Equivalence between short-time biphasic and incompressible elastic material responses.

PubMed

Ateshian, Gerard A; Ellis, Benjamin J; Weiss, Jeffrey A

2007-06-01

Porous-permeable tissues have often been modeled using porous media theories such as the biphasic theory. This study examines the equivalence of the short-time biphasic and incompressible elastic responses for arbitrary deformations and constitutive relations from first principles. This equivalence is illustrated in problems of unconfined compression of a disk, and of articular contact under finite deformation, using two different constitutive relations for the solid matrix of cartilage, one of which accounts for the large disparity observed between the tensile and compressive moduli in this tissue. Demonstrating this equivalence under general conditions provides a rationale for using available finite element codes for incompressible elastic materials as a practical substitute for biphasic analyses, so long as only the short-time biphasic response is sought. In practice, an incompressible elastic analysis is representative of a biphasic analysis over the short-term response deltat

Biphasic responses in multi-site phosphorylation systems.

PubMed

Suwanmajo, Thapanar; Krishnan, J

2013-12-06

Multi-site phosphorylation systems are repeatedly encountered in cellular biology and multi-site modification is a basic building block of post-translational modification. In this paper, we demonstrate how distributive multi-site modification mechanisms by a single kinase/phosphatase pair can lead to biphasic/partial biphasic dose-response characteristics for the maximally phosphorylated substrate at steady state. We use simulations and analysis to uncover a hidden competing effect which is responsible for this and analyse how it may be accentuated. We build on this to analyse different variants of multi-site phosphorylation mechanisms showing that some mechanisms are intrinsically not capable of displaying this behaviour. This provides both a consolidated understanding of how and under what conditions biphasic responses are obtained in multi-site phosphorylation and a basis for discriminating between different mechanisms based on this. We also demonstrate how this behaviour may be combined with other behaviour such as threshold and bistable responses, demonstrating the capacity of multi-site phosphorylation systems to act as complex molecular signal processors.

miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering.

PubMed

Stiefel, Fabian; Fischer, Simon; Sczyrba, Alexander; Otte, Kerstin; Hesse, Friedemann

2016-05-10

Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production modes for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where the culture temperature is decreased to maximize volumetric product yields. However, it remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37°C versus a temperature shift to 30°C. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which were differentially expressed in the different cell lines and cultivation phases. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. This study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch production process and functionally evaluated their potential for host cell engineering. Copyright © 2016. Published by Elsevier B.V.

Generation of useful energy from process fluids using the biphase turbine

NASA Astrophysics Data System (ADS)

Helgeson, N. L.

1981-01-01

The six largest energy consuming industries in the United States were surveyed to determine the energy savings that could result from applying the Biphase turbine to industrial process streams. A national potential energy savings of 58 million barrels of oil per year (technical market) was identified. This energy is recoverable from flashing gas liquid process streams and is separate and distinct from exhaust gas waste heat recovery. The industries surveyed in this program were the petroleum chemical, primary metals, paper and pulp, stone-clay-glass, and food. It was required to determine the applicability of the Biphase turbine to flashing operations connected with process streams, to determine the energy changes associated with these flashes if carried out in a Biphase turbine, and to determine the suitability (technical and economical feasibility) of applying the Biphase turbine to these processes.

Surface characterization of colloidal-sol gel derived biphasic HA/FA coatings.

PubMed

Cheng, Kui; Zhang, Sam; Weng, Wenjian

2007-10-01

Hydroxyapatite (HA) powders are ultrasonically dispersed in the precursor of fluoridated hydroxyapatite (FHA) or fluorapatite (FA) to form a "colloidal sol". HA/FA biphasic coatings are prepared on Ti6Al4V substrate via dip coating, 150 degrees C drying and 600 degrees C firing. The coatings show homogenous distribution of HA particles in the FA matrix. The relative phase proportion can be tailored by the amount of HA in the colloidal sol. The surfaces of the coatings consist of two kinds of distinct domains: HA and FA, resulting in a compositionally heterogeneous surface. The biphasic coating surface becomes increasingly rougher with HA powders, from around 200 nm of pure FA to 400-600 nm in Ra of biphasic coatings. The rougher biphasic HA/FA surfaces with chemically controllable domains will favor cell attachment, apatite layer deposition and necessary dissolution in clinical applications.

Cardioversion Efficacy Using Pulsed Biphasic or Biphasic Truncated Exponential Waveforms: A Randomized Clinical Trial.

PubMed

Schmidt, Anders S; Lauridsen, Kasper G; Adelborg, Kasper; Torp, Peter; Bach, Leif F; Jepsen, Simon M; Hornung, Nete; Deakin, Charles D; Rickers, Hans; Løfgren, Bo

2017-03-08

Several different defibrillators are currently used for cardioversion and defibrillation of cardiac arrhythmias. The efficacy of a novel pulsed biphasic (PB) waveform has not been compared to other biphasic waveforms. Accordingly, this study aims to compare the efficacy and safety of PB shocks with biphasic truncated exponential (BTE) shocks in patients undergoing cardioversion of atrial fibrillation or -flutter. This prospective, randomized study included patients admitted for elective direct current cardioversion. Patients were randomized to receive cardioversion using either PB or BTE shocks. We used escalating shocks until sinus rhythm was obtained or to a maximum of 4 shocks. Patients randomized to PB shocks received 90, 120, 150, and 200 J and patients randomized to BTE shocks received 100, 150, 200, and 250 J, as recommended by the manufacturers. In total, 69 patients (51%) received PB shocks and 65 patients (49%) BTE shocks. Successful cardioversion, defined as sinus rhythm 4 hours after cardioversion, was achieved in 43 patients (62%) using PB shocks and in 56 patients (86%) using BTE shocks; ratio 1.4 (95% CI 1.1-1.7) ( P =0.002). There was no difference in safety (ie, myocardial injury judged by changes in high-sensitive troponin I levels; ratio 1.1) (95% CI 1.0-1.3), P =0.15. The study was terminated prematurely because of an adverse event. Cardioversion using a BTE waveform was more effective when compared with a PB waveform. There was no difference in safety between the 2 waveforms, as judged by changes in troponin I levels. URL: http://www.clinicaltrials.gov. Unique identifier: NCT02317029. © 2017 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

A mixed-penalty biphasic finite element formulation incorporating viscous fluids and material interfaces.

PubMed

Chan, B; Donzelli, P S; Spilker, R L

2000-06-01

The fluid viscosity term of the fluid phase constitutive equation and the interface boundary conditions between biphasic, solid and fluid domains have been incorporated into a mixed-penalty finite element formulation of the linear biphasic theory for hydrated soft tissue. The finite element code can now model a single-phase viscous incompressible fluid, or a single-phase elastic solid, as limiting cases of a biphasic material. Interface boundary conditions allow the solution of problems involving combinations of biphasic, fluid and solid regions. To incorporate these conditions, the volume-weighted mixture velocity is introduced as a degree of freedom at interface nodes so that the kinematic continuity conditions are satisfied by conventional finite element assembly techniques. Results comparing our numerical method with an independent, analytic solution for the problem of Couette flow over rigid and deformable porous biphasic layers show that the finite element code accurately predicts the viscous fluid flows and deformation in the porous biphasic region. Thus, the analysis can be used to model the interface between synovial fluid and articular cartilage in diarthrodial joints. This is an important step toward modeling and understanding the mechanisms of joint lubrication and another step toward fully modeling the in vivo behavior of a diarthrodial joint.

Metal separations using aqueous biphasic partitioning systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaiko, D.J.; Zaslavsky, B.; Rollins, A.N.

1996-05-01

Aqueous biphasic extraction (ABE) processes offer the potential for low-cost, highly selective separations. This countercurrent extraction technique involves selective partitioning of either dissolved solutes or ultrafine particulates between two immiscible aqueous phases. The extraction systems that the authors have studied are generated by combining an aqueous salt solution with an aqueous polymer solution. They have examined a wide range of applications for ABE, including the treatment of solid and liquid nuclear wastes, decontamination of soils, and processing of mineral ores. They have also conducted fundamental studies of solution microstructure using small angle neutron scattering (SANS). In this report they reviewmore » the physicochemical fundamentals of aqueous biphase formation and discuss the development and scaleup of ABE processes for environmental remediation.« less

Evaluation of the finite element software ABAQUS for biomechanical modelling of biphasic tissues.

PubMed

Wu, J Z; Herzog, W; Epstein, M

1998-02-01

The biphasic cartilage model proposed by Mow et al. (1980) has proven successful to capture the essential mechanical features of articular cartilage. In order to analyse the joint contact mechanics in real, anatomical joints, the cartilage model needs to be implemented into a suitable finite element code to approximate the irregular surface geometries of such joints. However, systematic and extensive evaluation of the capacity of commercial software for modelling the contact mechanics with biphasic cartilage layers has not been made. This research was aimed at evaluating the commercial finite element software ABAQUS for analysing biphasic soft tissues. The solutions obtained using ABAQUS were compared with those obtained using other finite element models and analytical solutions for three numerical tests: an unconfined indentation test, a test with the contact of a spherical cartilage surface with a rigid plate, and an axi-symmetric joint contact test. It was concluded that the biphasic cartilage model can be implemented into the commercial finite element software ABAQUS to analyse practical joint contact problems with biphasic articular cartilage layers.

Biphasic Synergistic Gel Materials with Switchable Mechanics and Self-Healing Capacity.

PubMed

Zhao, Ziguang; Liu, Yuxia; Zhang, Kangjun; Zhuo, Shuyun; Fang, Ruochen; Zhang, Jianqi; Jiang, Lei; Liu, Mingjie

2017-10-16

A fabrication strategy for biphasic gels is reported, which incorporates high-internal-phase emulsions. Closely packed micro-inclusions within the elastic hydrogel matrix greatly improve the mechanical properties of the materials. The materials exhibit excellent switchable mechanics and shape-memory performance because of the switchable micro- inclusions that are incorporated into the hydrogel matrix. The produced materials demonstrated a self-healing capacity that originates from the noncovalent effect of the biphasic heteronetwork. The aforementioned characteristics suggest that the biphasic gels may serve as ideal composite gel materials with validity in a variety of applications, such as soft actuators, flexible devices, and biological materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Structurally and Functionally Biomimetic Biphasic Scaffold for Intervertebral Disc Tissue Engineering

PubMed Central

Choy, Andrew Tsz Hang; Chan, Barbara Pui

2015-01-01

Tissue engineering offers high hopes for the treatment of intervertebral disc (IVD) degeneration. Whereas scaffolds of the disc nucleus and annulus have been extensively studied, a truly biomimetic and mechanically functional biphasic scaffold using naturally occurring extracellular matrix is yet to be developed. Here, a biphasic scaffold was fabricated with collagen and glycosaminoglycans (GAGs), two of the most abundant extracellular matrix components in the IVD. Following fabrication, the scaffold was characterized and benchmarked against native disc. The biphasic scaffold was composed of a collagen-GAG co-precipitate making up the nucleus pulposus-like core, and this was encapsulated in multiple lamellae of photochemically crosslinked collagen membranes comprising the annulus fibrosus-like lamellae. On mechanical testing, the height of our engineered disc recovered by ~82-89% in an annulus-independent manner, when compared with the 99% recovery exhibited by native disc. The annulus-independent nature of disc height recovery suggests that the fluid replacement function of the engineered nucleus pulposus core might mimic this hitherto unique feature of native disc. Biphasic scaffolds comprised of 10 annulus fibrosus-like lamellae had the best overall mechanical performance among the various designs owing to their similarity to native disc in most aspects, including elastic compliance during creep and recovery, and viscous compliance during recovery. However, the dynamic mechanical performance (including dynamic stiffness and damping factor) of all the biphasic scaffolds was similar to that of the native discs. This study contributes to the rationalized design and development of a biomimetic and mechanically viable biphasic scaffold for IVD tissue engineering. PMID:26115332

Electron transport in zinc-blende wurtzite biphasic gallium nitride nanowires and GaNFETs

DOE PAGES

Jacobs, Benjamin W.; Ayres, Virginia M.; Stallcup, Richard E.; ...

2007-10-19

Two-point and four-point probe electrical measurements of a biphasic gallium nitride nanowire and current–voltage characteristics of a gallium nitride nanowire based field effect transistor are reported. The biphasic gallium nitride nanowires have a crystalline homostructure consisting of wurtzite and zinc-blende phases that grow simultaneously in the longitudinal direction. There is a sharp transition of one to a few atomic layers between each phase. Here, all measurements showed high current densities. Evidence of single-phase current transport in the biphasic nanowire structure is discussed.

A re-examination of the biphasic theory of skeletal muscle growth.

