Wellington, in semi-arid SE Australia are compared to the instrumental record to assess its efficacy as a proxy of past hydrological variability. Stalagmite δ18O was modulated by the frequency of recharge events and epikarst evaporation of storage water. Prolonged intervals between recharge events, such as droughts, resulted in higher stalagmite δ18O. Conversely, periods with more frequent recharge events and a positive water balance, resulted in lower δ18O. Disequilibrium cave processes are likely to be enhanced during dry conditions, although it is argued that these will modulate δ18Ospel in the same direction as epikarst evaporation, effectively amplifying the response of δ18Ospel. Extreme events, such as floods and droughts, were also captured in the stalagmite records, although potentially with a lag of several years. We verify that modern speleothems from semi-arid regions can be used to reconstruct hydroclimate due to variations in δ18Ospel modulated by karst processes. Such records are archives of past changes in recharge rather than precipitation amount or surface temperature, as is commonly applied to speleothem records from non-water-limited regions.

The ‘bomb-pulse’ method is a chronological approach to further constrain the age of speleothems that grew between 1950 CE – present. Establishing dependable chronological constraints is crucial for modern calibration studies of speleothems to instrumental climate records, which provides the basis for paleoclimate interpretations. However, a large unknown is how 14C is transferred from the atmosphere to any individual speleothem owing to the site-specific residence times of organic matter above cave systems. Here, we employ the bomb-pulse method to build chronologies from 14C measurements in combination with a new unsaturated zone C model which considers C decomposition as a continuum, to better understand unsaturated zone 14C dynamics. The bomb-pulse curves of eight speleothems from southern Australia from three contrasting climatic regions; the semi-arid Wellington Caves site, the mediterranean Golgotha Cave site and the montane Yarrangobilly Caves site, are investigated. Overall, the modelled 14C bomb-pulse curves produce excellent fits with actual measured 14C speleothem data (r2 = 0.82-0.99). The C modelling reveals that unsaturated zone C is predominately young at the semi-arid site, with a weighted-mean residence time of 32 years and that tree root respiration is likely an important source of vadose CO2. At the montane site, ∼39% of C is young (< 1 years), but the weighted-mean C ages are older (145-220 years). The mediterranean site has very little contribution from young C (< 12%: 0-1 years), with weighted-mean ages between 157 and 245 years, likely due to greater adsorption of organic matter in the upper vadose zone during matrix flow, and remobilisation of C from young syngenetic karst. New end members for low speleothem Dead Carbon Proportion (DCP) are identified (2.19% and 1.65%, respectively) for Australian montane and semi-arid zone speleothems, where oversupply of modern CO2 in the vadose zone leads to lower DCP. It was also demonstrated that DCP can be quite variable over small time scales, the processes may be difficult to untangle and a constant DCP assumption is likely invalid. DCP variability over time is mainly controlled by the changes vadose zone CO2, where vegetation regeneration, wild-fires and karst hydrology play an important role.

Measurement of glycerol dialkyl glycerol tetraethers (GDGTs) preserved in speleothems offers a potential proxy for past temperature but, in general, their origin is unknown. To understand the source of speleothem GDGTs, we undertook an irrigation experiment to activate drip sites within a hydrogeochemically well characterised cave. The cave drip water was analysed for GDGTs, inorganic elements (major ions and trace elements), stable isotopes and dissolved organic matter concentration and character. Published speleothem GDGT records from the site have been observed to be dominated by isoprenoid GDGTs and interpreted as deriving from in situ microbial communities within the cave or vadose zone. The drip water in our irrigation experiment had a GDGT distribution distinct from that of soil and speleothem samples, providing direct evidence that the distinctive GDGT signature in speleothems is derived from a subsurface source. Analysis of GDGTs in this context allowed further elucidation of their source and transport in cave systems, enhancing our understanding of how they might be used as a temperature proxy.

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.

