Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for initial calcite-aragonite composition of Lower Algal Chert Member ooids and stromatolites, Paleoproterozoic Gunflint Formation, Ontario, Canada

The chert members of the Paleoproterozoic Gunflint Formation, Ontario, Canada, are commonly regarded as examples of primary silica chemical sediments. This interpretation is founded upon the ubiquitous nature of silica, high fidelity of preservation of microfossils found within, and lack of observed primary carbonate. Previous arguments for silica replacement of carbonate are based on indirect evidence and are largely dismissed. Thus, Gunflint microfossils are regarded as having lived in a silica-rich environment, which makes them unusual compared to most other pre- Phanerozoic microfossils that are known from silicified carbonates. We present evidence that carbonate was a primary mineral species of the Lower Algal Chert Member (where most of the microbiota are found). Most compelling are iron-stained, low-Mg calcite ooids containing (1) well-preserved growth laminae, (2) textures indicating a disrupted tan - gential fabric of growth laminae, and (3) quartz crosscutting the growth laminae. These indicate the initial mineral was a carbonate, possibly aragonite. Less-compelling evidence is found in stromatolite columns. Specularite crystals in low- Mg calcite display crosscutting relationships with calcite and quartz indicating that calcite was primary, specularite sec- ondary, and quartz tertiary. The crosscutting relations show that silicification took place in at least two stages. One of the silicification events took place very early in diagenesis. Thus the Gunflint microbiota may not have existed in a radically different environment (silica precipitating) than those of most other known Proterozoic microbiota. High fidel- ity of preservation of microfossils does not always indicate that the mineral entombing them was the primary mineral precipitated from aqueous solution.
Mutation of CRE1 in Fusarium oxysporum reverts the pathogenicity defects of the FRP1 deletion mutant

The F‐box protein Frp1 is required for pathogenicity of Fusarium oxysporum f. sp. lycopersici towards tomato. The Δfrp1 mutant is deficient in expression of genes for cell wall‐degrading enzymes (CWDEs) and ICL1, encoding a key enzyme for the assimilation of C2 carbon sources. An explanation for the inability of the Δfrp1 mutant to express these genes may be found in constitutive carbon catabolite repression. Cre1 is the transcriptional repressor in filamentous fungi known to repress several CWDE genes and other genes required for assimilation of non‐sugar carbon sources. Here, we demonstrate that Frp1 and Cre1 both control the repression/derepression state of such genes. The replacement of CRE1 with GST::CRE1 resulted in a derepressed phenotype in wild‐type background, suggesting that this replacement affects Cre1 function. Strikingly, in the Δfrp1 mutant the replacement of CRE1 with GST::CRE1 restored pathogenicity, growth on ethanol and expression of ICL1 and CWDE genes. A GFP–Cre1 fusion protein is not degraded nor exported out of the nucleus during growth on ethanol, a derepressing carbon source, suggesting that Cre1 is not likely a target of Frp1 for degradation by the proteasome. We conclude that both proteins function together to regulate transcription of carbon source utilization genes.
Adenosine monophosphate–activated protein kinase modulates the activated phenotype of hepatic stellate cells

Adiponectin limits the development of liver fibrosis and activates adenosine monophosphate–activated protein kinase (AMPK). AMPK is a sensor of the cellular energy status, but its possible modulation of the fibrogenic properties of hepatic stellate cells (HSCs) has not been established. In this study, we investigated the role of AMPK activation in the biology of activated human HSCs. A time‐dependent activation of AMPK was observed in response to a number of stimuli, including globular adiponectin, 5‐aminoimidazole‐4‐carboxamide‐1‐beta‐4‐ribofuranoside (AICAR), or metformin. All these compounds significantly inhibited platelet‐derived growth factor (PDGF)‐stimulated proliferation and migration of human HSCs and reduced the secretion of monocyte chemoattractant protein‐1. In addition, AICAR limited the secretion of type I procollagen. Knockdown of AMPK by gene silencing increased the mitogenic effects of PDGF, confirming the negative modulation exerted by this pathway on HSCs. AMPK activation did not reduce PDGF‐dependent activation of extracellular signal‐regulated kinase (ERK) or Akt at early time points, whereas a marked inhibition was observed 24 hours after addition of PDGF, reflecting a block in cell cycle progression. In contrast, AICAR blocked short‐term phosphorylation of ribosomal S6 kinase (p70S6K) and 4E binding protein‐1 (4EBP1), 2 downstream effectors of the mammalian target of rapamycin (mTOR) pathway, by PDGF. The ability of interleukin‐a (IL‐1) to activate nuclear factor kappa B (NF‐κB) was also reduced by AICAR. Conclusion: Activation of AMPK negatively modulates the activated phenotype of HSCs. (HEPATOLOGY 2007.)
Synchronising radiocarbon dating and the Egyptian historical chronology by improved sample selection