PubMed Central

Levine, A S; Hegarty, P V

1977-01-01

Because of the importance of fibre diameter measurements it was decided to re-evaluate the biphasic theory of skeletal muscle growth and development. This theory proposes an initial memophasic distribution of muscle fibres which changes to a biphasic distribution during development. The theory is based on observations made on certain muscles in mice, where two distinct populations of fibre diameters (20 and 40 micronm) contribute to the biphasic distribution. In the present investigation corss sections of frozen biceps brachii of mice in rigor mortis were examined. The rigor state was used to avoid complications produced by thaw-rigor contraction. The diameters of the outermost and innermost fibres were found to be significantly different. However, if the outer and inner fibres were combined to form one group, no significant difference between this group and other random groups was found. The distributions of all groups were monophasic. The diameters of isolated fibres from mice and rats also displayed a monophasic distribution. This evidence leads to the conclusion that the biphasic theory of muscle growth is untenable. Some of the variables which may occur in fibre size and shape are discussed. Images Fig. 1 PMID:858691

Effect of coenzyme q10 on myopathic symptoms in patients treated with statins.

PubMed

Caso, Giuseppe; Kelly, Patricia; McNurlan, Margaret A; Lawson, William E

2007-05-15

Treatment of hypercholesterolemia with statins (3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors) is effective in the primary and secondary prevention of cardiovascular disease. However, statin use is often associated with a variety of muscle-related symptoms or myopathies. Myopathy may be related in part to statin inhibition of the endogenous synthesis of coenzyme Q10, an essential cofactor for mitochondrial energy production. The aim of this study is to determine whether coenzyme Q10 supplementation would reduce the degree of muscle pain associated with statin treatment. Patients with myopathic symptoms were randomly assigned in a double-blinded protocol to treatment with coenzyme Q10 (100 mg/day, n = 18) or vitamin E (400 IU/day, n = 14) for 30 days. Muscle pain and pain interference with daily activities were assessed before and after treatment. After a 30-day intervention, pain severity decreased by 40% (p <0.001) and pain interference with daily activities decreased by 38% (p <0.02) in the group treated with coenzyme Q10. In contrast, no changes in pain severity (+9%, p = NS) or pain interference with daily activities (-11%, p = NS) was observed in the group treated with vitamin E. In conclusion, results suggest that coenzyme Q10 supplementation may decrease muscle pain associated with statin treatment. Thus, coenzyme Q10 supplementation may offer an alternative to stopping treatment with these vital drugs.

Biphasic Dose Response in Low Level Light Therapy – An Update

PubMed Central

Huang, Ying-Ying; Sharma, Sulbha K; Carroll, James; Hamblin, Michael R

2011-01-01

Low-level laser (light) therapy (LLLT) has been known since 1967 but still remains controversial due to incomplete understanding of the basic mechanisms and the selection of inappropriate dosimetric parameters that led to negative studies. The biphasic dose-response or Arndt-Schulz curve in LLLT has been shown both in vitro studies and in animal experiments. This review will provide an update to our previous (Huang et al. 2009) coverage of this topic. In vitro mediators of LLLT such as adenosine triphosphate (ATP) and mitochondrial membrane potential show biphasic patterns, while others such as mitochondrial reactive oxygen species show a triphasic dose-response with two distinct peaks. The Janus nature of reactive oxygen species (ROS) that may act as a beneficial signaling molecule at low concentrations and a harmful cytotoxic agent at high concentrations, may partly explain the observed responses in vivo. Transcranial LLLT for traumatic brain injury (TBI) in mice shows a distinct biphasic pattern with peaks in beneficial neurological effects observed when the number of treatments is varied, and when the energy density of an individual treatment is varied. Further understanding of the extent to which biphasic dose responses apply in LLLT will be necessary to optimize clinical treatments. PMID:22461763

Biphasic decay of the Ca transient results from increased sarcoplasmic reticulum Ca leak

PubMed Central

Sankaranarayanan, Rajiv; Li, Yatong; Greensmith, David J.; Eisner, David A.

2016-01-01

Key points Ca leak from the sarcoplasmic reticulum through the ryanodine receptor (RyR) reduces the amplitude of the Ca transient and slows its rate of decay.In the presence of β‐adrenergic stimulation, RyR‐mediated Ca leak produces a biphasic decay of the Ca transient with a fast early phase and a slow late phase.Two forms of Ca leak have been studied, Ca‐sensitising (induced by caffeine) and non‐sensitising (induced by ryanodine) and both induce biphasic decay of the Ca transient.Only Ca‐sensitising leak can be reversed by traditional RyR inhibitors such as tetracaine.Ca leak can also induce Ca waves. At low levels of leak, waves occur. As leak is increased, first biphasic decay and then slowed monophasic decay is seen. The level of leak has major effects on the shape of the Ca transient. Abstract In heart failure, a reduction in Ca transient amplitude and contractile dysfunction can by caused by Ca leak through the sarcoplasmic reticulum (SR) Ca channel (ryanodine receptor, RyR) and/or decreased activity of the SR Ca ATPase (SERCA). We have characterised the effects of two forms of Ca leak (Ca‐sensitising and non‐sensitising) on calcium cycling and compared with those of SERCA inhibition. We measured [Ca2+]i with fluo‐3 in voltage‐clamped rat ventricular myocytes. Increasing SR leak with either caffeine (to sensitise the RyR to Ca activation) or ryanodine (non‐sensitising) had similar effects to SERCA inhibition: decreased systolic [Ca2+]i, increased diastolic [Ca2+]i and slowed decay. However, in the presence of isoproterenol, leak produced a biphasic decay of the Ca transient in the majority of cells while SERCA inhibition produced monophasic decay. Tetracaine reversed the effects of caffeine but not of ryanodine. When caffeine (1 mmol l−1) was added to a cell which displayed Ca waves, the wave frequency initially increased before waves disappeared and biphasic decay developed. Eventually (at higher caffeine concentrations), the

Hydroxyapatite/polylactide biphasic combination scaffold loaded with dexamethasone for bone regeneration.

PubMed

Son, Jun-Sik; Kim, Su-Gwan; Oh, Ji-Su; Appleford, Mark; Oh, Sunho; Ong, Joo L; Lee, Kyu-Bok

2011-12-15

This study presents a novel design of a ceramic/polymer biphasic combination scaffold that mimics natural bone structures and is used as a bone graft substitute. To mimic the natural bone structures, the outside cortical-like shells were composed of porous hydroxyapatite (HA) with a hollow interior using a polymeric template-coating technique; the inner trabecular-like core consisted of porous poly(D,L-lactic acid) (PLA) that was loaded with dexamethasone (DEX) and was directly produced using a particle leaching/gas forming technique to create the inner diameter of the HA scaffold. It was observed that the HA and PLA parts of the fabricated HA/PLA biphasic scaffold contained open and interconnected pore structures, and the boundary between both parts was tightly connected without any gaps. It was found that the structure of the combination scaffold was analogous to that of natural bone based on micro-computed tomography analysis. Additionally, the dense, uniform apatite layer was formed on the surface of the HA/PLA biphasic scaffold through a biomimetic process, and DEX was successfully released from the PLA of the biphasic scaffold over a 1-month period. This release caused human embryonic palatal mesenchyme cells to proliferate, differentiate, produce ECM, and form tissue in vitro. Therefore, it was concluded that this functionally graded scaffold is similar to natural bone and represents a potential bone-substitute material. Copyright © 2011 Wiley Periodicals, Inc.

Continuous Flow Science in an Undergraduate Teaching Laboratory: Bleach-Mediated Oxidation in a Biphasic System

ERIC Educational Resources Information Center

Kairouz, Vanessa; Collins, Shawn K.

2018-01-01

An undergraduate teaching laboratory experiment involving a continuous flow, bleach-mediated oxidation of aldehydes under biphasic conditions was developed that allowed students to explore concepts of mixing or mass transport, solvent sustainability, biphasic reactions, phase transfer catalysis, and continuous flow chemistry.

The added predictive value of biphasic events in ST analysis of the fetal electrocardiogram for intrapartum fetal monitoring.

PubMed

Becker, Jeroen H; Krikhaar, Anniek; Schuit, Ewoud; Mårtendal, Annika; Maršál, Karel; Kwee, Anneke; Visser, Gerard H A; Amer-Wåhlin, Isis

2015-02-01

To study the predictive value of biphasic ST-events for interventions for suspected fetal distress and adverse neonatal outcome, when using ST-analysis of the fetal electrocardiogram (FECG) for intrapartum fetal monitoring. Prospective cohort study. Three academic hospitals in Sweden. Women in labor with a high-risk singleton fetus in cephalic position beyond 36 weeks of gestation. In women in labor who were monitored with conventional cardiotocography, ST-waveform analysis was recorded and concealed. Traces with biphasic ST-events of the FECG (index) were compared with traces without biphasic events of the FECG. The ability of biphasic events to predict interventions for suspected fetal distress and adverse outcome was assessed using univariable and multivariable logistic regression analyses. Interventions for suspected fetal distress and adverse outcome (defined as presence of metabolic acidosis (i.e. umbilical cord pH <7.05 and base deficit in extracellular fluid >12 mmol), umbilical cord pH <7.00, 5-min Apgar score <7, admittance to neonatal intensive care unit or perinatal death). Although the presence of biphasic events of the FECG was associated with more interventions for fetal distress and an increased risk of adverse outcome compared with cases with no biphasic events, the presence of significant (i.e. intervention advised according to cardiotocography interpretation) biphasic events showed no independent association with interventions for fetal distress [odds ratio (OR) 1.71, 95% confidence interval (CI) 0.65-4.50] or adverse outcome (OR 1.96, 95% CI 0.74-5.24). The presence of significant biphasic events did not discriminate in the prediction of interventions for fetal distress or adverse outcome. Therefore, biphasic events in relation to ST-analysis monitoring during birth should be omitted if future studies confirm our findings. © 2014 Nordic Federation of Societies of Obstetrics and Gynecology.

Dissolved nutrients and atrazine removal by column-scale monophasic and biphasic rain garden model systems.

PubMed

Yang, Hanbae; McCoy, Edward L; Grewal, Parwinder S; Dick, Warren A

2010-08-01

Rain gardens are bioretention systems that have the potential to reduce peak runoff flow and improve water quality in a natural and aesthetically pleasing manner. We compared hydraulic performance and removal efficiencies of nutrients and atrazine in a monophasic rain garden design versus a biphasic design at a column-scale using simulated runoff. The biphasic rain garden was designed to increase retention time and removal efficiency of runoff pollutants by creating a sequence of water saturated to unsaturated conditions. We also evaluated the effect of C substrate availability on pollutant removal efficiency in the biphasic rain garden. Five simulated runoff events with various concentrations of runoff pollutants (i.e. nitrate, phosphate, and atrazine) were applied to the monophasic and biphasic rain gardens once every 5d. Hydraulic performance was consistent over the five simulated runoff events. Peak flow was reduced by approximately 56% for the monophasic design and 80% for the biphasic design. Both rain garden systems showed excellent removal efficiency of phosphate (89-100%) and atrazine (84-100%). However, significantly (p<0.001) higher removal of nitrate was observed in the biphasic (42-63%) compared to the monophasic rain garden (29-39%). Addition of C substrate in the form of glucose increased removal efficiency of nitrate significantly (p<0.001), achieving up to 87% removal at a treatment C/N ratio of 2.0. This study demonstrates the importance of retention time, environmental conditions (i.e. saturated/unsaturated conditions), and availability of C substrate for bioremediation of pollutants, especially nitrates, in rain gardens. (c) 2010 Elsevier Ltd. All rights reserved.

Operation and Performance of a Biphase Turbine Power Plant at the Cerro Prieto Geothermal Field (Final Report)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hays, Lance G.

2000-09-01

A full scale, wellhead Biphase turbine was manufactured and installed with the balance of plant at Well 103 of the Cerro Prieto geothermal resource in Baja, California. The Biphase turbine was first synchronized with the electrical grid of Comision Federal de Electricidad on August 20, 1997. The Biphase power plant was operated from that time until May 23, 2000, a period of 2 years and 9 months. A total of 77,549 kWh were delivered to the grid. The power plant was subsequently placed in a standby condition pending replacement of the rotor with a newly designed, higher power rotor andmore » replacement of the bearings and seals. The maximum measured power output of the Biphase turbine, 808 kWe at 640 psig wellhead pressure, agreed closely with the predicted output, 840 kWe. When combined with the backpressure steam turbine the total output power from that flow would be increased by 40% above the power derived only from the flow by the present flash steam plant. The design relations used to predict performance and design the turbine were verified by these tests. The performance and durability of the Biphase turbine support the conclusion of the Economics and Application Report previously published, (Appendix A). The newly designed rotor (the Dual Pressure Rotor) was analyzed for the above power condition. The Dual Pressure Rotor would increase the power output to 2064 kWe by incorporating two pressure letdown stages in the Biphase rotor, eliminating the requirement for a backpressure steam turbine. The power plant availability was low due to deposition of solids from the well on the Biphase rotor and balance of plant problems. A great deal of plant down time resulted from the requirement to develop methods to handle the solids and from testing the apparatus in the Biphase turbine. Finally an online, washing method using the high pressure two-phase flow was developed which completely eliminated the solids problem. The availability of the Biphase turbine itself was

Biphasic non-adrenergic, non-cholinergic relaxations of the mouse anococcygeus muscle.

PubMed Central

Gibson, A.; Yu, O.

