Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonally and regionally determined indication potential of bioassays in contaminated river sediments

River sediments are a dynamic system, especially in areas where floods occur frequently. In the present study, an integrative approach is used to investigate the seasonal and spatial dynamics of contamination of sediments from a regularly flooded industrial area in the Czech Republic, which presents a suitable model ecosystem for pollutant distribution research at a regional level. Surface sediments were sampled repeatedly to represent two different hydrological situations: spring (after the peak of high flow) and autumn (after longer period of low flow). Samples were characterized for abiotic parameters and concentrations of priority organic pollutants. Toxicity was assessed by Microtox test; genotoxicity by SOS‐chromotest and green fluorescent protein (GFP)‐yeast test; and the presence of compounds with specific mode of action by in vitro bioassays for dioxin‐like activity, anti‐/androgenicity, and anti‐/estrogenicity. Distribution of organic contaminants varied among regions and seasonally. Although the results of Microtox and genotoxicity tests were relatively inconclusive, all other specific bioassays led to statistically significant regional and seasonal differences in profiles and allowed clear separation of upstream and downstream regions. The outcomes of these bioassays indicated an association with concentrations of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) as master variables. There were significant interrelations among dioxin‐like activity, antiandrogenicity and content of organic carbon, clay, and concentration of PAHs and PCBs, which documents the significance of abiotic factors in accumulation of pollutants. The study demonstrates the strength of the specific bioassays in indicating the changes in contamination and emphasizes the crucial role of a well‐designed sampling plan, in which both spatial and temporal dynamics should be taken into account, for the correct interpretations of information in risk assessments. Environ. Toxicol. Chem. 2010;29:522–534. © 2009 SETAC
Immunological Profile of HTLV-1-Infected Patients Associated with Infectious or Autoimmune Dermatological Disorders

In the present study, the frequency, the activation and the cytokine and chemokine profile of HTLV-1 carriers with or without dermatological lesions were thoroughly described and compared. The results indicated that HTLV-1-infected patients with dermatological lesions have distinct frequency and activation status when compared to asymptomatic carriers. Alterations in the CD4+HLA-DR+, CD8+ T cell, macrophage-like and NKT subsets as well as in the serum chemokines CCL5, CXCL8, CXCL9 and CXCL10 were observed in the HTLV-1-infected group with skin lesions. Additionally, HTLV-1 carriers with dermatological skin lesions showed more frequently high proviral load as compared to asymptomatic carriers. The elevated proviral load in HTLV-1 patients with infectious skin lesions correlated significantly with TNF-α/IL-10 ratio, while the same significant correlation was found for the IL-12/IL-10 ratio and the high proviral load in HTLV-1-infected patients with autoimmune skin lesions. All in all, these results suggest a distinct and unique immunological profile in the peripheral blood of HTLV-1-infected patients with skin disorders, and the different nature of skin lesion observed in these patients may be an outcome of a distinct unbalance of the systemic inflammatory response upon HTLV-1 infection.
Increased expression of mitochondrial transcription factor A and nuclear respiratory factor-1 predicts a poor clinical outcome of breast cancer

Nuclear respiratory factor-1 (Nrf1) and mitochondrial transcription factor A (TFAM) are involved in the regulation of a variety of mitochondrial functional genes, which are associated with decreased sensitivity of tumor cells to chemotherapy. However, the expression status of Nrf1 and TFAM, as well as their clinical significance in breast cancer, is unknown. In the present study, tumor tissues and corresponding adjacent normal tissues were collected from 336 patients with breast cancer, and Nrf1 and TFAM expression was analyzed by immunohistochemistry using a tissue microarray. Expression of Nrf1 and TFAM was significantly increased in breast cancer tissue compared with adjacent normal tissues. In addition, patients positive for Nrf1 or TFAM had a poorer clinical prognosis than patients who were negative, and those positive for Nrf1 and TFAM had the shortest survival time. These results suggest that Nrf1 and TFAM are potential biomarkers for the determination of individualized therapy and the prognosis of breast cancer, and molecular targeting of Nrf1 and TFAM is a promising strategy for the sensitization of breast cancer cells to chemotherapeutics.
Syndecan-2 Functions as a Docking Receptor for Pro-matrix Metalloproteinase-7 in Human Colon Cancer Cells*