Egypt has some of the oldest written records and extended lists of named rulers. But radiocarbon dates have only fulfilled expectations 66 per cent of the time. So why haven&t the two types of dating made a better match? The authors provide a dozen excellent reasons, which will sound the alarm among researchers well beyond Dynastic Egypt.
Vancomycin-resistant enterococci in rooks (Corvus frugilegus) wintering throughout Europe.

This study's aims were to assess the prevalence of, and to characterize, vancomycin-resistant enterococci (VRE) from rooks (Corvus frugilegus) wintering in Europe during 2010/2011. Faeces samples were cultivated selectively for VRE and characterized. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) were used to examine epidemiologic relationships of vanA-containing VRE. The vanA-carrying VRE were tested in vitro for mobility of vancomycin resistance traits. VRE were found in 62 (6%) of 1073 rook samples. Enterococcal species diversity comprised Enterococcus gallinarum (48 isolates), followed by E. faecium (9) and E. faecalis (5). Eight VRE harboured the vanA and ermB genes. Seven vanA-carrying VRE originated from the Czech Republic and one from Germany. All vanA-carrying VRE were identified as E. faecium. Based on MLST analysis, six vanA-positive isolates were grouped as ST92 type, one isolate belonged to ST121, and the remaining one was described as a novel type ST671. Seven out of eight isolates were able to transfer the vancomycin resistance trait via filter mating with a transfer rate of 8.95 ± 3.25 × 10(-7) transconjugants per donor. In conclusion, wintering rooks in some European countries may disseminate clinically important enterococci and pose a risk for environmental contamination.
Inhibition of proliferation, migration and invasion of human non-small cell lung cancer cell line A549 by phlomisoside F from Phlomis younghusbandii Mukerjee

Purpose : To determine the effect of phlomisoside F (PMF) on the proliferation, migration and invasion of human non-small cell lung cancer cell line A549 and explore the possible mechanisms. Methods : The anti-proliferative effect of PMF on A549 cells was determined by CCK-8. Subsequently, migration and invasion were evaluated by Transwell and Transwell with matrigel assays, respectively. Furthermore, cell cycle and apoptosis were assessed by flow cytometry, while the mechanisms of action were determined by Western blotting. Results : PMF exhibited significant anti-proliferative effect on A549 cells in concentration-dependent and time-dependent manners, with half maximal inhibitory concentration (IC50) of 54.51 μM. Treatment with PMF (10, 20 and 40 μM) for 48 h resulted in significantly decreased migration and invasion in A549 cells. In addition, PMF at concentrations of 25, 50 and 75 μM induced cell cycle arrest in G0/G1phase and enhanced cell apoptosis in A549 cells. Furthermore, caspase-3, caspase-9 and Bax protein expressions were up-regulated while Bacl-2 and COX-2 protein expressions were significantly downregulated at 10, 20 and 40 μM concentrations of PMF. Conclusion : PMF suppresses A549 cell growth, migration and invasion. The mechanism may be related to the induction of mitochondria-mediated apoptosis pathway via regulation of caspase-3, caspase-9, Bcl-2 and Bax expressions, and inhibition of PGE2 synthesis by reducing COX-2 expression. Keywords : Phlomisoside F, Lung cancer, Cell mobility, Apoptosis, PGE2, COX-2 expression, Caspase, Cell cycle arrest
RNA transcription and splicing at early and intermediate times after adenovirus-2 infection.