1983-01-01

Trains of field stimulation of 60 s duration caused a biphasic relaxation of carbachol (50 microM)-induced tone in the mouse anococcygeus. The optimal pulse frequency and width were 10 Hz and 1 ms respectively. Tetrodotoxin (31, 124, and 310 nM) caused a dose-dependent reduction in the magnitude of both phases. Neither phase was affected by (+/-)-propranolol (1 microM), neostigmine (1 microM), (+)-tubocurarine (100 microM), or apamin (500 nM). Biphasic relaxations were observed in muscles from 6-hydroxydopamine pretreated mice. Haemolysed blood (10, 40, and 100 microliter/ml) reduced the magnitude of the first phase of nerve-induced relaxation to a greater extent than the second. This effect was reversible. Following a prolonged train of inhibitory nerve stimulation (10 Hz; 10 min) the magnitude of the first phase was reduced only slightly, but the second markedly. The possible relationships between the biphasic relaxation to field stimulation and putative non-adrenergic, non-cholinergic transmitters in the mouse anococcygeus are discussed. PMID:6652345

Evaluation of a biphasic in vitro dissolution test for estimating the bioavailability of carbamazepine polymorphic forms.

PubMed

Deng, Jia; Staufenbiel, Sven; Bodmeier, Roland

2017-07-15

The purpose of this study was to discriminate three crystal forms of carbamazepine (a BCS II drug) by in vitro dissolution testing and to correlate in vitro data with published in vivo data. A biphasic dissolution system (phosphate buffer pH6.8 and octanol) was used to evaluate the dissolution of the three polymorphic forms and to compare it with conventional single phase dissolution tests performed under sink and non-sink conditions. Similar dissolution profiles of three polymorphic forms were observed in the conventional dissolution test under sink conditions. Although a difference in dissolution was seen in the single phase dissolution test under non-sink conditions as well as in the aqueous phase of the biphasic test, little relevance for in vivo data was observed. In contrast, the biphasic dissolution system could discriminate between the different polymorphic forms in the octanol phase with a ranking of form III>form I>dihydrate form. This was in agreement with the in vivo performance. The dissolved drug available for oral absorption, which was dominated by dissolution and solution-mediated phase transformation, could be reflected in the biphasic dissolution test. Moreover, a good correlation was established between in vitro dissolution in the octanol phase of the biphasic test and in vivo pharmacokinetic data (R 2 =0.99). The biphasic dissolution method is a valuable tool to discriminate between different crystal forms in the formulations of poorly soluble drugs. Copyright © 2017. Published by Elsevier B.V.

Shock-induced termination of reentrant cardiac arrhythmias: Comparing monophasic and biphasic shock protocols

NASA Astrophysics Data System (ADS)

Bragard, Jean; Simic, Ana; Elorza, Jorge; Grigoriev, Roman O.; Cherry, Elizabeth M.; Gilmour, Robert F.; Otani, Niels F.; Fenton, Flavio H.

2013-12-01

In this article, we compare quantitatively the efficiency of three different protocols commonly used in commercial defibrillators. These are based on monophasic and both symmetric and asymmetric biphasic shocks. A numerical one-dimensional model of cardiac tissue using the bidomain formulation is used in order to test the different protocols. In particular, we performed a total of 4.8 × 106 simulations by varying shock waveform, shock energy, initial conditions, and heterogeneity in internal electrical conductivity. Whenever the shock successfully removed the reentrant dynamics in the tissue, we classified the mechanism. The analysis of the numerical data shows that biphasic shocks are significantly more efficient (by about 25%) than the corresponding monophasic ones. We determine that the increase in efficiency of the biphasic shocks can be explained by the higher proportion of newly excited tissue through the mechanism of direct activation.

Biphasic Effects of Alcohol on Delay and Probability Discounting

PubMed Central

Bidwell, L. Cinnamon; MacKillop, James; Murphy, James G.; Grenga, Andrea; Swift, Robert M.; McGeary, John E.

2014-01-01

Delay discounting and probability discounting are behavioral economic indices of impulsive and risky decision making that have been associated with addictive behavior, but the acute biphasic effects of alcohol on these decision-making processes are not well understood. This study sought to investigate the biphasic effects of alcohol on delay and probability discounting across the ascending and descending limbs of the breath alcohol concentration (BAC) curve, which are respectively characterized by the stimulant and sedative effects of alcohol. Delay and probability discounting were measured at four time points (Baseline, Ascending, Descending, and Endpoint) across the BAC curve at two target alcohol doses (40 mg/dl and 80 mg/dl) in healthy adults (N = 23 and 27, for both doses, respectively). There was no significant effect of alcohol on delay discounting at either dose. Alcohol significantly affected probability discounting, such that reduced discounting for uncertain rewards was evident during the descending limb of the BAC curve at the lower dose (p<.05) and during both the ascending and descending limb of the BAC curve at the higher dose (p<.05). Thus, alcohol resulted in increased risky decision making, particularly during the descending limb which is primarily characterized by the sedative effects of alcohol. These findings suggest that the biphasic effects of alcohol across the ascending and descending limbs of the BAC have differential effects on behavior related to decision-making for probabilistic, but not delayed, rewards. Parallels to and distinctions from previous findings are discussed. PMID:23750692

A hybrid composite system of biphasic calcium phosphate granules loaded with hyaluronic acid-gelatin hydrogel for bone regeneration.

PubMed

Faruq, Omar; Kim, Boram; Padalhin, Andrew R; Lee, Gun Hee; Lee, Byong-Taek

2017-10-01

An ideal bone substitute should be made of biocompatible materials that mimic the structure, characteristics, and functions of natural bone. Many researchers have worked on the fabrication of different bone scaffold systems including ceramic-polymer hybrid system. In the present study, we incorporated hyaluronic acid-gelatin hydrogel to micro-channeled biphasic calcium phosphate granules as a carrier to improve cell attachment and proliferation through highly interconnected porous structure. This hybrid system is composed of ceramic biphasic calcium phosphate granules measuring 1 mm in diameter with seven holes and hyaluronic acid-gelatin hydrogel. This combination of biphasic calcium phosphate and hyaluronic acid-gelatin retained suitable characteristics for bone regeneration. The resulting scaffold had a porosity of 56% with a suitable pore sizes. The mechanical strength of biphasic calcium phosphate granule increased after loading hyaluronic acid-gelatin from 4.26 ± 0.43 to 6.57 ± 0.25 MPa, which is highly recommended for cancellous bone substitution. Swelling and degradation rates decreased in the hybrid scaffold compared to hydrogel due to the presence of granules in hybrid scaffold. In vitro cytocompatibility studies were observed by preosteoblasts (MC3T3-E1) cell line and the result revealed that biphasic calcium phosphate/hyaluronic acid-gelatin significantly increased cell growth and proliferation compared to biphasic calcium phosphate granules. Analysis of micro-computed tomography data and stained tissue sections from the implanted samples showed that the hybrid scaffold had good osseointegration and better bone formation in the scaffold one and two months postimplantation. Histological section confirmed the formation of dense collagenous tissue and new bone in biphasic calcium phosphate/hyaluronic acid-gelatin scaffolds at two months. Our study demonstrated that such hybrid biphasic calcium phosphate/hyaluronic acid-gelatin scaffold is a

A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae.

PubMed

Atack, John M; Srikhanta, Yogitha N; Fox, Kate L; Jurcisek, Joseph A; Brockman, Kenneth L; Clark, Tyson A; Boitano, Matthew; Power, Peter M; Jen, Freda E-C; McEwan, Alastair G; Grimmond, Sean M; Smith, Arnold L; Barenkamp, Stephen J; Korlach, Jonas; Bakaletz, Lauren O; Jennings, Michael P

2015-07-28

Non-typeable Haemophilus influenzae contains an N(6)-adenine DNA-methyltransferase (ModA) that is subject to phase-variable expression (random ON/OFF switching). Five modA alleles, modA2, modA4, modA5, modA9 and modA10, account for over two-thirds of clinical otitis media isolates surveyed. Here, we use single molecule, real-time (SMRT) methylome analysis to identify the DNA-recognition motifs for all five of these modA alleles. Phase variation of these alleles regulates multiple proteins including vaccine candidates, and key virulence phenotypes such as antibiotic resistance (modA2, modA5, modA10), biofilm formation (modA2) and immunoevasion (modA4). Analyses of a modA2 strain in the chinchilla model of otitis media show a clear selection for ON switching of modA2 in the middle ear. Our results indicate that a biphasic epigenetic switch can control bacterial virulence, immunoevasion and niche adaptation in an animal model system.

Shock-induced termination of reentrant cardiac arrhythmias: Comparing monophasic and biphasic shock protocols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bragard, Jean, E-mail: jbragard@unav.es; Simic, Ana; Elorza, Jorge

2013-12-15

In this article, we compare quantitatively the efficiency of three different protocols commonly used in commercial defibrillators. These are based on monophasic and both symmetric and asymmetric biphasic shocks. A numerical one–dimensional model of cardiac tissue using the bidomain formulation is used in order to test the different protocols. In particular, we performed a total of 4.8 × 10{sup 6} simulations by varying shock waveform, shock energy, initial conditions, and heterogeneity in internal electrical conductivity. Whenever the shock successfully removed the reentrant dynamics in the tissue, we classified the mechanism. The analysis of the numerical data shows that biphasic shocksmore » are significantly more efficient (by about 25%) than the corresponding monophasic ones. We determine that the increase in efficiency of the biphasic shocks can be explained by the higher proportion of newly excited tissue through the mechanism of direct activation.« less

Preparation of highly infective Leishmania promastigotes by cultivation on SNB-9 biphasic medium.

PubMed

Grekov, Igor; Svobodová, Milena; Nohýnková, Eva; Lipoldová, Marie

2011-12-01

Protozoan hemoflagellates Leishmania are causative agents of leishmaniases and an important biological model for study of host-pathogen interaction. A wide range of methods of Leishmania cultivation on both biphasic and liquid media is available. Biphasic media are considered to be superior for initial isolation of the parasites and obtaining high promastigote infectivity; however, liquid media are more suitable for large-scale experiments. The aim of the present study was the adaptation and optimization of the cultivation of Leishmania promastigotes on a biphasic SNB-9 (saline-neopeptone-blood 9) medium that was originally developed for Trypanosoma cultivation and combines the advantages of biphasic and liquid media. SNB-9 medium is characterized with a large volume of the liquid phase, which facilitates the manipulation with the culture and provides parasite yields comparable to parasite yields on such liquid medium as Schneider's Insect Medium. We demonstrate that SNB-9 very considerably surpasses Schneider's Insect Medium in in vitro infectivity of the parasites. Additionally, we show that the ratio of apoptotic parasites, which are important for the infectivity of the inoculum, in Leishmania culture in SNB-9 is higher than in Leishmania culture in Schneider's Insect Medium. Thus, we demonstrate that the cultivation of Leishmania on SNB-9 reliably yields highly infective promastigotes suitable for experimental infection. Copyright © 2011 Elsevier B.V. All rights reserved.

Hearing loss in a patient with the myopathic form of mitochondrial DNA depletion syndrome and a novel mutation in the TK2 gene.

PubMed

Martí, Ramon; Nascimento, Andrés; Colomer, Jaume; Lara, Mari C; López-Gallardo, Ester; Ruiz-Pesini, Eduardo; Montoya, Julio; Andreu, Antoni L; Briones, Paz; Pineda, Mercè

2010-08-01

Mitochondrial DNA (mtDNA) depletion syndrome (MDS) is a devastating disorder of infancy caused by a significant reduction of the number of copies of mitochondrial DNA in one or more tissues. We report a Spanish patient with the myopathic form of MDS, harboring two mutations in the thymidine kinase 2 gene (TK2): a previously reported deletion (p.K244del) and a novel nucleotide duplication in the exon 2, generating a frameshift and premature stop codon. Sensorineural hearing loss was a predominant symptom in the patient and a novel feature of MDS due to TK2 mutations. The patient survived up to the age of 8.5 y, which confirms that survival above the age of 5 y is not infrequent in patients with MDS due to TK2 deficiency.

Pretreatment of Eucalyptus in biphasic system for furfural production and accelerated enzymatic hydrolysis.

PubMed

Zhang, Xiudong; Bai, Yuanyuan; Cao, Xuefei; Sun, Runcang

2017-08-01

Herein, an efficient biphasic pretreatment process was developed to improve the production of furfural (FF) and glucose from Eucalyptus. The influence of formic acid and NaCl on FF production from xylose in water and various biphasic systems was investigated. Results showed that the addition of formic acid and NaCl significantly promoted the FF yield, and the biphasic system of MIBK (methyl isobutyl ketone)/water exhibited the best performance for FF production. Then the Eucalyptus was pretreated in the MIBK/water system, and a maximum FF yield of 82.0% was achieved at 180°C for 60min. Surface of the pretreated Eucalyptus became relatively rough and loose, and its crystallinity index increased obviously due to the removal of hemicelluloses and lignin. The pretreated Eucalyptus samples showed much higher enzymatic hydrolysis rates (26.2-70.7%) than the raw Eucalyptus (14.5%). Copyright © 2017 Elsevier Ltd. All rights reserved.

