Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolomic Analysis of the Skeletal Muscle of Mice Overexpressing PGC-1α

Peroxisome proliferator-activated receptor (PPAR) γ coactivator 1α (PGC-1α) is a coactivator of various nuclear receptors and other transcription factors whose expression increases in the skeletal muscle during exercise. We have previously made transgenic mice overexpressing PGC-1α in the skeletal muscle (PGC-1α-Tg mice). PGC-1α upregulates the expression of genes associated with red fibers, mitochondrial function, fatty acid oxidation, and branched chain amino acid (BCAA) degradation. However, global analyses of the actual metabolic products have not been investigated. In this study, we conducted metabolomic analysis of the skeletal muscle in PGC-1α-Tg mice by capillary electrophoresis with electrospray ionization time-of-flight mass spectrometry. Principal component analysis and hierarchical cluster analysis showed clearly distinguishable changes in the metabolites between PGC-1α-Tg and wild-type control mice. Changes were observed in metabolite levels of various metabolic pathways such as the TCA cycle, pentose phosphate pathway, nucleotide synthesis, purine nucleotide cycle, and amino acid metabolism, including BCAA and β-alanine. Namely, metabolic products of the TCA cycle increased in PGC-1α-Tg mice, with increased levels of citrate (2.3-fold), succinate (2.2-fold), fumarate (2.8-fold), and malate (2.3-fold) observed. Metabolic products associated with the pentose phosphate pathway and nucleotide biosynthesis also increased in PGC-1α-Tg mice. Meanwhile, BCAA levels decreased (Val, 0.7-fold; Leu, 0.8-fold; and Ile, 0.7-fold), and Glu (3.1-fold) and Asp (2.2-fold) levels increased. Levels of β-alanine and related metabolites were markedly decreased in PGC-1α-Tg mice. Coordinated regulation of the TCA cycle and amino acid metabolism, including BCAA, suggests that PGC-1α plays important roles in energy metabolism. Moreover, our metabolomics data showing the activation of the purine nucleotide pathway, malate–aspartate shuttle, as well as creatine metabolism, which are known to be active during exercise, further suggests that PGC-1α regulates metabolism in exercise. Thus, we demonstrated the roles of PGC-1α in the skeletal muscle at the metabolite level.
Surface formation of CO2 ice at low temperatures

The surface formation of CO 2 at low temperatures through the reaction CO + OH and direct dissociation of the resulting HO-CO complex is shown by hydrogenation of a CO:O 2 ice mixture. Such a binary ice is not fully representative for an interstellar ice, but the hydrogenation of O 2 ice produces OH radicals, which allows the investigation of the interstellar relevant CO + OH solid state reaction under fully controlled laboratory conditions. Similar recent astrophysical ice studies have focused on the investigation of isolated surface reaction schemes, starting from the hydrogenation of pure ices, like solid CO or O 2 . For such ices, no CO 2 formation is observed upon H-atom exposure. The hydrogenation of binary ice mixtures presented here allows to investigate for the first time the influence of the presence of other species in the ice on the pure ice reaction shemes. Mixtures of CO:O 2 are deposited on a substrate in an ultra high vacuum setup at low temperatures (15 and 20 K) and subsequently hydrogenated. The ice is monitored by means of Reflection Absorption InfraRed Spectroscopy (RAIRS). Results show that solid CO 2 is formed in all studied CO:O 2 mixtures under our laboratory conditions. Within the experimental uncertainties no dependency on ice temperature or composition is observed. The laboratory results show a correlation between the formation of CO 2 and H 2 O, which is consistent with the astronomical observation of solid CO 2 in water-rich environments. The results also show that the contemporary presence of CO and O 2 molecules in the ice influences the final product yields of the separate CO + H (H 2 CO, CH 3 OH) and O 2 + H (H 2 O 2 and H 2 O) channels, even though the formation rates are not significantly affected.
Environmental distribution of Cryptococcus neoformans and Cryptococcus gattii around the Mediterranean basin

In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-15. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected, and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus, and two Olea trees. C. neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy, and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.
Permanent Oviduct Posteriorization after Neonatal Exposure to the Phytoestrogen Genistein

