Mathematics Experience and Format-specific Effects in Numerical Cognition

A persistent issue in numerical cognition research is how the format of numerical information influences numerical processing. The format-independent view postulates that information from various formats (e.g. ‘3’ or ‘three’) is represented in a uniform numerical code and that format should thus have no influence on number manipulation. The format-specific view assumes separate representational pathways for arabic digits and number words, which come into play during number processing as well as manipulation. Five experiments were undertaken with methods ranging from behavioural measures of reaction time to more refined measures of cognitive processes such as eye-tracking and eventrelated potentials (ERPs). In each experiment, effects of format were investigated at different levels of mathematics experience, in order to examine how the processing of numbers might differ in this regard. The first three experiments focused on basic number processing and processing differences that can occur for arabic digits, number words and quantifier words. In Experiment 1, a modified counting Stroop task was employed to investigate cognitive interference of arabic digits and number words. Participants took longer to respond on incongruent trials (e.g. 4 4 4; how many numbers are present? Correct response: ‘3’) relative to neutral (e.g. * * *; Correct response: ‘3’) and congruent (e.g. 3 3 3; Correct response: ‘3’) trials. Individuals with high mathematics experience showed greater interference on digit trials, whereas no effect of mathematics experience was found for word trials (e.g. three three; respond ‘2’). This suggests that the influence of format on number processing can be regulated by mathematics experience. Experiment 2 investigated this effect further by considering numerical (e.g. 5 2; which number is higher?) and physical size (e.g. 5 2; which number is physically bigger?) comparisons of digit and word stimuli. For both formats, participants responded faster on trials with a large numerical distance (e.g. 2 7) compared to trials with a small numerical distance (e.g. 2 3) suggesting that specific number meanings are accessed spontaneously from digits and number words, however the size congruity effect only occurred for digit stimuli. Individuals with greater mathematics experience showed an overall advantage for numerical comparison, regardless of format. Based on the findings from Experiments 1 and 2, Experiment 3 modified the counting Stroop task (Experiment 1) to investigate if mathematics experience can be related to the processing of quantifier words (e.g. many, few, each). Stimuli were presented as either specific (e.g. both both; correct response ‘2’) or general (e.g. some some) quantifier words and participants were required to count the items on-screen. While the effects were minimal in comparison with Experiment 1, any effects related to the congruity of the stimuli only emerged for the highly mathematics experienced participants, suggesting the involvement of number experience in quantifier word processing, and in turn for extracting number meaning from language in general. As the first three experiments demonstrated format-specific effects in basic number processing, the second part of the thesis investigated these effects for more advanced numerical processing such as arithmetic. The second part of the thesis also employed more refined measures of cognitive processing (eyetracking and event-related potential [ERP] technology) to investigate effects that might not be evident from behavioural data alone. Experiment 4 employed eye tracking technology to compare effects of problem size, operation and format at different levels of mathematics experience. Fixation patterns supported the format-specific view of number processing by suggesting that in comparison with digit-format, word-format impeded the use of direct memory retrieval in arithmetic, an effect that seemed to be more pronounced for individuals with low mathematics experience. Eye-tracking data also supported behavioural data as well as self-report data that have been noted in reports on strategy use in arithmetic. From this, inferences were made regarding the degree to which surface format influences subsequent calculation processes and how this might be moderated by mathematics experience. Experiment 5 investigated the interaction between the encoding and answer-retrieval stages in digit- and word-format arithmetic by separating the presentation of the first operand and the rest of the equation in a true–false verification task (e.g. ‘3’ and ‘x 4 = 12’; correct response ‘true’). Before each test block, participants were told which operation was to follow (addition or multiplication). ERP findings suggested that operands presented in the same format were encoded in the same way, with effects of operation only emerging during the second part of the equation, after participants had seen the operation sign (‘+’ or ‘x’). Regardless of format, the High Maths group showed greater left anterior potentials for multiplication than addition, suggesting an advantage for arithmetic fact retrieval. In the final chapter of the thesis the findings are discussed in relation to existing theoretical accounts on the influence of format in numerical cognition, with specific focus on the benefit of considering mathematics experience in this regard

