The Effect of Sample and Sample Matrix on DNA Processing: Mechanisms for the Detection and Management of Inhibition in Forensic Samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.

When group members go against the grain : an ironic interactive effect of group identification and normative content on healthy eating

Acknowledgements The research leading to these results has been funded by a Tandem Grant from the European Health Psychology Society/CREATE, awarded to the first and second author. The funder had no involvement in the study design, collection or analysis of data, writing the report, or the decision to submit this manuscript for publication.

The effects of centrally acting ACE inhibitors on the rate of cognitive and functional decline in dementia: a KDD approach

Alzheimer’s Disease and other dementias are one of the most challenging illnesses confronting countries with ageing populations. Treatment options for dementia are limited, and the costs are significant. There is a growing need to develop new treatments for dementia, especially for the elderly. There is also growing evidence that centrally acting angiotensin converting enzyme (ACE) inhibitors, which cross the blood-brain barrier, are associated with a reduced rate of cognitive and functional decline in dementia, especially in Alzheimer’s disease (AD). The aim of this research is to investigate the effects of centrally acting ACE inhibitors (CACE-Is) on the rate of cognitive and functional decline in dementia, using a three phased KDD process. KDD, as a scientific way to process and analysis clinical data, is used to find useful insights from a variety of clinical databases. The data used are from three clinic databases: Geriatric Assessment Tool (GAT), the Doxycycline and Rifampin for Alzheimer’s Disease (DARAD), and the Qmci validation databases, which were derived from several different geriatric clinics in Canada. This research involves patients diagnosed with AD, vascular or mixed dementia only. Patients were included if baseline and end-point (at least six months apart) Standardised Mini-Mental State Examination (SMMSE), Quick Mild Cognitive Impairment (Qmci) or Activities Daily Living (ADL) scores were available. Basically, the rates of change are compared between patients taking CACE-Is, and those not currently treated with CACE-Is. The results suggest that there is a statistically significant difference in the rate of decline in cognitive and functional scores between CACE-I and NoCACE-I patients. This research also validates that the Qmci, a new short assessment test, has potential to replace the current popular screening tests for cognition in the clinic and clinical trials.

COGNITIVE AND LINGUISTIC FACTORS OF READING ARABIC: THE ROLE OF MORPHOLOGICAL AWARENESS IN READING

Scientific reading research has produced substantial evidence linking specific reading components to a range of constructs including phonological awareness (PA), morphological awareness, orthographic processing (OP), rapid automatized naming, working memory and vocabulary. There is a paucity of research on Arabic, although 420 million people around the world (Gordon, 2005) speak Arabic. As a Semitic language, Arabic differs in many ways from Indo-European languages. Over the past three decades, literacy research has begun to elucidate the importance of morphological awareness (MA) in reading. Morphology is a salient aspect of Arabic word structure. This study was designed to (a) examine the dimensions underlying MA in Arabic; (b) determine how well MA predicts reading; (c) investigate the role of the standard predictors in different reading outcomes; and (d) investigate the construct of reading in Arabic. This study was undertaken in two phases. In Phase I, 10 MA measures and two reading measures were developed, and tested in a sample of 102 Grade 3 Arabic-speaking children. Factor analysis of the 10 MA tasks yielded one predominant factor supporting the construct validity of MA in Arabic. Hierarchical regression analyses, controlling for age and gender, indicated that the MA factor solution accounted for 41– 43% of the variance in reading. In Phase II, the widely studied predictor measures were developed for PA and OP in addition to one additional measure of MA (root awareness), and three reading measures In Phase II, all measures were administered to another sample of 201 Grade 3 Arabic-speaking children. The construct of reading in Arabic was examined using factor analysis. The joint and unique effects of all standard predictors were examined using different sets of hierarchical regression analyses. Results of Phase II showed that: (a) all five reading measures loaded on one factor; (b) MA consistently accounted for unique variance in reading, particularly in comprehension, above and beyond the standard predictors; and (c) the standard predictors had differential contributions. These findings underscore the contribution of MA to all components of Arabic reading. The need for more emphasis on including morphology in Arabic reading instruction and assessment is discussed.

