Subtle Signatures Research Articles

Seasonal variability of shallow cumuliform snowfall: A CloudSat perspective

Cumuliform snowfall seasonal variability is studied using a multi‐year CloudSat snowfall rate and cloud classification retrieval dataset. Microwave radiometer sea ice concentration datasets are also utilized to illustrate the intimate link between oceanic cumuliform snowfall production and decreased sea ice coverage. Three metrics are calculated to illustrate seasonal cumuliform snowfall signatures: (a) cumuliform snowfall frequency of occurrence, (b) mean cumuliform snowfall rate, and (c) fraction of snowfall attributed to cumuliform snowfall events. Distinct seasonal cumuliform snowfall cycles are observed over the Northern Hemispheric oceans. Cumuliform snowfall frequency of occurrence (mean snowfall rate) peaks in months SON (DJF) at most latitudes. Maximum mean cumuliform snowfall rates exceed 300 mm/year in various North Atlantic Ocean locations, with DJF exhibiting the largest areal extent of higher snowfall rates. Cumuliform snow occurrence fraction frequently exceeds 0.5, but regional seasonal sensitivity is observed where transient sea ice coverage exists. Annual snowfall rate fraction attributed to cumuliform snow does not vary appreciably during SON, DJF and MAM north of ∼70°N, but seasonal zonal variability is evident south of this latitudinal threshold. Land cumuliform snowfall features do not universally display strong seasonal signals. Southern Hemisphere seasonal results indicate a strong mean cumuliform snowfall rate maximum (minimum) in JJA (DJF) accompanied by a seasonal latitudinal shift in the snowfall rate peak. Maximum regional snowfall rates exceed 300 mm/year over a broader area compared to the Northern Hemisphere. Cumuliform snowfall production is again strongly linked to seasonal sea ice coverage. Southern Hemispheric cumuliform snowfall occurrence and snowfall rate fraction seasonality is not as obvious as in the Northern Hemisphere, but some latitudinal zones experience ∼5–20% seasonal variability in these quantities. Typical cumuliform snowfall fractions range from 0.4 to 0.6 in the prominent cumuliform snowfall belt covering most of the Southern Ocean. Some subtle seasonal cumuliform snowfall signatures are observed over Antarctica.

Identifying the subtle signatures of feedback from distant AGN using ALMA observations and the EAGLE hydrodynamical simulations

AbstractWe present sensitive 870 μm continuum measurements from our ALMA programmes of 114 X-ray selected active galactic nuclei (AGN) in the Chandra Deep Field-South and Cosmic Evolution Survey fields. We use these observations in combination with data from Spitzer and Herschel to construct a sample of 86 X-ray selected AGN, 63 with ALMA constraints at z = 1.5–3.2 with stellar mass >2 × 1010 M⊙. We constructed broad-band spectral energy distributions in the infrared band (8–1000 μm) and constrain star-formation rates (SFRs) uncontaminated by the AGN. Using a hierarchical Bayesian method that takes into account the information from upper limits, we fit SFR and specific SFR (sSFR) distributions. We explore these distributions as a function of both X-ray luminosity and stellar mass. We compare our measurements to two versions of the Evolution and Assembly of GaLaxies and their Environments (EAGLE) hydrodynamical simulations: the reference model with AGN feedback and the model without AGN. We find good agreement between the observations and that predicted by the EAGLE reference model for the modes and widths of the sSFR distributions as a function of both X-ray luminosity and stellar mass; however, we found that the EAGLE model without AGN feedback predicts a significantly narrower width when compared to the data. Overall, from the combination of the observations with the model predictions, we conclude that (1) even with AGN feedback, we expect no strong relationship between the sSFR distribution parameters and instantaneous AGN luminosity and (2) a signature of AGN feedback is a broad distribution of sSFRs for all galaxies (not just those hosting an AGN) with stellar masses above ≈1010 M⊙.

Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity.

Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired-end restriction site-associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.