Although elevated syndecan-2 expression is known to be crucial for the tumorigenic activity in colon carcinoma cells, how syndecan-2 regulates colon cancer is unclear. In human colon adenocarcinoma tissue samples, we found that both mRNA and protein expression of syndecan-2 were increased, compared with the neighboring normal epithelium, suggesting that syndecan-2 plays functional roles in human colon cancer cells. Consistent with this notion, syndecan-2-overexpressing HT-29 colon adenocarcinoma cells showed enhanced migration/invasion, anchorage-independent growth, and primary tumor formation in nude mice, paralleling their morphological changes into highly tumorigenic cells. In addition, our experiments revealed that syndecan-2 enhanced both expression and secretion of matrix metalloproteinase-7 (MMP-7), directly interacted with pro-MMP-7, and potentiated the enzymatic activity of pro-MMP-7 by activating its processing into the active MMP-7. Collectively, these data strongly suggest that syndecan-2 functions as a docking receptor for pro-MMP-7 in colon cancer cells.
Optimization and stabilization of networked control systems: An Estimation of Distribution Algorithm approach

This paper addresses the optimization and stabilization problem for networked control systems (NCSs). The memoryless state feedback controller is considered, and the resulting closed-loop NCS is modeled as a discrete-time switch system. By defining a state-dependent Lyapunov function, the stability conditions are derived for NCSs in terms of linear matrix inequalities (LMIs). Based on the obtained stability conditions, the corresponding controller design problem is solved, and estimation of distribution algorithm (EDA) is used to select the optimal state feedback stabilizing gain. It is shown that the proposed method can be easily implemented to various applications, since it is simple and has no assumptions on time delays and packet losses. Simulation results are given to demonstrate the effectiveness of the proposed approach.
Synthesis of CDP-Activated Ribitol for Teichoic Acid Precursors in Streptococcus pneumoniae

ABSTRACT Streptococcus pneumoniae has unusually complex cell wall teichoic acid and lipoteichoic acid, both of which contain a ribitol phosphate moiety. The lic region of the pneumococcal genome contains genes for the uptake and activation of choline, the attachment of phosphorylcholine to teichoic acid precursors, and the transport of these precursors across the cytoplasmic membrane. The role of two other, so far uncharacterized, genes, spr1148 and spr1149, in the lic region was determined. TarJ (spr1148) encodes an NADPH-dependent alcohol dehydrogenase for the synthesis of ribitol 5-phosphate from ribulose 5-phosphate. TarI (spr1149) encodes a cytidylyl transferase for the synthesis of cytidine 5′-diphosphate (CDP)-ribitol from ribitol 5-phosphate and cytidine 5′-triphosphate. We also present the crystal structure of TarI with and without bound CDP, and the structures present a rationale for the substrate specificity of this key enzyme. No transformants were obtained with insertion plasmids designed to interrupt the tarIJ genes, indicating that their function could be essential for cell growth. CDP-activated ribitol is a precursor for the synthesis of pneumococcal teichoic acids and some of the capsular polysaccharides. Thus, all eight genes in the lic region have a role in teichoic acid synthesis.
Discourse Coherence and Shifting Centers in Japanese Texts

In languages such as Japanese, the use of {\it zeros}, unexpressed arguments of the verb, in utterances that shift the topic involves a risk that the meaning intended by the speaker may not be transparent to the hearer. However, this potentially undesirable conversational strategy often occurs in the course of naturally-occurring discourse. In this chapter, I report on an empirical study of 250 utterances with {\it zeros} in 20 Japanese newspaper articles. Each utterance is analyzed in terms of centering transitions and the form in which centers are realized by referring expressions. I also examine lexical subcategorization information, and tense and aspect in order to test the hypothesis that the speaker expects the hearer to use this information in determining global discourse structure. I explain the occurrence of {\it zeros} in {\sc retain} and {\sc rough-shift} centering transitions, by claiming that a {\it zero} can only be used in these cases when the shift of centers is supported by contextual information such as lexical semantics, tense and aspect, and agreement features. I then propose an algorithm by which centering can incorporate these observations to integrate centering with global discourse structure, and thus enhance its ability for non-local pronoun resolution.
The cyclin encoded by Kaposi's sarcoma-associated herpesvirus stimulates cdk6 to phosphorylate the retinoblastoma protein and histone H1