Transcription of human adenovirus-2 (Ad2) DNA1 has generally been recognized to have an early phase (from 1 to 8 hours after infection of permissive human cells) and a late phase, essentially coincident with DNA replication (from 8 hours until cell death at 48–72 hours after infection). Solution-hybridization studies have shown that about one fourth of the genome is expressed as cytoplasmic RNA at early times after infection and that these RNAs come from four widely separated regions, two on each DNA strand (Green et al. 1971; Sharp et al. 1975; Pettersson et al. 1976). Electron microscopic studies of R loops formed with early Ad2 RNA in double-stranded Ad2 DNA (Chow et al. 1977b; Westphal and Lai 1977) as well as nuclease-S1 mapping of RNA-single-stranded-DNA heteroduplexes (Berk and Sharp 1977b) produced evidence that early region 1 is subdivided into two segments, 1A and 1B.
Occurrence and Predictors of Developmental Impairments in 3-Year-Old Children with Congenital Heart Defects

Objective: To examine the occurrence of developmental impairments in 3-year-old children with varying severity of congenital heart defects (CHD) and to identify predictors associated with developmental impairment in children with severe CHD. Methods: Prospective data collected at birth, 6, 18, and 36 months from the Norwegian Mother and Child Cohort Study (MoBa), conducted by the Norwegian Institute of Public Health, were linked with a nationwide medical CHD registry, and 175 three year olds with CHD in a cohort of 44,044 children were identified. Children with mild/moderate (n = 115) and severe (n = 60) CHD were compared with children without CHD (43,929) on motor, communication, and social impairments as reported by mothers in Norwegian Mother and Child Cohort Study questionnaires. Predictors of developmental impairment were analyzed for the group with severe CHD. Results: Children with severe CHD had >3 times higher odds of communication and gross motor impairments compared with controls, and had 2 times higher odds of any developmental impairment compared with controls. Children with mild and moderate CHD had >2 times higher odds of gross motor impairment but did not otherwise differ from controls. Predictors of impairment identified were previous developmental impairments and smaller head circumference at birth. Conclusion: Children with severe CHD have increased odds of developmental impairments at age 3 years. Early developmental impairments are associated with later developmental impairments, suggesting lasting impairments and not merely temporary delay. Patient-specific conditions at birth should be considered and motor and communication support provided to potentially improve outcomes in children with CHD.
Deduced amino-acid sequence of a calcium-free alpha-amylase from a strain of Bacillus: implications from molecular modeling of high oxidation stability and chelator resistance of the enzyme.

Alkaline alpha-amylase (AmyK38) from the alkaliphilic Bacillus sp. strain KSM-K38 is a unique enzyme in that it is highly chelator-resistant and oxidatively stable [Hagihara, H. , Igarashi, K. , Hayashi, Y. , Endo, K. , Ikawa-Kitayama, K. , Ozaki, K. , Kawai, S. & Ito, S. (2001) Appl. Environ. Microbiol. 67, 1744-1750]. This enzyme was found to contain no Ca and require Na (or monovalent cations) for manifestation of activity. The nucleotide sequence of the gene for the novel enzyme was determined, and it harbored an ORF of 1503 bp encoding the enzyme of 501 amino acids, including a 21-amino-acid signal peptide. The deduced amino-acid sequence of the mature enzyme (55 097 Da) showed moderate homology to those of alpha-amylases from Bacillus licheniformis, Bacillus stearothermophilus and Bacillus amyloliquefaciens, with approximately 63% identity. A methionine residue, which is conserved and susceptible to chemical oxidation, was replaced with leucine in AmyK38. Moreover, many conserved residues that are crucial ligands for Ca were replaced with other amino acids, thereby leading to loss of the Ca coordination geometries. By building a molecular model, we showed the calcium-independent, oxidatively stable active-site topology and structural integrity of AmyK38.
Pokémon GO May Increase Physical Activity and Decrease Sedentary Behaviors.

