Miracle-dz/UniFAR-FTUs huggingface dataset:
Cannabinoid Receptor 2 Modulates Neutrophil Recruitment in a Murine Model of Endotoxemia

The endocannabinoid system consists of endogenous lipid mediators and cannabinoid receptors (CB) 1 and 2. It has previously been demonstrated that activation of the leukocyte-expressed CB2 has anti-inflammatory effects in vivo. Here, we report its role under baseline conditions and in a model of low-dose endotoxemia by comparing CB2 knockout to littermate control mice. CB2-deficient mice displayed significantly more neutrophils and fewer monocytes in the bone marrow under steady state. In initial validation experiments, administration of 1 mg/kg LPS to male C57BL/6J mice was shown to transiently upregulate systemic proinflammatory mediators (peaked at 2 hours) and mobilise bone marrow neutrophils and monocytes into circulation. In CB2 knockout mice, the level of the metalloproteinase MMP-9 was significantly elevated by 2 hours and we also observed augmented recruitment of neutrophils to the spleen in addition to increased levels of Ccl2, Ccl3, Cxcl10, and Il6. Collectively, our data show that the absence of CB2 receptor increases the levels of innate immune cell populations in the bone marrow under steady state. Furthermore, during an acute systemic inflammatory insult, we observe a highly reproducible and site-specific increase in neutrophil recruitment and proinflammatory chemokine expression in the spleen of CB2 knockout mice.
Burial/exhumation histories for the Cooper–Eromanga Basins and implications for hydrocarbon exploration, Eastern Australia

The Cooper–Eromanga Basins of South Australia and Queensland are not at their maximum burial depth due to Late Cretaceous–Tertiary, and Late Triassic–Early Jurassic exhumation. Apparent exhumation (maximum burial depth–present burial depth) for the Cooper Basin has been quantified using the compaction methodology. The results show that exhumation of the Cooper Basin for the majority of the wells is greater than the exhumation of the Eromanga Basin. Using the compaction methodology, apparent exhumation of Early to Middle Triassic age Arrabury and Tinchoo Formatios has been quantified. Both units yield similar results and do not support that the Arrabury/Tinchoo boundary represents the Cooper–Eromanga boundary. Hence, the Cooper Basin is believed to have reached its maximum burial depth in Late Triassic times. Sonic log data are not available for the units overlying the Late Cretaceous Winton Formation; thus, it is not possible to date exhumation beyond the Late Cretaceous–Tertiary using the compaction methodology. Tertiary sequences as are preserved are relatively thin and separated by marked unconformities and weathered surfaces; hence, exhumation rather than sedimentation dominated the Tertiary, and in exhumed areas, maximum burial depth was attained in Late Cretaceous times. The burial/exhumation history of representative wells was synthesized using sediment decompaction and establishing porosity/depth relations for the Cooper–Eromanga units. Considering the relative significance of the major periods of exhumation in the Cooper/Eromanga Basins, three broad types of burial/exhumation histories can be distinguished. Maximum burial depth of the Cooper Basin sequence was attained before the deposition of the Eromanga Basin sequence, i.e. Late Triassic–Early Jurassic times; maximum burial depth of the Cooper and Eromanga Basin sequences attained in Late Cretaceous times; and Cooper and Eromanga Basin sequences are currently at maximum burial‐depth. Incorporation of exhumation into burial history has major implications for hydrocarbon exploration.
Numerical predictions of aerosol charging and electrical conductivity of the lower atmosphere of Mars

The charging of aerosols and the conductivity of the lower, night time atmosphere of Mars are calculated. The charge distribution of aerosols was obtained by the simultaneous solution of the ion‐aerosol charge balance equations. Galactic cosmic rays are the dominant ionizing process in the night time lower atmosphere producing molecular ions and ion clusters. The ion production rates for different solar activities are considered. The ion‐ion recombination rates and the ion‐aerosols attachment coefficients are calculated for altitudes from 0 to 70 km. Both the steady state and time dependent concentration of charged aerosols are calculated. The conductivity produced by ion‐attachment of aerosols was found to decrease by a factor of five yielding a value of about 4 × 10−12 Ohm−1 m−1 close to the surface. The effect on the conductivity of the temperature vs. altitude and the aerosol density are also estimated.
Estimating earthquake source depths by combining surface wave amplitude spectra and teleseismic depth phase observations