Background: Preimplantation embryo loss during oviduct transit has been observed in adult mice after a 5-day neonatal exposure to the phytoestrogen genistein (Gen; 50 mg/kg/day). Objective: We investigated the mechanisms underlying the contribution of the oviduct to infertility. Methods: Female mice were treated on postnatal days 1–5 with corn oil or Gen (50 mg/kg/day). We compared morphology, gene expression, and protein expression in different regions of the reproductive tracts of Gen-treated mice with those of control littermates at several time points. Results: Neonatal Gen treatment resulted in substantial changes in expression of genes that modulate neonatal oviduct morphogenesis, including Hoxa (homeobox A cluster), Wnt (wingless-related MMTV integration site), and hedgehog signaling genes. An estrogen receptor antagonist blocked these effects, indicating that they were induced by the estrogenic activity of Gen. Oviducts of adults treated neonatally with Gen had abnormal morphology and were stably “posteriorized,” as indicated by altered Hoxa gene patterning during the time of treatment and dramatic, permanent up-regulation of homeobox genes (e.g., Pitx1, Six1) normally expressed only in the cervix and vagina. Conclusions: Neonatal exposure to estrogenic environmental chemicals permanently disrupts oviduct morphogenesis and adult gene expression patterns, and these changes likely contribute to the infertility phenotype.
The Impact of Strong El Niño and La Niña Events on the North Atlantic

The impact of strong La Niña events on January–February North Atlantic mean sea level pressure is unknown, as these events have never been observed. Using large ensembles from the Met Office decadal prediction system, examples of strong La Niña events are simulated and the Atlantic response to these is found to be a positive North Atlantic Oscillation. This is very different to the wavelike response observed and simulated for strong El Niño events. The reason for this difference is traced to the fact that the December‐January‐February mean tropospheric teleconnection of El Niño–Southern Oscillation to the North Atlantic dominates for strong El Niño events, while the stratospheric teleconnection dominates for strong La Niña events. The strength of the tropospheric pathway grows linearly and symmetrically with El Niño–Southern Oscillation. The stratospheric pathway is the source of the asymmetry between January and February surface responses to strong El Niño and strong La Niña events.
Ocurrence of Staphylococcus aureus and multiplex pcr detection of classic enterotoxin genes in cheese and meat products

Multiplex PCR was used to investigate the presence of enterotoxins genes (sea, seb, sec, sed and see) and femA gene (specific for Staphylococcus aureus) in coagulase-positive staphylococci (CPS) isolated from cheese and meat products. From 102 CPS isolates, 91 were positive for femA, 10 for sea, 12 for sed and four for see.
The Impact of Information Security Awareness Training on Information Security Behaviour: The Case for Further Research

Information Security awareness initiatives are seen as critical to any information security programme. But, how do we determine the effectiveness of these awareness initiatives? We could get our employees to write a test afterwards to determine how well they understand the policies, but this does not show how it affects the employee’s on the job behaviour. Does awareness training have a direct influence on the security behaviour of individuals, and what is the direct benefit of awareness training? This paper represents a study in progress that aims to answer the question: to what extent does information security awareness training influence information security behaviour? Research carried out on information security has traditionally been slanted towards technical aspects of security, typically rooted in computer science and mathematics. Security was traditionally seen as a service to be provided and not something that was influenced by users. However, it was soon recognised that focusing on technical issues alone is inadequate. Technologies meant to provide security ultimately depend on the effective implementation and operation of these technologies by people. Thus awareness of policies is needed by all individuals in an organisation to ensure that policies are well understood and not misinterpreted. Some researchers have maintained that educating users is futile mainly because it is believed that it is difficult to teach users complex security issues and secondly, because security is seen as secondary by the user they will not pay enough attention to it. This paper reflects research in progress and discusses some of the problems with existing information security awareness research and proposes a model to be tested for examining the impact of information security awareness training on information security behaviour.
Mechanisms of (local) anaesthetics on voltage-gated sodium and other ion channels.

Local anaesthetics have been used clinically for well over a century, but the molecular mechanisms by which they alter specific functions of the peripheral nerve system remained unclear for a long time. Investigations during the last few decades presented evidence implicating the sodium (Na + ) channel protein as a target for specific, clinically important, local anaesthetic effects on mammalian neurones. In this review I will present the state of knowledge of the action of local anaesthetics at the molecular level, with an emphasis on Na + channels. After a brief survey of the history of concepts of local anaesthetic actions, the structure of the Na + channel will be described with regard to its function in order to understand the recent findings that have followed the description of the amino acid sequence of the Na + channel protein. 46 At clinically relevant concentrations local anaesthetics can also affect potassium (K + ) and calcium (Ca 2+ ) channels, which might help explain some of their side-effects. General anaesthetics also interact with these targets (ion channels), but differences in selectivity compared with local anaesthetics have been reported. Current findings indicate that local anaesthetics also act on intracellular mechanisms, which raises the question of whether these might explain toxicity and other side-effects.
Sparse Linear Prediction and Its Applications to Speech Processing