The authors argue that Pokemon Go mobile application game may help video game users increase their physical activity levels and decrease sedentary behaviors, and it mentions a Pokemon Go-related pilot study conducted by a University of Hawaii institutional review board. A revised Godin Leisure-Time Exercise Questionnaire is addressed, along with data which supports the idea that Internet games can help promote health behaviors. Television viewing and strenuous physical activity are assessed.
Patterns of gastrointestinal parasitic infections in the bushbuck Tragelaphus scriptus from the Queen Elizabeth National Park, Uganda

Abstract Seasonal, host sex and age-related variations in helminth egg and coccidian oocyst counts were investigated in a naturally infected wild bushbuck (Tragelaphus scriptus) population in Queen Elizabeth National Park, western Uganda from April 2000 to February 2002. The prevalence and mean intensity quantified as the number of eggs and oocysts per gram of faeces were taken as a measure of parasite burdens. Host sex and age-related differences in prevalence values were not found but the overall prevalence of Eimeria sp. was significantly higher during the rainy season, and peak counts were recorded either during or soon after a peak rainfall. A similar trend was observed for Moniezia spp. , although the results were marginally not significant. There were also no significant differences in mean intensity values, relative to host sex, age or season.
Early Gut Barrier Dysfunction in Patients with Severe Acute Pancreatitis: Attenuated by Continuous Blood Purification Treatment

Objectives The aim of this study was to investigate the effect of continuous blood purification (CBP) on early gut mucosal dysfunction in patients with severe acute pancreatitis (SAP). Methods Patients with SAP were randomized to receive 24 hours of continuous veno-venous hemofiltration (CVVH; n=33) or no CVVH (n=30). Blood samples were taken from the patients at 0, 6, 12, and 24 hours during CVVH therapy. Serum diamine oxidase (DAO) and endotoxin, epithelial permeability, transepithelial electrical resistance (TER) and F-actin rearrangement of the epithelial monolayer were used as the markers for the assessment of gut barrier function and the effect of CBP therapy in patients with SAP. Results Patients with SAP had increased levels of serum DAO, endotoxin, and epithelial permeability when compared with normal controls, and the increase was more pronounced in patients with organ dysfunction (p<0.01). F-actin rearrangement, loose cell-cell junction, and iNOS mRNA upregulation were found in all patients. After CBP treatment, Acute Physiology and Chronic Health Evaluation II score and SOFA score improved significantly; levels of serum DAO, endotoxin, and epithelial permeability decreased (p<0.05). CBP also significantly attenuated reorganization of actin and downregulated iNOS mRNA expression and NO production (p<0.05). Conclusions CBP can not only improve the general conditions but also effectively improve gut barrier dysfunction. The beneficial effect of CBP on gut barrier dysfunction is associated with the improvement of cytoskeletal instability, by downregulating iNOS through the removal of excess proinflammatory factors.
Barking, Dominance, and Territoriality in Male Sea Lions

Experiments in which male sea lions (Zalophus californianus) were removed and reintroduced into a social group demonstrate that barking by larger males restricts movement and barking by other smaller males. Barking and aggression were primarily directed toward animals of most nearly equal size. Two 6-year-olds seeking to establish and maintain territorial status used aggressive tactics similar to those observed in breeding males in the field.
Increased expression of integrin-linked kinase is correlated with melanoma progression and poor patient survival.

PURPOSE Integrin-linked kinase (ILK), a key component of the extracellular matrix adhesion, has been studied extensively in recent years. Overexpression of ILK in epithelial cells results in anchorage-independent cell growth with increased cell cycle progression. Furthermore, increased ILK expression is correlated with progression of several human tumor types, including breast, prostate, and colon carcinomas. However, the role of ILK overexpression in human melanoma pathogenesis is not known. To investigate whether ILK plays a role in melanoma progression, we measured ILK expression in primary melanoma biopsies at various stages of invasion and evaluated the prognostic value of ILK expression in human melanoma. EXPERIMENTAL DESIGN We used tissue microarray and immunohistochemistry to determine ILK expression in 67 primary melanomas and analyzed the correlation between ILK expression and melanoma progression and 5-year patient survival. RESULTS We show that strong ILK expression is significantly associated with melanoma thickness. Strong ILK expression was observed in 0, 22, 33, and 63% in melanoma biopsies </=0.75, 0.76-1.50, 1.51-3.0, and >3.0 mm in thickness, respectively. Furthermore, strong ILK expression was detected in 83% of the tumors with lymph node invasion compared with only 18% for tumors without lymph node invasion (P < 0.01). Strikingly, our data revealed that strong ILK expression is inversely correlated with 5-year patient survival (P < 0.05). CONCLUSION ILK expression increases dramatically with melanoma invasion and progression and is inversely correlated with patient survival.
Extrema of mass, stationarity, and staticity, and solutions to the Einstein-Yang-Mills equations.