Oxygen isotope ratios in speleothems may be affected by external processes that are independent of climate, such as karst hydrology and kinetic fractionation. Consequently, there has been a shift towards characterising and understanding these processes through cave monitoring studies, particularly focussing on temperate zones where precipitation exceeds evapotranspiration. Here, we investigate oxygen isotope systematics at Wellington Caves in semi-arid, SE Australia, where evapotranspiration exceeds precipitation. We use a novel D2O isotopic tracer in a series of artificial irrigations, supplemented by pre-irrigation data comprised four years of drip monitoring and three years of stable isotope analysis of both drip waters and rainfall. This study reveals that: (1) evaporative processes in the unsaturated zone dominate the isotopic composition of drip waters; (2) significant soil zone ‘wetting up’ is required to overcome soil moisture deficits in order to achieve infiltration, which is highly dependent on antecedent hydro-climatic conditions; (3) lateral flow, preferential flow and sorption in the soil zone are important in redistributing subsurface zone water; (4) isotopic breakthrough curves suggest clear evidence of piston-flow at some drip sites where an older front of water discharged prior to artificial irrigation water; and (5) water residence times in a shallow vadose zone (

While several studies explore cave climate and thermal regimes, little is known about the controls on cave drip water temperature. Yet water temperature significantly influences biogeochemical processes associated with cave drips. To identify the processes that control the cave drip water temperature, we measured the temperatures at multiple locations along a speleothem flow path and drip sources (stalactites) concurrently with the drip rates in Cathedral Cave, Wellington, Australia. We monitored long-term drip water temperature, drip rates, surface and cave climate and in-cave evaporation rates and conducted 3 infiltration experiments with different flow, temperature and isotopic conditions. Our results show that the drip water temperature is controlled by multiple superimposed heat transport mechanisms that act upon the infiltrating water in the epikarst, the water film after it enters the cave and before it becomes a drip. The two main heat sources/sinks for drip water are the cave air and the surrounding rock. The subsurface temperature is coupled to the surface temperature by conduction through the soil and rock mass, but the cave climate is also coupled to the surface climate by venting. On a regional scale, drip temperatures are mainly driven by the annual ground surface temperature signal but damped with depth and shifted in time compared to the surface. On a local scale, the drip water temperature can differ significantly from cave air and speleothem temperature due to the latent heat exchange of evaporation and localised water film convection. The main controls are ground surface temperature, subsurface depth, air density induced ventilation, distance from entry and drip rate. We present a conceptual model that explains drip water temperature signals and provide signal driven guidance on best type and location for speleothem sampling. We anticipate that our results will significantly improve the understanding of temperature-dependent paleoclimate signals from speleothem archives.

Cathedral Cave, Wellington, Australia, is a natural laboratory for studying water movement and geochemical processes in the unsaturated zone by using artificial irrigation to activate drip sites within the cave. Water sampled from two drip sites activated by irrigations carried out in summer 2014 was analysed for dissolved inorganic ions and fluorescent organic matter. The analysis allowed the development of a conceptual flow path model for each drip site. DOM analysis was further complemented by liquid chromatography with organic carbon detection (LC-OCD), applied for the first time to karst drip waters, allowing the characterisation of six organic matter fractions. The differences in organic matter fractions at each drip site are interpreted as a signature of the proposed flow paths. LC-OCD was also compared with parallel factor analysis (PARAFAC) of the fluorescence and good correlations were observed for high molecular weight organic matter. Strong positive correlations were also observed for high molecular weight matter and Cu and Ni. This is suggestive of colloidal transport of Cu and Ni by organic matter with high molecular weight, while small molecular weight colloids were not efficient transporters. LC-OCD uniquely provides information on non-fluorescent organic matter and can be used to further quantify drip water organic matter composition.

