Connecting to the Data-Intensive Future of Scientific Research

In recent years enormous amounts of digital data have become available to scientific researchers. This flood of data is transforming the way scientific research is conducted. Independent researchers are in serious need of tools that will help them managed and preserve the large volumes of data being created in their own labs. Data management will not only help researchers get or keep a handle on their data, it will also help them stay relevant and competitive in increasingly strict funding environments. This paper provides summaries of best practices and case studies of data management that relate to three common data management challenges – multitudinous sensor data, short-term data loss, and digital images. We use a combination of open system solutions such as HydroServer Lite, an open system database for time series data, and proprietary tools such as Adobe Photoshop Lightroom. Each lab may require its own unique suite of tools, but these are becoming numerous and readily available, making it easier to archive and share data with collaborators and to discover and integrate published data sets

The Effects of Acute and Chronic Hypoxia on Cortisol, Glucose and Lactate Concentrations in Different Populations of Three-Spined Stickleback

The response of individuals from three different populations of three-spined sticklebacks to acute and chronic periods of hypoxia (4.4 kPa DO, 2.2 mg l-1) were tested using measures of whole-body (WB) cortisol, glucose and lactate. Although there was no evidence of a neuroendocrine stress response to acute hypoxia, fish from the population least likely to experience hypoxia in their native habitat had the largest response to low oxygen, with significant evidence of anaerobic glycolysis after two hours of hypoxia. However, there was no measurable effect of a more prolonged period (seven days) of hypoxia on any of the fish in this study, suggesting that they acclimated to this low level of oxygen over time. Between-population differences in the analytes tested were observed in the control fish of the acute hypoxia trial, which had been in the laboratory for 16 days. However, these differences were not apparent among the control fish in the chronic exposure groups that had been held in the laboratory for 23 days suggesting that these site-specific trends in physiological status were acclimatory. Overall, the results of this study suggest that local environmental conditions may shape sticklebacks’ general physiological profile as well as influencing their response to hypoxia

Ernest Everett Just, PhD: Pioneer in Ecological Developmental (Eco-Devo) Biology

Ernest Everett Just, a pioneering American biologist, discovered the fundamental role of the environment in the development of embryos. His work led to the creation of the area of biology known as ecological developmental (Eco-Devo) biology. However, both his work and the context of his scientific contributions are not widely known. His work covered a diversity of fields of biology, including marine biology, cytology, and parthogenesis (asexual reproduction where growth and development of embryos occur without fertilization). His findings provided important concepts in developmental biology that are used to this day. Specifically, he demonstrated the importance of the cellular cytoplasm and ectoplasm, in addition to the nucleus, in determining how development occurs in embryos. His worked was unique for its use of in vivo conditions using a variety of marine organisms. His publications on the “Basic Methods for Experiments on Eggs of Marine Mammals” in 1922 and “The Biology of the Cell Surface” in 1939 are still regarded as two of the most comprehensive reviews in cell biology. In this manuscript we present Dr. Just’s childhood in Charleston, SC, unlikely attendance and success at Dartmouth College, and his groundbreaking work, which was developed at the Marine Biological Laboratory (MBL) at Woods Hole, Europe, and Howard University

Effect of Applied Biosolids to Bahiagrass Pastures on Copper Status of Cattle

When grazing ruminants consume forages high in Mo but adequate in S, there is a risk of molybdenosis (a Mo-induced Cu deficiency). This occurs when Mo, S, and Cu join to form Cu-thiomolybdate complexes in the rumen that are not readily absorbed (Suttle, 1991). High dietary S reduces Cu absorption, possibly due to unabsorbable Cu sulphide formation, independent from its part in thiomolybdate complexes. The use of municipal sludge (biosolids) as a pasture fertiliser is of interest since some contain high Mo which may induce Cu deficiency. The objective of this study was to evaluate the performance and Cu status of cattle grazing pastures fertilized with biosolids

The impact of mining and mining exploration on range resources and pastoral pursuits in the Pilbara, Gascoyne, Murchison and Goldfields regions of Western Australia

Mining activity occurs very widely over relatively small areas of the rangelands. However, it is an intense landuse which can create significant offsite effects. Mining activity is most common around metamorphic \u27greenstone\u27 belts and broad drainages. Pastoralists reported both benefits and adverse affects as a consequence of mining activity. The main grievances related to unnecessary and excessive disturbance of pastoral land and the failure of operators to inform the pastoralist of their intentions

Phase Ib/II Study of the Safety and Efficacy of Combination Therapy with Multikinase VEGF Inhibitor Pazopanib and MEK Inhibitor Trametinib In Advanced Soft Tissue Sarcoma.