A simple formula is derived for the variation of mass and other asymptotic conserved quantities in Einstein-Yang-Mills theory. For asymptotically flat initial data with a single asymptotic region and no interior boundary, it follows directly from our mass-variation formula that initial data for stationary solutions are extrema of mass at fixed electric charge. When generalized to include an interior boundary, this formula provides a simple derivation of a generalized form of the first law of black-hole mechanics. We also argue, but do not rigorously prove, that in the case of a single asymptotic region with no interior boundary stationarity is necessary for an extremum of mass at fixed charge; when an interior boundary is present, we argue that a necessary condition for an extremum of mass at fixed angular momentum, electric charge, and boundary area is that the solution be a stationary black hole, with the boundary serving as the bifurcation surface of the horizon. Then, by a completely different argument, we prove that if a foliation by maximal slices (i.e., slices with a vanishing trace of extrinsic curvature) exists, a necessary condition for an extremum of mass when no interior boundary is present is that the solution be static. A generalization of the argument to the case in which an interior boundary is present proves that a necessary condition for a solution of the Einstein-Yang-Mills equation to be an extremum of mass at fixed area of the boundary surface is that the solution be static.
A comparison of methods for meta‐analysis of a small number of studies with binary outcomes

Meta‐analyses often include only a small number of studies (≤5). Estimating between‐study heterogeneity is difficult in this situation. An inaccurate estimation of heterogeneity can result in biased effect estimates and too narrow confidence intervals. The beta‐binominal model has shown good statistical properties for meta‐analysis of sparse data. We compare the beta‐binominal model with different inverse variance random (eg, DerSimonian‐Laird, modified Hartung‐Knapp, and Paule‐Mandel) and fixed effects methods (Mantel‐Haenszel and Peto) in a simulation study. The underlying true parameters were obtained from empirical data of actually performed meta‐analyses to best mirror real‐life situations. We show that valid methods for meta‐analysis of a small number of studies are available. In fixed effects situations, the Mantel‐Haenszel and Peto methods performed best. In random effects situations, the beta‐binominal model performed best for meta‐analysis of few studies considering the balance between coverage probability and power. We recommended the beta‐binominal model for practical application. If very strong evidence is needed, using the Paule‐Mandel heterogeneity variance estimator combined with modified Hartung‐Knapp confidence intervals might be useful to confirm the results. Notable most inverse variance random effects models showed unsatisfactory statistical properties also if more studies (10‐50) were included in the meta‐analysis.
CASP2: Report on ab initio predictions

Submissions in the ab initio category included predictions of secondary structure, three‐dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 ≥ 68 (Q3 = % of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three‐dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK‐lysin (target 42), a 78‐residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue‐residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Benner for segment contacts. Proteins, Suppl. 1:151–166, 1997. © 1998 Wiley‐Liss, Inc.
Prediction of power production from a single axis photovoltaic system by Artificial Neural Networks

The power production from a photovoltaic module depends on environmental factors such as radiation, air temperature, wind speed and direction and relative humidity. This study aimed to predict some atmospheric indicators which may affect upon the power production from a single axis (East-West) tracking PV module by using Artificial Neural Network architecture. The novelty side of this research is to use a single axis tracking PV system as first in the literature to predict effective factors of the power production. Besides, unlike previous study, many atmospheric indicators were used to estimate the power production. In this study, the performance of Artificial Neural Network is measured with Mean Square Error, Root Mean Square Error, Mean Absolute Error, Relative Absolute Error, Root Relative Square Error and correlation coefficient. In the established Artificial Neural Network model for sunny and cloudy days, the correlation coefficients are computed as 0.995 and 0.990, respectively. The models of the study will project for future estimation of power production from a single axis photovoltaic module.