Tree Sequences as a General-Purpose Tool for Population Genetic Inference.

As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks applied to population genetic alignments. To better utilize these new data structures, we propose and implement a graph convolutional network to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format.

Mechanical and suture-holding properties of a UV-cured atelocollagen membrane with varied crosslinked architecture.

The mechanical competence and suturing ability of collagen-based membranes are paramount in guided bone regeneration (GBR) therapy, to ensure damage-free implantation, fixation and space maintenance. However, contact with the biological medium can induce swelling of collagen molecules, yielding risks of membrane sinking into the bone defect, early loss of barrier function, and irreversibly compromised clinical outcomes. To address these challenges, this study investigates the effect of the crosslinked network architecture on both mechanical and suture-holding properties of a new atelocollagen (AC) membrane.

Tree sequences as a general-purpose tool for population genetic inference.

As population genetics data increases in size new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient, but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks (CNNs) applied to population genetic alignments. To better utilize these new data structures we propose and implement a graph convolutional network (GCN) to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format.

Collaborative Recognition of Wellbeing Needs: A Novel Approach to Universal Psychosocial Screening on the Neonatal Unit.

Universal screening for the psychological needs of families in neonatal care is internationally recommended, but is not routinely practiced in the United Kingdom (UK). The present quality improvement project explores the clinical and operational feasibility of a novel approach to universal screening on a neonatal intensive care unit in the UK. The approach to screening taken adopts collaborative, strengths-based and dialogical methods for recognising the psychological needs of families whose baby is in hospital.

PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature.

Summary: Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of the National Center for Biotechnology Information Taxonomy and Global Biodiversity Information Facility databases to find associated synonyms with given target species names.

PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature.

Summary: Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of two commonly used taxonomic databases to find associated synonyms with given target species names.

Timesweeper: accurately identifying selective sweeps using population genomic time series.

Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations, only a single period of time can be sampled.

Effects of juvenile thermal preconditioning on the heat-shock, immune, and stress responses of rainbow trout upon a secondary thermal challenge.

Higher water temperatures and pathogens are both significant factors that negatively affect the welfare of teleost fish. In aquaculture, compared to natural populations, these problems are especially exacerbated, as the animals have relatively limited mobility, and the higher density promotes faster spread of infectious diseases. Because of the potential harm these stressors can inflict, methods that can limit the damage of these stressors are particularly valuable.

Bioactive molecules for regenerative pulp capping.

Since the discovery of bioactive molecules sequestered in dentine, researchers have been exploring ways to harness their activities for dental regeneration. One specific area, discussed in this review, is that of dental-pulp capping. Dental-pulp caps are placed when the dental pulp is exposed due to decay or trauma in an attempt to enhance tertiary dentine deposition.

The intersection of stress, sex and immunity in fishes.

While sexual dimorphism in immune responses has been documented in other vertebrates, evidence for a similar phenomenon in fish is lacking. Here, we review the relationship between immunity, stress, spawning, and sex hormones in fish to gain a better understanding of sex-based differences in fish immune responses and its consequences for aquaculture. It is well known that there is a strong link between the stress response and immune function in fish.

Hypoxia affects the ontogeny of the hypothalamus-pituitary-interrenal axis functioning in the lake whitefish (Coregonus clupeaformis).

Early life stages are sensitive to environmental insults and changes during critical developmental periods; this can often result in altered adult behaviour and physiology. Examining the development of the hypothalamus-pituitary-interrenal (HPI) axis and its responsiveness, or lack thereof, during development are important for understanding the short- and long-term impacts of stressors on embryonic and larval fish. We examined the ontogeny of the HPI axis in embryonic (21, 38, 63, 83 and 103 days post-fertilisation (dpf)) and larval (1, 2, 3 and 4 weeks post-hatch (wph)) lake whitefish (Coregonus clupeaformis) by quantifying changes in mRNA levels of several genes associated with HPI axis functioning and whole animal cortisol levels throughout development and in response to a severe or mild hypoxic stress.

A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta.

Amelogenesis is the process of enamel formation. For amelogenesis to proceed, the cells of the inner enamel epithelium (IEE) must first proliferate and then differentiate into the enamel-producing ameloblasts. Amelogenesis imperfecta (AI) is a heterogeneous group of genetic conditions that result in defective or absent tooth enamel.

Hedgehog Pathway Activation Alters Ciliary Signaling in Primary Hypothalamic Cultures.

Primary cilia dysfunction has been associated with hyperphagia and obesity in both ciliopathy patients and mouse models of cilia perturbation. Neurons throughout the brain possess these solitary cellular appendages, including in the feeding centers of the hypothalamus. Several cell biology questions associated with primary neuronal cilia signaling are challenging to address .

