Semantics of Database Transformations

Database transformations arise in many different settings including database integrations, evolution of database systems, and implementing user views and data-entry tools. This paper surveys approaches that have been taken to problems in these settings, assesses their strengths and weaknesses, and develops requirements on a formal model for specifying and implementing database transformations. We also consider the problem of insuring the correctness of database transformations. In particular, we demonstrate that the usefulness of correctness conditions such as information preservation are hindered by the interactions of transformations and database constraints, and the limited expressive power of established database constraint languages. We conclude that more general notions of correctness are required, and that there is a need for a uniform formalism for expressing both database transformations and constraints, and reasoning about their interactions. Finally we introduce WOL, a declarative language for specifying and implementing database transformations and constraints. We briefly describe the WOL language and its semantics, and argue that it addresses many of the requirements of a formalism for dealing with general database transformations

Facilitating Transformations in a Human Genome Project Database

Human Genome Project databases present a confluence of interesting database challenges: rapid schema and data evolution, complex data entry and constraint management, and the need to integrate multiple data sources and software systems which range over a wide variety of models and formats. While these challenges are not necessarily unique to biological databases, their combination, intensity and complexity are unusual and make automated solutions imperative. We illustrate these problems in the context of the Human Genome Database for Chromosome 22 (Chr22DB), and describe a new approach to a solution for these problems, by means of a deductive language for expressing database transformations and constraints

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease.

PurposeAlterations in the urinary microbiome have been associated with urological diseases. The microbiome of patients with urethral stricture disease (USD) remains unknown. Our objective is to examine the microbiome of USD with a focus on inflammatory USD caused by lichen sclerosus (LS).MethodsWe collected mid-stream urine samples from men with LS-USD (cases; n = 22) and non-LS USD (controls; n = 76). DNA extraction, PCR amplification of the V4 hypervariable region of the 16S rRNA gene, and sequencing was done on the samples. Operational taxonomic units (OTUs) were defined using a > 97% sequence similarity threshold. Alpha diversity measurements of diversity, including microbiome richness (number of different OTUs) and evenness (distribution of OTUs) were calculated and compared. Microbiome beta diversity (difference between microbial communities) relationships with cases and controls were also assessed.ResultsFifty specimens (13 cases and 37 controls) produced a 16S rRNA amplicon. Mean sample richness was 25.9 vs. 16.8 (p = 0.076) for LS-USD vs. non-LS USD, respectively. LS-USD had a unique profile of bacteria by taxonomic order including Bacillales, Bacteroidales and Pasteurellales enriched urine. The beta variation of observed bacterial communities was best explained by the richness.ConclusionsMen with LS-USD may have a unique microbiologic richness, specifically inclusive of Bacillales, Bacteroidales and Pasteurellales enriched urine compared to those with non-LS USD. Further work will be required to elucidate the clinical relevance of these variations in the urinary microbiome

Therapeutic Periocular Vaccination with a Subunit Vaccine Induces Higher Levels of Herpes Simplex Virus-Specific Tear Secretory Immunoglobulin A Than Systemic Vaccination and Provides Protection against Recurrent Spontaneous Ocular Shedding of Virus in Latently Infected Rabbits

AbstractRabbits latently infected with herpes simplex virus type 1 (HSV-1) were vaccinated either periocularly or systemically with a subunit vaccine (gB2 + gD2) plus adjuvant or adjuvant alone. Tear films were collected daily to measure recurrent infectious HSV-1 shedding. After systemic vaccination, the latently infected rabbits were not protected against recurrent ocular viral shedding (HSV-1-positive tear film cultures/total cultures) compared with either the systemic or periocular adjuvant controls (systemic vaccination = 49 of 972, 5.0%; systemic control = 46 of 972, 4.7%; periocular control = 43 of 930, 4.6%;P> 0.8). In contrast, latently infected rabbits vaccinated periocularly with the same vaccine had significantly reduced recurrent shedding (20 of 1026, 2.0%) compared with controls (P< 0.001) or systemic vaccination (P= 0.0002). Thus, recurrent HSV-1 shedding was significantly reduced by therapeutic local periocular subunit vaccination but not by therapeutic systemic subunit vaccination. Neutralizing antibody titers in the serum of systemically and ocularly vaccinated rabbits was similar. In contrast, HSV-specific tear secretory immunoglobulin A was significantly higher in the ocularly vaccinated group (P< 0.01). These results strongly suggest that in the rabbit, and presumably in humans, the local ocular (mucosal) immune response is much more important than the systemic immune response for therapeutic protection against recurrent ocular HSV-1. Thus development of a therapeutic vaccine against recurrent ocular HSV-1 should be directed at enhancing the local ocular (mucosal) immune response

