VictorJuiz/thesis huggingface dataset:
Identification and characterisation of the shwachman-diamond syndrome gene and its orthologues

Shwachman-Diamond syndrome (OMIM 260400) is a rare, autosomal recessive disorder characterized by pancreatic exocrine insufficiency, hematological dysfunction, and skeletal abnormalities. Clinical diagnosis of SDS can be challenging due to the variable and intermittent nature of phenotypic components. Diagnosis would be facilitated by identification of the SDS gene, and development of a rapid molecular test. Elucidation of the molecular etiology of SDS should lead to improved treatments, including pharmacological and gene-based therapies. Eighteen positional candidate genes were identified in extant sequences and prioritised for mutation screening based on ascribed functions and expression profiling. Disease-associated mutations were identified in the SBDS gene, which was locally duplicated at 7q11. Sixty percent of mutations were gene conversions that arose due to recombination between SBDS and a highly homologous pseudogene. Patient mutation data and model organism studies suggested the gene is essential, with symptoms arising due to hypomorphic alleles. Indirect evidence suggests that SBDS functions in RNA metabolism or ribosome assembly or function. SBDS is ubiquitously expressed, and highly conserved, with homologues in all sequenced archaeal and eukaryotic genomes. The recent crystal structure of an archaeal homologue revealed a three domain arrangement. Alignment of homologues revealed that domain one was the most highly conserved across species, followed by domains two and three, respectively. A functional complementation assay was developed in Saccharomyces cerevisiae and used to assess chimeric proteins. Domain one was functionally interchangeable between distantly related Eukaryotes. Domain two imparted species specificity, while domain three was non-essential. Genetic studies in multiplex families identified a single 1.9 cM co-segregating locus at 7q11, but had exhausted informative families and genetic markers. Physical mapping was initiated as part of a positional cloning approach to gene identification. A partial map of the interval was constructed from available genomic sequences. This was comprised of 3.5 Mb and four gaps of unknown size. Features of the region were typical of other characterised pericentromeric loci. For example, a proximal region was composed of a mosaic of recent segmental duplications.
Functional characterization of human kallikrein 14

Human tissue kallikrein 14 (KLK14) is a novel extracellular serine protease. Clinical data links KLK14 expression to several pathologic conditions, including cancer and skin dermatoses, however, little is known of its (patho)physiological role. In order to functionally characterize KLK14, we expressed and purified recombinant KLK14 in mature and pro-enzyme forms, determined its expression profile, substrate specificity, regulation and potential in vivo substrates. As quantified by a newly developed immunoassay, KLK14 is most highly expressed in the normal and/or diseased tissues of the skin, breast and prostate and is significantly elevated in the serum of a proportion of prostate cancer patients. A collective assessment of KLK14 specificity using fluorogenic tripeptides, phage display substrate and positional-scanning synthetic combinatorial libraries suggests that KLK14 is a dual specificity enzyme, with both trypsin and chymotrypsin-like activity and a P1 preference for Arg over Tyr and Lys. A modest preference for P1'-Ser and P4'-Pro was also observed. KLK14 activity could be regulated by: (1) autolytic cleavage within surface loops leading to enzymatic inactivation, (2) endogenous inhibitors including: the inhibitory serpins alpha1-antitrypsin, alpha 2-antiplasmin, antithrombin III and alpha1-antichymotrypsin (with second-order rate constants (k+2/ Ki) of 49.8, 23.8, 1.48 and 0.224 muM-1min -1 respectively), and plasminogen activator inhibitor-1 as well as lympho-epithelial Kazal-type related inhibitor [LEKTI; 3 recombinant fragments containing inhibitory domains 1-6, rLEKTI(1-6); 6-8 and partial domain 9, rLEKTI(6-9'); and 9-12, rLEKTI(9-12)] with Ki values of 0.22, 3.41 and 10.26 nM for rLEKTI(1-6), rLEKTI(6-9') and rLEKTI(9-12), respectively and (3) citrate and zinc ions, which exerted stimulatory and inhibitory effects on KLK14 activity, respectively. We also expanded the potential in vivo target repertoire of KLK14 to include desmoglein-1, collagens I-IV, fibronectin, laminin, matrilin-4, kininogen, fibrinogen, plasminogen, vitronectin and insulin-like growth factor binding proteins 2 and 3. Our results indicate that KLK14 may be implicated in several facets of tumour progression, including growth, invasion and angiogenesis, in arthritic disease via digestion of cartilage and skin desquamation under normal and pathological conditions. These findings may have clinical implications for the management of cancer and other disorders in which KLK14 activity is elevated.
Teaching composing in the classroom: What teachers know