Former des espaces climatisés soutenables

Qu'engage la fonction "climatiser" dans le contexte actuel de l'effet de serre anthropique ? Les enjeux qu'implique la production de climats artificiels ont des conséquences directes sur le climat et le milieu dit naturel. Nous nous trouvons face à une multiplicité d'attitudes quand il s'agit de réaliser, former et présenter des climats domestiques, c'est-à-dire des espaces habités. Ce travail examine les formes que prennent différents modes de climatiser (standards et alternatifs) à travers trois exemples d'architecture ou conceptions d'intérieur. Il envisage de redéfinir la fonction "climatiser" et de saisir les voies soutenables quant à ces formes ainsi que leur modalité de présentation. Un climat domestique soutenable serait un climat intérieur composé et conçu en tant qu'espace formellement perceptible, exposant sa relation d'interdépendance au climat culturel avec lequel il tenterait de "négocier"

Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method

Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situHybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.699.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis.This work was supported by European Union funds (FEDER/COMPETE) and by national funds (FCT) under the project FCOMP-01-0124-FEDER-008991 (PTDC/BIA-MIC/098228/2008). Antonio Machado was funded by the FCT individual fellowship SFRH/BD/62375/2009. Other fundings came from the FCT Strategic Project PEst-OE/EQB/LA0023/2013, the Project NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regional do Norte (ON.2-O Novo Norte), QREN, FEDER, and the project FCOMP-01-0124-FEDER-008991 (RECI/BBB-EBI/0179/2012). Nuno Cerca is an Investigador FCT (Portuguese national funds). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus spp. in milk samples

Lactobacillus species constitute one of the dominant and beneficial bacteria in our body and are used in developed countries as a microbial adjuvant. Identification of these probiotic bacteria is traditionally performed by culture-based techniques. However, such methods are very time-consuming and can give inaccurate results, especially when Lactobacillus is present in mixed bacterial complex communities. Our study aimed to accurately identify Lactobacillus spp. using a novel Peptide Nucleic Acid (PNA) Fluorescence In Situ Hibridization (FISH) probe. The probe (Lac663) was tested on 36 strains belonging to different Lactobacillus species and on 20 strains of other bacterial species. The sensitivity and specificity of the method were 100% (95% confidence interval (CI), 88.0 to 100.0%) and 95.0% (95% CI, 73.1 to 99.7%), respectively. Additionally, we tested the applicability of the method on milk samples added with Lactobacillus strains at probiotic range concentrations and others taxonomically related bacteria, as well as pathogenic bacteria. The Lac663 probe bound exclusively to Lactobacillus strains and the described PNA-FISH method was capable of directly quantifying Lactobacillus spp. in concentrations at which these potential probiotic bacteria are considered to have an effective benefit on human health.This work was supported by European Union funds (FEDER/COMPETE) and by national funds (FCT) under the project with reference FCOMP-01-0124-FEDER-008991 (PTDC/BIA-MIC/098228/2008. Antonio Machado acknowledges the FCT individual fellowship-SFRH/BD/62375/2009. However, it is important to refer that FCT did not have any role in the design of the experiments or manuscript writing

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a w) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a w. Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a w). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 a w for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a w for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life

Water-in-oil-in-water double emulsion for the delivery of starter cultures in reduced-salt moromi fermentation of soy sauce

This study investigated the application of water-oil-water (W1/O/W2) double emulsions (DE) for yeast encapsulation and sequential inoculation of Zygosaccharomyces rouxii and Tetragenococcus halophilus in moromi stage of soy sauce fermentation with reduced NaCl and/or substitution with KCl. Z. rouxii and T. halophilus were incorporated in the internal W1 and external W2 phase of DE, respectively. NaCl reduction and substitution promoted T. halophilus growth to 8.88 log CFU/mL, accompanied with faster sugar depletion and enhanced lactic acid production. Reducing NaCl without substitution increased the final pH (5.49) and decreased alcohols, acids, esters, furan and phenol content. However, the application of DE resulted in moromi with similar microbiological and physicochemical characteristics to that of high-salt. Principal component analysis of GC–MS data demonstrated that the reduced-salt moromi had identical aroma profile to that obtained in the standard one, indicating the feasibility of producing low-salt soy sauce without compromising its quality

Thick juice degradation: study of the microbial population dynamics and control of the causative flora during storage