Soil-gas and weak partial soil extractions for nickel exploration through transported cover in Western Australia

Traditional, near surface geochemical techniques have been effective in mineral discovery but to explore in deeper transported cover (>10 m) and find new resources, as demanded by a growing global population, new and improved exploration methods are required. As mineral exploration transitions from exploring in residual outcropping terrains into deeper covered terrains, geochemical signatures are diluted and the ability to successfully discern subtle geochemical signatures is essential. At the ‘geochemically-blind’ North Miitel Ni deposit in Western Australia, we compared passive soil-gas hydrocarbons and weakly extracted elements from soil (10 – 20 cm depth) with both proving successful. The primary mineralization is >200 m below the surface, but a weak zone of secondary Ni enrichment occurs in the saprolite at 15 – 20 m depth. This enriched zone is covered by 10 – 15 m of transported cover. Minimum hypergeometric probability (MHP) statistics were used to evaluate the near surface geochemical signatures of c. 100 samples from three traverses over the mineralization. Soil samples from 10–20 cm were subjected to distilled water, 0.1 M cold hydroxylamine hydrochloride and aqua regia extractions. The water-extractable concentrations of Ni, Co, Mo, Sb, and Sn were successful in identifying mineralization (MHP <1%, type II error). The hydrocarbons, 2-methylbutane, pentane and 1-pentene were also successful (MHP <1%) at identifying the zone of mineralization using the Amplified Geochemical Imaging (AGI) passive soil-gas collectors. Of the techniques used, the water extraction performed the best using MHP classified accuracy to identify mineralization. The passive soil-gas data were the second most effective, and superior to the stronger partial extractions using hydroxylamine and aqua regia that did not identify the mineralized zone (MHP>>1%). The water extraction and the passive soil-gas showed a greater degree of variability than the stronger extractions. The results indicate that depth of sampling, interaction with organic carbon and potential mechanisms of metal migration greatly influence the geochemical anomaly near the surface. These mechanisms are evident as hydromorphic dispersion at depth, with potential capillarity and gaseous migration up through the profile above the water table. Integrating an understanding of metal migration mechanisms, genesis and evolution of target and pathfinder compounds (particularly hydrocarbons) related to deposit types will improve future exploration. Extending into much deeper cover (>20 m), the viability of passive soil-gas methods may become more relevant and warrant further study for mineral exploration.

Salt marsh plant response to vertical deformation resulting from the February 2011 Christchurch earthquake

ABSTRACTInvestigations of modern coseismic ground surface deformation where fault rupture is absent typically rely on remote sensing techniques. We used monitoring of salt marsh vegetation and substrate for 3 years after the 22 February 2011 Christchurch earthquake (MW 6.2) to document the biological response to vertical deformation, to provide estimates of the amount of uplift and subsidence and ground-truth remote sensing data. Comparison of vegetation-derived vertical deformation with estimates from remote-sensing techniques (Light Detection and Ranging, Global Positioning System and Differential Interferometric Synthetic Aperture Radar) shows good agreement at sites where several decimetres of vertical movement occurred, and less agreement where smaller amounts of vertical movement occurred and/or where vegetation-monitoring sites were affected by differential movement of artificial structures such as roads and breakwaters. Biological and sedimentological changes observed in salt marshes around the Avon–Heathcote Estuary/Ihutai (AHEI) as a result of the 22 February 2011 Christchurch earthquake are likely to be preserved as subtle geological signatures in restricted locations around the AHEI.

Genomic responses to the socio-sexual environment in male Drosophila melanogaster exposed to conspecific rivals.

Socio-sexual environments have profound effects on fitness. Local sex ratios can alter the threat of sexual competition, to which males respond via plasticity in reproductive behaviors and ejaculate composition. In Drosophila melanogaster, males detect the presence of conspecific, same-sex mating rivals prior to mating using multiple, redundant sensory cues. Males that respond to rivals gain significant fitness benefits by altering mating duration and ejaculate composition. Here we investigated the underlying genome-wide changes involved. We used RNA-seq to analyze male transcriptomic responses 2, 26, and 50 h after exposure to rivals, a time period that was previously identified as encompassing the major facets of male responses to rivals. The results showed a strong early activation of multiple sensory genes in the head–thorax (HT), prior to the expression of any phenotypic differences. This gene expression response was reduced by 26 h, at the time of maximum phenotypic change, and shut off by 50 h. In the abdomen (A), fewer genes changed in expression and gene expression responses appeared to increase over time. The results also suggested that different sets of functionally equivalent genes might be activated in different replicates. This could represent a mechanism by which robustness is conferred upon highly plastic traits. Overall, our study reveals that mRNA-seq can identify subtle genomic signatures characteristic of flexible behavioral phenotypes.