Summary High-frequency, spatially-dense discharge monitoring was conducted over fifteen months to characterise unsaturated zone flow at Harrie Wood Cave (HWC), in the Snowy Mountains, Yarrangobilly (SE Australia). The cave was formed in the Late Silurian Yarrangobilly Limestone, a fractured rock associated with very low primary porosity due to past diagenesis. Over our monitoring period we simultaneously measured rainfall, soil moisture saturation and drip discharge rate at fourteen sites to characterise infiltration–discharge relationships. All drip discharge sites exhibited non-Gaussian distributions, indicating long periods where low discharge predominates, punctuated by short infrequent periods of high discharge. However, there was significant variability in discharge between sites and consequently no spatial correlation in the cave. We investigated the depth–discharge relationship at HWC and found a moderate relationship between depth and drip discharge lag (response) times to soil moisture content, but only weak relationships between depth and mean and maximum discharge. This highlights that the karst architecture plays an important role in controlling drip discharge dynamics. Principal Component Analysis (PCA) and Agglomerative Hierarchal Clustering (AHC) were used to classify similar drip types, revealing five unique drip regimes. Two-phase flow and non-linear response to recharge behaviour were observed, suggesting secondary porosity is controlling unsaturated zone flow in mature limestone environments with low primary porosity. Using the data presented here, the first coupled conceptual and box hydrological flow model was developed. This study highlights the heterogeneous nature of hydrological flow in karst and the need to understand unsaturated zone hydrology at the individual drip discharge level, to inform speleothem studies for high-resolution paleoclimate reconstruction.

Our current understanding of cancer genetics is grounded on the principle that cancer arises from a clone that has accumulated the requisite somatically acquired genetic aberrations, leading to the malignant transformation. It also results in aberrent of gene and protein expression. Next generation sequencing (NGS) or deep sequencing platforms are being used to create large catalogues of changes in copy numbers, mutations, structural variations, gene fusions, gene expression, and other types of information for cancer patients. However, inferring different types of biological changes from raw reads generated using the sequencing experiments is algorithmically and computationally challenging. In this article, we outline common steps for the quality control and processing of NGS data. We highlight the importance of accurate and application-specific alignment of these reads and the methodological steps and challenges in obtaining different types of information. We comment on the importance of integrating these data and building infrastructure to analyse it. We also provide exhaustive lists of available software to obtain information and point the readers to articles comparing software for deeper insight in specialised areas. We hope that the article will guide readers in choosing the right tools for analysing oncogenomic datasets.

A series of four short-term infiltration experiments which revealed hydrochemical responses relevant to semi-arid karst environments were carried out above Cathedral Cave, Wellington, New South Wales (NSW), Australia. Dripwater samples were collected at two sites for trace element and organic matter analysis. Organic matter was characterised using fluorescence and interpreted using a PARAFAC model. Three components were isolated that represented unprocessed, soil-derived humic-like and fulvic-like material, processed humic/fulvic-like material and tryptophan-like fluorescence. Principal Component Analysis (PCA) performed on the entire dataset comprising trace element concentrations and PARAFAC scores revealed two dominant components that were identified as soil and limestone bedrock. The soil component was assigned based on significant contributions from the PARAFAC scores and additionally included Ba, Cu, Ni and Mg. The bedrock component included the expected elements of Ca, Mg and Sr as well as Si. The same elemental behaviour was observed in recent stalagmite growth collected from the site. Our experiments demonstrate that existing paleoclimate interpretations of speleothem Mg and Sr, developed in regions of positive water balance, are not readily applicable to water limited environments. We provide a new interpretation of trace element signatures unique to speleothems from water limited karst environments.

Speleothems (cave deposits), used for paleoenvironmental reconstructions, are deposited from cave dripwaters. Differentiating climate and karst processes within a dripwater signal is fundamental for the correct identification of paleoenvironmental proxies and ultimately their interpretation within speleothem records. We investigate the potential use of trace element and stable oxygen-isotope (δ18O) variations in cave dripwaters as paleorainfall proxies in an Australian alpine karst site. This paper presents the first extensive hydrochemical and δ18O dataset from Yarrangobilly Caves, in the Snowy Mountains, south-east Australia. Using a 7-year long rainfall δ18O and dripwater Ca, Cl, Mg / Ca, Sr / Ca and δ18O dataset from three drip sites, we determined that the processes of mixing, dilution, flow path change, carbonate mineral dissolution and Prior Calcite Precipitation (PCP) accounted for the observed variations in the dripwater geochemical composition. We identify that the three monitored drip sites are fed by fracture flow from a well-mixed epikarst storage reservoir; supplied by variable concentrations of dissolved ions from soil and bedrock dissolution. We constrained the influence of multiple processes and controls on dripwater composition in a region dominated by ENSO. During the El Niño and dry periods, enhanced PCP, a flow path change and dissolution due to increased soil CO2 production occurred in response to decreased rainfall, in distinction to the La Niña phase where dilution dominated and reduced PCP was observed. We present a conceptual model, illustrating the key processes impacting the dripwater chemistry. We identified a robust relationship between ENSO and dripwater trace element concentrations and propose variations in speleothem Mg / Ca and Sr / Ca ratios may be interpreted to reflect paleorainfall conditions. These findings inform paleorainfall reconstruction from speleothems regionally and provide a basis for paleoclimate studies globally, in regions where there is intermittent recharge variability.