Kaposi's sarcoma-associated herpesvirus (KSHV or human herpesvirus 8) is a novel gammaherpesvirus implicated in the cause of Kaposi's sarcoma and certain malignancies of lymphatic origin. One of the candidate genes possibly involved in promoting tumor development is an open reading frame (ORF) with sequence similarity to human type D cyclin genes. This cyclin-like gene, when expressed in tissue culture cells, promotes phosphorylation and inactivation of the retinoblastoma tumor suppressor protein and thereby may result in deregulation of cell division control. We report here the biochemical characterization of this cyclin (KSHV-cyc) and the kinase activity that it elicits upon expression in tissue culture cells. We demonstrate that the kinase activity associated with KSHV-cyc is sensitive to the cdk inhibitor p27 (KIP) and due to activation of cdk6. However, in contrast to cdk6 activated by cellular type D cyclins, the cdk6 activated by KSHV-cyc is capable of phosphorylating not only the retinoblastoma protein but also histone H1. This finding implies that activation by KSHV-cyc alters the substrate preference of this cdk. This may have important physiological consequences in that the kinase activity triggered by this viral cyclin may abrogate cell cycle checkpoints in addition to those targeted by cellular cyclin D-cdk6 kinase.
Oscillation Criteria for Forced Second-Order Functional Dynamic Equations with Mixed Nonlinearities on Time Scales

We are concerned with the oscillation of certain forced second-order functional dynamic equation with mixed nonlinearities. Our results in a particular case solve a problem posed by Anderson, and our results in the special cases when the time scale is the set of real numbers and the set of integers involve and improve some oscillation results for second-order differential and difference equations, respectively.
Characterization of the sediment bacterial community in groundwater discharge zones of an alkaline fen: a seasonal study

The cell density, activity, and community structure of the bacterial community in wetland sediments were monitored over a 13-month period. The study was performed at Cedar Bog, an alkaline fen. The objective was to characterize the relationship between the sediment bacterial community in groundwater upwelling zones and the physical and chemical factors which might influence the community structure and activity. DNA, protein, and lipid synthesis were measured at three different upwelling zones by using [3H]thymidine, [14C]leucine, and [14C]glucose incorporation, respectively. The physiological status (apparent stress) of the consortium was assessed by comparing [14C]glucose incorporation into membrane and that into storage lipids. Bacterial cell density was determined by acridine orange direct counts, and gross bacterial community structure was determined by bisbenzimidazole-cesium chloride gradient analysis of total bacterial community DNA. Both seasonal and site-related covariation were observed in all estimates of bacterial biomass and activity. Growth rate estimates and cell density peaked in late July at 2.5 x 10(8) cells/g/day and 2.7 x 10(9) cells/g, respectively, and decreased in December to 2.0 x 10(7) cells/g/day and 1.5 x 10(9) cells/g, respectively. Across sites, membrane-to-storage-lipid ratios were generally highest in late spring and peaked in September for one site. Overall, the data indicate dynamic seasonal differences in sediment bacterial community activity and physiology, possibly in response to changing physical and chemical environmental factors which included the C/N/P ratios of the perfusing groundwater. By contrast, total cell numbers were rather constant, and community structure analysis indicated that the overall community structure was similar throughout the study.
The Lyn Tyrosine Kinase Differentially Regulates Dendritic Cell Generation and Maturation1