Oral microbiome in HIV-associated periodontitis.

HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV- individuals at different levels of PD severity.This cross-sectional study included both HIV+ and HIV- patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations.Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV-) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome.HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites.

The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens.

Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut.

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes.

Multi-proxy evidence for small historical tsunamis leaving little or no sedimentary record

There has been considerable progress in tsunami research in recent years, yet most work has been focussed on identifying and understanding the evidence of large events. This study aimed to identify the evidence of small historical tsunamis in Lyttelton Harbour, New Zealand. The study area has been inundated by multiple relatively small historical tsunamis that left atypical sedimentary evidence (no sand) or no sediment. Shallow trenches revealed discontinuous layers of small grey mud clasts at various depths across the study area, most likely transported from the nearby tidal flats. The origin of these mud clast layers was investigated using a multi-proxy approach comprising sedimentological, geochemical and diatom analyses complemented by dating from 137Cs activity profiles and historical data. Subtle variations consistent with inclusions of marine mud such as a decrease in organic content and magnetic susceptibility and increases in geochemical markers (e.g. Ca/kcps, K/kcps, K/Rb, Si/Rb and Sr/Rb) were found in the sediment profile. Variations in diatom assemblages suggesting a marine influence were also recorded at similar depths, aligning with layers of mud clasts. Using 137Cs activity profiles and historical data, these deposits were attributed to the 1960 Chile Valdivia and 1964 Alaska tsunamis, as well as a possible earlier event. Sedimentary evidence for the 2010 Chile Maule tsunami was not found at the study site, but geochemical analysis of surface samples revealed marked changes in Ca, Cl, Sr and Ti concentrations, indicative of a change from a terrestrial to marine influence. This was used to identify the landward extent of inundation by the 2010 event. Ultimately, this study shows that a broad multi-proxy analysis can distinguish even the subtle signatures of an inconspicuous deposit laid down by a small tsunami.

Tectonic geomorphology of the Sudetes (Central Europe) – a review and re-appraisal

The Sudetes are a mountain range in Central Europe, which owes its emergence to the Cenozoic rejuvenation of an old Variscan orogen, subject to stresses from the Alps and the Carpathians. The gross morphological features of the Sudetes are typically explained as reflecting the superposition of the effects of long-term, rock-controlled denudation and Late Cenozoic differential uplift and subsidence. In this paper, early conceptual models, developed in the 1950s and 1960s and emphasizing alternating uplift and planation phases, are presented first. A review of more recent work focused on tectonic landforms and geomorphic indicators of tectonic movements follows, with special attention to fault-generated escarpments, valley morphology, stream longitudinal profiles, terraces and fans, drainage basin characteristics and regional geomorphometric studies. Attempts to provide a timeframe of tectonic relief differentiation are also summarized. In the closing part of the paper, the existing approaches and findings are re-evaluated in order to identify challenges and perspectives for future work. The availability of high-resolution digital terrain models creates a unique opportunity to quantify relief features and detect even the subtle topographic signatures of recent tectonics. A need to reconcile the results of geomorphological analysis with those emerging from other studies focused on faults is highlighted.

Signatures of Subacute Potentially Catastrophic Illness in the ICU: Model Development and Validation.

