Methods to split cognitive task data for estimating split-half reliability: A comprehensive review and systematic assessment

Estimating the reliability of cognitive task datasets is commonly done via split-half methods. We review four methods that differ in how the trials are split into parts: a first-second half split, an odd-even trial split, a permutated split, and a Monte Carlo-based split. Additionally, each splitting method could be combined with stratification by task design. These methods are reviewed in terms of the degree to which they are confounded with four effects that may occur in cognitive tasks: effects of time, task design, trial sampling, and non-linear scoring. Based on the theoretical review, we recommend Monte Carlo splitting (possibly in combination with stratification by task design) as being the most robust method with respect to the four confounds considered. Next, we estimated the reliabilities of the main outcome variables from four cognitive task datasets, each (typically) scored with a different non-linear algorithm, by systematically applying each splitting method. Differences between methods were interpreted in terms of confounding effects inflating or attenuating reliability estimates. For three task datasets, our findings were consistent with our model of confounding effects. Evidence for confounding effects was strong for time and task design and weak for non-linear scoring. When confounding effects occurred, they attenuated reliability estimates. For one task dataset, findings were inconsistent with our model but they may offer indicators for assessing whether a split-half reliability estimate is appropriate. Additionally, we make suggestions on further research of reliability estimation, supported by a compendium R package that implements each of the splitting methods reviewed here

Critical role of metals in biochemical properties of xylose isomerase

Improving the activity of xylose isomerase (XI) is highly desired for achieving efficient fermentation of xylose in lignocellulosic biomass using XI-expressing S. cerevisiae. XI is a metalloenzyme which requires two bivalent metals for its catalytic activity. The enzyme from Piromyces sp. E2 (PirXI)[1],[2] is activated with various metal ions including Mg2+, Mn2+, Ca2+, Co2+, Zn2+ and Fe2+. The biochemical properties of PirXI are dependent on the types of its metal cofactors. Moreover, the enzyme shows different affinities towards these metals. Characterization of these properties is critical for understanding the enzyme behavior in vivo and to further adapt the enzyme to the cytosolic metal environment. Recently, we have shown that altered intracellular metal composition can improve anaerobic growth of a xylose-fermenting strain by enhancing the activity of PirXI[3]. Furthermore, our current study on PirXI and other studies on different XIs have shown that it is also possible to change the metal preferences of the enzyme[4]. A PirXI variant with a single amino acid substitution in the proximity of the metal binding residues showed significant changes in metal preference compared to the wild-type PirXI. Further exploration on metal specificity of PirXI is necessary to optimize the in vivo enzyme activity. References: 1.Kuyper M, Harhangi HR, Stave AK, Winkler AA, Jetten MS, de Laat WT, den Ridder JJ, Op den Camp HJ, van Dijken JP, Pronk JT, FEMS Yeast Research 4 (2003) 69-78 2.van Maris AJ, Winkler AA, Kuyper M, de Laat WT, van Dijken JP, Pronk JT, Adv Biochem Engin/Biotechnol (2007) 108: 179–204 3.Verhoeven MD, Lee M, Kamoen L, van den Broek M, Janssen DB, Daran JG, van Maris AJA, Pronk JT, Sci. Rep (2017) 7, 46155 4.van Tilbeurgh H, Jenkins J, Chiadmi M, Janin J, Wodak SJ, Mrabet NT, Lambeir AM, Biochemistry (1992) 31: 5467-547

Self-perception but not peer reputation of bullying victimization is associated with non-clinical psychotic experiences in adolescents

Background Bullying victimization may be linked to psychosis but only self-report measures of victimization have been used so far. This study aimed (a) to investigate the differential associations of peer-nominated versus self-reported victim status with non-clinical psychotic experiences in a sample of young adolescents, and (b) to examine whether different types of self-reported victimization predict non-clinical psychotic experiences in these adolescents. Method A combination of standard self-report and peer nomination procedures was used to assess victimization. The sample (n = 724) was divided into four groups (exclusively self-reported victims, self- and peer-reported victims, exclusively peer-reported victims, and non-victims) to test for a group effect on non-clinical psychotic experiences. The relationship between types of victimization and non-clinical psychotic experiences was examined by a regression analysis. Results Self-reported victims, along with self- and peer-reported victims, scored higher than peer-reported victims and non-victims on non-clinical psychotic experiences. Self-reports of direct relational, indirect relational and physical victimization significantly improved the prediction of non-clinical psychotic experiences whereas verbal and possession-directed victimization had no significant predictive value. Conclusions The relationship between victimization and non-clinical psychotic experiences is only present for self-reported victimization, possibly indicative of an interpretation bias. The observed discrepancy between self-report and peer-report highlights the importance of implementing a combination of both measures for future research. Copyright © Cambridge University Press 2012

Physiological and genome-wide transcriptional responses of Saccharomyees cerevisiae to high carbon dioxide concentrations

Microbial Biotechnolog

Phosphoenolpyruvate Carboxykinase as the Sole Anaplerotic Enzyme in Saccharomyces cerevisiae

