OncoThreads: visualization of large-scale longitudinal cancer molecular data.

MOTIVATION: Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. RESULTS: To address this need we developed OncoThreads, a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, for example, emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2-4 timepoints. AVAILABILITY AND IMPLEMENTATION: Freely available at http://oncothreads.gehlenborglab.org. Implemented in Java Script using the cBioPortal web API as a backend. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluation of the effect of ultrasound guidance on the accuracy of intercostal nerve injection: a canine cadaveric study.

OBJECTIVE: To develop an ultrasound-guided approach to intercostal nerve injection and to compare the success rate of intercostal nerve injections using blind or ultrasound-guided technique in canine cadavers. STUDY DESIGN: Prospective, randomized, descriptive, experimental anatomic study. ANIMALS: A total of 14 mid-sized adult canine cadavers. METHODS: Ultrasound landmarks were identified by dissection of four cadavers and used to develop an ultrasound-guided technique. The remaining 10 cadavers were randomly assigned to blind (five cadavers) or ultrasound-guided (five cadavers) injections of the third to the ninth intercostal nerves bilaterally with 0.03 mL kg-1 of colorant per injection. The target for intercostal injections was the caudal border of the respective rib, between the internal intercostal membrane and the parietal pleura. Additionally, displacement of the parietal pleura without visible intramuscular distribution was considered the end point for ultrasound-guided injections. For each cadaver, a practitioner in training performed the blocks on one hemithorax, while an experienced practitioner performed the blocks on the opposite hemithorax. Injections were considered successful if ≥1 cm of the target nerve was stained with colorant upon dissection. Success rates and length of nerve staining were analyzed with Fisher's exact and t tests, respectively. Data were considered statistically different with p < 0.05. RESULTS: Success rates of blind and ultrasound-guided technique were 57.1% and 91.4%, respectively (p < 0.0001). The length of intercostal nerve staining was 3.1 ± 1.2 cm and 3.6 ± 1.0 cm using blind and ultrasound-guided techniques, respectively (p = 0.02). No differences were observed between the two practitioners for blind (p = 0.33) and ultrasound-guided techniques (p = 0.67). CONCLUSIONS AND CLINICAL RELEVANCE: Ultrasound guidance improves the accuracy of intercostal nerve injections when compared with blind technique, independently of the level of expertise in regional anesthesia.

Comparison between two approaches for the transversus abdominis plane block in canine cadavers.

OBJECTIVE: To compare the dye distribution following either two lateral abdominal or one lateral abdominal and one subcostal ultrasound-guided transversus abdominis plane (TAP) injections of a clinically relevant volume of dye solution in dogs. STUDY DESIGN: Randomized cadaveric study. ANIMALS: A total of eight canine cadavers. METHODS: On one side of each cadaver, two TAP injections were performed on the lateral aspect of the abdomen (approach LL), caudal to the last rib and cranial to the iliac crest. On the contralateral hemiabdomen, one subcostal (caudal to the costal arch) and one lateral abdominal injection (between last rib and iliac crest), were performed (approach SL). Side allocation was randomly determined. A spinal needle was introduced in-plane to the transducer for each injection of methylene blue (0.25 mL kg-1). All cadavers were dissected to assess dye distribution and number of stained target nerves. RESULTS: All injections were performed in the TAP. The proportion of target nerve staining was 53.5% versus 80.4% with approaches LL and SL, respectively (p = 0.005). Approach LL stained the first lumbar (L1) spinal nerve in 100% of injections and ninth thoracic (T9), T10, T11, T12, T13 and L2 were stained in 0%, 0%, 37.5%, 62.5%, 87.5% and 87.5% of injections, respectively. Approach SL stained T11, L1 and L2 in 100% of injections and T9, T10, T12 and T13 were stained in 37.5%, 87.5%, 75% and 62.5% of injections, respectively. Approach SL resulted in greater staining of nerves cranial to T12 compared with approach LL. The two approaches were equivalent in staining nerves caudal to T12. CONCLUSIONS AND CLINICAL RELEVANCE: Approach SL provided a broader distribution of the injected solution than approach LL, which may result in a larger blocked area in live animals undergoing celiotomy.

Bioenergetics underlying single-cell migration on aligned nanofiber scaffolds.