Patients in ICUs are susceptible to subacute potentially catastrophic illnesses such as respiratory failure, sepsis, and hemorrhage that present as severe derangements of vital signs. More subtle physiologic signatures may be present before clinical deterioration, when treatment might be more effective. We performed multivariate statistical analyses of bedside physiologic monitoring data to identify such early subclinical signatures of incipient life-threatening illness. We report a study of model development and validation of a retrospective observational cohort using resampling (Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis type 1b internal validation) and a study of model validation using separate data (type 2b internal/external validation). University of Virginia Health System (Charlottesville), a tertiary-care, academic medical center. Critically ill patients consecutively admitted between January 2009 and June 2015 to either the neonatal, surgical/trauma/burn, or medical ICUs with available physiologic monitoring data. None. We analyzed 146 patient-years of vital sign and electrocardiography waveform time series from the bedside monitors of 9,232 ICU admissions. Calculations from 30-minute windows of the physiologic monitoring data were made every 15 minutes. Clinicians identified 1,206 episodes of respiratory failure leading to urgent unplanned intubation, sepsis, or hemorrhage leading to multi-unit transfusions from systematic individual chart reviews. Multivariate models to predict events up to 24 hours prior had internally validated C-statistics of 0.61-0.88. In adults, physiologic signatures of respiratory failure and hemorrhage were distinct from each other but externally consistent across ICUs. Sepsis, on the other hand, demonstrated less distinct and inconsistent signatures. Physiologic signatures of all neonatal illnesses were similar. Subacute potentially catastrophic illnesses in three diverse ICU populations have physiologic signatures that are detectable in the hours preceding clinical detection and intervention. Detection of such signatures can draw attention to patients at highest risk, potentially enabling earlier intervention and better outcomes.

Large-scale phenome analysis defines a behavioral signature for Huntington's disease genotype in mice.

Rapid technological advances for the frequent monitoring of health parameters have raised the intriguing possibility that an individual's genotype could be predicted from phenotypic data alone. Here we used a machine learning approach to analyze the phenotypic effects of polymorphic mutations in a mouse model of Huntington's disease that determine disease presentation and age of onset. The resulting model correlated variation across 3,086 behavioral traits with seven different CAG-repeat lengths in the huntingtin gene (Htt). We selected behavioral signatures for age and CAG-repeat length that most robustly distinguished between mouse lines and validated the model by correctly predicting the repeat length of a blinded mouse line. Sufficient discriminatory power to accurately predict genotype required combined analysis of >200 phenotypic features. Our results suggest that autosomal dominant disease-causing mutations could be predicted through the use of subtle behavioral signatures that emerge in large-scale, combinatorial analyses. Our work provides an open data platform that we now share with the research community to aid efforts focused on understanding the pathways that link behavioral consequences to genetic variation in Huntington's disease.

Accurate X-ray Absorption Spectra of Dilute Systems: Absolute Measurements and Structural Analysis of Ferrocene and Decamethylferrocene

X-ray absorption fine structure (XAFS) of ferrocene (Fc) and Decamethylferrocene (DmFc) have been determined on an absolute scale using transmission measurements of multiple solutions of differing concentrations (15 mM, 3 mM, pure solvent) at operating temperatures of 10–20 K. Mass attenuation coefficients and photoelectric absorption cross sections are measured and tabulated for both molecules for an extended energy range in excess of 1.5 keV from the Fe K-shell absorption edge. At these temperatures, the minimization of of dynamic disorder has enabled a critical determination of the oscillatory absorption structures created by multiple-scattering paths of the excited photoelectron. These oscillatory structures are highly sensitive to the local conformation environment of the iron absorber in organometallic structures. Crystallographic and scattering studies have reported both structures characterized by staggered cyclopentadienyl rings, in contrast with low temperature crystallography and recent density functional theoretical predictions. Phase changes in the crystallographic space groups are reported for Fc at different temperatures, raising the possibility of alternative conformation states. Robust experimental techniques are described which have allowed the measurement of XAFS spectra of dilute systems by transmission at accuracies ranging from 0.2% to 2%, and observe statistically significant fine structure at photoelectron wavenumbers extending to >12 Å–1. The subtle signatures of the conformations are then investigated via extensive analysis of the XAFS spectra using the full multiple scattering theory as implemented by the FEFF package. Results indicate a near-eclipsed D5h geometry for low-temperature Fc, in contrast with a staggered D5d geometry observed for DmFc. The ability of this experimental approach and data analysis methodology combined with advanced theory to investigate and observe such subtle conformational differences using XAFS is a powerful tool for future challenges and widens the capacity of advanced XAFS to solve a broad range of challenging systems.