Sugar thick juice degradation: study of the microbial commuity dynamics and control of the causative microflora during storage Storing sugar extracts as thick juice, a form of sucrose syrup, is widely practiced in the sugar industry because it allows to spread sugar production over an entire season. However, thick juice storage as currently practiced commonly faces problems due to juice degradation. The precise cause for this problem was ill defined but believed to be of microbial origin. The major challenge at the start of the research described inthis thesis was to describe the microbial population dynamics during thick juice storage, in order to identify the causative degradation flora and to define improved good storage practices with the ultimate goal of preventing thick juice degradation. In the last two decades, major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have driven the development of culture-independent techniques, which are primary based on the analysis of nucleic acids. In this research, thick juice microflora has been thoroughly studied with molecular tools, encompassing the application of 16S rRNA gene clone libraries and Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis, providing a more comprehensive representation of the thick juice microflora than the previous studies. The initial, heterogeneous microflora in freshly produced thick juice evolved to the dominance (>99%) of Tetragenococcus halophilus during storage. Basedon its high population density (10*6 10*7 cfu/ml), the ability to consume sucrose and the similar acidification pattern of artificially infested sterile thick juice, T. halophilus is proposed to be the key player in thick juice degradation. Remarkably, T. halophilus has thus far been associated only with high salt food products and ourwork is the first to associate it with high sugar matrices. Therefore, different T. halophilus strains either from thick juice or from high salt environments were compared in depth. Using a range of genetic typing methods and physiological tests including repetitive extragenic palindrome analysis (REP-PCR), random amplification of polymorphic DNA(RAPD), and determination of carbon utilization patterns (Biolog), clear differences were found between T. halophilus strains isolated from salt and sugar rich environments. Irrespective these differences,DNA-DNA hybridization grouped all strains within the species T.halophilus , except two isolates from sugar thick juice that appear to represent two new species of Tetragenococcus .In addition to T. halophilus , other bacteria such as Staphylococcus and Bacillus species were consistently present, though in lower steady concentrations of 10*3 cfu/ml. In order to simultaneously detect the different bacteria that may occur in thick juice, a DNA array was developed containing detector oligonucleotides for the genera Bacillus , Kocuria , Staphylococccus and Tetragenococcus , and the species Aerococcus viridans , Leuconostoc mesenteroides and T. halophilus . The developed macroarray was shown reliable and sensitive and has potential for monitoring the thick juice microflora during storage as an early warning system. Finally, best available storage practiceswere defined based on laboratory and pilot scale storage experiments using the independent variables solids content, pH, storage temperature and biocide concentration.In conclusion, this work has contributed to a better description of themicrobial population dynamics during thick juice storage and degradation, and to the definition of improved storage practices that will be useful for the sugar industry.Table of contents Abstract i Samenvatting iii Publications v List of abbreviations vii 1. CURRENT KNOWLEDGE ABOUT SUGAR THICK JUICE PRODUCTION 1 1.1 SUGAR PRODUCTION FROM SUGAR BEETS 2 1.2 THICK JUICE DEGRADATION DURING STORAGE 4 1.3 MICROBIAL COMMUNITY ANALYSIS TECHNIQUES IN FOOD AND FOOD- ASSOCIATED MATRICES 9 1.3.1 Choice of target genes 10 1.3.1.1. Ubiquitously conserved genes 10 1.3.1.2. Functional genes 11 1.3.2 Microbial community analysis techniques 12 1.3.2.1. Microbial diversity 12 1.3.2.2. Identity 