Dental Hygienists\u27 Knowledge of HIV, Attitudes Towards People with HIV and Willingness to Conduct Rapid HIV Testing

This study was aimed to determine the dental hygienists\u27 knowledge of HIV, attitudes towards people living with HIV and willingness to conduct rapid HIV testing

Bite force and cranial bone strain in four species of lizards

In vivo bone strain data provide direct evidence of strain patterns in the cranium during biting. Compared to mammals, in vivo bone strains in lizard skulls are poorly documented. This paper presents strain data from the skulls of Anolis equestris, Gekko gecko, Iguana iguana and Salvator merianae during transducer biting. Analysis of variance was used to investigate effects of bite force, bite point, diet, cranial morphology and cranial kinesis on strain magnitudes. Within individuals the most consistent determinants of variance in bone strain magnitudes are gage location and bite point, with the importance of bite force varying between individuals. Inter-site variance in strain magnitudes—strain gradient—is present in all individuals, and varies with bite point. Between individuals within species, variance in strain magnitude is driven primarily by variation in bite force, not gage location or bite point, suggesting that inter-individual variation in patterns of strain magnitude is minimal. Between species, variation in strain magnitudes is significantly impacted by bite force and species membership, as well as by interactions between gage location, species, and bite point. Independent of bite force, species differences in cranial strain magnitudes may reflect selection for different cranial morphology in relation to feeding function, but what these performance criteria are is not clear. The relatively low strain magnitudes in Iguana and Uromastyx compared to other lizards may be related to their herbivorous diet. Cranial kinesis and the presence or absence of postorbital and supratemporal bars are not important determinants of inter-specific variation in strain magnitudes

Experiences and barriers to Health-Related Quality of Life following liver transplantation: a qualitative analysis of the perspectives of pediatric patients and their parents

This paper examines health-related quality of life (HRQOL) experiences and barriers facing young people who have received a liver transplant (LT). Semi-structured qualitative interviews were conducted with children and adolescents who have undergone LT and their parents. Findings indicate that LT fosters substantially improved child and adolescent HRQOL; however, young people also experience challenges such as difficulties with medication compliance, self-management of care routines, physical activity restrictions, and undesirable medical procedures. Implications and recommendations for clinical practice and research are discussed

The CS sulphation motifs 4C3, 7D4, 3B3[-]; and perlecan identify stem cell populations and niches, activated progenitor cells and transitional tissue development in the fetal human elbow

We compared the immunohistochemical distribution of (i) the novel chondroitin sulphate (CS) sulphation motifs 7D4, 4C3 and 3B3[-], (ii) native heparan sulphate (HS) and Δ-HS ‘stubs’ generated by heparitinase III digestion and (iii) the HS-proteoglycan, perlecan, in the foetal human elbow joint. Putative stem cell populations associated with hair bulbs, humeral perichondrium, humeral and ulnar rudiment stromal/perivascular tissues expressed the CS motifs 4C3, 7D4 and 3B3[-] as well as perlecan in close association but not co-localised. Chondrocytes in the presumptive articular cartilage of the foetal elbow expressed the 4C3 and 7D4 CS sulphation motifs consistent with earlier studies on the expression of these motifs in knee cartilage following joint cavitation. The present study also indicated that hair bulbs, skin, perichondrium and rudiment stroma were all perlecan rich progenitor cell niches that contributed to the organisation and development of the human foetal elbow joint and associated connective tissues. One of the difficulties in determining the precise role of stem cells in tissue development and repair processes is their short engraftment period and the lack of specific markers which differentiate the activated stem cell lineages from the resident cells. The CS sulphation motifs 7D4, 4C3 and 3B3[-] decorate cell surface proteoglycans on activated stem/progenitor cells and thus can be used to identify these cells in transitional areas of tissue development and in repair tissues and may be applicable to determining a more precise mode of action of stem cells in these processes. Isolation of perlecan from 12-14 week gestational age foetal knee rudiments demonstrated that perlecan in these foetal tissues was a HS-CS hybrid proteoglyca

Airborne Lidar Simulator for the Lidar Surface Topography (LIST) Mission

In 2007, the National Research Council (NRC) completed its first decadal survey for Earth science at the request of NASA, NOAA, and USGS. The Lidar Surface Topography (LIST) mission is one of fifteen missions recommended by NRC, whose primary objectives are to map global topography and vegetation structure at 5 m spatial resolution, and to acquire global surface height mapping within a few years. NASA Goddard conducted an initial mission concept study for the LIST mission in 2007, and developed the initial measurement requirements for the mission