S U M M A R Y The ability to confidently estimate the depths of small-to-medium sized (3.5 ≤ mb ≤ 5.5) seismic disturbances is important both in plate tectonics studies, and when monitoring compliance with the Comprehensive Nuclear-Test-Ban Treaty (CTBT). Seismic source depths can be determined by identification of the teleseismic depth phases pP and sP, and also by modelling surface wave amplitude spectra. The radiation pattern of the teleseismic depth phase pP and fundamental mode Rayleigh amplitudes show that the effectiveness of these methods of earthquake depth estimation is dependent on the orientation of the focal mechanism and the station locations. For some focal mechanisms, the predicted amplitude of the teleseismic depth phase pP will only be large for stations in certain locations, and the Rayleigh wave spectral nulls that tightly constrain the seismic source depth when modelling surface wave amplitude spectra often only occur for a limited range of azimuths. In this study, we show that for sources where Rayleigh wave spectral nulls are not observed and the source depth cannot be constrained using the surface wave amplitude spectra, the focal mechanism obtained by modelling Rayleigh and Love wave amplitude spectra can be used to identify the locations of stations where pP should have a large amplitude and hence be easiest for an analyst to identify. The increased global coverage of seismometer stations means that there is an increased likelihood that stations exist in the locations where the predicted amplitude of pP is large. As the identified depth phases are consistent with the focal mechanism this approach allows increased confidence to be placed in the identified depth phases and hence the estimated source depth. This approach could potentially be used with other methods of focal mechanism estimation provided that the method used to estimate the focal mechanism is independent of the source depth.
Localization of ASV Integrase-DNA Contacts by Site-Directed Crosslinking and their Structural Analysis

Background We applied crosslinking techniques as a first step in preparation of stable avian sarcoma virus (ASV) integrase (IN)-DNA complexes for crystallographic investigations. These results were then compared with the crystal structures of the prototype foamy virus (PFV) intasome and with published data for other retroviral IN proteins. Methodology/Results Photoaffinity crosslinking and site-directed chemical crosslinking were used to localize the sites of contacts with DNA substrates on the surface of ASV IN. Sulfhydryl groups of cysteines engineered into ASV IN and amino-modified nucleotides in DNA substrates were used for attachment of photocrosslinkers. Analysis of photocrosslinking data revealed several specific DNA-protein contacts. To confirm contact sites, thiol-modified nucleotides were introduced into oligo-DNA substrates at suggested points of contact and chemically crosslinked to the cysteines via formation of disulfide bridges. Cysteines incorporated in positions 124 and 146 in the ASV IN core domain were shown to interact directly with host and viral portions of the Y-mer DNA substrate, respectively. Crosslinking of an R244C ASV IN derivative identified contacts at positions 11 and 12 on both strands of viral DNA. The most efficient disulfide crosslinking was observed for complexes of the ASV IN E157C and D64C derivatives with linear viral DNA substrate carrying a thiol-modified scissile phosphate. Conclusion Analysis of our crosslinking results as well as published results of retroviral IN protein from other laboratories shows good agreement with the structure of PFV IN and derived ASV, HIV, and MuLV models for the core domain, but only partial agreement for the N- and C-terminal domains. These differences might be explained by structural variations and evolutionary selection for residues at alternate positions to perform analogous functions, and by methodological differences: i.e., a static picture of a particular assembly from crystallography vs. a variety of interactions that might occur during formation of functional IN complexes in solution.
Risk for animal and human health related to the presence of dioxins and dioxin‐like PCBs in feed and food