Cell migration is centrally involved in a myriad of physiological processes, including morphogenesis, wound healing, tissue repair, and metastatic growth. The bioenergetics that underlie migratory behavior are not fully understood, in part because of variations in cell culture media and utilization of experimental cell culture systems that do not model physiological connective extracellular fibrous networks. In this study, we evaluated the bioenergetics of C2C12 myoblast migration and force production on fibronectin-coated nanofiber scaffolds of controlled diameter and alignment, fabricated using a nonelectrospinning spinneret-based tunable engineered parameters (STEP) platform. The contribution of various metabolic pathways to cellular migration was determined using inhibitors of cellular respiration, ATP synthesis, glycolysis, or glucose uptake. Despite immediate effects on oxygen consumption, mitochondrial inhibition only modestly reduced cell migration velocity, whereas inhibitors of glycolysis and cellular glucose uptake led to striking decreases in migration. The migratory metabolic sensitivity was modifiable based on the substrates present in cell culture media. Cells cultured in galactose (instead of glucose) showed substantial migratory sensitivity to mitochondrial inhibition. We used nanonet force microscopy to determine the bioenergetic factors responsible for single-cell force production and observed that neither mitochondrial nor glycolytic inhibition altered single-cell force production. These data suggest that myoblast migration is heavily reliant on glycolysis in cells grown in conventional media. These studies have wide-ranging implications for the causes, consequences, and putative therapeutic treatments aimed at cellular migration.

Assembly of the TgrB1-TgrC1 cell adhesion complex during Dictyostelium discoideum development.

In Dictyostelium discoideum, TgrB1 and TgrC1 are partners of a heterophilic cell-adhesion system. To investigate its assembly process, the split GFP complementation assay was used to track the oligomeric status of both proteins. The ability of TgrC1 to form cis-homodimers spontaneously was demonstrated by fluorescence complementation studies and confirmed by chemical cross-linking. In contrast, TgrB1 failed to form cis-homodimers in the absence of TgrC1. Treatment of cell aggregates with antibodies against TgrB1 or TgrC1 did not affect TgrC1 dimerization, but inhibited TgrB1 dimer formation, suggesting that TgrB1 cis-homodimerization is dependent on trans-interaction with TgrC1. When TgrB1 and TgrC1 conjugated with the complementary halves of GFP were co-expressed in cells, cis-heterodimers were not detected. However, weak FRET signals were detected in cells expressing TgrB1-RFP and TgrC1-GFP, suggesting that TgrB1 dimers and TgrC1 dimers were arranged juxtapose to each other in the adhesion complex. The results of the present study suggest that the assembly process is initiated upon trans-interaction of monomeric TgrB1 with TgrC1 homodimers on adjacent cells, which triggers the formation of TgrB1 dimers. The homodimerization of TgrB1 in turn induces the clustering of TgrB1 and TgrC1, and the coalescence of TgrB1-TgrC1 clusters results in the formation of large adhesion complexes.

Pharmacokinetics and tolerability of single-dose enteral cannabidiol and cannabidiolic acid rich hemp in horses (Equus caballus).

The pharmacokinetics and tolerability of cannabinoids and their metabolites were determined in eight horses after enteral administration of a commercial CBD/CBDA-rich hemp oil product. Each horse was administered 2 mg/kg or 8 mg/kg CBD/CBDA or no treatment in a randomized cross-over design. Serial serum samples collected over 48 h were analyzed by high performance liquid chromatography with tandem mass spectrometry. Plasma chemistry analysis was performed at 0 h and 24 h. Vital parameters, pedometry, and blinded mentation and gait evaluations were recorded at intervals up to 24 h. Manure production and gastrointestinal transit time were tracked for 48 h after oil administration. The median maximal concentration of CBD and CBDA were 5.2 and 36.95 ng/mL in the 2 mg/kg group, respectively; and 40.35 and 353.56 ng/mL in the 8 mg/kg group. The median half-life of elimination was not calculated for the 2 mg/kg CBD treatment due to lack of time points above the lower quantifiable limit beyond the Cmax while it was 7.75 h in the 8 mg/kg group. CBDA absorption was biphasic. Pharmacokinetic parameters for tetrahydrocannabinol, tetrahydrocannabinolic acid, cannabigerolic acid, and 7-carboxy cannabidiol are also reported. No significant differences in any of the measured tolerability parameters were demonstrated between treatment groups. Single-dose enteral administration of CBD/CBDA-rich hemp extract up to 8 mg/kg does not appear to produce neurologic, behavioral, or gastrointestinal effects in horses.

Connectome-driven neural inventory of a complete visual system.

Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial features requires a large and diverse network of neurons, such that in animals as distant as flies and humans, visual regions comprise half the brain's volume. These visual brain regions often reveal remarkable structure-function relationships, with neurons organized along spatial maps with shapes that directly relate to their roles in visual processing. To unravel the stunning diversity of a complex visual system, a careful mapping of the neural architecture matched to tools for targeted exploration of that circuitry is essential. Here, we report a new connectome of the right optic lobe from a male Drosophila central nervous system FIB-SEM volume and a comprehensive inventory of the fly's visual neurons. We developed a computational framework to quantify the anatomy of visual neurons, establishing a basis for interpreting how their shapes relate to spatial vision. By integrating this analysis with connectivity information, neurotransmitter identity, and expert curation, we classified the ~53,000 neurons into 727 types, about half of which are systematically described and named for the first time. Finally, we share an extensive collection of split-GAL4 lines matched to our neuron type catalog. Together, this comprehensive set of tools and data unlock new possibilities for systematic investigations of vision in Drosophila, a foundation for a deeper understanding of sensory processing.

Beyond the biomedical: an evaluation of the introduction of social gerontology into a postgraduate geriatric medicine education program.

Geriatric Medicine education tends to adopt a biomedical lens, despite the practice of Geriatric Medicine involving the comprehensive assessment of the functional, psychological, and social aspects of older people's lives. In this commentary, we describe the delivery of a Social Gerontology education program for Geriatric Medicine trainees in the Northwest of England. Education in Social Gerontology-a field that focuses on how social, cultural, economic, and environmental factors shape the lives of older adults-is thought to mitigate against ageism, a pervasive and multifaceted form of discrimination. We describe the rationale for, and context of, the program delivery, before presenting an overview of trainee's feedback. Thematic analysis of feedback centered around three main themes: knowledge acquisition, change in clinical practice, and enjoyment of the sessions. Trainees (n = 20) reported enjoying the sessions, with 100% likely to recommend to peers. The focus on underserved groups, the novel content of the sessions, which were not taught elsewhere, and the non-medical perspective of the speakers were described as particularly valuable. By sharing our approach and reflecting on the early success of the program, we argue for an increased focus on Social Gerontology in Geriatric Medicine education.

Platypnoea-orthodeoxia in an elderly man with patent foramen ovale and dilated ascending aorta.

We report the case of an 85-year-old male with platypnoea-orthodeoxia associated with patent foramen ovale (PFO) and ectatic ascending aorta, in the absence of any significant pulmonary pathology.

Current Concepts in Head and Neck Surgery.

This article is intended to "brush up" on the literature updates for the management of head and neck surgeries, particularly mandibulectomy and maxillectomy. Few new techniques have been described in the past decade in dental and oral oncological surgery. A tendency of developing more aggressive surgical strategies to treat complex oral tumors is evident from the recent veterinary literature and the emerging novel techniques for bone regeneration of maxillofacial defects. In addition, this article also focuses on the basic oral surgical oncology principles, an important part of any maxillofacial surgery.

14-3-3σ and p63 play opposing roles in epidermal tumorigenesis.

14-3-3σ plays a regulatory role in epidermal epithelial differentiation and loss of 14-3-3σ leads to increased proliferation and impaired differentiation. A tumor suppressor function for 14-3-3σ has been proposed based on the fact that some epithelial-derived tumors lose 14-3-3σ expression. p63, a p53 family member, is a master regulator of epidermal epithelial proliferation and differentiation and is necessary for the epidermal development. The function of p63 in tumorigenesis is still controversial and poorly defined as multiple isoforms have been found to play either collaborative or opposing roles. By using 'repeated epilation' heterozygous (Er/+) mice containing a dominant-negative 14-3-3σ mutation, the functional relationship of p63 with 14-3-3σ in epidermal proliferation, differentiation and tumorigenesis was investigated. It was found that p63, particularly the ΔNp63α isoform, was strongly expressed in 14-3-3σ-deficient keratinocytes and knockdown of p63 remarkably inhibited proliferation in these cells. To study the functional roles of 14-3-3σ and p63 in epidermal tumorigenesis, we adopted a 7,12-dimethylbenzanthracene/12-O-tetradecanoyl-phorbol-13-acetate (DMBA/TPA) two-stage tumorigenesis procedure to induce formation of skin papillomas and squamous cell carcinomas in Er/+ mice and identified strong p63 expression in resultant tumors. The loss of one allele of p63 caused by the generation of Er/+/p63(+/-) double compound mice decreased the sensitivity to DMBA-/TPA-induced tumorigenesis as compared with Er/+ mice. This study shows that p63 and 14-3-3σ play opposing roles in the development of skin tumors and that the accumulation of p63 is essential for Ras/14-3-3σ mutation-induced papilloma formation and squamous cell carcinoma carcinogenesis.