The aim of this paper is to provide an overview of Sparse Linear Prediction, a set of speech processing tools created by introducing sparsity constraints into the linear prediction framework. These tools have shown to be effective in several issues related to modeling and coding of speech signals. For speech analysis, we provide predictors that are accurate in modeling the speech production process and overcome problems related to traditional linear prediction. In particular, the predictors obtained offer a more effective decoupling of the vocal tract transfer function and its underlying excitation, making it a very efficient method for the analysis of voiced speech. For speech coding, we provide predictors that shape the residual according to the characteristics of the sparse encoding techniques resulting in more straightforward coding strategies. Furthermore, encouraged by the promising application of compressed sensing in signal compression, we investigate its formulation and application to sparse linear predictive coding. The proposed estimators are all solutions to convex optimization problems, which can be solved efficiently and reliably using, e.g., interior-point methods. Extensive experimental results are provided to support the effectiveness of the proposed methods, showing the improvements over traditional linear prediction in both speech analysis and coding.
Climate not to blame for African civil wars

Vocal actors within policy and practice contend that environmental variability and shocks, such as drought and prolonged heat waves, drive civil wars in Africa. Recently, a widely publicized scientific article appears to substantiate this claim. This paper investigates the empirical foundation for the claimed relationship in detail. Using a host of different model specifications and alternative measures of drought, heat, and civil war, the paper concludes that climate variability is a poor predictor of armed conflict. Instead, African civil wars can be explained by generic structural and contextual conditions: prevalent ethno-political exclusion, poor national economy, and the collapse of the Cold War system.
High-accuracy mapping of protein binding stability on nucleosomal DNA using a single-molecule method.

Dear Editor, The conformation of nucleosomal DNA is significantly different from that of B-form double stranded DNA (dsDNA) (Richmond and Davey, 2003). In nucleosomal DNA, specific DNA sequences are less flexible and less accessible than in free dsDNA, which might be due to the tight association of histone cores. The allosteric effect via DNA has been documented recently (Kim et al., 2013), suggesting that DNA is not merely a solid rod providing recognition sequences. Previous studies of nucleosom-al DNA – protein interactions only demonstrated the key mechanism involved—histone How conformation-al changes in nucleosomal DNA, compared with free dsDNA, affect nucleosomal DNA– protein interactions remains unknown. The glucocorticoid receptor (GR)-binding sequence GREs3 (5 ′-AGAACATCATGTTCT-3 ′) (Luisi et al., 1991) was inserted into a specific histone core-binding sequence W601 (Lowary and Widom, 1998) at the position from 2 16 to 4 bp around central dyad of the nucleosome (Supplementary Figure S1). Each nucleosomal construct was tethered onto a functional coverslip of a flow-cell using a biotin-streptavidin connector (Figure 1A). Using a sensitive single-molecule technique (Kim et al., 2013), we measured the stochastic residence time of Cy3B-labeled GR DNA-binding domain (GRDBD) on each nucleosomal GREs3. The average residence time (ART, t) for each construct was calculated by fitting the stochastic residence time to a single-exponential decay and extracting the decay constant (Figure 1B), which reflects the stability of GRDBD binding to each nu-cleosomal GREs3 (see Supplementary Figure S2 and Supplementary Methods for details). The ARTs of GRDBD binding to constructs without histone core, as control (labeled as DG instead of NG in Figure 1B), are very similar, suggesting inconspicuous influence of the flanking sequence of GREs3. Interestingly, the strongest binding (longest ART) occurred within the nucleo-somal DNA– GRDBD complex (Figure 1B, NG-12) rather than the free DNA– GRDBD complex, demonstrating that the binding stability increased 1.5-fold on nucleo-some. The main trend of the ART of all different rotationally positioned nucleosomal GREs3 was found modulated by the orientation (Red trendline in Figure 1C), agreed with previous ensemble data (Li and Wrange, 1993). Yet there are a few positions (NG-11, NG-10, and NG0) that could not be fitted on the trendline and showed a sudden reduction by 3.7-fold (Figure 1C). Not coincidently, these outliers were all positioned on the outward-facing segment of the nucleosome and were separated by 10– 11 bps, which is identical with the DNA helical pitch on nucleosome (Richmond and Davey, 2003). …
Invasive treatment in complicated monochorionic twin pregnancies: indications and outcome of 120 consecutively treated pregnancies