Abstract The European Commission asked EFSA for a scientific opinion on the risks for animal and human health related to the presence of dioxins (PCDD/Fs) and DL‐PCBs in feed and food. The data from experimental animal and epidemiological studies were reviewed and it was decided to base the human risk assessment on effects observed in humans and to use animal data as supportive evidence. The critical effect was on semen quality, following pre‐ and postnatal exposure. The critical study showed a NOAEL of 7.0 pg WHO2005‐TEQ/g fat in blood sampled at age 9 years based on PCDD/F‐TEQs. No association was observed when including DL‐PCB‐TEQs. Using toxicokinetic modelling and taking into account the exposure from breastfeeding and a twofold higher intake during childhood, it was estimated that daily exposure in adolescents and adults should be below 0.25 pg TEQ/kg bw/day. The CONTAM Panel established a TWI of 2 pg TEQ/kg bw/week. With occurrence and consumption data from European countries, the mean and P95 intake of total TEQ by Adolescents, Adults, Elderly and Very Elderly varied between, respectively, 2.1 to 10.5, and 5.3 to 30.4 pg TEQ/kg bw/week, implying a considerable exceedance of the TWI. Toddlers and Other Children showed a higher exposure than older age groups, but this was accounted for when deriving the TWI. Exposure to PCDD/F‐TEQ only was on average 2.4‐ and 2.7‐fold lower for mean and P95 exposure than for total TEQ. PCDD/Fs and DL‐PCBs are transferred to milk and eggs, and accumulate in fatty tissues and liver. Transfer rates and bioconcentration factors were identified for various species. The CONTAM Panel was not able to identify reference values in most farm and companion animals with the exception of NOAELs for mink, chicken and some fish species. The estimated exposure from feed for these species does not imply a risk.
Detachment faults at Mid-Ocean Ridges garner interest

The recent discovery of low-angle faults known as detachments on the Mid-Atlantic Ridge requires a major reevaluation of how the oceanic crust forms at slow spreading ridges. Detachment faults can expose large areas of plutonic and ultramafic rocks on the seafloor, without an overlying volcanic carapace. They could profoundly influence the thermal structure, rheology, composition, and style of magmatic accretion at ridges. Oceanic detachments have many parallels with continental detachment faults, with the added advantage that the morphology of the fault surface is pristine, unaffected by subareal erosion.
Geodynamic significance of ophiolites within the Calabrian Arc

Abstract Slices of oceanic lithosphere belonging to the neo‐Tethys realm crop out discontinuously in the northern Calabrian Arc, Southern Apennines. They consist of high‐pressure–low‐temperature metamorphic ophiolitic sequences formed from metaultramafics, metabasites and alternating metapelites, metarenites, marbles and calcschist. Ophiolites occupy an intermediate position in the northern Calabrian Arc nappe pile, situated between overlying Hercynian continental crust and the underlying Apenninic limestone units. In the literature, these ophiolitic sequences are subdivided into several tectonometamorphic units. Geochemical characteristics indicate that metabasites were derived from subalkaline basalts with tholeiitic affinity (transitional mid‐oceanic ridge basalt type), and a harzburgitic‐lherzolitic protolith is suggested for the serpentinites. The pressure–temperature‐deformation paths of the metabasites from different outcrops display similar features: (i) the prograde segment follows a typical Alpine geothermal gradient up to a metamorphic climax at 350°C and 0.9 GPa and crystallization of the high‐pressure mineral assemblage occurs along a pervasive foliation developed during a compressive tectonic event; and (ii) the retrogression path can be subdivided in two segments, the first is characterized by nearly isothermal decompression to approximately 400°C and 0.3 GPa and the second follows a cooling trajectory. During low‐pressure conditions, a second deformation event produces millimetric to decametric scale asymmetric folds that describe west‐verging major structures. The third deformation event is characterized by brittle extensional structures. The tectonometamorphic evolution of the ophiolitic sequences from the different outcrops is similar. Both thermobarometric modeling and tectonic history indicate that the studied rocks underwent Alpine subduction and exhumation processes as tectonic slices inside a west‐verging accretionary wedge. The subduction of oceanic lithosphere was towards the present east; therefore, the Hercynian continental crust, overthrusted on the ophiolitic accretionary wedge after the neo‐Tethys closure, was part of the African paleomargin or a continental microplate between Africa and Europe.
HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