Biphasic Effect of Nitric Oxide on the Cardiac Voltage-dependent Anion Channel

PubMed Central

Cheng, Qunli; Sedlic, Filip; Pravdic, Danijel; Bosnjak, Zeljko J.; Kwok, Wai-Meng

2010-01-01

Nitric oxide (NO˙) effects on the cardiac mitochondrial voltage-dependent anion channel (VDAC) are unknown. The effects of exogenous NO˙ on VDAC purified from rat hearts were investigated in this study. When incorporated into lipid bilayers, VDAC was inhibited directly by an NO˙ donor, PAPA NONOate, in a concentration-dependent biphasic manner. This was prevented by an NO˙ scavenger, PTIO. The effect paralleled that of NO˙ in delaying the opening of the mitochondrial permeability transition (PT) pore. These biphasic effects on the cardiac VDAC and the PT pore reveal a tandem impact of NO˙ on the two mitochondrial entities. PMID:21156174

Enhancing productivity for cascade biotransformation of styrene to (S)-vicinal diol with biphasic system in hollow fiber membrane bioreactor.

PubMed

Gao, Pengfei; Wu, Shuke; Praveen, Prashant; Loh, Kai-Chee; Li, Zhi

2017-03-01

Biotransformation is a green and useful tool for sustainable and selective chemical synthesis. However, it often suffers from the toxicity and inhibition from organic substrates or products. Here, we established a hollow fiber membrane bioreactor (HFMB)-based aqueous/organic biphasic system, for the first time, to enhance the productivity of a cascade biotransformation with strong substrate toxicity and inhibition. The enantioselective trans-dihydroxylation of styrene to (S)-1-phenyl-1,2-ethanediol, catalyzed by Escherichia coli (SSP1) coexpressing styrene monooxygenase and an epoxide hydrolase, was performed in HFMB with organic solvent in the shell side and aqueous cell suspension in the lumen side. Various organic solvents were investigated, and n-hexadecane was found as the best for the HFMB-based biphasic system. Comparing to other reported biphasic systems assisted by HFMB, our system not only shield much of the substrate toxicity but also deflate the product recovery burden in downstream processing as the majority of styrene stayed in organic phase while the diol product mostly remained in the aqueous phase. The established HFMB-based biphasic system enhanced the production titer to 143 mM, being 16-fold higher than the aqueous system and 1.6-fold higher than the traditional dispersive partitioning biphase system. Furthermore, the combination of biphasic system with HFMB prevents the foaming and emulsification, thus reducing the burden in downstream purification. HFMB-based biphasic system could serve as a suitable platform for enhancing the productivity of single-step or cascade biotransformation with toxic substrates to produce useful and valuable chemicals.

Cell–material interactions on biphasic polyurethane matrix

PubMed Central

Dicesare, Patrick; Fox, Wade M.; Hill, Michael J.; Krishnan, G. Rajesh; Yang, Shuying; Sarkar, Debanjan

2013-01-01

Cell–matrix interaction is a key regulator for controlling stem cell fate in regenerative tissue engineering. These interactions are induced and controlled by the nanoscale features of extracellular matrix and are mimicked on synthetic matrices to control cell structure and functions. Recent studies have shown that nanostructured matrices can modulate stem cell behavior and exert specific role in tissue regeneration. In this study, we have demonstrated that nanostructured phase morphology of synthetic matrix can control adhesion, proliferation, organization and migration of human mesenchymal stem cells (MSCs). Nanostructured biodegradable polyurethanes (PU) with segmental composition exhibit biphasic morphology at nanoscale dimensions and can control cellular features of MSCs. Biodegradable PU with polyester soft segment and hard segment composed of aliphatic diisocyanates and dipeptide chain extender were designed to examine the effect polyurethane phase morphology. By altering the polyurethane composition, morphological architecture of PU was modulated and its effect was examined on MSC. Results show that MSCs can sense the nanoscale morphology of biphasic polyurethane matrix to exhibit distinct cellular features and, thus, signifies the relevance of matrix phase morphology. The role of nanostructured phases of a synthetic matrix in controlling cell–matrix interaction provides important insights for regulation of cell behavior on synthetic matrix and, therefore, is an important tool for engineering tissue regeneration. PMID:23255285

A pilot trial of square biphasic pulse deep brain stimulation for dystonia: The BIP dystonia study.

PubMed

Almeida, Leonardo; Martinez-Ramirez, Daniel; Ahmed, Bilal; Deeb, Wissam; Jesus, Sol De; Skinner, Jared; Terza, Matthew J; Akbar, Umer; Raike, Robert S; Hass, Chris J; Okun, Michael S

2017-04-01

Dystonia often has inconsistent benefits and requires more energy-demanding DBS settings. Studies suggest that squared biphasic pulses could provide significant clinical benefit; however, dystonia patients have not been explored. To assess safety and tolerability of square biphasic DBS in dystonia patients. This study included primary generalized or cervical dystonia patients with bilateral GPi DBS. Square biphasic pulses were implemented and patients were assessed at baseline, immediately postwashout, post-30-minute washout, 1 hour post- and 2 hours postinitiation of investigational settings. Ten participants completed the study. There were no patient-reported or clinician-observed side effects. There was improvement across time on the Toronto Western Spasmodic Torticollis Rating Scale (χ 2  = 10.7; P = 0.031). Similar improvement was detected in objective gait measurements. Square biphasic stimulation appears safe and feasible in dystonia patients with GPi DBS. Further studies are needed to evaluate possible effectiveness particularly in cervical and gait features. © 2016 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

Fabrication and tritium release property of Li2TiO3-Li4SiO4 biphasic ceramics

NASA Astrophysics Data System (ADS)

Yang, Mao; Ran, Guangming; Wang, Hailiang; Dang, Chen; Huang, Zhangyi; Chen, Xiaojun; Lu, Tiecheng; Xiao, Chengjian

2018-05-01

Li2TiO3-Li4SiO4 biphasic ceramic pebbles have been developed as an advanced tritium breeder due to the potential to combine the advantages of both Li2TiO3 and Li4SiO4. Wet method was developed for the pebble fabrication and Li2TiO3-Li4SiO4 biphasic ceramic pebbles were successfully prepared by wet method using the powders synthesized by hydrothermal method. The tritium release properties of the Li2TiO3-Li4SiO4 biphasic ceramic pebbles were evaluated. The biphasic pebbles exhibited good tritium release property at low temperatures and the tritium release temperature was around 470 °C. Because of the isotope exchange reaction between H2 and tritium, the addition of 0.1%H2 to purge gas He could significantly enhance the tritium gas release and the fraction of molecular form of tritium increased from 28% to 55%. The results indicate that the Li2TiO3-Li4SiO4 biphasic ceramic pebbles fabricated by wet method exhibit good tritium release property and hold promising potential as advanced breeder pebbles.

HIV-1 dynamics revisited: biphasic decay by cytotoxic T lymphocyte killing?

PubMed Central

Arnaout, R A; Nowak, M A; Wodarz, D

2000-01-01

The biphasic decay of blood viraemia in patients being treated for human immunodeficiency virus type 1 (HIV-1) infection has been explained as the decay of two distinct populations of cells: the rapid death of productively infected cells followed by the much slower elimination of a second population the identity of which remains unknown. Here we advance an alternative explanation based on the immune response against a single population of infected cells. We show that the biphasic decay can be explained simply, without invoking multiple compartments: viral load falls quickly while cytotoxic T lymphocytes (CTL) are still abundant, and more slowly as CTL disappear. We propose a method to test this idea, and develop a framework that is readily applicable to treatment of other infections. PMID:10972131

Triple-channel microreactor for biphasic gas-liquid reactions: Photosensitized oxygenations.

PubMed

Maurya, Ram Awatar; Park, Chan Pil; Kim, Dong-Pyo

2011-01-01

A triple-channel microreactor fabricated by means of a soft-lithography technique was devised for efficient biphasic gas-liquid reactions. The excellent performance of the microreactor was demonstrated by carrying out photosensitized oxygenations of α-terpinene, citronellol, and allyl alcohols.

Monophasic versus biphasic defibrillation for pediatric out-of-hospital cardiac arrest patients: a nationwide population-based study in Japan

PubMed Central

2012-01-01

Introduction Conventional monophasic defibrillators for out-of-hospital cardiac-arrest patients have been replaced with biphasic defibrillators. However, the advantage of biphasic over monophasic defibrillation for pediatric out-of-hospital cardiac-arrest patients remains unknown. This study aimed to compare the survival outcomes of pediatric out-of-hospital cardiac-arrest patients who underwent monophasic defibrillation with those who underwent biphasic defibrillation. Methods This prospective, nationwide, population-based observational study included pediatric out-of-hospital cardiac-arrest patients from January 1, 2005, to December 31, 2009. The primary outcome measure was survival at 1 month with minimal neurologic impairment. The secondary outcome measures were survival at 1 month and the return of spontaneous circulation before hospital arrival. Multivariable logistic regression analysis was performed to identify the independent association between defibrillator type (monophasic or biphasic) and outcomes. Results Among 5,628 pediatric out-of-hospital cardiac-arrest patients (1 through 17 years old), 430 who received defibrillation shock with monophasic or biphasic defibrillator were analyzed. The number of patients who received defibrillation shock with monophasic defibrillator was 127 (30%), and 303 (70%) received defibrillation shock with biphasic defibrillator. The survival rates at 1 month with minimal neurologic impairment were 17.5% and 24.4%, the survival rates at 1 month were 32.3% and 35.6%, and the rates of return of spontaneous circulation before hospital arrival were 24.4% and 27.4% in the monophasic and biphasic defibrillator groups, respectively. Hierarchic logistic regression analyses by using generalized estimation equations found no significant difference between the two groups in terms of 1-month survival with minimal neurologic impairment (odds ratio (OR), 1.57; 95% confidence interval (CI), 0.87 to 2.83; P = 0.14) and 1-month survival (OR

Aqueous biphasic extraction process with pH and particle control

DOEpatents

Chaiko, David J.; Mensah-Biney, R.

1995-01-01

A process for aqueous biphasic extraction of metallic oxides and the like from substances containing silica. Control of media pH enables efficient and effective partition of mixture components. The inventive method may be employed to remove excess silica from kaolin clay.

Triple-channel microreactor for biphasic gas–liquid reactions: Photosensitized oxygenations

PubMed Central

Maurya, Ram Awatar; Park, Chan Pil

2011-01-01

Summary A triple-channel microreactor fabricated by means of a soft-lithography technique was devised for efficient biphasic gas–liquid reactions. The excellent performance of the microreactor was demonstrated by carrying out photosensitized oxygenations of α-terpinene, citronellol, and allyl alcohols. PMID:21915221

Lipase in biphasic alginate beads as a biocatalyst for esterification of butyric acid and butanol in aqueous media.

PubMed

Ng, Choong Hey; Yang, Kun-Lin

2016-01-01

Esterification of organic acids and alcohols in aqueous media is very inefficient due to thermodynamic constraints. However, fermentation processes used to produce organic acids and alcohols are often conducted in aqueous media. To produce esters in aqueous media, biphasic alginate beads with immobilized lipase are developed for in situ esterification of butanol and butyric acid. The biphasic beads contain a solid matrix of calcium alginate and hexadecane together with 5 mg/mL of lipase as the biocatalyst. Hexadecane in the biphasic beads serves as an organic phase to facilitate the esterification reaction. Under optimized conditions, the beads are able to catalyze the production of 0.16 mmol of butyl butyrate from 0.5 mmol of butyric acid and 1.5 mmol of butanol. In contrast, when monophasic beads (without hexadecane) are used, only trace amount of butyl butyrate is produced. One main application of biphasic beads is in simultaneous fermentation and esterification (SFE) because the organic phase inside the beads is very stable and does not leach out into the culture medium. SFE is successfully conducted with an esterification yield of 6.32% using biphasic beads containing iso-octane even though the solvent is proven toxic to the butanol-producing Clostridium spp. Copyright © 2015 Elsevier Inc. All rights reserved.

Biphasic Kinetic Behavior of Nitrate Reductase from Heterocystous, Nitrogen-Fixing Cyanobacteria 1

PubMed Central

Martin-Nieto, José; Flores, Enrique; Herrero, Antonia

1992-01-01

Nitrate reductase activity from filamentous, heterocyst-forming cyanobacteria showed a biphasic kinetic behavior with respect to nitrate as the variable substrate. Two kinetic components were detected, the first showing a higher affinity for nitrate (Km, 0.05-0.25 mm) and a lower catalytic activity and the second showing a lower affinity for nitrate (Km, 5-25 mm) and a higher (3- to 5-fold) catalytic activity. In contrast, among unicellular cyanobacteria, most representatives studied exhibited a monophasic, Michaelis-Menten kinetic pattern for nitrate reductase activity. Biphasic kinetics remained unchanged with the use of different assay conditions (i.e. cell disruption or permeabilization, two different electron donors) or throughout partial purification of the enzyme. PMID:16652939

High-throughput bone and cartilage micropellet manufacture, followed by assembly of micropellets into biphasic osteochondral tissue.