Objective. Monochorionic twin pregnancies are associated with increased risk of severe complications. Umbilical cord occlusion (UCO) and fetoscopic selective laser coagulation (FSLC) are used as invasive treatment. The study aim was to document treatment indications and pregnancy outcome where UCO and FSLC were used for treating fetal discrepancies and twin‐to‐twin transfusion syndrome (TTTS). Design. Cohort study of all consecutively treated monochorionic twin pregnancies 2004–2010. Setting. Tertiary care center. Population. One hundred and twenty pregnancies treated by FSLC (55) or UCO (65). Umbilical cord occlusion was undertaken in 49 TTTS cases, in four cases with fetal abnormality and TTTS and in 12 cases because of fetal anomaly only. Main outcome measures. Overall survival per fetus, survival per pregnancy of at least one fetus and further survival according to the Quintero stages. Infant survival until at least one week after birth. Results. Of the pregnancies studied, 84% had TTTS, 13% had a fetal malformation and 3% had both. Of TTTS cases, 69% were Quintero stage 3 and 4. In the UCO group with TTTS, 87% were in stage 3 and 4. Survival in the UCO group was 82%. In the laser group, the survival of at least one fetus was 85%. Overall survival per fetus was 60%. Conclusions. By far the most common indication for invasive treatment was TTTS in Quintero stage 3. Outcome by means of survival after FSLC and UCO were similar to what has been reported elsewhere. Cord occlusion was an acceptable treatment alternative to fetoscopic selective laser coagulation in severe TTTS cases.
Influência do Rompimento da Barragem do Valo Grande (Iguape, SP) nas Associações de Foraminíferos e Tecamebas.

This paper deals with the probable consequences of the increase of water flow on the hydrographic and sedimentological parameters of the Cananeia-Iguape estuary and their relationship with the foraminifera and thecamoebians assemblages found before and after the Valo Grande dam's disruption. The sedimentological and biological parameters were obtained from each of the sixty samples of the collected bottom sediments. Before the dam’s disruption, the distribution of foraminifera and thecamoebians was apparently influenced by the substrate properties, such as grain size sorting and organic carbon content. After the dam's disruption, the bottom temperature was probably the responsible for the distribution of foraminifera and thecamoebians and for the total Textulariina and Ammonia tepida and Arenoparrella mexicana distribution patterns. Besides. very fine sand and bottom water salinity were probably the most influential factors in the distribution of Difflugia oblonga. Centropyxis aculeate and Centropyxis constricta.
Beaver (Castor fiber) Activity in an Archaeological Context: A Mid-Holocene Beaver Burrow Feature and a Late-Holocene Ecofact at the Late Palaeolithic Grabow Site, Northern Germany*

ABSTRACT Bioturbation and intrusive ecofacts are major concerns for the analysis of archaeological sites in wetland environments. Post-sedimentary influence of beavers (Castor fiber) is described for a well dated Late Palaeolithic archaeological record situated in a floodplain in Northern Germany. An extensive burrow system was documented and analysed according to its spatial dimensions and sedimentological properties; it was interpreted to be the result of beaver activity. Palynological analyses proved a Mid-Holocene origin of the infill material and helped in understanding the history of site formation. In addition, a pointed piece of wood was examined and identified as ecofact, which had been gnawed by a small rodent, possibly Arvicola amphibius (water vole). Our study thus illustrates the potential complexity of post-sedimentary site-alteration, describes the sub-surface morphology of a burrow system in a wetland context and documents risks for erroneous archaeological interpretation.
The design of a high speed ASIC unit for the hash function SHA-256 (384, 512)

After recalling the basic algorithms published by NIST for implementing the hash functions SHA-256 (384, 512), a basic circuit characterized by a cascade of full adder arrays is given. Implementation options are discussed and two methods for improving speed are exposed: the delay balancing and the pipelining. An application of the former is first given, obtaining a circuit that reduces the length of the critical path by a full adder array. A pipelined version is then given, obtaining a reduction of two full adder arrays in the critical path. The two methods are afterwards combined and the results obtained through hardware synthesis are exposed, where a comparison between the new circuits is also given.
The Application of "Three Dimensional" Model in the Teaching Design of EFL Writing

As an indispensable and most difficult part of language acquisition, the importance of English writing has been intensified by the economic globalization and internet revolution due to the special role of English as a universal language (Warshauer, 2000). However, writing teaching and learning has been long perplexing language teachers and learners even in the first language. Therefore many studies have been conducted on the revelation of the nature of writing and how to achieve it in pursuit of solutions to this problem. Consequently, the paradigm of teaching design of EFL Writing has experienced corresponding shift with the development of science, technology and social culture. Based on the analyses of various paradigms, the paper proposes the framework of a “three dimensional” model as well as its application in the teaching of EFL Business English discourse composition so as to cultivate the learners’ all-round writing skills in the aspect of teaching design.