Abstract Housekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping and Reference Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 11 281 and 507 high-quality RNA-seq samples from 52 human non-disease tissues/cells and 14 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2158 human HK transcripts from 2176 HK genes and 3024 mouse HK transcripts from 3277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with a regulatory elements resource from Epiregio server.
Turbulence Structures in Flow over Two-Dimensional Dunes

This paper presents a large eddy simulation (LES) of turbulent open channel flow over two-dimensional periodic dunes. The Reynolds number R based on the bulk velocity U (bulk) and the maximum flow depth h , is approximately 25,000. The instantaneous flow field is investigated with special emphasis on the occurrence of coherent structures. Instantaneous vortices were visualized and it is shown that separated vortices are formed downstream of the dune crest due to Kelvin–Helmholtz instabilities. Near the point of reattachment the so-called kolk-boil vortex evolves in form of a hairpin vortex. Also present are previously separated vortices, which are convected along the stoss side of the downstream dune and elevated toward the water surface. The existence of near wall streaks which reform shortly after reattachment is also shown. The spacing between two low-speed streaks is very similar to that observed previously over smooth and rough walls. For validation, profiles of the time-averaged velocities, streamwi.
Wet phases in tropical southern Africa during the last glacial period

A 45,000‐year high‐resolution sedimentary record from Lake Masoko in Tanzania shows the climate in this part of East Africa to have been characterized by a short and less severe dry season during the Last Glacial Maximum. Moisture and lake‐level proxies, pollen assemblages and magnetic susceptibility, indicate that rainfall in the Masoko area was strongly controlled by low‐latitude insolation (i.e., precessional forcing). Such observations contrast with the climatic patterns previously reconstructed in East Africa for the last glacial. Indeed, widespread dry conditions are generally observed and are attributed to the predominant control of high latitude glacial forcing over insolation forcing on the tropical hydrology. However, during the Younger Dryas cold event, out of phase with regional insolation behaviour, wetter conditions prevailed in this area, suggesting that the rainfall belt over Africa was probably shifted to the South, bringing moisture to the southernmost tropics.
Characteristics and formation of Eastern South Pacific Intermediate Water

Newly gathered hydrographic data from the Eastern South Pacific is combined with other high‐quality data (mainly WOCE) to reassess the properties and boundaries of the Eastern South Pacific Intermediate Water (ESPIW); to date the ESPIW has been only poorly described. The ESPIW core is found off central and northern Chile, between the coast and 90°W and 20–38°S. Located at 50–400 m of depth, its temperature varies between 11–13°C, salinity ranges from 34.1–34.3, and its sigma‐t lies between 25.75–26.25 kgm−3. ESPIW spreads with the subtropical gyre circulation and can be traced to at least 150°W. Formed through the process of subduction southeastward of the wind‐driven gyre circulation, the ESPIW communicates surface properties of the waters off central Chile to tropical latitudes.
Therapeutic landscapes as assemblages, actor-networks and contingent affordances : the example of Saltwell Park

