Promises and Perils of Big Data: Philosophical Constraints on Chemical Ontologies.

Chemistry is experiencing a paradigm shift in the way it interacts with data. So-called "big data" are collected and used at unprecedented scales with the idea that algorithms can be designed to aid in chemical discovery. As data-enabled practices become ever more ubiquitous, chemists must consider the organization and curation of their data, especially as it is presented to both humans and increasingly intelligent algorithms. One of the most promising organizational schemes for big data is a construct termed an ontology. In data science, ontologies are systems that represent relations among objects and properties in a domain of discourse. As chemistry encounters larger and larger data sets, the ontologies that support chemical research will likewise increase in complexity, and the future of chemistry will be shaped by the choices made in developing big data chemical ontologies. How such ontologies will work should therefore be a subject of significant attention in the chemical community. Now is the time for chemists to ask questions about ontology design and use: How should chemical data be organized? What can be reasonably expected from an organizational structure? Is a universal ontology tenable? As some of these questions may be new to chemists, we recommend an interdisciplinary approach that draws on the long history of philosophers of science asking questions about the organization of scientific concepts, constructs, models, and theories. This Perspective presents insights from these long-standing studies and initiates new conversations between chemists and philosophers.

Does Thoracic Manipulation Cause Extravasation at Joint Following Facet Injections?

Facet injections and other pain management interventions are commonly performed in combination with conservative therapy to address spinal pain. Joint mobilizations are a highly utilized intervention for manual practitioners to treat patients with spinal pain. Clinical reasoning and decision making models have not been well described in the literature assessing if and when joint mobilizations are appropriate interventions immediately or shortly following facet injection procedures. It has not been well studied if joint mobilizations immediately following facet injections negatively impact the injected solution at the respective joint and thus influence therapeutic effect. More specifically, there is a paucity of evidence assessing this at the thoracic spine. The purpose of this study was to assess if thoracic joint high-velocity low amplitude thrust manipulations caused extravasation of injected radiolucent material at respective thoracic facet joints on a cadaver. This study included an expert physician performing ultrasound-guided facet injections, an experienced manual physical therapist performing joint mobilization techniques, and fluoroscopic assessment of radiolucent material pre- and post-manipulation by a board-certified radiologist with experience in this field of study. Imaging interpretation confirmed that extravasation at respective joints did not occur following manipulation. This basic research can help guide clinical reasoning for practitioners considering implementing manual therapy techniques following facet injections and help guide further research.

Seeing Double: A Case of ACL Tears in Monozygotic Twin Female Athletes Within 48 Hours.

Anterior cruciate ligament (ACL) injuries are a serious issue for young athletes. These injuries are devastating and costly, leading to significant time away from sports, and substantial financial cost. A case is presented in which monozygotic twin sisters sustained ACL injuries within 48 hours of one another. Limited research is available studying twins with ACL tears and the risk factors associated with them. This is the first reported case of monozygotic sisters that are high-level athletes with ACL tears in such close proximity to one another. Enhanced knowledge of genetic contribution to ACL injuries is important to better understand predisposing factors and to develop preventative approaches. More research is needed to support a distinct association between ACL rupture and genetic variants.

Cervicothoracic Manipulation Techniques Reviewed Utilizing Three-Dimensional Spine Model.

Currently, there is a paucity of studies that describe prone cervicothoracic joint high-velocity low-amplitude (HVLA) thrust techniques using an anatomically accurate, biomimetic three-dimensional (3D) spine model for educational demonstration. The purpose of this technical report was to present a learning model for two prone cervicothoracic HVLA thrust techniques using a 3D model, review intersegmental mobility observed on a 3D spine model with application of the techniques, and lastly discuss potential applications of this learning model.

Luminal Toxin-Binding Agents for Clostridium difficile Infection.

OBJECTIVE: To systematically search the literature for trials evaluating luminal toxin-binding agents (LTBAs) for Clostridium difficile infection (CDI). METHODS: A systematic search was conducted utilizing PubMed and International Pharmaceutical Abstracts with the following terms: anion-exchange resins, C difficile, cholestyramine, tolevamer, and colestipol. Articles were included if published in the English language and reported clinical outcomes of more than 5 adult humans with CDI treated with LTBAs. RESULTS: Nearly all clinical trials evaluated LTBA as monotherapy for CDI and LTBAs are inferior to standard therapy. In contemporary practice, LTBAs are employed as adjunctive or sequential therapy for which there is a paucity of data. Some data suggest potential efficacy for recurrent CDI. Current guidelines for CDI assert LTBAs are contraindicated due to drug-drug interactions with vancomycin. However, the impact of this interaction on clinical outcomes has not been evaluated, and it is unknown whether higher doses of vancomycin or separating the administration of LTBAs from vancomycin would mitigate this interaction. CONCLUSION: LTBA monotherapy is inferior to vancomycin and metronidazole for CDI. Some data indicate possible benefit in reducing recurrent CDI, but outcomes with adjunctive and/or sequential LTBAs are unavailable. Further studies are needed to investigate the role of LTBAs for CDI.