Purpose: Pazopanib, a multireceptor tyrosine kinase inhibitor targeting primarily VEGFRs1–3, is approved for advanced soft tissue sarcoma (STS) and renal cell cancer. Downstream of VEGFR, trametinib is an FDA-approved MEK inhibitor used for melanoma. We hypothesized that vertical pathway inhibition using trametinib would synergize with pazopanib in advanced STS. Experimental Design: In an open-label, multicenter, investigator-initiated National Comprehensive Cancer Network (NCCN)-sponsored trial, patients with metastatic or advanced STS received pazopanib 800 mg and 2 mg of trametinib continuously for 28-day cycles. The primary endpoint was 4-month progression-free survival (PFS). Secondary endpoints were overall survival, response rate, and disease control rate. Results: Twenty-five patients were enrolled. The median age was 49 years (range, 22–77 years) and 52% were male. Median PFS was 2.27 months [95% confidence interval (CI), 1.9–3.9], and the 4-month PFS rate was 21.1% (95% CI, 9.7–45.9), which was not an improvement over the hypothesized null 4-month PFS rate of 28.3% (P ¼ 0.79). Median overall survival was 9.0 months (95% CI, 5.7–17.7). A partial response occurred in 2 (8%) of the evaluable patients (95% CI, 1.0–26.0), one with PIK3CA E542K-mutant embryonal rhabdomyosarcoma and another with spindle cell sarcoma. The disease control rate was 14/25 (56%; 95% CI, 34.9–75.6). The most common adverse events were diarrhea (84%), nausea (64%), and fatigue (56%). Conclusions: The combination of pazopanib and trametinib was tolerable without indication of added activity of the combination in STS. Further study may be warranted in RAS/RAF aberrant sarcomas. ©2017 AACR

Biofabrication of human articular cartilage: a path towards the development of a clinical treatment

Cartilage injuries cause pain and loss of function, and if severe may result in osteoarthritis (OA). 3D bioprinting is now a tangible option for the delivery of bioscaffolds capable of regenerating the deficient cartilage tissue. Our team has developed a handheld device, the Biopen, to allow in situ additive manufacturing during surgery. Given its ability to extrude in a core/shell manner, the Biopen can preserve cell viability during the biofabrication process, and it is currently the only biofabrication tool tested as a surgical instrument in a sheep model using homologous stem cells. As a necessary step toward the development of a clinically relevant protocol, we aimed to demonstrate that our handheld extrusion device can successfully be used for the biofabrication of human cartilage. Therefore, this study is a required step for the development of a surgical treatment in human patients. In this work we specifically used human adipose derived mesenchymal stem cells (hADSCs), harvested from the infrapatellar fat pad of donor patients affected by OA, to also prove that they can be utilized as the source of cells for the future clinical application. With the Biopen, we generated bioscaffolds made of hADSCs laden in gelatin methacrylate, hyaluronic acid methacrylate and cultured in the presence of chondrogenic stimuli for eight weeks in vitro. A comprehensive characterisation including gene and protein expression analyses, immunohistology, confocal microscopy, second harmonic generation, light sheet imaging, atomic force mycroscopy and mechanical unconfined compression demonstrated that our strategy resulted in human hyaline-like cartilage formation. Our in situ biofabrication approach represents an innovation with important implications for customizing cartilage repair in patients with cartilage injuries and OA

Wireless ion selective electrode autonomous sensing system

A paradigm shift in sensing methods and principles is required to meet the legislative demands for detecting hazardous substances in the molecular world. This will encompass the development of new sensing technologies capable of performing very selective and sensitive measurements at an acceptable cost, developed by multidisciplinary teams of chemists, engineers and computer scientists to harvest information from a multitude of molecular targets in health, food and the environment. In this study we present the successful implementation of a low-cost, wireless chemical sensing system that employs a minimum set of components for effective operation. Specifically, our efforts resulted in a wireless, tri-electrode, ISE pH sensor for use in environmental monitoring. Sensor calibration and validated insitu field trials have been carried out and are presented in this paper

Seasonal Performance of White Clover in Mixed-Sward Grazing Pasture Highlights Genotype by Environment Interaction

White clover is an important forage crop because of its nutritional value, ability to provide plantavailable nitrogen via symbiosis with Rhizobium soil bacteria, and year-round availability of dry matter (DM) yield. However, its performance in mixed sward-based pastures is characterised by seasonal variability and declining DM yield over time. The identification of white clover genotypes adapted for across seasonal performance is an important goal in white clover breeding. In this study, we evaluated the seasonal performance of 200 white clover half-sib families using visual growth scores and calibrated dry matter yield based on growth scores measured for three years in two locations. Results showed significant variation for growth scores across years, seasons and locations. Significant G×E was observed in the form of year, location and season interactions. Calibrated DM yield was highest in the second-year summer with clover content declining in the third year. Spring and winter were identified as potential vulnerable periods for white clover growth in pastures