Linear Hyperspectral Unmixing Using L0-norm Approximations and Nonnegative Matrix Factorization

Spectral unmixing (SU) is a technique to characterize mixed pixels of the hyperspectral images measured by remote sensors. Most of the existing spectral unmixing algorithms are developed using the linear mixing models. Since the number of endmembers/materials present at each mixed pixel is normally scanty compared with the number of total endmembers (the dimension of spectral library), the problem becomes sparse. This thesis introduces sparse hyperspectral unmixing methods for the linear mixing model through two different scenarios. In the first scenario, the library of spectral signatures is assumed to be known and the main problem is to find the minimum number of endmembers under a reasonable small approximation error. Mathematically, the corresponding problem is called the $\ell_0$-norm problem which is NP-hard problem. Our main study for the first part of thesis is to find more accurate and reliable approximations of $\ell_0$-norm term and propose sparse unmixing methods via such approximations. The resulting methods are shown considerable improvements to reconstruct the fractional abundances of endmembers in comparison with state-of-the-art methods such as having lower reconstruction errors. In the second part of the thesis, the first scenario (i.e., dictionary-aided semiblind unmixing scheme) will be generalized as the blind unmixing scenario that the library of spectral signatures is also estimated. We apply the nonnegative matrix factorization (NMF) method for proposing new unmixing methods due to its noticeable supports such as considering the nonnegativity constraints of two decomposed matrices. Furthermore, we introduce new cost functions through some statistical and physical features of spectral signatures of materials (SSoM) and hyperspectral pixels such as the collaborative property of hyperspectral pixels and the mathematical representation of the concentrated energy of SSoM for the first few subbands. Finally, we introduce sparse unmixing methods for the blind scenario and evaluate the efficiency of the proposed methods via simulations over synthetic and real hyperspectral data sets. The results illustrate considerable enhancements to estimate the spectral library of materials and their fractional abundances such as smaller values of spectral angle distance (SAD) and abundance angle distance (AAD) as well.

Modest elevation in BNP in asymptomatic hypertensive patients reflects sub-clinical cardiac remodeling, inflammation and extracellular matrix changes

In asymptomatic subjects B-type natriuretic peptide (BNP) is associated with adverse cardiovascular outcomes even at levels well below contemporary thresholds used for the diagnosis of heart failure. The mechanisms behind these observations are unclear. We examined the hypothesis that in an asymptomatic hypertensive population BNP would be associated with sub-clinical evidence of cardiac remodeling, inflammation and extracellular matrix (ECM) alterations. We performed transthoracic echocardiography and sampled coronary sinus (CS) and peripheral serum from patients with low (n = 14) and high BNP (n = 27). Peripheral BNP was closely associated with CS levels (r = 0.92, p<0.001). CS BNP correlated significantly with CS levels of markers of collagen type I and III turnover including: PINP (r = 0.44, p = 0.008), CITP (r = 0.35, p = 0.03) and PIIINP (r = 0.35, p = 0.001), and with CS levels of inflammatory cytokines including: TNF-α (r = 0.49, p = 0.002), IL-6 (r = 0.35, p = 0.04), and IL-8 (r = 0.54, p<0.001). The high BNP group had greater CS expression of fibro-inflammatory biomarkers including: CITP (3.8±0.7 versus 5.1±1.9, p = 0.007), TNF-α (3.2±0.5 versus 3.7±1.1, p = 003), IL-6 (1.9±1.3 versus 3.4±2.7, p = 0.02) and hsCRP (1.2±1.1 versus 2.4±1.1, p = 0.04), and greater left ventricular mass index (97±20 versus 118±26 g/m(2), p = 0.03) and left atrial volume index (18±2 versus 21±4, p = 0.008). Our data provide insight into the mechanisms behind the observed negative prognostic impact of modest elevations in BNP and suggest that in an asymptomatic hypertensive cohort a peripheral BNP measurement may be a useful marker of an early, sub-clinical pathological process characterized by cardiac remodeling, inflammation and ECM alterations.

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

Enhancer regions and transcription start sites of estrogen-target regulated genes are connected by means of Estrogen Receptor long-range chromatin interactions. Yet, the complete molecular mechanisms controlling the transcriptional output of engaged enhancers and subsequent activation of coding genes remain elusive. Here, we report that CTCF binding to enhancer RNAs is enriched when breast cancer cells are stimulated with estrogen. CTCF binding to enhancer regions results in modulation of estrogen-induced gene transcription by preventing Estrogen Receptor chromatin binding and by hindering the formation of additional enhancer-promoter ER looping. Furthermore, the depletion of CTCF facilitates the expression of target genes associated with cell division and increases the rate of breast cancer cell proliferation. We have also uncovered a genomic network connecting loci enriched in cell cycle regulator genes to nuclear lamina that mediates the CTCF function. The nuclear lamina and chromatin interactions are regulated by estrogen-ER. We have observed that the chromatin loops formed when cells are treated with estrogen establish contacts with the nuclear lamina. Once there, the portion of CTCF associated with the nuclear lamina interacts with enhancer regions, limiting the formation of ER loops and the induction of genes present in the loop. Collectively, our results reveal an important, unanticipated interplay between CTCF and nuclear lamina to control the transcription of ER target genes, which has great implications in the rate of growth of breast cancer cells.