This study describes the first use of concurrent high-precision temperature and drip rate monitoring to explore what controls the temperature of speleothem forming drip water. Two contrasting sites, one with fast transient and one with slow constant dripping, in a temperate semi-arid location (Wellington, NSW, Australia), exhibit drip water temperatures which deviate significantly from the cave air temperature. We confirm the hypothesis that evaporative cooling is the dominant, but so far unattributed, control causing significant disequilibrium between drip water and host rock/air temperatures. The amount of cooling is dependent on the drip rate, relative humidity and ventilation. Our results have implications for the interpretation of temperature-sensitive, speleothem climate proxies such as δ18O, cave microecology and the use of heat as a tracer in karst. Understanding the processes controlling the temperature of speleothem-forming cave drip waters is vital for assessing the reliability of such deposits as archives of climate change.

Microarray technology changed the landscape of contemporary life sciences by providing vast amounts of expression data. Researchers are building up repositories of experiment results with various conditions and samples which serve the scientific community as a precious resource. Ensuring that the sample is of high quality is of utmost importance to this effort. The task is complicated by the fact that in many cases datasets lack information concerning pre-experimental quality assessment. Transcription profiling of tissue samples may be invalidated by an error caused by heterogeneity of the material. The risk of tissue cross contamination is especially high in oncological studies, where it is often difficult to extract the sample. Therefore, there is a need of developing a method detecting tissue contamination in a post-experimental phase. We propose Microarray Inspector: customizable, user-friendly software that enables easy detection of samples containing mixed tissue types. The advantage of the tool is that it uses raw expression data files and analyses each array independently. In addition, the system allows the user to adjust the criteria of the analysis to conform to individual needs and research requirements. The final output of the program contains comfortable to read reports about tissue contamination assessment with detailed information about the test parameters and results. Microarray Inspector provides a list of contaminant biomarkers needed in the analysis of adipose tissue contamination. Using real data (datasets from public repositories) and our tool, we confirmed high specificity of the software in detecting contamination. The results indicated the presence of adipose tissue admixture in a range from approximately 4% to 13% in several tested surgical samples.

Gene expression profiling is one of the most explored methods for studying cancers and microarray data repositories have become a rich and important resource. The most common human cancers develop in organs that are walled by smooth muscles. The only method of sample extraction free of unintentional contamination with surrounding tissue is microdissection. Nevertheless, such an approach is implemented infrequently. In the light of the above, there is a possibility of smooth muscle contamination in a large portion of publicly available data. In this study, 2292 publicly available microarrays were analysed to develop a simple screening method for detecting smooth muscle contamination. Microarray Inspector software was used to perform the tests since it has the unique ability to use many selected genes and probesets in a single group as a tissue definition. Furthermore, the test was dataset-independent. Two strategies of tissue definition were explored and compared. The first one depended on Tissue Specific Genes Database (TiSGeD) and BioGPS web resources, which themselves were based on meta-analysis of thousands of microarrays. The second method was based on a differential gene expression analysis of a few hundred preselected arrays. The comparison of the two methods proved the latter to be superior. Among the tested samples of undefined contamination, nearly half were identified to possibly contain significant smooth muscle traces. The obtained results equip researches with a simple method of examining microarray data for smooth muscle contamination. The presented work serves as an example of how to create definitions when searching for other possible contaminations.