My doctoral research is situated within Geographies of Health, asking whether and how an urban public park is therapeutic. Specifically, the thesis is concerned with theorising what the physical, social and symbolic environments of the park consist of and how individual park users interact with those environments. The thesis used Gesler’s therapeutic landscape concept and typology as its starting point, but I have critiqued this typology for its boundedness, lack of temporal and material flux and implicit normative assumptions. The therapeutic landscape literature has rarely engaged with Post-structuralist and Non-Representational thinking, which are relatively rarely used within wider health geography discourse. I sought to include all observable elements within the composition of the park fabric, including, for example, weather and wildlife, and cultural images and individual representations, following from assemblagic and actor network thinking. I sought to gain as many perspectives about the park’s form and usage, obtaining empirical data through an innovative year-long mixed-methods approach of repeated ethnographic observation, participation observation, and purposive sampling semi-structured interviews, augmented where possible with an accompanying photovoice and mapping exercises. I spoke to nearly 60 people, respondents ranging from primary school children to new mothers to five male mental health service users. Within the text of this thesis, the empirical data has been mapped against the therapeutic landscapes’ typology of natural, social and symbolic environments. The ability of an individual to access and make beneficial use of the park depends upon their ability to gain physical, social and emotional access,. This is dependent upon factors such as physical proximity, social inclusion and the perception of the park. As such, the “therapeutic” is relational, a function of park-person interactions. The natural, social and symbolic environments typology should be seen as a series of assemblages of human and nonhuman elements that co-function under specific circumstances, and into which the park users situate themselves.
Cytoskeletal protein flightless I inhibits apoptosis, enhances tumor cell invasion and promotes cutaneous squamous cell carcinoma progression

Flightless I (Flii) is an actin remodeling protein that affects cellular processes including adhesion, proliferation and migration. In order to determine the role of Flii during carcinogenesis, squamous cell carcinomas (SCCs) were induced in Flii heterozygous (Flii+/−), wild-type and Flii overexpressing (FliiTg/Tg) mice by intradermal injection of 3-methylcholanthrene (MCA). Flii levels were further assessed in biopsies from human SCCs and the human SCC cell line (MET-1) was used to determine the effect of Flii on cellular invasion. Flii was highly expressed in human SCC biopsies particularly by the invading cells at the tumor edge. FliiTg/Tg mice developed large, aggressive SCCs in response to MCA. In contrast Flii+/− mice had significantly smaller tumors that were less invasive. Intradermal injection of Flii neutralizing antibodies during SCC initiation and progression significantly reduced the size of the tumors and, in vitro, decreased cellular sphere formation and invasion. Analysis of the tumors from the Flii overexpressing mice showed reduced caspase I and annexin V expression suggesting Flii may negatively regulate apoptosis within these tumors. These studies therefore suggest that Flii enhances SCC tumor progression by decreasing apoptosis and enhancing tumor cell invasion. Targeting Flii may be a potential strategy for reducing the severity of SCCs.
FliZ Is a Global Regulatory Protein Affecting the Expression of Flagellar and Virulence Genes in Individual Xenorhabdus nematophila Bacterial Cells

Heterogeneity in the expression of various bacterial genes has been shown to result in the presence of individuals with different phenotypes within clonal bacterial populations. The genes specifying motility and flagellar functions are coordinately regulated and form a complex regulon, the flagellar regulon. Complex interplay has recently been demonstrated in the regulation of flagellar and virulence gene expression in many bacterial pathogens. We show here that FliZ, a DNA-binding protein, plays a key role in the insect pathogen, Xenorhabdus nematophila, affecting not only hemolysin production and virulence in insects, but efficient swimming motility. RNA-Seq analysis identified FliZ as a global regulatory protein controlling the expression of 278 Xenorhabdus genes either directly or indirectly. FliZ is required for the efficient expression of all flagellar genes, probably through its positive feedback loop, which controls expression of the flhDC operon, the master regulator of the flagellar circuit. FliZ also up- or downregulates the expression of numerous genes encoding non-flagellar proteins potentially involved in key steps of the Xenorhabdus lifecycle. Single-cell analysis revealed the bimodal expression of six identified markers of the FliZ regulon during exponential growth of the bacterial population. In addition, a combination of fluorescence-activated cell sorting and RT-qPCR quantification showed that this bimodality generated a mixed population of cells either expressing (“ON state”) or not expressing (“OFF state”) FliZ-dependent genes. Moreover, studies of a bacterial population exposed to a graded series of FliZ concentrations showed that FliZ functioned as a rheostat, controlling the rate of transition between the “OFF” and “ON” states in individuals. FliZ thus plays a key role in cell fate decisions, by transiently creating individuals with different potentials for motility and host interactions.