PubMed

Babur, Betul Kul; Futrega, Kathryn; Lott, William B; Klein, Travis Jacob; Cooper-White, Justin; Doran, Michael Robert

2015-09-01

Engineered biphasic osteochondral tissues may have utility in cartilage defect repair. As bone-marrow-derived mesenchymal stem/stromal cells (MSC) have the capacity to make both bone-like and cartilage-like tissues, they are an ideal cell population for use in the manufacture of osteochondral tissues. Effective differentiation of MSC to bone-like and cartilage-like tissues requires two unique medium formulations and this presents a challenge both in achieving initial MSC differentiation and in maintaining tissue stability when the unified osteochondral tissue is subsequently cultured in a single medium formulation. In this proof-of-principle study, we used an in-house fabricated microwell platform to manufacture thousands of micropellets formed from 166 MSC each. We then characterized the development of bone-like and cartilage-like tissue formation in the micropellets maintained for 8-14 days in sequential combinations of osteogenic or chondrogenic induction medium. When bone-like or cartilage-like micropellets were induced for only 8 days, they displayed significant phenotypic changes when the osteogenic or chondrogenic induction medium, respectively, was swapped. Based on these data, we developed an extended 14-day protocol for the pre-culture of bone-like and cartilage-like micropellets in their respective induction medium. Unified osteochondral tissues were formed by layering 12,000 osteogenic micropellets and 12,000 chondrogenic micropellets into a biphasic structure and then further culture in chondrogenic induction medium. The assembled tissue was cultured for a further 8 days and characterized via histology. The micropellets had amalgamated into a continuous structure with distinctive bone-like and cartilage-like regions. This proof-of-concept study demonstrates the feasibility of micropellet assembly for the formation of osteochondral-like tissues for possible use in osteochondral defect repair.

Aqueous biphasic extraction process with pH and particle control

DOEpatents

Chaiko, D.J.; Mensah-Biney, R.

1995-05-02

A process for aqueous biphasic extraction of metallic oxides and the like from substances containing silica. Control of media pH enables efficient and effective partition of mixture components. The inventive method may be employed to remove excess silica from kaolin clay. 2 figs.

Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus

PubMed Central

Jehee, Janneke F. M.; Ballard, Dana H.

2009-01-01

Biphasic neural response properties, where the optimal stimulus for driving a neural response changes from one stimulus pattern to the opposite stimulus pattern over short periods of time, have been described in several visual areas, including lateral geniculate nucleus (LGN), primary visual cortex (V1), and middle temporal area (MT). We describe a hierarchical model of predictive coding and simulations that capture these temporal variations in neuronal response properties. We focus on the LGN-V1 circuit and find that after training on natural images the model exhibits the brain's LGN-V1 connectivity structure, in which the structure of V1 receptive fields is linked to the spatial alignment and properties of center-surround cells in the LGN. In addition, the spatio-temporal response profile of LGN model neurons is biphasic in structure, resembling the biphasic response structure of neurons in cat LGN. Moreover, the model displays a specific pattern of influence of feedback, where LGN receptive fields that are aligned over a simple cell receptive field zone of the same polarity decrease their responses while neurons of opposite polarity increase their responses with feedback. This phase-reversed pattern of influence was recently observed in neurophysiology. These results corroborate the idea that predictive feedback is a general coding strategy in the brain. PMID:19412529

Biphasic papillary renal cell carcinoma is a rare morphological variant with frequent multifocality: a study of 28 cases.

PubMed

Trpkov, Kiril; Athanazio, Daniel; Magi-Galluzzi, Cristina; Yilmaz, Helene; Clouston, David; Agaimy, Abbas; Williamson, Sean R; Brimo, Fadi; Lopez, Jose I; Ulamec, Monika; Rioux-Leclercq, Nathalie; Kassem, Maysoun; Gupta, Nilesh; Hartmann, Arndt; Leroy, Xavier; Bashir, Samir Al; Yilmaz, Asli; Hes, Ondřej

2018-04-01

To further characterise biphasic squamoid renal cell carcinoma (RCC), a recently proposed variant of papillary RCC. We identified 28 tumours from multiple institutions. They typically showed two cell populations-larger cells with eosinophilic cytoplasm and higher-grade nuclei, surrounded by smaller, amphophilic cells with scanty cytoplasm. The dual morphology was variable (median 72.5% of tumour, range 5-100%); emperipolesis was found in all cases. The male/female ratio was 2:1, and the median age was 55 years (range 39-86 years). The median tumour size was 20 mm (range 9-65 mm). Pathological stage pT1a was found in 21 cases, pT1b in three, and pT3a and pT3b in one each (two not available). Multifocality was found in 32%: multifocal biphasic RCC in one case, biphasic + papillary RCC in two cases, biphasic + clear cell RCC in three cases, biphasic + low-grade urothelial carcinoma of the renal pelvis in one case, and biphasic + Birt-Hogg-Dubé syndrome in one case. Positive immunostains included: PAX8, cytokeratin (CK) 7, α-methylacyl-CoA racemase, epithelial membrane antigen, and vimentin. Cyclin D1 was expressed only in the larger cells. The Ki67 index was higher in the larger cells (median 5% versus ≤1%). Negative stains included: carbonic anhydrase 9, CD117, GATA-3, WT1, CK5/6, and CK20; CD10 and 34βE12 were variably expressed. Gains of chromosomes 7 and 17 were found in two evaluated cases. Follow-up was available for 23 patients (median 24 months, range 1-244 months): 19 were alive without disease, one was alive with recurrence, and one had died of disease (two had died of other causes). Biphasic papillary RCC is a rare variant of papillary RCC, and is often multifocal. © 2017 John Wiley & Sons Ltd.

Biphasic patterns of diversification and the emergence of modules

PubMed Central

Mittenthal, Jay; Caetano-Anollés, Derek; Caetano-Anollés, Gustavo

2012-01-01

The intricate molecular and cellular structure of organisms converts energy to work, which builds and maintains structure. Evolving structure implements modules, in which parts are tightly linked. Each module performs characteristic functions. In this work we propose that a module can emerge through two phases of diversification of parts. Early in the first phase of this biphasic pattern, the parts have weak linkage—they interact weakly and associate variously. The parts diversify and compete. Under selection for performance, interactions among the parts increasingly constrain their structure and associations. As many variants are eliminated, parts self-organize into modules with tight linkage. Linkage may increase in response to exogenous stresses as well as endogenous processes. In the second phase of diversification, variants of the module and its functions evolve and become new parts for a new cycle of generation of higher-level modules. This linkage hypothesis can interpret biphasic patterns in the diversification of protein domain structure, RNA and protein shapes, and networks in metabolism, codes, and embryos, and can explain hierarchical levels of structural organization that are widespread in biology. PMID:22891076

Biphasic synovial sarcoma in the cervical spine: Case report.

PubMed

Foreman, Stephen M; Stahl, Michael J

2011-05-23

Synovial sarcoma is a rare malignant neoplasm of soft tissue that typically arising near large joints of the upper and lower extremities in young adult males. Only 3% of these neoplasms have been found to arise in the head and neck region. To our knowledge, there are limited reports in the literature of this neoplasm in the cervical spine.A case of biphasic synovial sarcoma of the cervical spine is reviewed. A 29 year-old male presented with pain on the left side of the cervical spine. Physical examination revealed a global loss of cervical motion and large, palpable mass in the left paravertebral area. The long-delayed Magnetic Resonance (MR) scan revealed a soft tissue mass measuring 8.3 centimeters (cm) × 5.7 cm that was surgically removed. A malignant biphasic synovial sarcoma was diagnosed on pathologic examination.The clinical and imaging findings of an atypically located synovial sarcoma are reviewed. This case report emphasizes the consequences of a limited differential diagnosis, prolonged treatment and the failure to perform timely diagnostic imaging in the presence of a paraspinal mass.

Clinical, biochemical and molecular aspects of cerebellar ataxia and Coenzyme Q10 deficiency.

PubMed

Montero, Raquel; Pineda, Mercé; Aracil, Asun; Vilaseca, Maria-Antonia; Briones, Paz; Sánchez-Alcázar, José-Antonio; Navas, Plácido; Artuch, Rafael

2007-01-01

Coenzyme Q(10) (CoQ) deficiency is an autosomal recessive disorder presenting five phenotypes: a myopathic form, a severe infantile neurological syndrome associated with nephritic syndrome, an ataxic variant, Leigh syndrome and a pure myopathic form. The third is the most common phenotype related with CoQ deficiency and it will be the focus of this review. This new syndrome presents muscle CoQ deficiency associated with cerebellar ataxia and cerebellar atrophy as the main neurological signs. Biochemically, the hallmark of CoQ deficiency syndrome is a decreased CoQ concentration in muscle and/or fibroblasts. There is no molecular evidence of the enzyme or gene involved in primary CoQ deficiencies associated with cerebellar ataxia, although recently a family has been reported with mutations at COQ2 gene who present a distinct phenotype. Patients with primary CoQ deficiency may benefit from CoQ supplementation, although the clinical response to this therapy varies even among patients with similar phenotypes. Some present an excellent response to CoQ while others show only a partial improvement of some symptoms and signs. CoQ deficiency is the mitochondrial encephalomyopathy with the best clinical response to CoQ supplementation, highlighting the importance of an early identification of this disorder.

Usefulness of p16/CDKN2A fluorescence in situ hybridization and BAP1 immunohistochemistry for the diagnosis of biphasic mesothelioma.

PubMed

Wu, Di; Hiroshima, Kenzo; Yusa, Toshikazu; Ozaki, Daisuke; Koh, Eitetsu; Sekine, Yasuo; Matsumoto, Shinji; Nabeshima, Kazuki; Sato, Ayuko; Tsujimura, Tohru; Yamakawa, Hisami; Tada, Yuji; Shimada, Hideaki; Tagawa, Masatoshi

2017-02-01

Malignant mesothelioma is a highly aggressive neoplasm, and the histologic subtype is one of the most reliable prognostic factors. Some biphasic mesotheliomas are difficult to distinguish from epithelioid mesotheliomas with atypical fibrous stroma. The aim of this study was to analyze p16/CDKN2A deletions in mesotheliomas by fluorescence in situ hybridization (FISH) and BAP1 immunohistochemistry to evaluate their potential role in the diagnosis of biphasic mesothelioma. We collected 38 cases of pleural mesotheliomas. The results of this study clearly distinguished 29 cases of biphasic mesothelioma from 9 cases of epithelioid mesothelioma. The proportion of biphasic mesotheliomas with homozygous deletions of p16/CDKN2A in total was 96.6% (28/29). Homozygous deletion of p16/CDKN2A was observed in 18 (94.7%) of 19 biphasic mesotheliomas with 100% concordance of the p16/CDKN2A deletion status between the epithelioid and sarcomatoid components in each case. Homozygous deletion of the p16/CDKN2A was observed in 7 (77.8%) of 9 epithelioid mesotheliomas but not in fibrous stroma. BAP1 loss was observed in 5 (38.5%) of 13 biphasic mesotheliomas and in both epithelioid and sarcomatoid components. BAP1 loss was observed in 5 (62.5%) of 8 epithelioid mesotheliomas but not in fibrous stroma. Homozygous deletion of p16/CDKN2A is common in biphasic mesotheliomas, and the analysis of only one component of mesothelioma is sufficient to show that the tumor is malignant. However, compared with histology alone, FISH analysis of the p16/CDKN2A status and BAP1 immunohistochemistry in the spindled mesothelium provide a more objective means to differentiate between biphasic mesothelioma and epithelioid mesothelioma with atypical stromal cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysis of the Angle of Maximal Stability and Flow Regime Transitions in Different Proportions of Bi-phasic Granular Matter Mixtures

NASA Astrophysics Data System (ADS)

Maquiling, Joel Tiu; Visaga, Shane Marie

This study investigates the dependence of the critical angle θc of stability on different mass ratios γ of layered bi-phasic granular matter mixtures and on the critical angle of its mono-disperse individual components. It also aims to investigate and explain regime transitions of granular matter flowing down a tilted rough inclined plane. Critical angles and flow regimes for a bi-phasic mixture of sago spheres and bi-phasic pepper mixture of fine powder and rough spheres were observed and measured using video analysis. The critical angles θc MD of mono-disperse granular matter and θc BP of biphasic granular matter mixtures were observed and compared. All types of flow regimes and a supramaximal critical angle of stability exist at mass ratio γ = 0.5 for all biphasic granular matter mixtures. The θc BP of sago spheres was higher than the θc MD of sago spheres. Moreover, the θc BP of the pepper mixture was in between the θc MD of fine pepper and θc MD of rough pepper spheres. Comparison of different granular material shows that θc MD is not simply a function of particle diameter but of particle roughness as well. Results point to a superposition mechanism of the critical angles of biphasic sphere mixtures.

A Simplified Whole-Organ CT Perfusion Technique with Biphasic Acquisition: Preliminary Investigation of Accuracy and Protocol Feasibility in Kidneys.