Subtle signatures of seeps: Record of groundwater in a Dryland, DK, Olduvai Gorge, Tanzania

AbstractFew proxies exist to identify aridity in the depositional record, although drylands cover ca 30% of the modern continental surface. New exposures in a siliciclastic and carbonate sequence in an arid to hyperarid basin at Olduvai Gorge, Tanzania provide a unique multi‐proxy record of a 1·85 Ma landscape that was exploited by early humans. The 2 m thick sequence of clastics and carbonates that are exposed along a 450 m outcrop records climate change over a single precession (dry‐wet‐dry) cycle. Siliciclastic data (sedimentary structures, grain size, mineralogy) and biological data are combined with data for a 10 to 35 cm thick limestone (stable isotopes, elemental geochemistry, petrography) to generate a depositional facies model for a site DK (Douglass Korongo) on this dry rift basin landscape. This site was situated on a low gradient, distal portion of a volcaniclastic alluvial fan. The clastics are intercalated distal alluvial fan sandy silts and lake clays that accumulated in a low energy environment. Groundwater discharge and the alkaline springs and seeps during wet‐to‐dry change in climate made a freshwater carbonate‐rich environment. Bedded lithofacies (a lime mudstone with fossils) were deposited in shallow standing (spring‐fed) pools, while nodular lithofacies with calcite spherulites indicate permanently saturated ground (seeps). Both environments experienced similar diagenesis, that is, the precipitation of authigenic barite from supersaturated groundwater, desiccation and pedogenesis, and late‐stage calcite precipitation. Compositional and isotopic data suggest that a fresh groundwater‐fed system was available to early humans even during dry intervals of the precession cycle.

Recognizing sulfate and phosphate complexes chemisorbed onto nanophase weathering products on Mars using in-situ and remote observationsk

Orbital and in-situ data from the surface of Mars indicate that nanophase weathering products are important constituents of martian rocks and soils. Nanophase minerals have the capacity to chemisorb anions like sulfate and phosphate onto their surfaces, but it is not known whether chemisorption is an important or even detectable process via orbital and in-situ observations. The detection of chemisorbed sulfate and phosphate anions on nanophase minerals would constrain the speciation of these anions and past aqueous environmental conditions. Here, we synthesized two nanophase weathering products that are common in terrestrial volcanic soils and have been identified on the martian surface: allophane and nanophase ferric oxide as represented by ferrihydrite. We specifically adsorbed sulfate and phosphate separately onto the nanophase mineral surfaces (4.5 and 1.6 wt% SO42−, and 6.7 and 8.9 wt% PO43− on allophane and ferrihydrite, respectively) and analyzed the untreated and chemisorbed materials using instruments similar to those on orbital and landed Mars missions (including X-ray diffraction, evolved gas analysis, Mossbauer spectroscopy, and VNIR and thermal-IR spectroscopy). Evolved gas analysis is the optimum method to detect chemisorbed sulfate, with SO2(g) being released at >900 °C for allophane and 400–800 °C for ferrihydrite. Chemisorbed sulfate and phosphate anions affect the thermal-IR spectra of allophane and ferrihydrite in the S-O and P-O stretching region when present in abundances of only a few weight percent; S-O and P-O stretching bands are apparent as short-wavelength shoulders on Si-O stretching bands. Sulfate and phosphate anions chemisorbed to allophane have small but measurable effects on the position of the OH-H2O bands at 1.4 and 1.9 μm in near-IR spectra. Chemisorbed sulfate and phosphate anions did not affect the X-ray diffraction patterns, Mossbauer spectra, and visible/near-IR spectra of ferrihydrite. These data suggest that sulfate chemisorbed onto the surfaces of nanophase minerals can be detected with the Sample Analysis at Mars (SAM) instrument on the Mars science laboratory Curiosity rover, and subtle signatures of chemisorbed sulfate and phosphate may be detectable by IR spectrometers on landed missions. The combined use of SAM, the Chemistry and Mineralogy (CheMin) instrument, and the Alpha Particle X-ray Spectrometer (APXS) on Curiosity allows for the most detailed characterization to date of nanophase minerals in martian rocks and soils and the potential presence of chemisorbed anionic complexes.