Enhanced delivery of microRNA mimics to cardiomyocytes using ultrasound responsive microbubbles reverses hypertrophy in an in-vitro model.

BACKGROUND: Cardiovascular diseases (CVD) account for 36% of deaths in Europe and the United States. Gene therapy can act as a therapeutic modality for the treatment of CVD. The use of microRNA mimetics may be advantageous as they regulate important processes in health and pathology. A major hurdle for using miRNA therapies relates to site specific delivery and sufficient cellular uptake of material to achieve efficacy OBJECTIVE: To assess the feasibility of ultrasound responsive microbubble mediated delivery of miR mimics to cardiomyocytes. METHODS: Liposome/microbubble formulations were added to HL-1 cardiomyocytes in the presence/absence of ultrasound (US). Transfection efficacy and functionality was assessed using epifluorescent microscopy, flow cytometry and qRT-PCR. DNA Quantification post-ultrasound mediated transfection of HL-1s using microbubbles was quantified. The capability of miR-133 microbubble formulations to suppress hypertrophy were measured by quantifying changes in cell size. RESULTS: Ultrasound mediated microbubble formulations enhanced intracellular delivery of miR mimics in cardiomyocytes. Both complexed/encapsulated miR-microbubble formulations delivered functional miR mimics and showed no adverse effect on cardiomyocyte viability. Furthermore, ultrasound mediated microbubble transfection of miR-133 mimics reversed cardiomyocyte hypertrophy in an in-vitro model. CONCLUSIONS: This novel delivery method has the potential for further development as a targeted delivery strategy for miR therapeutics to the heart.

Orchestrating osteogenic differentiation of mesenchymal stem cells--identification of placental growth factor as a mechanosensitive gene with a pro-osteogenic role.

Skeletogenesis is initiated during fetal development and persists through adult life as either a remodeling process in response to homeostatic regulation or as a regenerative process in response to physical injury. Mesenchymal stem cells (MSCs) play a crucial role providing progenitor cells from which osteoblasts, bone matrix forming cells are differentiated. The mechanical environment plays an important role in regulating stem cell differentiation into osteoblasts, however, the mechanisms by which MSCs respond to mechanical stimuli are yet to be fully elucidated. To increase understanding of MSC mechanotransuction and osteogenic differentiation, this study aimed to identify novel, mechanically augmented genes and pathways with pro-osteogenic functionality. Using collagen glycoaminoglycan scaffolds as mimics of native extracellular matrix, to create a 3D environment more representative of that found in bone, MSC-seeded constructs were mechanically stimulated in a flow-perfusion bioreactor. Global gene expression profiling techniques were used to identify potential candidates warranting further investigation. Of these, placental growth factor (PGF) was selected and expression levels were shown to strongly correlate to both the magnitude and duration of mechanical stimulation. We demonstrated that PGF gene expression was modulated through an actin polymerization-mediated mechanism. The functional role of PGF in modulating MSC osteogenic differentiation was interrogated, and we showed a concentration-dependent response whereby low concentrations exhibited the strongest pro-osteogenic effect. Furthermore, pre-osteoclast migration and differentiation, as well as endothelial cell tubule formation also maintained concentration-dependent responses to PGF, suggesting a potential role for PGF in bone resorption and angiogenesis, processes key to bone remodeling and fracture repair.

Visualizing feasible operating ranges within tissue engineering systems using a "windows of operation" approach: a perfusion-scaffold bioreactor case study.

Tissue engineering approaches to developing functional substitutes are often highly complex, multivariate systems where many aspects of the biomaterials, bio-regulatory factors or cell sources may be controlled in an effort to enhance tissue formation. Furthermore, success is based on multiple performance criteria reflecting both the quantity and quality of the tissue produced. Managing the trade-offs between different performance criteria is a challenge. A "windows of operation" tool that graphically represents feasible operating spaces to achieve user-defined levels of performance has previously been described by researchers in the bio-processing industry. This paper demonstrates the value of "windows of operation" to the tissue engineering field using a perfusion-scaffold bioreactor system as a case study. In our laboratory, perfusion bioreactor systems are utilized in the context of bone tissue engineering to enhance the osteogenic differentiation of cell-seeded scaffolds. A key challenge of such perfusion bioreactor systems is to maximize the induction of osteogenesis but minimize cell detachment from the scaffold. Two key operating variables that influence these performance criteria are the mean scaffold pore size and flow-rate. Using cyclooxygenase-2 and osteopontin gene expression levels as surrogate indicators of osteogenesis, we employed the "windows of operation" methodology to rapidly identify feasible operating ranges for the mean scaffold pore size and flow-rate that achieved user-defined levels of performance for cell detachment and differentiation. Incorporation of such tools into the tissue engineer's armory will hopefully yield a greater understanding of the highly complex systems used and help aid decision making in future translation of products from the bench top to the market place.