PubMed

Yuan, XiaoDong; Zhang, Jing; Quan, ChangBin; Tian, Yuan; Li, Hong; Ao, GuoKun

2016-04-01

To determine the feasibility and accuracy of a protocol for calculating whole-organ renal perfusion (renal blood flow [RBF]) and regional perfusion on the basis of biphasic computed tomography (CT), with concurrent dynamic contrast material-enhanced (DCE) CT perfusion serving as the reference standard. This prospective study was approved by the institutional review board, and written informed consent was obtained from all patients. Biphasic CT of the kidneys, including precontrast and arterial phase imaging, was integrated with a first-pass dynamic volume CT protocol and performed and analyzed in 23 patients suspected of having renal artery stenosis. The perfusion value derived from biphasic CT was calculated as CT number enhancement divided by the area under the arterial input function and compared with the DCE CT perfusion data by using the paired t test, correlation analysis, and Bland-Altman plots. Correlation analysis was made between the RBF and the extent of renal artery stenosis. All postprocessing was independently performed by two observers and then averaged as the final result. Mean ± standard deviation biphasic and DCE CT perfusion data for RBF were 425.62 mL/min ± 124.74 and 419.81 mL/min ± 121.13, respectively (P = .53), and for regional perfusion they were 271.15 mL/min per 100 mL ± 82.21 and 266.33 mL/min per 100 mL ± 74.40, respectively (P = .31). Good correlation and agreement were shown between biphasic and DCE CT perfusion for RBF (r = 0.93; ±10% variation from mean perfusion data [P < .001]) and for regional perfusion (r = 0.90; ±13% variation from mean perfusion data [P < .001]). The extent of renal artery stenosis was negatively correlated with RBF with biphasic CT perfusion (r = -0.81, P = .012). Biphasic CT perfusion is clinically feasible and provides perfusion data comparable to DCE CT perfusion data at both global and regional levels in the kidney. Online supplemental material is available for this article.

Development and Characterization of Biphasic Hydroxyapatite/β-TCP Cements

PubMed Central

Gallinetti, Sara; Canal, Cristina; Ginebra, Maria-Pau; Ferreira, J

2014-01-01

Biphasic calcium phosphate bioceramics composed of hydroxyapatite (HA) and β-tricalcium phosphate (β-TCP) have relevant properties as synthetic bone grafts, such as tunable resorption, bioactivity, and intrinsic osteoinduction. However, they have some limitations associated to their condition of high-temperature ceramics. In this work self-setting Biphasic Calcium Phosphate Cements (BCPCs) with different HA/β-TCP ratios were obtained from self-setting α-TCP/β-TCP pastes. The strategy used allowed synthesizing BCPCs with modulated composition, compressive strength, and specific surface area. Due to its higher solubility, α-TCP was fully hydrolyzed to a calcium-deficient HA (CDHA), whereas β-TCP remained unreacted and completely embedded in the CDHA matrix. Increasing amounts of the non-reacting β-TCP phase resulted in a linear decrease of the compressive strength, in association to the decreasing amount of precipitated HA crystals, which are responsible for the mechanical consolidation of apatitic cements. Ca2+ release and degradation in acidic medium was similar in all the BCPCs within the timeframe studied, although differences might be expected in longer term studies once β-TCP, the more soluble phase was exposed to the surrounding media. PMID:25866411

Development and Characterization of Biphasic Hydroxyapatite/β-TCP Cements.

PubMed

Gallinetti, Sara; Canal, Cristina; Ginebra, Maria-Pau; Ferreira, J

2014-04-01

Biphasic calcium phosphate bioceramics composed of hydroxyapatite (HA) and β-tricalcium phosphate (β-TCP) have relevant properties as synthetic bone grafts, such as tunable resorption, bioactivity, and intrinsic osteoinduction. However, they have some limitations associated to their condition of high-temperature ceramics. In this work self-setting Biphasic Calcium Phosphate Cements (BCPCs) with different HA/β-TCP ratios were obtained from self-setting α-TCP/β-TCP pastes. The strategy used allowed synthesizing BCPCs with modulated composition, compressive strength, and specific surface area. Due to its higher solubility, α-TCP was fully hydrolyzed to a calcium-deficient HA (CDHA), whereas β-TCP remained unreacted and completely embedded in the CDHA matrix. Increasing amounts of the non-reacting β-TCP phase resulted in a linear decrease of the compressive strength, in association to the decreasing amount of precipitated HA crystals, which are responsible for the mechanical consolidation of apatitic cements. Ca 2+ release and degradation in acidic medium was similar in all the BCPCs within the timeframe studied, although differences might be expected in longer term studies once β-TCP, the more soluble phase was exposed to the surrounding media.

Aqueous biphasic plutonium oxide extraction process with pH and particle control

DOEpatents

Chaiko, D.J.; Mensah-Biney, R.

1997-04-29

A method is described for simultaneously partitioning a metal oxide and silica from a material containing silica and the metal oxide, using a biphasic aqueous medium having immiscible salt and polymer phases. 2 figs.

Learning new meanings for known words: Biphasic effects of prior knowledge.

PubMed

Fang, Xiaoping; Perfetti, Charles; Stafura, Joseph

2017-01-01

In acquiring word meanings, learners are often confronted by a single word form that is mapped to two or more meanings. For example, long after how to roller-"skate", one may learn that "skate" is also a kind of fish. Such learning of new meanings for familiar words involves two potentially contrasting processes, relative to new form-new meaning learning: 1) Form-based familiarity may facilitate learning a new meaning, and 2) meaning-based interference may inhibit learning a new meaning. We examined these two processes by having native English speakers learn new, unrelated meanings for familiar (high frequency) and less familiar (low frequency) English words, as well as for unfamiliar (novel or pseudo-) words. Tracking learning with cued-recall tasks at several points during learning revealed a biphasic pattern: higher learning rates and greater learning efficiency for familiar words relative to novel words early in learning and a reversal of this pattern later in learning. Following learning, interference from original meanings for familiar words was detected in a semantic relatedness judgment task. Additionally, lexical access to familiar words with new meanings became faster compared to their exposure controls, but no such effect occurred for less familiar words. Overall, the results suggest a biphasic pattern of facilitating and interfering processes: Familiar word forms facilitate learning earlier, while interference from original meanings becomes more influential later. This biphasic pattern reflects the co-activation of new and old meanings during learning, a process that may play a role in lexicalization of new meanings.

Learning new meanings for known words: Biphasic effects of prior knowledge

PubMed Central

Fang, Xiaoping; Perfetti, Charles; Stafura, Joseph

2017-01-01

In acquiring word meanings, learners are often confronted by a single word form that is mapped to two or more meanings. For example, long after how to roller-“skate”, one may learn that “skate” is also a kind of fish. Such learning of new meanings for familiar words involves two potentially contrasting processes, relative to new form-new meaning learning: 1) Form-based familiarity may facilitate learning a new meaning, and 2) meaning-based interference may inhibit learning a new meaning. We examined these two processes by having native English speakers learn new, unrelated meanings for familiar (high frequency) and less familiar (low frequency) English words, as well as for unfamiliar (novel or pseudo-) words. Tracking learning with cued-recall tasks at several points during learning revealed a biphasic pattern: higher learning rates and greater learning efficiency for familiar words relative to novel words early in learning and a reversal of this pattern later in learning. Following learning, interference from original meanings for familiar words was detected in a semantic relatedness judgment task. Additionally, lexical access to familiar words with new meanings became faster compared to their exposure controls, but no such effect occurred for less familiar words. Overall, the results suggest a biphasic pattern of facilitating and interfering processes: Familiar word forms facilitate learning earlier, while interference from original meanings becomes more influential later. This biphasic pattern reflects the co-activation of new and old meanings during learning, a process that may play a role in lexicalization of new meanings. PMID:29399593

Reversion of mtDNA depletion in a patient with TK2 deficiency.

PubMed

Vilà, M R; Segovia-Silvestre, T; Gámez, J; Marina, A; Naini, A B; Meseguer, A; Lombès, A; Bonilla, E; DiMauro, S; Hirano, M; Andreu, A L

2003-04-08

Mutations in the thymidine kinase 2 (TK2) gene cause a myopathic form of the mitochondrial DNA depletion syndrome (MDS). Here, the authors report the unusual clinical, biochemical, and molecular findings in a 14-year-old patient in whom pathogenic mutations were identified in the TK2 gene. This report extends the phenotypic expression of primary TK2 deficiency and suggests that factors other than TK2 may modify expression of the clinical phenotype in patients with MDS syndrome.

A case of mumps-related acute encephalopathy with biphasic seizures and late reduced diffusion.

PubMed

Hazama, Kyoko; Shiihara, Takashi; Tsukagoshi, Hiroyuki; Hasegawa, Shunji; Dowa, Yuri; Watanabe, Mio

2017-10-01

Mumps is a common childhood viral disease characterized by fever and swelling of the parotid gland. The prognosis is generally good, although some complications, such as encephalitis (0.1%), exist. Acute encephalopathy with biphasic seizures and late reduced diffusion is the most common type of acute encephalopathy. However, this type of encephalopathy has not been reported in association with mumps infection. A previously healthy 3-year-old Japanese boy had a brief convulsion after fever for 3days, and then had conscious disturbance and parotitis. After several days, he had a second brief convulsion and was admitted. Increased serum amylase levels and presence of anti-mumps immunoglobulin M antibody confirmed mumps parotitis. The patient had another brief seizure later the day of admission. He did not have status or cluster seizures, although the biphasic nature of his seizures, conscious disturbance between the seizures, no pleocytosis in cerebrospinal fluid, and brain magnetic resonance images were consistent with acute encephalopathy with biphasic seizures and late reduced diffusion. In Japan, the mumps vaccine is not administered as a part of routine immunizations. It thus has low coverage (30-40%), and as a result, mumps infections are still common. However, this is the first case of mumps-related acute encephalopathy with biphasic seizures and late reduced diffusion. This case may be representative of only a minority of patients with mumps-associated central nervous system involvement. Nevertheless, this diagnostic possibility may be considered. In order to prevent mumps-related complications, routine mumps vaccination might be warranted. Copyright © 2017 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Biphasic Effects of Alcohol as a Function of Circadian Phase

PubMed Central

Van Reen, Eliza; Rupp, Tracy L.; Acebo, Christine; Seifer, Ronald; Carskadon, Mary A.

2013-01-01

Study Objectives: To assess how alcohol affects multiple sleep latency tests (MSLT) and subjective measures of stimulation/sedation when alcohol is given at different circadian phases. Participants: Twenty-seven healthy young adults (age 21-26 yr) were studied. Design: Double-blind placebo and alcohol (vodka tonic targeting 0.05 g% concentration) beverages were each administered three times during the 20-h forced desynchrony protocol. Sleep latency tests and Biphasic Effects of Alcohol Scale (BAES) were administered on each forced desynchrony day. The outcome variables for this study include sleep onset latency (SOL) and stimulation and sedation value (from the BAES). Each outcome variable was associated with the ascending or descending limb of the breath alcohol concentration (BrAC) curve and assigned a circadian phase within a 90° bin. Measurements and Results: BrAC confirmed targeted maximal levels. Only outcome variables associated with the ascending and descending limb of the alcohol curve were analyzed for this article. Alcohol administered at a circadian time associated with greatest sleepiness showed longer SOL compared with placebo when measured on the ascending limb of the BrAC curve. We also found longer SOL with alcohol on the ascending limb of the BrAC curve in a circadian bin that favors greatest alertness. We observed shorter SOLs on the descending limb of the BrAC curve, but with no circadian phase interaction. The subjective data were partially consistent with the objective data. Conclusions: The physiologic findings in this study support the biphasic stimulating and sedating properties of alcohol, but limit the effect to specific circadian times. Citation: Van Reen E; Rupp TL; Acebo C; Seifer R; Carskadon MA. Biphasic effects of alcohol as a function of circadian phase. SLEEP 2013;36(1):137-145. PMID:23288980

Attenuated adult biphasic shocks for prolonged pediatric ventricular fibrillation: support for pediatric automated defibrillators.

PubMed

Berg, Robert A

2004-09-01

To evaluate published data regarding the treatment of prolonged pediatric defibrillation, with special emphasis on the use of attenuated adult biphasic shocks for pediatric defibrillation. Review relevant human and animal literature. Rhythm analysis algorithms from two manufacturers of automated external defibrillators can accurately distinguish shockable from nonshockable rhythms in children. Theoretical considerations and transthoracic impedance data from animals and children suggest that pediatric defibrillation doses should not necessarily vary in a simple weight-based manner. Two piglet studies have established that an attenuated adult biphasic dosage can be successfully used for 3.5- to 24-kg animals in ventricular fibrillation. One study established that the attenuated adult biphasic dosage was at least as safe and effective as the standard monophasic weight-based dosing. This review supports the American Heart Association's new guidelines for pediatric automated external defibrillator usage: "Automated external defibrillators may be used for children 1 to 8 yrs of age who have no signs of circulation. Ideally the device should deliver a pediatric dose. The arrhythmia detection system used in the device should demonstrate high specificity for pediatric shockable rhythms, i.e., it will not recommend delivery of a shock for nonshockable rhythms."