The Src family kinase Lyn plays both stimulatory and inhibitory roles in hemopoietic cells. In this report we provide evidence that Lyn is involved in dendritic cell (DC) generation and maturation. Loss of Lyn promoted DC expansion in vitro from bone marrow precursors due to enhanced generation and accelerated differentiation of Lyn-deficient DC progenitors. Differentiated Lyn-deficient DCs also had a higher survival rate. Similarly, the CD11c-positive cell number was increased in aged Lyn-deficient mice in vivo. In contrast to their enhanced generation, lyn−/− DCs failed to mature appropriately in response to innate stimuli, resulting in DCs with lower levels of MHC class II and costimulatory molecules. In addition, IL-12 production and Ag-specific T cell activation were reduced in lyn−/− DCs after maturation, resulting in impaired Th1 responses. This is the first study to characterize Lyn-deficient DCs. Our results suggest that Lyn kinase plays uniquely negative and positive regulatory roles in DC generation and maturation, respectively.
Cloning and Functional Characterization of a System ASC-like Na+-dependent Neutral Amino Acid Transporter*

A cDNA was isolated from mouse testis which encodes a Na+-dependent neutral amino acid transporter. The encoded protein, designated ASCT2, showed amino acid sequence similarity to the mammalian glutamate transporters (40–44% identity), Na+-dependent neutral amino acid transporter ASCT1 (57% identity; Arriza, J. L., Kavanaugh, M. P., Fairman, W. A., Wu, Y.-N., Murdoch, G. H., North, R. A., and Amara, S. G. (1993) J. Biol. Chem. 268, 15329-15332; Shafqat, S. , Tamarappoo, B. K. , Kilberg, M. S. , Puranam, R. S. , McNamara, J. O. , Guadano-Ferraz, A. , and Fremeau, T. , Jr. (1993) J. Biol. Chem. 268, 15351-15355) and a mouse adipocyte differentiation-associated gene product AAAT (94% identity; Liao, K., and Lane, D. (1995) Biochem. Biophys. Res. Commun. 208, 1008-1015). When expressed in Xenopus laevis oocytes, ASCT2 exhibited Na+-dependent uptakes of neutral amino acids such as L-alanine, L-serine, L-threonine, L-cysteine, and L-glutamine at high affinity with Km values around 20 μM. L-Methionine, L-leucine, L-glycine, and L-valine were also transported by ASCT2 but with lower affinity. The substrate selectivity of ASCT2 was typical of amino acid transport system ASC, which prefers neutral amino acids without bulky or branched side chains. ASCT2 also transported L-glutamate at low affinity (Km = 1.6 mM). L-Glutamate transport was enhanced by lowering extracellular pH, suggesting that L-glutamate was transported as protonated form. In contrast to electrogenic transport of glutamate transporters and the other ASC isoform ASCT1, ASCT2-mediated amino acid transport was electroneutral. Na+ dependence of L-alanine uptake fits to the Michaelis-Menten equation, suggesting a single Na+ cotransported with one amino acid, which was distinct from glutamate transporters coupled to two Na+. Northern blot hybridization revealed that ASCT2 was mainly expressed in kidney, large intestine, lung, skeletal muscle, testis, and adipose tissue. Functional characterization of ASCT2 provided fruitful information on the properties of substrate binding sites and the mechanisms of transport of Na+-dependent neutral and acidic amino acid transporter family, which would facilitate the structure-function analyses based on the comparison of the primary structures of ASCT2 and the other members of the family.
Simulation of electrical tree growth in solid dielectrics containing voids of arbitrary shape

In this paper the electrical tree growth in solid insulating materials containing voids of arbitrary shape is modelled using von Neumann's cellular automata (CA). The model is based upon the assumption that the electric stress at the end of a conducting tip quite often approaches the dielectric strength of the material and that progressive breakdown may occur by electrical tree formation. Because of tree advancement, the potential distribution within the insulating material changes with time, and it is calculated at each time step. An algorithm, based on this model, for the simulation of electrical tree growth in solid dielectrics containing voids of arbitrary shape has been developed. Simulation results show that voids constitute a danger for solid insulation, because they act as sources of secondary electrical trees. An interaction mechanism between voids within a dielectric is proposed and discussed.
Universally measurable subgroups of countable index