Influence of shear stress in perfusion bioreactor cultures for the development of three-dimensional bone tissue constructs: a review.

Bone tissue engineering aims to generate clinically applicable bone graft substitutes in an effort to ease the demands and reduce the potential risks associated with traditional autograft and allograft bone replacement procedures. Biomechanical stimuli play an important role under physiologically relevant conditions in the normal formation, development, and homeostasis of bone tissue--predominantly, strain (predicted levels in vivo for humans <2000 µÎµ) caused by physical deformation, and fluid shear stress (0.8-3 Pa), generated by interstitial fluid movement through lacunae caused by compression and tension under loading. Therefore, in vitro bone tissue cultivation strategies seek to incorporate biochemical stimuli in an effort to create more physiologically relevant constructs for grafting. This review is focused on collating information pertaining to the relationship between fluid shear stress, cellular deformation, and osteogenic differentiation, providing further insight into the optimal culture conditions for the creation of bone tissue substitutes.

Sub-population analysis of human cancer vaccine cells--ultra scale-down characterization of response to shear.

The allogeneic whole cell therapy field presents a novel challenge for cell line selection. Large numbers of candidates will he screened for desirable traits including cell growth rates and maintenance of critical product attributes. Screening cell lines for susceptibility to large scale processing conditions has become of increasing importance; innovators do not wish to face the quandary of clinically efficacious cell lines that show poor manufacturability. We have previously described an ultra scale-down method for assessing the impact of the hydrodynamic environment on human cells (McCoy et al., 2009). This body of work describes the validation of this experimental approach using a second, clinically tested, human prostate cancer cell line and describes an additional level of sub-population characterisation. The small-scale conditions set were similar to those expected in downstream process, formulation and vial filling operations with maximum shear rates ranging from 30 x 10(3) to 90 x 10(3) s(-1)(equivalent maximum power dissipation rates of 1.5 x 10(3) to 14 x 10(3) W kg(-1)). Changes to critical cell quality attributes such as membrane integrity retention, cell surface marker staining levels (CD9, CD59, CD147) and cell surface marker density is described. Evaluation of two sub-populations which are formed in response to shear showed distinct staining profiles. Identification of these phenotypically distinct populations, derived in response to the same hydrodynamic environment, poses an interesting bio-processing challenge with regards to both maintenance of product quality, but also highlights the potential benefit of process manipulation through shear-rate intervention with regards to product efficacy.

Ultra scale-down studies of the effect of shear on cell quality; Processing of a human cell line for cancer vaccine therapy.

Whole cell therapy is showing potential in the clinic for the treatment of many chronic diseases. The translation of laboratory-scale methods for cell harvesting and formulation to commercial-scale manufacturing offers major bioprocessing challenges. This is especially the case when the cell properties determine the final product effectiveness. This study is focused on developing an ultra scale-down method for assessing the impact of the hydrodynamic environment on human cells that constitute the therapeutic product. Small volumes of a prostate cancer cell line, currently being developed in late phase II clinical trials as an allogeneic whole cell vaccine therapy for prostate cancer, were exposed to hydrodynamic shear rates similar to those present in downstream process, formulation and vial filling operations. A small scale rotating disc shear device (20 mL) was used over a range of disc speeds to expose cells to maximum shear rates ranging from 90 x 10(3) to 175 x 10(3) s(-1) (equivalent maximum power dissipation rates of 14 x 10(3) to 52 x 10(3) W kg(-1)). These cells were subsequently analyzed for critical cell quality attributes such as the retention of membrane integrity and cell surface marker profile and density. Three cell surface markers (CD9, CD147, and HLAA-C) were studied. The cell markers exhibited different levels of susceptibility to hydrodynamic shear but in all cases this was less than or equal to the loss of membrane integrity. It is evident that the marker, or combination or markers, which might provide the required immunogenic response, will be affected by hydrodynamic shear environment during bioprocessing, if the engineering environment is not controlled to within the limits tolerated by the cell components.