Hypoxia alters the expression of hif-1a mRNA and downstream HIF-1 response genes in embryonic and larval lake whitefish (Coregonus clupeaformis).

Lake whitefish (Coregonus clupeaformis) embryos and larvae were exposed to hypoxia at different developmental ages to determine when the cellular response to hypoxia could be initiated. mRNA levels of hypoxia-inducible factor 1α (hif-1α), hsp70, and several HIF-1 target genes were quantified in embryos at 21, 38, 63, 83- and 103-days post fertilisation (dpf) and in larvae at 1, 2, 3- and 4-weeks post hatch (wph) following a 6-hour hypoxia exposure. hsp70 mRNA levels were increased in response to hypoxia at all embryonic ages.

Novel DLX3 variants in amelogenesis imperfecta with attenuated tricho-dento-osseous syndrome.

Objectives: Variants in DLX3 cause tricho-dento-osseous syndrome (TDO, MIM #190320), a systemic condition with hair, nail and bony changes, taurodontism and amelogenesis imperfecta (AI), inherited in an autosomal dominant fashion. Different variants found within this gene are associated with different phenotypic presentations. To date, six different DLX3 variants have been reported in TDO.

Teaching professionalism: some features in Canadian physiotherapy programs.

The role of "professionalism" is core to many health professions including Physical Therapy (PT), and the development of competence in professionalism is a key requirement of entry-to-practice PT programs. However, the actual curriculum, teaching methodologies, and evaluation methods currently used to develop professional competence during PT training programs in Canada are unclear. This study explored current teaching practices, evaluation and curricular content related to professionalism in Canadian entry-to-practice PT programs.

A CreER mouse to study melanin concentrating hormone signaling in the developing brain.

The neuropeptide, melanin concentrating hormone (MCH), and its G protein-coupled receptor, melanin concentrating hormone receptor 1 (Mchr1), are expressed centrally in adult rodents. MCH signaling has been implicated in diverse behaviors such as feeding, sleep, anxiety, as well as addiction and reward. While a model utilizing the Mchr1 promoter to drive constitutive expression of Cre recombinase (Mchr1-Cre) exists, there is a need for an inducible Mchr1-Cre to determine the roles for this signaling pathway in neural development and adult neuronal function.

Development of the embryonic heat shock response and the impact of repeated thermal stress in early stage lake whitefish (Coregonus clupeaformis) embryos.

Lake whitefish (Coregonus clupeaformis) embryos were exposed to thermal stress (TS) at different developmental stages to determine when the heat shock response (HSR) can be initiated and if it is altered by exposure to repeated TS. First, embryos were subject to one of three different TS temperatures (6, 9, or 12°C above control) at 4 points in development (21, 38, 60 and 70 days post-fertilisation (dpf)) for 2h followed by a 2h recovery to understand the ontogeny of the HSR. A second experiment explored the effects of repeated TS on the HSR in embryos from 15 to 75 dpf.

Defects in the acid phosphatase ACPT cause recessive hypoplastic amelogenesis imperfecta.

We identified two homozygous missense variants (c.428C>T, p.(T143M) and c.

Cactus Spine Wounds: A Case Report and Short Review of the Literature.

Introduction: Cactus plants are commonly seen in arid southwestern regions of the United States. Due to their ready availability, they have become a popular houseplant. The spines or glochidia can easily puncture the skin with only minor pressure (ie, bumping or touching the cactus).

Therapeutic hepatocyte transplant for inherited metabolic disorders: functional considerations, recent outcomes and future prospects.

The applications, outcomes and future strategies of hepatocyte transplantation (HTx) as a corrective intervention for inherited metabolic disease (IMD) are described. An overview of HTx in IMDs, as well as preclinical evaluations in rodent and other mammalian models, is summarized. Current treatments for IMDs are highlighted, along with short- and long-term outcomes and the potential for HTx to supplement or supplant these treatments.

A retrospective observational study of the relationship between family history and survival from colorectal cancer.

Background: Although family history is well established to be a risk factor for developing colorectal cancer (CRC), much less is known about its impact on patient survival. This study aimed to link CRC patient data from the National Study of Colorectal Cancer Genetics (NSCCG) to the National Cancer Data Repository (NCDR) to examine the relationship between family history and the characteristics and outcomes of CRC.

Methods: All eligible NSCCG patients underwent a matching process to the NCDR using combinations of their personal identifiers.

Population-based study of laparoscopic colorectal cancer surgery 2006-2008.

Background: Clinical guidelines recommend that, where clinically appropriate, laparoscopic tumour resections should be available for patients with colorectal cancer. This study aimed to examine the introduction of laparoscopic surgery in the English National Health Service.

Methods: Data were extracted from the National Cancer Data Repository on all patients who underwent major resection for a primary colorectal cancer diagnosed between 2006 and 2008.