17 1.3.2.3. Quantification 21 1.3.3 General pitfalls and limitations 26 1.3.3.1. Sampling 26 1.3.3.2. DNA extraction and PCR amplification 26 1.3.3.3. Viable versus non-viable 28 1.3.3.4. Active versus non-active 29 1.3.3.5. Sequence databases: availability and quality 29 1.3.4 Automation 29 1.3.5 Concluding Remarks 30 1.4 AIM AND OUTLINE OF THE THESIS 32 2. EFFECT OF HOP EXTRACT, SOLIDS CONTENT AND STORAGE TEMPERATURE ON MICROBIAL DEGRADATION OF THICK JUICE 33 2.1 INTRODUCTION 33 2.2 MATERIALS AND METHODS 35 2.2.1 Thick juice storage experiments and sampling 35 2.2.2 Microbiological analysis 38 2.2.3 Biochemical and chemical analyses 39 2.2.4 Sequencing of bacterial 16S rRNA genes 39 2.2.5 Susceptibility of fastidious bacteria in thick juice to hop ß-acids 39 2.2.6 Data analysis 40 2.3 RESULTS 40 2.3.1 Effect of total soluble solids (°Bx) on thick juice degradation 40 2.3.2 Stability of hop ß-acids during thick juice storage 41 2.3.3 Effect of hop ß-acids and temperature on thick juice degradation 42 2.3.4 Effect of hop ß-acids on thick juice microflora 43 2.3.5 Preliminary identification of the Fastidious Bacteria (FB) 44 2.3.6 Sensitivity of fastidious bacteria to hop ß-acids 46 2.4 DISCUSSION 47 3. DOMINANCE OF TETRAGENOCOCCUS HALOPHILUS DURING THICK JUICE DEGRADATION 51 3.1 INTRODUCTION 51 3.2 MATERIALS AND METHODS 52 3.2.1 Thick juice storage experiment and sampling 52 3.2.2 Viable counts 53 3.2.3 Acid analysis 53 3.2.4 DNA extraction 54 3.2.5 Analysis of 16S rDNA T-RFLP 54 3.2.6 Application of clone libraries 54 3.2.7 Sequencing of bacterial 16S rRNA gene fragments 55 3.2.8 Specific PCR assay development and verification 55 3.3 RESULTS AND DISCUSSION 56 3.3.1 Culturable microflora: viable counts and identification 56 3.3.2 Acids Analysis 61 3.3.3 T-RFLP analyses and application of clone libraries 63 3.3.4 Tetragenococcus halophilus can cause thick juice degradation 68 3.3.5 Specific PCR for Tetragenococcus halophilus 70 4. GENETIC AND PHYSIOLOGICAL DIVERSITY OF TETRAGENOCOCCUS HALOPHILUS STRAINS ISOLATED FROM SUGAR- AND SALT-RICH ENVIRONMENTS 75 4.1 INTRODUCTION 75 4.2 MATERIALS AND METHODS 76 4.2.1 Bacterial strains 76 4.2.2 DNA extraction 76 4.2.3 RAPD fingerprinting 78 4.2.4 16S rRNA gene sequence analysis 78 4.2.5 REP-PCR fingerprinting 79 4.2.6 DNA-DNA hybridization 79 4.2.7 Carbon source metabolic fingerprint 79 4.2.8 Salt and sucrose tolerance 80 4.3 RESULTS 80 4.3.1 RAPD fingerprinting 80 4.3.2 16S rRNA gene sequencing and phylogenetic analysis 82 4.3.3 REP-PCR fingerprinting 85 4.3.4 DNA-DNA hybridization 86 4.3.5 Biochemical characterization 86 4.3.6 Physiological characterization: salt and sucrose tolerance 88 4.4 DISCUSSION 91 5. DEVELOPMENT OF A DNA ARRAY FOR DETECTION AND IDENTIFICATION OF THICK JUICE CONTAMINANTS DURING THICK JUICE STORAGE 95 5.1 INTRODUCTION 95 5.2 MATERIALS AND METHODS 96 5.2.1 Bacterial isolates and DNA extraction 96 5.2.2 Selection of oligonucleotides 96 5.2.3 DNA array production 98 5.2.4 PCR amplification, labeling and hybridization 98 5.2.4.1. Validation of the DNA array 100 5.2.4.2. Monitoring thick juice contaminants during storage and degradation 101 5.2.4.3. Stability of Recovery of hybridized sequences 102 5.2.4.4. Stability of DNA in thick juice 102 5.3 RESULTS AND DISCUSSION 103 5.3.1 Design of the DNA array 103 5.3.2 Evaluation of the specificity and sensitivity of the DNA array 106 5.3.3 Validation of the DNA array 110 5.3.4 Monitoring thick juice contaminants 111 5.3.5 Stability of DNA in thick juice 116 6. INFLUENCE OF INDUSTRIALLY RELEVANT PROCESS AND STORAGE PARAMETERS ON MICROBIAL THICK JUICE DEGRADATION BY TETRAGENOCOCCUS HALOPHILUS 119 6.1 INTRODUCTION 119 6.2 MATERIAL AND METHODS 120 6.2.1 Thick juice storage experiments and sampling 120 6.2.2 Microbiological analyses 121 6.2.3 Biochemical and chemical analyses 121 6.2.4 Data analysis 121 6.3 RESULTS 122 6.3.1 Evolution of Tetragenococcus halophilus counts 122 6.3.2 pH evolution 122 6.3.3 Evolution of other degradation parameters 124 6.3.4 Case study: pilot scale storage experiment 127 6.4 DISCUSSION 130 7. GENERAL CONCLUSIONS 131 References 136status: publishe