In this research I employed multi-site qualitative case study methodology to explore and analyze three secondary school teachers' personal understandings of their teaching-composing practices. I developed three separate case studies, each one representing the participant's personal knowledge of teaching composing. The rich knowledge revealed in each case study subsequently informed the development of a cross-case substantive-level grounded theory to explain the teaching-composing process as carried out by my participants. The knowledge developed includes some of the conditions that cause teachers to teach composing: (1) having personal composing experience, (2) valuing student composing, (3) recognizing that students themselves value composing, and (4) curriculum requirements. Some of the tools that teachers provide include: (1) composing confidence, (2) music theory and compositional technique---carefully provided in moderation, 3) collaborative composing opportunities, and (4) computer-facilitated composing. Strategies for guiding students through the composing process include: (1) enabling students to hear their works-in-progress; (2) offering suggestions; (3) sequencing tasks; (4) allowing the time, space, and freedom for exploration; and (5) encouraging students to seek, offer, and receive peer feedback. In order to manage the teaching-composing context, teachers may: (1) respect and connect to students' worlds, and to students' needs; and (2) ensure a safe and supportive classroom ethos. In order to manage the teaching-composing process, teachers may: (1) teach 'from the side'---providing resources, assistance, and guidance, but otherwise leaving students alone; (2) draw from and share their own personal composer knowledge; and (3) engage in ongoing development and modification of teaching-composing practices. Students benefit from composing by (1) experiencing success; (2) experiencing enjoyment; (3) exercising self-expression; and (4) gaining composing confidence and continuing to compose---both in the classroom and beyond. Strategies to engage students in composing activities include: (1) designing assignments with a carefully considered balance of freedoms and constraints; (2) inspiring students (presenting compositional models, offering inspirational triggers, and connecting to students' interests); (3) motivating with praise, encouragement, and nagging; (4) imbuing students with ownership over---and personal involvement in---their work; (5) the showcasing and sharing of student work; and (6) enabling enjoyment.
The use of breeding bird atlases and remotely sensed data provides a means to determine the minimum area of different land cover types needed for species persistence

Knowledge of the land cover area size below which species will no longer persist will contribute to the planning efforts of landholders and policy makers as land quality deteriorates over time due to various forms of degradation and loss. Using the British Trust for Ornithology (BTO) atlas (1988-1991), I related the change in distributions of focal bird species over time with areas of land cover assemblages that were quantified using remotely sensed data from the Land Cover Map of Great Britain (LCMGB, 1990). I studied two species known to be specializing in declining land covers to determine when suitable land cover had been reduced to a non-persistence threshold. Logistic regression and principal component analysis results suggest that resident Black Grouse species are well suited to such analyses (limited by the resolution of the BTO atlases), with the approximate minimum suitable woodland land cover area needed for persistence being 2.5 km2.
An alternative education program for students at risk of dropping out of high school in a large suburban school board

Interviews were conducted with teachers and administrators in a school board in the Greater Toronto Area (GTA) to investigate Alternative Education Programs in the board. The school board has two different alternative programs available to students. These programs are intended to serve students who are experiencing difficulty in the regular school system. In one program students leave their high school and attend a off-site program. The other program allows students to remain at their current high school but attend an on-site program. The on-site program, which is the current model for alternative education in the board, provides a model for alternative education not previously investigated. The benefit of the on-site alternative education program is that students remain with peers and teachers who know them and are best able to support them. Interviews explored the reasons that students experience difficulty in the regular school system, the process for admission to the alternative program as well as the structure and goals of the program.
Thermophilic fermentative hydrogen production from glucose

A laboratory-scaled anaerobic reactor fed with glucose was used to test the suitability of using mesophilic digester sludge to produce hydrogen thermophilically and to examine different startup procedures. The procedures tested included different pH values, ranging from 7.0 to 5.5; different configurations, sequencing batch, semicontinuous and continuous; and different solids retention times, ranging from theoretically infinite to 9 h. Different concentrations of products were observed in each condition. The smallest SRT at pH 5.5 favoured the highest production of hydrogen and butyric acid, and limited the production of alcohols and lactic acid, while the longest SRT favoured the growth of lactic acid bacteria, which inhibited hydrogen production. High concentrations of acids also caused inhibition. A high concentration of methane was found in the biogas, even under operational conditions that are adverse to methanogens. This excessive methane production was believed to be related with a biofilm that grew on the internal walls of the reactor.
Children with physical disabilities: friendship, self-concept and the role of social attributions