Abstract It is proved that any countable index, universally measurable subgroup of a Polish group is open. By consequence, any universally measurable homomorphism from a Polish group into the infinite symmetric group S∞ is continuous. It is also shown that a universally measurable homomorphism from a Polish group into a second countable, locally compact group is necessarily continuous.
On the Choice of Shear Correction Factor in Sandwich Structures

The first-order shear deformation theory (FSDT) is a relatively simple tool that has been found to yield accurate results in the non-local problems of sandwich structures, such as buckling and free vibration. However, a key factor in practical application of the theory is determination of the transverse shear correction factor (K), which appears as a coefficient in the expression for the transverse shear stress resultant. The physical basis for this factor is that it is supposed to compensate for the FSDT assumption that the shear strain is uniform through the depth of the cross section. In the present paper, the philosophies and results of K determination for homogeneous rectangular cross sections are first reviewed, followed by a review and discussion for the case of sandwich structures. The analysis presented in the paper results in the conclusion that K should be taken equal to unity, as a first approximation, for both two-skin as well as for multi-skin sandwich structures.
High prevalence of adynamic bone disease diagnosed by biochemical markers in a wide sample of the European CAPD population.

BACKGROUND Adynamic bone disease (ABD) has been described in the current dialysis population to have an unexpectedly high prevalence. Moreover, it is clearly more prevalent in CAPD patients, compared to haemodialysis patients. Recently we demonstrated that both a low (< or = 27 U/1) level of bone alkaline phosphatase (BAP) as determined by an optimized agarose gel electrophoretic technique and a low (< or = 150 pg/ml ) level of iPTH are good markers of ABD with sensitivities of 78.1% and 80.6% and specificities of 86.4% and 76.2% respectively. METHODS In this study (n = 212), the prevalence of ABD in the European CAPD population was evaluated by means of these biochemical markers. Clinical data on the patients included were recorded at the moment of blood sampling. In patients under CAPD treatment for longer than 9 months, we calculated an index of calcium exposure through PD fluid. RESULTS In this population with a low exposure to aluminium, the prevalence of ABD as indicated by either a low level of BAP or PTH was 43%. The following risk factors could be identified: advanced age, shorter time on renal replacement therapy, male gender, and high calcium content of PD fluid. The index of calcium exposure was significantly higher in the patients with low BAP and low iPTH levels compared to those with either BAP > or = 27 U/1 or iPTH > 150 pg/ml. The latter finding gives further support to the hypothesis that a high calcium load administered to renal failure patients may lead to 'oversuppressed' parathyroids in ABD. In a subgroup of patients with a high level of BAP associated with a low iPTH level a profile previously shown to be associated in the presence of aluminium overload, significantly higher serum aluminium levels were noted. suggesting that even in patients with low exposure to aluminium, this element still can affect bone metabolism. CONCLUSION A high prevalence of ABD--as diagnosed by biochemical markers--was observed in the European CAPD population. A number of risk factors could be put forward. The aetiology and pathogenesis of this type of renal osteodystrophy remain to be elucidated, but appear, however, to be multifactorial.
Preoperative 18F‐FDG PET/CT and high‐risk HPV in patients with oropharyngeal squamous cell carcinoma

To evaluate the association of 18F‐fluorodeoxyglucose‐positron emission tomography (18F‐FDG PET/CT) and high‐risk human papillomavirus (HPV) status and to establish the histologic correlates in oropharyngeal cancer (OPSCC).
Combining ocFLIM and FIDSAM reveals fast and dynamic physiological responses at subcellular resolution in living plant cells

For a deeper understanding of molecular mechanisms within cells and for the realization of predictive biology for intracellular processes at subcellular level, quantitative biology is required. Therefore, novel optical and spectroscopic technologies with quantitative and dynamic output are needed in cell biology. Here, we present a combined approach of novel one‐chromophore fluorescence lifetime imaging microscopy to probe the local environment of fluorescent fusion proteins and fluorescence intensity decay shape analysis microscopy to suppress interfering autofluorescence. By applying these techniques, we are able to analyse the subcellular localization and partitioning of a green fluorescence protein fusion of the salt stress‐induced protein low temperature induced (LTI)6b in great detail with high spatial and temporal resolution in living cells of Arabidopsis plants.