Mathematical methods for the configuration of transportation systems with a focus on continuous and modular matrix conveyors

The lack of flexibility in logistic systems currently on the market leads to the development of new innovative transportation systems. In order to find the optimal configuration of such a system depending on the current goal functions, for example minimization of transport times and maximization of the throughput, various mathematical methods of multi-criteria optimization are applicable. In this work, the concept of a complex transportation system is presented. Furthermore, the question of finding the optimal configuration of such a system through mathematical methods of optimization is considered.

Quality of life predictors and normative data

Purpose: Identify predictors and normative data for quality of life (QOL) in a sample of Portuguese adults from general population Methods: A cross-sectional correlational study was undertaken with two hundred and fifty-five (N=255) individuals from Portuguese general population (mean age 43yrs, range 25-84yrs; 148 females, 107 males). Participants completed the European Portuguese version of the World Health Organization Quality of Life short-form instrument (WHOQOL-Bref) and the European Portuguese version of the Center for Epidemiologic Studies Depression Scale (CES-D). Demographic information was also collected. Results: Portuguese adults reported their QOL as good. The physical, psychological and environmental domains predicted 44% of the variance of QOL. The strongest predictor was the physical domain and the weakest was social relationships. Age, educational level, socioeconomic status and emotional status were significantly correlated with QOL and explained 25% of the variance of QOL. The strongest predictor of QOL was emotional status followed by education and age. QOL was significantly different according to: marital status; living place (mainland or islands); type of cohabitants; occupation; health. Conclusions: The sample of adults from general Portuguese population reported high levels of QOL. The life domain that better explained QOL was the physical domain. Among other variables, emotional status best predicted QOL. Further variables influenced overall QOL. These findings inform our understanding on adults from Portuguese general population QOL

New tools for cognitive and motor rehabilitation: development and clinical validation

Nervous system disorders are associated with cognitive and motor deficits, and are responsible for the highest disability rates and global burden of disease. Their recovery paths are vulnerable and dependent on the effective combination of plastic brain tissue properties, with complex, lengthy and expensive neurorehabilitation programs. This work explores two lines of research, envisioning sustainable solutions to improve treatment of cognitive and motor deficits. Both projects were developed in parallel and shared a new sensible approach, where low-cost technologies were integrated with common clinical operative procedures. The aim was to achieve more intensive treatments under specialized monitoring, improve clinical decision-making and increase access to healthcare. The first project (articles I – III) concerned the development and evaluation of a web-based cognitive training platform (COGWEB), suitable for intensive use, either at home or at institutions, and across a wide spectrum of ages and diseases that impair cognitive functioning. It was tested for usability in a memory clinic setting and implemented in a collaborative network, comprising 41 centers and 60 professionals. An adherence and intensity study revealed a compliance of 82.8% at six months and an average of six hours/week of continued online cognitive training activities. The second project (articles IV – VI) was designed to create and validate an intelligent rehabilitation device to administer proprioceptive stimuli on the hemiparetic side of stroke patients while performing ambulatory movement characterization (SWORD). Targeted vibratory stimulation was found to be well tolerated and an automatic motor characterization system retrieved results comparable to the first items of the Wolf Motor Function Test. The global system was tested in a randomized placebo controlled trial to assess its impact on a common motor rehabilitation task in a relevant clinical environment (early post-stroke). The number of correct movements on a hand-to-mouth task was increased by an average of 7.2/minute while the probability to perform an error decreased from 1:3 to 1:9. Neurorehabilitation and neuroplasticity are shifting to more neuroscience driven approaches. Simultaneously, their final utility for patients and society is largely dependent on the development of more effective technologies that facilitate the dissemination of knowledge produced during the process. The results attained through this work represent a step forward in that direction. Their impact on the quality of rehabilitation services and public health is discussed according to clinical, technological and organizational perspectives. Such a process of thinking and oriented speculation has led to the debate of subsequent hypotheses, already being explored in novel research paths.