This study compared children with physical disabilities (PD), learning disabilities (LD) and no disabilities (ND) in terms of their reported numbers of friends, quality of friendships, self-concept and social attributions. It further explored the relationship between these facets of social functioning in all three groups. Seventy-one 10 to 14-year-old participants were recruited from four settings: a full-time special education program for children with physical disabilities (PD-FT) (n = 15), an integrated program for children with physical disabilities (PD-RC) (n = 12), a program for students with learning disabilities (LD) (n = 16), and a regular classroom program (ND) (n = 27). All participants were administered the Self-Perception Profile for Children (Harter, 1985), a friendship nomination measure (Wiener, 1995), the Friendship Quality Questionnaire (Parker & Asher, 1993), the Peer Social Attributions Questionnaire (Hoza, 1993), a friendship attributions interview, and, where applicable, a modified version of the Mossford Assessment Chart for the Physically Handicapped (Whitehouse, 1983). Questionnaires were given to all participants' teachers, and telephone interviews conducted with their parents. Results indicated that there were no group differences in self-concept. However, children with PD differed from both their LD and ND peers in reporting friendships of poorer quality. Students in the PD-FT group further reported lower quality of friendship than their PD-RC peers. Moreover, children with PD displayed different attributional patterns for both actual and hypothetical friendship situations than children with ND. Children with PD attributed positive social outcome less often to others than their ND peers, and less often acknowledged the importance of their own lack of effort in negative friendship interactions. These findings are significant in the context of results from the entire sample, which revealed a positive relationship between self-attributions and self-concept as well as quality of friendship. The present findings help explain the controversial accounts of intact self-concept coupled with poor peer relations often reported in the literature on children with PD. Implications for educational and clinical practice are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved)

Keywords: Children with disabilities
Learning disabled children
Friendship in children
Self-perception in children
Attribution (Social psychology) in children
Social interaction in children
Interpersonal relations in children
Neuraminidase-1, a subunit of the elastin receptor, alters mitogenic growth factor receptors and down-regulates proliferation of arterial smooth muscle cells

Elastic fibers are extracellular matrix components that contribute to vascular cell quiescence by sequestering certain mitogenic growth factors. The present study demonstrates that neuraminidase-1 (Neu1), a member of the cell surface elastin receptor, can also down-regulate proliferation of human arterial smooth muscle cells (SMCs). Inhibition of endogenous Neu1 induced a significant up-regulation in SMC proliferation. Conversely, treatment of SMCs with an exogenous bacterial neuraminidase (Nase), which mimicked over-expression of Neu1, decreased cellular proliferation. Most notably, the activity of neuraminidase abolished mitogenic responsiveness of human arterial SMCs to PDGF-BB and IGF-II. Furthermore, fibroblasts derived from patients with congenital sialidosis (genetically deficient in Neu1) were significantly more responsive to PDGF-BB and IGF-II than normal fibroblasts. In conclusion, the current findings suggest that Neu1 down-regulates cellular proliferation by: (1) up-regulation of elastic fiber deposition and by (2) de-sialylation of cell-surface receptors for PDGF-BB and IGF-II.
Aryl Imines: (A) stereoselective recognition of aziridines with a salen based Co(III) complex ; (B) conversion of aryl imines to vicinal diamides

Our investigation of the stereoselective recognition of aziridines by a salen Co(III) complex provides insight into the origin of stereoselectivity for ring opening reactions of terminal epoxides. We have determined by computation, 1H NMR analysis and X-ray crystal data, that aziridine and epoxide coordination are similar. We have also found that pi-pi stacking is important for selective recognition of aziridines. The aminolytic kinetic resolution of terminal epoxides with N-methyl aniline catalyzed by salen Co(III) complex obeyed first order kinetics with respect to the catalyst. In this example of monomeric catalysis, approach of the nucleophile was found to be substrate specific. The aminolysis of (+/- ) propylene oxide resulted in 8% enantiomeric excess of unreacted R -propylene oxide while that of (+/- ) styrene oxide gave 37% enantiomeric excess of S-styrene oxide. Krel values are 1.2 and 2.4 for propylene oxide and styrene oxide respectively. It was also proposed that in hydrolysis, the observed selectivity is determined by the approach of the nucleophile. The equilibrium between aryl mono-imine and di-imine formation was studied for several aldehydes. This gives insight into what controls 1,2-diamine synthesis. Initial studies have shown that there is no significant steric or electronic effect when resonance assisted hydrogen bonds are absent. However, in the presence of resonance assisted hydrogen bonding, exclusive formation of the mono-imine is observed. Through this study, we have also identified a stable aryl mono-imine (119) derived from 2,4,6-trimethoxybenzaldehyde. As a result of unfavourable lone pair-lone pair interaction, formation of the di-imine does not occur. Hence, aryl mono-imines are preferred when resonance assisted hydrogen bonds are present, or the di-imine is destabilized. The conversion of the mono-imine 119 to vicinal diamides was also studied. Formation of the 1,2-diamides is achieved through a diaza-Cope rearrangement with aryl diketones. Conversion occurs quantitatively and under mild conditions. Novel meso 1,2-diamides were isolated and characterized. Preliminary indications are that this rearrangement can also proceed stereoselectively because only dl 1,2-benzamide was observed. As such, chiral diamines can be prepared in a convenient way.
Identification of in vivo targets of Chx10, a homeodomain protein critical for retinal development

