A long-term time series of global and diffuse photosynthetically active radiation in the Mediterranean: interannual variability and cloud effects

Abstract. Measurements of global and diffuse photosynthetically active radiation (PAR) have been carried out on the island of Lampedusa, in the central Mediterranean Sea, since 2002. PAR is derived from observations made with multi-filter rotating shadowband radiometers (MFRSRs) by comparison with a freshly calibrated PAR sensor and by relying on the on-site Langley plots. In this way, a long-term calibrated record covering the period 2002–2016 is obtained and is presented in this work. The monthly mean global PAR peaks in June, with about 160 W m−2, while the diffuse PAR reaches 60 W m−2 in spring or summer. The global PAR displays a clear annual cycle with a semi amplitude of about 52 W m−2. The diffuse PAR annual cycle has a semi amplitude of about 12 W m−2. A simple method to retrieve the cloud-free PAR global and diffuse irradiances in days characterized by partly cloudy conditions has been implemented and applied to the dataset. This method allows retrieval of the cloud-free evolution of PAR and calculation of the cloud radiative effect, CRE, for downwelling PAR. The cloud-free monthly mean global PAR reaches 175 W m−2 in summer, while the diffuse PAR peaks at about 40 W m−2. The cloud radiative effect, CRE, on global and diffuse PAR is calculated as the difference between all-sky and cloud-free measurements. The annual average CRE is about −14.7 W m−2 for the global PAR and +8.1 W m−2 for the diffuse PAR. The smallest CRE is observed in July, due to the high cloud-free condition frequency. Maxima (negative for the global, and positive for the diffuse component) occur in March–April and in October, due to the combination of elevated PAR irradiances and high occurrence of cloudy conditions. Summer clouds appear to be characterized by a low frequency of occurrence, low altitude, and low optical thickness, possibly linked to the peculiar marine boundary layer structure. These properties also contribute to produce small radiative effects on PAR in summer. The cloud radiative effect has been deseasonalized to remove the influence of annual irradiance variations. The monthly mean normalized CRE for global PAR can be well represented by a multi-linear regression with respect to monthly cloud fraction, cloud top pressure, and cloud optical thickness, as determined from satellite MODIS observations. The behaviour of the normalized CRE for diffuse PAR can not be satisfactorily described by a simple multi-linear model with respect to the cloud properties, due to its non-linear dependency, in particular on the cloud optical depth. The analysis suggests that about 77 % of the global PAR interannual variability may be ascribed to cloud variability in winter

Sexual epigenetic dimorphism in the human placenta: implications for susceptibility during the prenatal period

Sex-based differences in response to adverse prenatal environments and infant outcomes have been observed, yet the underlying mechanisms for this are unclear. The placental epigenome may be a driver of these differences

In Vitro Identification and Characterization of CD133pos Cancer Stem-Like Cells in Anaplastic Thyroid Carcinoma Cell Lines

Background: Recent publications suggest that neoplastic initiation and growth are dependent on a small subset of cells, termed cancer stem cells (CSCs). Anaplastic Thyroid Carcinoma (ATC) is a very aggressive solid tumor with poor prognosis, characterized by high dedifferentiation. The existence of CSCs might account for the heterogeneity of ATC lesions. CD133 has been identified as a stem cell marker for normal and cancerous tissues, although its biological function remains unknown. Methodology/Principal Findings: ATC cell lines ARO, KAT-4, KAT-18 and FRO were analyzed for CD133 expression. Flow cytometry showed CD133pos cells only in ARO and KAT-4 (6469% and 57612%, respectively). These data were confirmed by qRT-PCR and immunocytochemistry. ARO and KAT-4 were also positive for fetal marker oncofetal fibronectin and negative for thyrocyte-specific differentiating markers thyroglobulin, thyroperoxidase and sodium/iodide symporter. Sorted ARO/ CD133pos cells exhibited higher proliferation, self-renewal, colony-forming ability in comparison with ARO/CD133neg. Furthermore, ARO/CD133pos showed levels of thyroid transcription factor TTF-1 similar to the fetal thyroid cell line TAD-2, while the expression in ARO/CD133neg was negligible. The expression of the stem cell marker OCT-4 detected by RT-PCR and flow cytometry was markedly higher in ARO/CD133pos in comparison to ARO/CD133neg cells. The stem cell markers c- KIT and THY-1 were negative. Sensitivity to chemotherapy agents was investigated, showing remarkable resistance to chemotherapy-induced apoptosis in ARO/CD133pos when compared with ARO/CD133neg cells. Conclusions/Significance: We describe CD133pos cells in ATC cell lines. ARO/CD133pos cells exhibit stem cell-like features - such as high proliferation, self-renewal ability, expression of OCT-4 - and are characterized by higher resistance to chemotherapy. The simultaneous positivity for thyroid specific factor TTF-1 and onfFN suggest they might represent putative thyroid cancer stem-like cells. Our in vitro findings might provide new insights for novel therapeutic approaches

Shared probe design and existing microarray reanalysis using PICKY

<p>Abstract</p> <p>Background</p> <p>Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations.</p> <p>Results</p> <p><smcaps>PICKY</smcaps> 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. <smcaps>PICKY</smcaps> 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, <smcaps>PICKY</smcaps> does not sacrifice the quality of shared probes when choosing them. The latest <smcaps>PICKY</smcaps> 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making <smcaps>PICKY</smcaps> 2.1 more versatile to microarray users.</p> <p>Conclusions</p> <p>Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.</p

In Vitro Phenotypic, Genomic and Proteomic Characterization of a Cytokine-Resistant Murine β-TC3 Cell Line

Type 1 diabetes mellitus (T1DM) is caused by the selective destruction of insulin-producing β-cells. This process is mediated by cells of the immune system through release of nitric oxide, free radicals and pro-inflammatory cytokines, which induce a complex network of intracellular signalling cascades, eventually affecting the expression of genes involved in β-cell survival

RNAstructure: software for RNA secondary structure prediction and analysis

<p>Abstract</p> <p>Background</p> <p>To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.</p> <p>Results</p> <p>RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.</p> <p>Conclusion</p> <p>The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at <url>http://rna.urmc.rochester.edu/RNAstructure.html</url>.</p