Regulation of spatiotemporal expression of cell-cell adhesion molecules during development of Dictyostelium discoideum.

The social amoeba Dictyostelium discoideum is a simple but powerful model organism for the study of cell-cell adhesion molecules and their role in morphogenesis during development. Three adhesive systems have been characterized and studied in detail. The spatiotemporal expression of these adhesion proteins is stringently regulated, often coinciding with major shifts in the morphological complexity of development. At the onset of development, amoeboid cells express the Ca(2+) -dependent cell-cell adhesion molecule DdCAD-1, which initiates weak homophilic interactions between cells and assists in the recruitment of individuals into cell streams. DdCAD-1 is unique because it is synthesized as a soluble protein in the cytoplasm. It is targeted for presentation on the cell surface by an unconventional protein transport mechanism via the contractile vacuole. Concomitant with the aggregation stage is the expression of the contact sites A glycoprotein csA/gp80 and TgrC1, both of which mediate Ca(2+) /Mg(2+) -independent cell-cell adhesion. Whereas csA/gp80 is a homophilic binding protein, TgrC1 binds to a heterophilic receptor on the cell. During cell aggregation, csA/gp80 associates preferentially with lipid rafts, which facilitate the rapid assembly of adhesion complexes. TgrC1 is synthesized at low levels during aggregation and rapid accumulation occurs initially in the peripheral cells of loose mounds. The extracellular portion of TgrC1 is shed and becomes part of the extracellular matrix. Additionally, analyses of knockout mutants have revealed important biological roles played by these adhesion proteins, including size regulation, cell sorting and cell-type proportioning.

Core Strategies to Increase the Uptake and Use of Potassium-Enriched Low-Sodium Salt.

Excess sodium consumption and insufficient potassium intake contribute to high blood pressure and thus increase the risk of heart disease and stroke. In low-sodium salt, a portion of the sodium in salt (the amount varies, typically ranging from 10 to 50%) is replaced with minerals such as potassium chloride. Low-sodium salt may be an effective, scalable, and sustainable approach to reduce sodium and therefore reduce blood pressure and cardiovascular disease at the population level. Low-sodium salt programs have not been widely scaled up, although they have the potential to both reduce dietary sodium intake and increase dietary potassium intake. This article proposes a framework for a successful scale-up of low-sodium salt use in the home through four core strategies: availability, awareness and promotion, affordability, and advocacy. This framework identifies challenges and potential solutions within the core strategies to begin to understand the pathway to successful program implementation and evaluation of low-sodium salt use.

Common gut microbial metabolites of dietary flavonoids exert potent protective activities in ß-cells and skeletal muscle cells.

Flavonoids are dietary compounds with potential anti-diabetes activities. Many flavonoids have poor bioavailability and thus low circulating concentrations. Unabsorbed flavonoids are metabolized by the gut microbiota to smaller metabolites, which are more bioavailable than their precursors. The activities of these metabolites may be partly responsible for associations between flavonoids and health. However, these activities remain poorly understood. We investigated bioactivities of flavonoid microbial metabolites [hippuric acid (HA), homovanillic acid (HVA), and 5-phenylvaleric acid (5PVA)] in primary skeletal muscle and ß-cells compared to a native flavonoid [(-)-epicatechin, EC]. In muscle, EC was the most potent stimulator of glucose oxidation, while 5PVA and HA simulated glucose metabolism at 25 µM, and all compounds preserved mitochondrial function after insult. However, EC and the metabolites did not uncouple mitochonndrial respiration, with the exception of 5PVA at10 µM. In ß-cells, all metabolites more potently enhanced glucose-stimulated insulin secretion (GSIS) compared to EC. Unlike EC, the metabolites appear to enhance GSIS without enhancing ß-cell mitochondrial respiration or increasing expression of mitochondrial electron transport chain components, and with varying effects on ß-cell insulin content. The present results demonstrate the activities of flavonoid microbial metabolites for preservation of ß-cell function and glucose utilization. Additionally, our data suggest that metabolites and native compounds may act by distinct mechanisms, suggesting complementary and synergistic activities in vivo which warrant further investigation. This raises the intriguing prospect that bioavailability of native dietary flavonoids may not be as critical of a limiting factor to bioactivity as previously thought.