Cognitive and structural aspects of addiction: Relation between iris patterns, time perception, eyeblink rate, impulsivity and cigarette addiction

Objectif : Le but de ce travail est d'étudier les corrélations existantes entre les patterns de l'iris, la perception du temps et la fréquence de clignement des paupières (eye blink rate) et ceci en relation avec l'addiction à la cigarette. Méthodologie: Revue de la littérature existante. Expériences sur une cohorte d'au moins trente sujets fumeurs/non-fumeurs. Analyses statistiques. Résultats: Nos résultats confirment qu'il existe des relations entre l'impulsivité, les patterns d'iris, l'eye blink rate spontané et la perception du temps. Nous observons également que l'addiction à la cigarette et son niveau de dépendance ont une influence sur ces différentes mesures. En effet, les sujets fumeurs tendent à avoir une personnalité plus impulsive par rapport aux sujets contrôles. On remarque également une nette diminution de l'eye blink rate dans le groupe des fumeurs et une tendance à la sur-estimation du temps qui passe. Conclusion : Ce travail nous permet de mieux comprendre les différentes corrélations qui existent entre les différentes variables que nous avons mesurées (patterns d'iris, score d'impulsivité et eye blink rate) ainsi que leur relation à l'addiction à la cigarette. Dès lors qu'il est avéré que les fumeurs peuvent avoir une perception du temps altérée par rapport au groupe contrôle, il serait intéressant d'en étudier l'évolution sur le long terme (aggravation avec la durée du tabagisme actif) ainsi que les conséquences qui en découlent écologiquement au moyen d'études longitudinales et de terrain.

Indigofera tinctoria Linn (Fabaceae) attenuates cognitive and behavioral deficits in scopolamine-induced amnesic mice

Purpose: To investigate the cognition-enhancing effects of aqueous extract of Indigofera tinctoria Linn (ITE, Fabaceae) in experimental amnesic mice. Methods: Scopolamine (2 mg/kg, i.p.) was used to induce amnesia in mice. The cognitive-enhancing activity of the ITE (5, 10 and 20 μg/mL) was studied by passive avoidance response, elevated plus maze and Y-maze behavioral paradigm in normal and scopolamine-induced amnesic mice. Antioxidant activities were also determined based on the ability of ITE to inhibit lipid peroxide, superoxide and hydroxyl radicals. Results: Scopolamine-induced cognitive deficits were significantly reversed by ITE (p < 0.001 at 20 mg/kg) in a dose-dependent fashion in all the behavioral paradigms tested. Furthermore, ITE dosedependently scavenged lipid peroxide, superoxide and hydroxyl free radicals with 50 % inhibition concentration (IC50) of 7.28 ± 0.37, 5.25 ± 0.28 and 7.62 ± 0.43 μg/mL, respectively. Conclusion: ITE possesses cognitive-enhancing properties in amnesic mice due to its potent antioxidant action.

The effect of sample and sample matrix on DNA processing: Mechanisms for the detection and management of inhibition in forensic samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.^

Cognitive and Visual Speech Contributions to Speech Perception in Challenging Listening Conditions

Speech perception routinely takes place in noisy or degraded listening environments, leading to ambiguity in the identity of the speech token. Here, I present one review paper and two experimental papers that highlight cognitive and visual speech contributions to the listening process, particularly in challenging listening environments. First, I survey the literature linking audiometric age-related hearing loss and cognitive decline and review the four proposed causal mechanisms underlying this link. I argue that future research in this area requires greater consideration of the functional overlap between hearing and cognition. I also present an alternative framework for understanding causal relationships between age-related declines in hearing and cognition, with emphasis on the interconnected nature of hearing and cognition and likely contributions from multiple causal mechanisms. I also provide a number of testable hypotheses to examine how impairments in one domain may affect the other. In my first experimental study, I examine the direct contribution of working memory (through a cognitive training manipulation) on speech in noise comprehension in older adults. My results challenge the efficacy of cognitive training more generally, and also provide support for the contribution of sentence context in reducing working memory load. My findings also challenge the ubiquitous use of the Reading Span test as a pure test of working memory. In a second experimental (fMRI) study, I examine the role of attention in audiovisual speech integration, particularly when the acoustic signal is degraded. I demonstrate that attentional processes support audiovisual speech integration in the middle and superior temporal gyri, as well as the fusiform gyrus. My results also suggest that the superior temporal sulcus is sensitive to intelligibility enhancement, regardless of how this benefit is obtained (i.e., whether it is obtained through visual speech information or speech clarity). In addition, I also demonstrate that both the cingulo-opercular network and motor speech areas are recruited in difficult listening conditions. Taken together, these findings augment our understanding of cognitive contributions to the listening process and demonstrate that memory, working memory, and executive control networks may flexibly be recruited in order to meet listening demands in challenging environments.