Chx10 is a homeodomain protein essential to normal eye development in both mice and humans. Homeodomain proteins regulate gene expression by activating or inhibiting genes involved in cell-type determination during development. In Chx10 null mice, retinal bipolar neurons fail to differentiate properly. We have shown that Chx10 represses gene expression and hypothesize that Chx10 allows bipolar cells to differentiate by inhibiting genes required for differentiation of other retinal cell types. Here, we characterize Chx10 antibodies and use them to demonstrate that Chx10 and photoreceptor proteins are expressed reciprocally during retinal development, that endogenous Chx10 binds photoreceptor specific gene elements in vitro, and that Chx10 binds the arrestin and IRBP promoters in vivo. These data provide strong evidence that Chx10 promotes bipolar cell differentiation at least in part by regulating photoreceptor gene expression.
Effects of wind on lake plankton patchiness and trophic interactions

Over thirty years of research has shown that zooplankton and phytoplankton exist in patches generated by physical (e.g., water movement caused by wind) and biological processes (e.g., vertical migration). These patches constantly change in response to weather conditions, however the trophic effects of this have not been thoroughly evaluated because previous studies have included relatively few transects. In this study, 150 sampling transects were collected from two basins (South Arm and Annie Bay) of Lake Opeongo (ON, Canada) under varying wind conditions. While the basins are biologically similar, South Arm is more exposed to the prevailing westerly winds, due to its size and orientation. On each transect, water temperature, chlorophyll concentration (proxy for phytoplankton) and zooplankton size were simultaneously recorded with a spatial resolution of 1.5m. The spatial patterns of each recorded variable were described at a wide range of scales using wavelet analysis, since spectral analysis was inappropriate due to the presence of large-scale trends and abrupt changes in variability. Statistically significant changes in variability were detected in all of the variables and the locations of these changes were mapped. The results showed that change points were relatively uniformly distributed along the sheltered Annie Bay transects, but were more concentrated in the most exposed region of the South Arm transects. Changes in wind conditions were correlated with the spatial patterns of the recorded variables. The results showed that large-scale downwind accumulations were more frequent in South Arm, where winds were generally stronger and more persistent. Small-scale variability was associated with strong winds in both basins. Carbon-budget simulations were used to investigate the link between wind-driven spatial patchiness and trophic interactions. Spatially-explicit budgets evaluated zooplankton growth potential against uniform conditions, which assumed median values of temperature and chlorophyll concentration. Regardless of basin, a growth advantage was observed more frequently than a disadvantage. However, statistical models show that the basins had different spatial patterns of chlorophyll concentration and wind conditions responsible for generating this growth advantage. The results demonstrate that observed spatial patterns should be incorporated into carbon budget simulations.
The significance of french after immersion: a qualitative case study

The main purpose of this study is to understand the significance of French language for French immersion high school graduates, professionally and socially. Based on an ethnographic study focused on the present language practices of four participants, this thesis examines similarities and differences of French immersion experiences and its significance in their lives. Through discourse analysis, results show that French has been significant throughout their lives and reveals the importance of this program as academic stage. All claim to have had a satisfying French immersion experience, but at the same time state to have a lack of opportunity to use their French and a lack of confidence in their French skills. Furthermore, these graduates argue that French is important because it is a way to distinguish themselves from the general English population. They seemed to have formed a separate identity group, one of Canadian immersion graduates.

Keywords: French language, Study and teaching
French language, Canada
French language, Study and teaching
Education, Bilingual, Canada
Immersion method (Language teaching)
A parallel adaptive mesh refinement scheme for hypersonic flows with an equilibrium high-temperature equation of state

An explicit parallel adaptive mesh refinement (AMR) scheme is proposed and developed for the solution of the partial differential equations governing two-dimensional hypersonic turbulent flows in conjunction with a high temperature equilibrium equation of state and the k-ω turbulence model. A finite-volume spatial discretization procedure is applied to the conservative form of the five governing equations: continuity, momentum and energy with two equations for the turbulence model, on structured body-fitted quadrilateral meshes. Limited piecewise-linear solution reconstruction with various approximate Riemann solvers modified to account for the high temperature equation of state is used in the numerical evaluation of the inviscid fluxes. The gradients for evaluating the viscous fluxes are calculated using centrally-weighted diamond path reconstruction. A block-based AMR scheme is used that allows for local anisotropic refinement of the grid and efficient parallel implementation via domain decomposition. The system of non-linear ordinary differential equations resulting from the finite volume discretization of steady-state boundary value problems is solved using explicit time marching methods with multigrid acceleration. Numerical results are presented and discussed for flows having Mach numbers in the range M<8. The results demonstrate the validity of the equilibrium high-temperature equation of state and the computational efficiency of the parallel explicit AMR schemes.