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.

In this study, we trace developmental stages using epigenome changes in human embryonic stem cells (hESCs) treated with drugs modulating either self-renewal or differentiation. Based on microscopy, qPCR and flow cytometry, we classified the treatment outcome as inducing pluripotency (hESC, flurbiprofen and gatifloxacin), mesendoderm (sinomenine), differentiation (cyamarin, digoxin, digitoxin, selegeline and theanine) and lineage-commitment (RA). When we analyzed histone PTMs that imprinted these gene and protein expressions, the above classification was reassorted. Hyperacetylation at H3K4, 9, 14, 18, 56 and 122 as well as H4K5, 8, 12 and 16 emerged as the pluripotency signature of hESCs. Methylations especially of H3 at K9, K20, K27 and K36 characterized differentiation initiation as seen in no-drug control and fluribiprofen. Sinomenine-treated cells clustered close to "differentiation initiators", consistent with flow cytometry where it induced mesendoderm, along with cyamarin and possibly selegnine. Neurectoderm, induced by RA and theanine manifested methylations on H3 shifts to H3.3. By both flow cytometry and histone PTM clustering, it appears that cells treated with gatifloxacin, flurbiprofen, digitoxin and digoxin were not yet lineage-committed or mixed cell types. Taken together, our moderate-throughput histone PTM profiling approach highlighted subtle epigenetic signatures that permitted us to predict divergent lineage progression even in differentiating cells with similar phenotype and gene expression.

Monkeys display classic signatures of human symbolic arithmetic.

Non-human primates compare quantities in a crude manner, by approximating their values. Less is known about the mental transformations that non-humans can perform over approximate quantities, such as arithmetic transformations. There is evidence that human symbolic arithmetic has a deep psychological connection with the primitive, approximate forms of quantification of non-human animals. Here, we ask whether the subtle performance signatures that humans exhibit during symbolic arithmetic also bear a connection to primitive arithmetic. Specifically, we examined the problem size effect, the tie effect, and the practice effect-effects which are commonly observed in children's math performance in school. We show that, like humans, monkeys exhibited the problem size and tie effects, indicating commonalities in arithmetic algorithms with humans. Unlike humans, however, monkeys did not exhibit a practice effect. Together, these findings provide new evidence for a cognitive relation between non-symbolic and symbolic arithmetic.

Functional hyperspectral imaging captures subtle details of cell metabolism in olfactory neurosphere cells, disease-specific models of neurodegenerative disorders

Hyperspectral imaging uses spectral and spatial image information for target detection and classification. In this work hyperspectral autofluorescence imaging was applied to patient olfactory neurosphere-derived cells, a cell model of a human metabolic disease MELAS (mitochondrial myopathy, encephalomyopathy, lactic acidosis, stroke-like syndrome). By using an endogenous source of contrast subtle metabolic variations have been detected between living cells in their full morphological context which made it possible to distinguish healthy from diseased cells before and after therapy. Cellular maps of native fluorophores, flavins, bound and free NADH and retinoids unveiled subtle metabolic signatures and helped uncover significant cell subpopulations, in particular a subpopulation with compromised mitochondrial function. Taken together, our results demonstrate that multispectral spectral imaging provides a new non-invasive method to investigate neurodegenerative and other disease models, and it paves the way for novel cellular characterisation in health, disease and during treatment, with proper account of intrinsic cellular heterogeneity.

9 Tracing Everyday Life at Trimithis (Dakhleh Oasis, Egypt)

ABSTRACTThis article explores how concepts of “trace” might help archaeologists disentangle and interpret the material remains of ordinary life. Trace is a theoretical vantage long exploited by social theorists to explore the unintentional, quotidian residues of ordinary people. The term trace is relevant to archaeology because it refocuses attention from active agency to more subtle undercurrents within daily life rhythms. I explore two Romano‐Egyptian houses from the same city from a trace perspective in order to reveal the small‐scale daily life choices of individuals. The results of this exploration suggest future directions for the archaeological use of trace to explore materiality, everyday life, and subtle signatures of multi‐cultural scenarios.