Mathematics Experience and Format-specific Effects in Numerical Cognition

A persistent issue in numerical cognition research is how the format of numerical information influences numerical processing. The format-independent view postulates that information from various formats (e.g. ‘3’ or ‘three’) is represented in a uniform numerical code and that format should thus have no influence on number manipulation. The format-specific view assumes separate representational pathways for arabic digits and number words, which come into play during number processing as well as manipulation. Five experiments were undertaken with methods ranging from behavioural measures of reaction time to more refined measures of cognitive processes such as eye-tracking and eventrelated potentials (ERPs). In each experiment, effects of format were investigated at different levels of mathematics experience, in order to examine how the processing of numbers might differ in this regard. The first three experiments focused on basic number processing and processing differences that can occur for arabic digits, number words and quantifier words. In Experiment 1, a modified counting Stroop task was employed to investigate cognitive interference of arabic digits and number words. Participants took longer to respond on incongruent trials (e.g. 4 4 4; how many numbers are present? Correct response: ‘3’) relative to neutral (e.g. * * *; Correct response: ‘3’) and congruent (e.g. 3 3 3; Correct response: ‘3’) trials. Individuals with high mathematics experience showed greater interference on digit trials, whereas no effect of mathematics experience was found for word trials (e.g. three three; respond ‘2’). This suggests that the influence of format on number processing can be regulated by mathematics experience. Experiment 2 investigated this effect further by considering numerical (e.g. 5 2; which number is higher?) and physical size (e.g. 5 2; which number is physically bigger?) comparisons of digit and word stimuli. For both formats, participants responded faster on trials with a large numerical distance (e.g. 2 7) compared to trials with a small numerical distance (e.g. 2 3) suggesting that specific number meanings are accessed spontaneously from digits and number words, however the size congruity effect only occurred for digit stimuli. Individuals with greater mathematics experience showed an overall advantage for numerical comparison, regardless of format. Based on the findings from Experiments 1 and 2, Experiment 3 modified the counting Stroop task (Experiment 1) to investigate if mathematics experience can be related to the processing of quantifier words (e.g. many, few, each). Stimuli were presented as either specific (e.g. both both; correct response ‘2’) or general (e.g. some some) quantifier words and participants were required to count the items on-screen. While the effects were minimal in comparison with Experiment 1, any effects related to the congruity of the stimuli only emerged for the highly mathematics experienced participants, suggesting the involvement of number experience in quantifier word processing, and in turn for extracting number meaning from language in general. As the first three experiments demonstrated format-specific effects in basic number processing, the second part of the thesis investigated these effects for more advanced numerical processing such as arithmetic. The second part of the thesis also employed more refined measures of cognitive processing (eyetracking and event-related potential [ERP] technology) to investigate effects that might not be evident from behavioural data alone. Experiment 4 employed eye tracking technology to compare effects of problem size, operation and format at different levels of mathematics experience. Fixation patterns supported the format-specific view of number processing by suggesting that in comparison with digit-format, word-format impeded the use of direct memory retrieval in arithmetic, an effect that seemed to be more pronounced for individuals with low mathematics experience. Eye-tracking data also supported behavioural data as well as self-report data that have been noted in reports on strategy use in arithmetic. From this, inferences were made regarding the degree to which surface format influences subsequent calculation processes and how this might be moderated by mathematics experience. Experiment 5 investigated the interaction between the encoding and answer-retrieval stages in digit- and word-format arithmetic by separating the presentation of the first operand and the rest of the equation in a true–false verification task (e.g. ‘3’ and ‘x 4 = 12’; correct response ‘true’). Before each test block, participants were told which operation was to follow (addition or multiplication). ERP findings suggested that operands presented in the same format were encoded in the same way, with effects of operation only emerging during the second part of the equation, after participants had seen the operation sign (‘+’ or ‘x’). Regardless of format, the High Maths group showed greater left anterior potentials for multiplication than addition, suggesting an advantage for arithmetic fact retrieval. In the final chapter of the thesis the findings are discussed in relation to existing theoretical accounts on the influence of format in numerical cognition, with specific focus on the benefit of considering mathematics experience in this regard