A biphasic dialytic strategy for the treatment of neonatal hyperammonemia

PubMed Central

Avasare, Sonal; Tsai, Eileen; Yadin, Ora; Zaritsky, Joshua

2018-01-01

Background Neonates with inborn errors of metabolism (IEM) often develop hyperammonemia which, if not corrected quickly, may result in poor neurologic outcomes. As pharmacologic therapy cannot rapidly lower ammonia levels, dialysis is frequently required. Both hemodialysis (HD) and standard-dose continuous renal replacement therapy (CRRT) are effective; however, HD may be followed by post-dialytic ammonia rebound, and standard-dose CRRT may not effect a rapid enough decrease in ammonia levels. Case-Diagnosis/Treatment We present two cases of IEM-associated neonatal hyperammonemia in which we employed a biphasic, high-dose CRRT treatment strategy, initially using dialysate flow rates of 5,000 mL/h (approximately 40,000 mL/h/1.73 m2) in order to rapidly decrease ammonia levels, then decreasing the dialysate flow rates to 500 mL/h (approximately 4,000 mL/h/1.73 m2) in order to prevent ammonia rebound. Conclusions This biphasic dialytic treatment strategy for neonatal hyperammonemia effected rapid ammonia reduction without rebound and accomplished during a single dialysis run without equipment changes. PMID:24122260

A New Biphasic Dicalcium Silicate Bone Cement Implant.

PubMed

Zuleta, Fausto; Murciano, Angel; Gehrke, Sergio A; Maté-Sánchez de Val, José E; Calvo-Guirado, José L; De Aza, Piedad N

2017-07-06

This study aimed to investigate the processing parameters and biocompatibility of a novel biphasic dicalcium silicate (C₂S) cement. Biphasic α´ L + β-C₂S ss was synthesized by solid-state processing, and was used as a raw material to prepare the cement. In vitro bioactivity and biocompatibility studies were assessed by soaking the cement samples in simulated body fluid (SBF) and human adipose stem cell cultures. Two critical-sized defects of 6 mm Ø were created in 15 NZ tibias. A porous cement made of the high temperature forms of C₂S, with a low phosphorous substitution level, was produced. An apatite-like layer covered the cement's surface after soaking in SBF. The cell attachment test showed that α´ L + β-C₂S ss supported cells sticking and spreading after 24 h of culture. The cement paste (55.86 ± 0.23) obtained higher bone-to-implant contact (BIC) percentage values (better quality, closer contact) in the histomorphometric analysis, and defect closure was significant compared to the control group (plastic). The residual material volume of the porous cement was 35.42 ± 2.08% of the initial value. The highest BIC and bone formation percentages were obtained on day 60. These results suggest that the cement paste is advantageous for initial bone regeneration.

A New Biphasic Dicalcium Silicate Bone Cement Implant

PubMed Central

Murciano, Angel; Maté-Sánchez de Val, José E.

2017-01-01

This study aimed to investigate the processing parameters and biocompatibility of a novel biphasic dicalcium silicate (C2S) cement. Biphasic α´L + β-C2Sss was synthesized by solid-state processing, and was used as a raw material to prepare the cement. In vitro bioactivity and biocompatibility studies were assessed by soaking the cement samples in simulated body fluid (SBF) and human adipose stem cell cultures. Two critical-sized defects of 6 mm Ø were created in 15 NZ tibias. A porous cement made of the high temperature forms of C2S, with a low phosphorous substitution level, was produced. An apatite-like layer covered the cement’s surface after soaking in SBF. The cell attachment test showed that α´L + β-C2Sss supported cells sticking and spreading after 24 h of culture. The cement paste (55.86 ± 0.23) obtained higher bone-to-implant contact (BIC) percentage values (better quality, closer contact) in the histomorphometric analysis, and defect closure was significant compared to the control group (plastic). The residual material volume of the porous cement was 35.42 ± 2.08% of the initial value. The highest BIC and bone formation percentages were obtained on day 60. These results suggest that the cement paste is advantageous for initial bone regeneration. PMID:28773119

Efficient asymmetric hydrolysis of styrene oxide catalyzed by Mung bean epoxide hydrolases in ionic liquid-based biphasic systems.

PubMed

Chen, Wen-Jing; Lou, Wen-Yong; Zong, Min-Hua

2012-07-01

The asymmetric hydrolysis of styrene oxide to (R)-1-phenyl-1,2-ethanediol using Mung bean epoxide hydrolases was, for the first time, successfully conducted in an ionic liquid (IL)-containing biphasic system. Compared to aqueous monophasic system, IL-based biphasic systems could not only dissolve the substrate, but also effectively inhibit the non-enzymatic hydrolysis, and therefore markedly improve the reaction efficiency. Of all the tested ILs, the best results were observed in the biphasic system containing C(4)MIM·PF(6), which exhibited good biocompatibility with the enzyme and was an excellent solvent for the substrate. In the C(4)MIM·PF(6)/buffer biphasic system, it was found that the optimal volume ratio of IL to buffer, reaction temperature, buffer pH and substrate concentration were 1/6, 35°C, 6.5 and 100 mM, respectively, under which the initial reaction rate, the yield and the product e.e. were 18.4 mM/h, 49.4% and 97.0%. The biocatalytic process was shown to be feasible on a 500-mL preparative scale. Copyright © 2011 Elsevier Ltd. All rights reserved.

Changes in Muscle Cell Metabolism and Mechanotransduction Are Associated with Myopathic Phenotype in a Mouse Model of Collagen VI Deficiency

PubMed Central

De Palma, Sara; Leone, Roberta; Grumati, Paolo; Vasso, Michele; Polishchuk, Roman; Capitanio, Daniele; Braghetta, Paola; Bernardi, Paolo; Bonaldo, Paolo; Gelfi, Cecilia

2013-01-01

This study identifies metabolic and protein phenotypic alterations in gastrocnemius, tibialis anterior and diaphragm muscles of Col6a1−/− mice, a model of human collagen VI myopathies. All three muscles of Col6a1−/− mice show some common changes in proteins involved in metabolism, resulting in decreased glycolysis and in changes of the TCA cycle fluxes. These changes lead to a different fate of α-ketoglutarate, with production of anabolic substrates in gastrocnemius and tibialis anterior, and with lipotoxicity in diaphragm. The metabolic changes are associated with changes of proteins involved in mechanotransduction at the myotendineous junction/costameric/sarcomeric level (TN-C, FAK, ROCK1, troponin I fast) and in energy metabolism (aldolase, enolase 3, triose phosphate isomerase, creatine kinase, adenylate kinase 1, parvalbumin, IDH1 and FASN). Together, these change may explain Ca2+ deregulation, impaired force development, increased muscle-relaxation-time and fiber damage found in the mouse model as well as in patients. The severity of these changes differs in the three muscles (gastrocnemius

Changes in muscle cell metabolism and mechanotransduction are associated with myopathic phenotype in a mouse model of collagen VI deficiency.

PubMed

De Palma, Sara; Leone, Roberta; Grumati, Paolo; Vasso, Michele; Polishchuk, Roman; Capitanio, Daniele; Braghetta, Paola; Bernardi, Paolo; Bonaldo, Paolo; Gelfi, Cecilia

2013-01-01

This study identifies metabolic and protein phenotypic alterations in gastrocnemius, tibialis anterior and diaphragm muscles of Col6a1(-/-) mice, a model of human collagen VI myopathies. All three muscles of Col6a1(-/-) mice show some common changes in proteins involved in metabolism, resulting in decreased glycolysis and in changes of the TCA cycle fluxes. These changes lead to a different fate of α-ketoglutarate, with production of anabolic substrates in gastrocnemius and tibialis anterior, and with lipotoxicity in diaphragm. The metabolic changes are associated with changes of proteins involved in mechanotransduction at the myotendineous junction/costameric/sarcomeric level (TN-C, FAK, ROCK1, troponin I fast) and in energy metabolism (aldolase, enolase 3, triose phosphate isomerase, creatine kinase, adenylate kinase 1, parvalbumin, IDH1 and FASN). Together, these change may explain Ca(2+) deregulation, impaired force development, increased muscle-relaxation-time and fiber damage found in the mouse model as well as in patients. The severity of these changes differs in the three muscles (gastrocnemius

Non-conventional solvents in liquid phase microextraction and aqueous biphasic systems.

PubMed

An, Jiwoo; Trujillo-Rodríguez, María J; Pino, Verónica; Anderson, Jared L

2017-06-02

The development of rapid, convenient, and high throughput sample preparation approaches such as liquid phase microextraction techniques have been continuously developed over the last decade. More recently, significant attention has been given to the replacement of conventional organic solvents used in liquid phase microextraction techniques in order to reduce toxic waste and to improve selectivity and/or extraction efficiency. With these objectives, non-conventional solvents have been explored in liquid phase microextraction and aqueous biphasic systems. The utilized non-conventional solvents include ionic liquids, magnetic ionic liquids, and deep eutectic solvents. They have been widely used as extraction solvents or additives in various liquid phase microextraction modes including dispersive liquid-liquid microextraction, single-drop microextraction, hollow fiber-liquid phase microextraction, as well as in aqueous biphasic systems. This review provides an overview into the use of non-conventional solvents in these microextraction techniques in the past 5 years (2012-2016). Analytical applications of the techniques are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Biphasic magnetic nanoparticles-nanovesicle hybrids for chemotherapy and self-controlled hyperthermia.

PubMed

Gogoi, Manashjit; Sarma, Haladhar D; Bahadur, Dhirendra; Banerjee, Rinti

2014-05-01

The aim was to develop magnetic nanovesicles for chemotherapy and self-controlled hyperthermia that prevent overheating of tissues. Magnetic nanovesicles containing paclitaxel and a dextran-coated biphasic suspension of La0.75Sr0.25MnO3 and Fe3O4 nanoparticles (magnetic nanoparticles) were developed. Encapsulation efficiencies of magnetic nanoparticles and paclitaxel were 67 ± 5 and 83 ± 3%, respectively. Sequential release performed at 37°C for 1 h followed by 44°C for another 1 h (as expected for intratumoral injection), showed a cumulative release of 6.6% (109.6 µg), which was above the IC50 of the drug. In an alternating current magnetic field, the temperature remained controlled at 44°C and a synergistic cytotoxicity of paclitaxel and hyperthermia was observed in MCF-7 cells. Magnetic nanovesicles containing biphasic suspensions La0.75Sr0.25MnO3 and Fe3O4 nanoparticles encapsulating paclitaxel have potential for combined self-controlled hyperthermia and chemotherapy.

Separation and recovery of food coloring dyes using aqueous biphasic extraction chromatographic resins.

PubMed

Huddleston, J G; Willauer, H D; Boaz, K R; Rogers, R D

1998-06-26

Aqueous biphasic systems (ABS) and aqueous biphasic extraction chromatographic (ABEC) resins are currently under investigation for their utility in the removal of color from textile plant wastes. The structures of several widely used food colorings, suggest that these dyes would also be retained on the resins. In work currently in progress, we have begun to investigate the retention and resolution of several common food colorings including indigo carmine, amaranth, carminic acid. erythrosin B, tartrazine and quinoline yellow. The relationship between the uptake of these dyes on ABEC resins in terms of the binding strengths and capacities of the resins and their partitioning behavior in ABS is illustrated. Some possible theoretical and practical approaches to the prediction of the partitioning and retention behavior is discussed.

CORRELATION OF A BIPHASIC METABOLIC RESPONSE WITH A BIPHASIC RESPONSE IN RESISTANCE TO TUBERCULOSIS IN RABBITS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allison, M.J.; Zappasodi, P.; Lurie, M.B.

Peritoneal exudate mononuclear cells obtained from BCG-vaccinated rabbits showed higher utilization of succinate, glycerophosphate, beta - hydroxybutyrate, and glycerol than cells from control animals. No differences in utilization of the following substrates were noted: lactate, glucose-6-phosphate, malate, isocitrate, alpha -ketoglutarate, and glutamic acid. A second, later stage of elevated metabolic activity was associated with heightened resistance to infection. When rabbits which had been irradiated with 400 r 2 years previously were vaccinated with BCG, they failed to respond as shown by their lack of resistance to infection and failure of their mononuclear cells to show the biphasic metabolic stimulation. Themore » results demonstrate the close relation between the metabolic capabilities of reticuloendothelial cells and their resistance to tuberculosis. (H.H.D.)« less

A Biphasic Calcium Sulphate/Hydroxyapatite Carrier Containing Bone Morphogenic Protein-2 and Zoledronic Acid Generates Bone

PubMed Central

Raina, Deepak Bushan; Isaksson, Hanna; Hettwer, Werner; Kumar, Ashok; Lidgren, Lars; Tägil, Magnus

2016-01-01

In orthopedic surgery, large amount of diseased or injured bone routinely needs to be replaced. Autografts are mainly used but their availability is limited. Commercially available bone substitutes allow bone ingrowth but lack the capacity to induce bone formation. Thus, off-the-shelf osteoinductive bone substitutes that can replace bone grafts are required. We tested the carrier properties of a biphasic, calcium sulphate and hydroxyapatite ceramic material, containing a combination of recombinant human bone morphogenic protein-2 (rhBMP-2) to induce bone, and zoledronic acid (ZA) to delay early resorption. In-vitro, the biphasic material released 90% of rhBMP-2 and 10% of ZA in the first week. No major changes were found in the surface structure using scanning electron microscopy (SEM) or in the mechanical properties after adding rhBMP-2 or ZA. In-vivo bone formation was studied in an abdominal muscle pouch model in rats (n = 6/group). The mineralized volume was significantly higher when the biphasic material was combined with both rhBMP-2 and ZA (21.4 ± 5.5 mm3) as compared to rhBMP-2 alone (10.9 ± 2.1 mm3) when analyzed using micro computed tomography (μ-CT) (p < 0.01). In the clinical setting, the biphasic material combined with both rhBMP-2 and ZA can potentially regenerate large volumes of bone. PMID:27189411

Deriving sulfamethoxazole dissipation endpoints in pasture soils using first order and biphasic kinetic models.