Pyruvate carboxylase is the sole anaplerotic enzyme in glucose-grown cultures of wild-type Saccharomyces cerevisiae. Pyruvate carboxylase-negative (Pyc–) S. cerevisiae strains cannot grow on glucose unless media are supplemented with C4 compounds, such as aspartic acid. In several succinate-producing prokaryotes, phosphoenolpyruvate carboxykinase (PEPCK) fulfills this anaplerotic role. However, the S. cerevisiae PEPCK encoded by PCK1 is repressed by glucose and is considered to have a purely decarboxylating and gluconeogenic function. This study investigates whether and under which conditions PEPCK can replace the anaplerotic function of pyruvate carboxylase in S. cerevisiae. Pyc– S. cerevisiae strains constitutively overexpressing the PEPCK either from S. cerevisiae or from Actinobacillus succinogenes did not grow on glucose as the sole carbon source. However, evolutionary engineering yielded mutants able to grow on glucose as the sole carbon source at a maximum specific growth rate of ca. 0.14 h–1, one-half that of the (pyruvate carboxylase-positive) reference strain grown under the same conditions. Growth was dependent on high carbon dioxide concentrations, indicating that the reaction catalyzed by PEPCK operates near thermodynamic equilibrium. Analysis and reverse engineering of two independently evolved strains showed that single point mutations in pyruvate kinase, which competes with PEPCK for phosphoenolpyruvate, were sufficient to enable the use of PEPCK as the sole anaplerotic enzyme. The PEPCK reaction produces one ATP per carboxylation event, whereas the original route through pyruvate kinase and pyruvate carboxylase is ATP neutral. This increased ATP yield may prove crucial for engineering of efficient and low-cost anaerobic production of C4 dicarboxylic acids in S. cerevisiae

When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

Within the first 5 min after a sudden relief from glucose limitation, Saccharomyces cerevisiae exhibited fast changes of intracellular metabolite levels and a major transcriptional reprogramming. Integration of transcriptome and metabolome data revealed tight relationships between the changes at these two levels. Transcriptome as well as metabolite changes reflected a major investment in two processes: adaptation from fully respiratory to respiro-fermentative metabolism and preparation for growth acceleration. At the metabolite level, a severe drop of the AXP pools directly after glucose addition was not accompanied by any of the other three NXP. To counterbalance this loss, purine biosynthesis and salvage pathways were transcriptionally upregulated in a concerted manner, reflecting a sudden increase of the purine demand. The short-term dynamics of the transcriptome revealed a remarkably fast decrease in the average half-life of downregulated genes. This acceleration of mRNA decay can be interpreted both as an additional nucleotide salvage pathway and an additional level of glucose-induced regulation of gene expression

Islands of conformational stability for Filopodia

Filopodia are long, thin protrusions formed when bundles of fibers grow outwardly from a cell surface while remaining closed in a membrane tube. We study the subtle issue of the mechanical stability of such filopodia and how this depends on the deformation of the membrane that arises when the fiber bundle adopts a helical configuration. We calculate the ground state conformation of such filopodia, taking into account the steric interaction between the membrane and the enclosed semiflexible fiber bundle. For typical filopodia we find that a minimum number of fibers is required for filopodium stability. Our calculation elucidates how experimentally observed filopodia can obviate the classical Euler buckling condition and remain stable up to several tens of . We briefly discuss how experimental observation of the results obtained in this work for the helical-like deformations of enclosing membrane tubes in filopodia could possibly be observed in the acrosomal reactions of the sea cucumber Thyone, and the horseshoe crab Limulus. Any realistic future theories for filopodium stability are likely to rely on an accurate treatment of such steric effects, as analysed in this work

Phase I study on docetaxel and ifosfamide in patients with advanced solid tumours.

Docetaxel and ifosfamide have shown significant activity against a variety of solid tumours. This prompted a phase I trial on the combination of these drugs. This phase I study was performed to assess the feasibility of the combination, to determine the maximum tolerated dose (MTD) and the side effects, and to propose a safe schedule for further phase II studies. A total of 34 patients with a histologically confirmed solid tumour, who were not pretreated with taxanes or ifosfamide and who had received no more than one line of chemotherapy for advanced disease were entered into the study. Treatment consisted of docetaxel given as a 1-h infusion followed by ifosfamide as a 24-h infusion (schedule A), or ifosfamide followed by docetaxel (schedule B) every 3 weeks. Docetaxel doses ranged from 60 to 85 mg m(-2) and ifosfamide doses from 2.5 to 5.0 g m(-2). Granulocytopenia grade 3 and 4 were common (89%), short lasting and ifosfamide dose dependent. Febrile neutropenia and sepsis occurred in 17% and 2% of courses respectively. Non-haematological toxicities were mild to moderate and included alopecia, nausea, vomiting, mucositis, diarrhoea, sensory neuropathy, skin and nail toxicity and oedema. There did not appear to be any pharmacokinetic interaction between docetaxel and ifosfamide. One complete response (CR) (soft tissue sarcoma) and two partial responses (PRs) were documented. A dose of 75 mg m(-2) of docetaxel combined with 5.0 g m(-2) ifosfamide appeared to be manageable. Schedule A was advocated for further treatment

Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics?

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Temperature strongly affects microbial growth, and many microorganisms have to deal with temperature fluctuations in their natural environment. To understand regulation strategies that underlie microbial temperature responses and adaptation, we studied glycolytic pathway kinetics in Saccharomyces cerevisiae during temperature changes. RESULTS: Saccharomyces cerevisiae was grown under different temperature regimes and glucose availability conditions. These included glucose-excess batch cultures at different temperatures and glucose-limited chemostat cultures, subjected to fast linear temperature shifts and circadian sinoidal temperature cycles. An observed temperature-independent relation between intracellular levels of glycolytic metabolites and residual glucose concentration for all experimental conditions revealed that it is the substrate availability rather than temperature that determines intracellular metabolite profiles. This observation corresponded with predictions generated in silico with a kinetic model of yeast glycolysis, when the catalytic capacities of all glycolytic enzymes were set to share the same normalized temperature dependency. CONCLUSIONS: From an evolutionary perspective, such similar temperature dependencies allow cells to adapt more rapidly to temperature changes, because they result in minimal perturbations of intracellular metabolite levels, thus circumventing the need for extensive modification of enzyme levels