PubMed

Srinivasan, Prakash; Sarmah, Ajit K; Rohan, Maheswaran

2014-08-01

Single first-order (SFO) kinetic model is often used to derive the dissipation endpoints of an organic chemical in soil. This model is used due to its simplicity and requirement by regulatory agencies. However, using the SFO model for all types of decay pattern could lead to under- or overestimation of dissipation endpoints when the deviation from first-order is significant. In this study the performance of three biphasic kinetic models - bi-exponential decay (BEXP), first-order double exponential decay (FODED), and first-order two-compartment (FOTC) models was evaluated using dissipation datasets of sulfamethoxazole (SMO) antibiotic in three different soils under varying concentration, depth, temperature, and sterile conditions. Corresponding 50% (DT50) and 90% (DT90) dissipation times for the antibiotics were numerically obtained and compared against those obtained using the SFO model. The fit of each model to the measured values was evaluated based on an array of statistical measures such as coefficient of determination (R(2)adj), root mean square error (RMSE), chi-square (χ(2)) test at 1% significance, Bayesian Information Criteria (BIC) and % model error. Box-whisker residual plots were also used to compare the performance of each model to the measured datasets. The antibiotic dissipation was successfully predicted by all four models. However, the nonlinear biphasic models improved the goodness-of-fit parameters for all datasets. Deviations from datasets were also often less evident with the biphasic models. The fits of FOTC and FODED models for SMO dissipation datasets were identical in most cases, and were found to be superior to the BEXP model. Among the biphasic models, the FOTC model was found to be the most suitable for obtaining the endpoints and could provide a mechanistic explanation for SMO dissipation in the soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Sub-threshold depolarizing pre-pulses can enhance the efficiency of biphasic stimuli in transcutaneous neuromuscular electrical stimulation.

PubMed

Vargas Luna, Jose Luis; Mayr, Winfried; Cortés-Ramirez, Jorge-Armando

2018-06-09

There is multiple evidence in the literature that a sub-threshold pre-pulse, delivered immediately prior to an electrical stimulation pulse, can alter the activation threshold of nerve fibers and motor unit recruitment characteristics. So far, previously published works combined monophasic stimuli with sub-threshold depolarizing pre-pulses (DPPs) with inconsistent findings-in some studies, the DPPs decreased the activation threshold, while in others it was increased. This work aimed to evaluate the effect of DPPs during biphasic transcutaneous electrical stimulation and to study the possible mechanism underlying those differences. Sub-threshold DPPs between 0.5 and 15 ms immediately followed by biphasic or monophasic pulses were administered to the tibial nerve; the electrophysiological muscular responses (motor-wave, M-wave) were monitored via electromyogram (EMG) recording from the soleus muscle. The data show that, under the specific studied conditions, DPPs tend to lower the threshold for nerve fiber activation rather than elevating it. DPPs with the same polarity as the leading phase of biphasic stimuli are more effective to increase the sensitivity. This work assesses for the first time the effect of DPPs on biphasic pulses, which are required to achieve charge-balanced stimulation, and it provides guidance on the effect of polarity and intensity to take full advantage of this feature. Graphical abstract In this work, the effect of sub-threshold depolarizing pre-pulses (DPP) is investigated in a setup with transcutaneous electrical stimulation. We found that, within the tested 0-15 ms DPP duration range, the DPPs administered immediately before biphasic pulses proportionally increase the nerve excitability as visible in the M-waves recorded from the soleus muscle. Interestingly, these findings oppose published results, where DPPs, administered immediately before monophasic stimuli via implanted electrodes, led to decrease of nerve excitability.

Anti-prelog reduction of prochiral carbonyl compounds by Oenococcus oeni in a biphasic system.

PubMed

Hu, Jian; Xu, Yan

2006-07-01

An aqueous-organic biphasic system was established and used with whole cells of Oenococcus oeni to reduce 2-octanone to (R)-2-octanol. The conversion reached 99% when the Tris/borate buffer was increased from 50 mM to 300 mM in the aqueous phase. In addition, the conversion increased as the log P value of the organic solvent changed from 0.5 to 6.6. Under optimized conditions, the conversion of (R)-2-octanol reached 99% from 0.5 M 2-octanone with an optical purity of 99% e.e. The biphasic system allows the anti-Prelog reduction of aliphatic and aromatic ketones to furnish (R)-configurated alcohols in high optical purity as well.

The effect of collagen fibril orientation on the biphasic mechanics of articular cartilage.

PubMed

Meng, Qingen; An, Shuqiang; Damion, Robin A; Jin, Zhongmin; Wilcox, Ruth; Fisher, John; Jones, Alison

2017-01-01

The highly inhomogeneous distribution of collagen fibrils may have important effects on the biphasic mechanics of articular cartilage. However, the effect of the inhomogeneity of collagen fibrils has mainly been investigated using simplified three-layered models, which may have underestimated the effect of collagen fibrils by neglecting their realistic orientation. The aim of this study was to investigate the effect of the realistic orientation of collagen fibrils on the biphasic mechanics of articular cartilage. Five biphasic material models, each of which included a different level of complexity of fibril reinforcement, were solved using two different finite element software packages (Abaqus and FEBio). Model 1 considered the realistic orientation of fibrils, which was derived from diffusion tensor magnetic resonance images. The simplified three-layered orientation was used for Model 2. Models 3-5 were three control models. The realistic collagen orientations obtained in this study were consistent with the literature. Results from the two finite element implementations were in agreement for each of the conditions modelled. The comparison between the control models confirmed some functions of collagen fibrils. The comparison between Models 1 and 2 showed that the widely-used three-layered inhomogeneous model can produce similar fluid load support to the model including the realistic fibril orientation; however, an accurate prediction of the other mechanical parameters requires the inclusion of the realistic orientation of collagen fibrils. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Two cases of traumatic head injury mimicking acute encephalopathy with biphasic seizures and late reduced diffusion.

PubMed

Nishiyama, Masahiro; Fujita, Kyoko; Maruyama, Azusa; Nagase, Hiroaki

2014-11-01

Acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) presents a distinct clinical course of biphasic seizures and impaired consciousness. These symptoms are followed by reduced diffusion in the subcortical white matter on magnetic resonance imaging that is typically observed between 3 and 9 days after illness onset. Here, we report two cases of traumatic head injury with clinical and radiological features similar to those for AESD. The similarities between our cases and AESD may be useful in understanding the pathogenesis of AESD. Copyright © 2013 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Comparison of outcomes after use of biphasic or monophasic defibrillators among out-of-hospital cardiac arrest patients: a nationwide population-based observational study.

PubMed

Tanabe, Seizan; Yasunaga, Hideo; Ogawa, Toshio; Koike, Soichi; Akahane, Manabu; Horiguchi, Hiromasa; Hatanaka, Tetsuo; Yokota, Hiroyuki; Imamura, Tomoaki

2012-09-01

The use and popularity of the biphasic waveform defibrillator as a replacement for the monophasic waveform defibrillator are increasing, but it is unclear whether this can improve the rate of survival among out-of-hospital cardiac arrest patients. This study aimed to verify the hypothesis that the outcome of out-of-hospital cardiac arrest patients who received defibrillation shock with the biphasic waveform defibrillator was better than that of patients who received defibrillation shock with the monophasic defibrillator. This prospective, nationwide, population-based, observational study included 21 172 out-of-hospital cardiac arrest patients with initial ventricular fibrillation or pulseless ventricular tachycardia from January 1, 2005, through December 31, 2007. Defibrillation shock was performed by monophasic defibrillator on 8224 (39%) patients and by biphasic defibrillator on 12 948 (61%) patients. The rate of survival at 1 month with minimal neurological impairment was 11.6% (951/8192) in the monophasic defibrillator group and 12.8% (1653/12 928) in the biphasic defibrillator group. Hierarchical logistic regression analysis using a generalized estimation equation showed no significant difference between the biphasic and monophasic groups in 1-month survival with minimal neurological impairment (adjusted odds ratio, 1.07; 95% confidence interval, 0.91-1.26; P=0.42). Confirmatory propensity score analyses showed similar results. Although monophasic defibrillators are being replaced by biphasic defibrillators, our nationwide population-based observational study failed to demonstrate a statistically significant association between defibrillation waveform and 1-month survival rate with minimal neurological impairment.

Production of Furfural from Process-Relevant Biomass-Derived Pentoses in a Biphasic Reaction System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mittal, Ashutosh; Black, Stuart K.; Vinzant, Todd B.

Furfural is an important fuel precursor which can be converted to hydrocarbon fuels and fuel intermediates. In this work, the production of furfural by dehydration of process-relevant pentose rich corn stover hydrolyzate using a biphasic batch reaction system has been investigated. Methyl isobutyl ketone (MIBK) and toluene have been used to extract furfural and enhance overall furfural yield by limiting its degradation to humins. The effects of reaction time, temperature, and acid concentration (H 2SO 4) on pentose conversion and furfural yield were investigated. For the dehydration of 8 wt % pentose-rich corn stover hydrolyzate under optimum reaction conditions, 0.05more » M H 2SO 4, 170 degrees C for 20 min with MIBK as the solvent, complete conversion of xylose (98-100%) and a furfural yield of 80% were obtained. Under these same conditions, except with toluene as the solvent, the furfural yield was 77%. Additionally, dehydration of process-relevant pentose rich corn stover hydrolyzate using solid acid ion-exchange resins under optimum reaction conditions has shown that Purolite CT275 is as effective as H 2SO 4 for obtaining furfural yields approaching 80% using a biphasic batch reaction system. In conclusion, this work has demonstrated that a biphasic reaction system can be used to process biomass-derived pentose rich sugar hydrolyzates to furfural in yields approaching 80%.« less

Production of Furfural from Process-Relevant Biomass-Derived Pentoses in a Biphasic Reaction System

DOE PAGES

Mittal, Ashutosh; Black, Stuart K.; Vinzant, Todd B.; ...

2017-05-16

Furfural is an important fuel precursor which can be converted to hydrocarbon fuels and fuel intermediates. In this work, the production of furfural by dehydration of process-relevant pentose rich corn stover hydrolyzate using a biphasic batch reaction system has been investigated. Methyl isobutyl ketone (MIBK) and toluene have been used to extract furfural and enhance overall furfural yield by limiting its degradation to humins. The effects of reaction time, temperature, and acid concentration (H 2SO 4) on pentose conversion and furfural yield were investigated. For the dehydration of 8 wt % pentose-rich corn stover hydrolyzate under optimum reaction conditions, 0.05more » M H 2SO 4, 170 degrees C for 20 min with MIBK as the solvent, complete conversion of xylose (98-100%) and a furfural yield of 80% were obtained. Under these same conditions, except with toluene as the solvent, the furfural yield was 77%. Additionally, dehydration of process-relevant pentose rich corn stover hydrolyzate using solid acid ion-exchange resins under optimum reaction conditions has shown that Purolite CT275 is as effective as H 2SO 4 for obtaining furfural yields approaching 80% using a biphasic batch reaction system. In conclusion, this work has demonstrated that a biphasic reaction system can be used to process biomass-derived pentose rich sugar hydrolyzates to furfural in yields approaching 80%.« less

Computational solvent system screening for the separation of tocopherols with centrifugal partition chromatography using deep eutectic solvent-based biphasic systems.

PubMed

Bezold, Franziska; Weinberger, Maria E; Minceva, Mirjana

2017-03-31

Tocopherols are a class of molecules with vitamin E activity. Among those, α-tocopherol is the most important vitamin E source in the human diet. The purification of tocopherols involving biphasic liquid systems can be challenging since these vitamins are poorly soluble in water. Deep eutectic solvents (DES) can be used to form water-free biphasic systems and have already proven applicable for centrifugal partition chromatography separations. In this work, a computational solvent system screening was performed using the predictive thermodynamic model COSMO-RS. Liquid-liquid equilibria of solvent systems composed of alkanes, alcohols and DES, as well as partition coefficients of α-tocopherol, β-tocopherol, γ-tocopherol, and σ-tocopherol in these biphasic solvent systems were calculated. From the results the best suited biphasic solvent system, namely heptane/ethanol/choline chloride-1,4-butanediol, was chosen and a batch injection of a tocopherol mixture, mainly consisting of α- and γ-tocopherol, was performed using a centrifugal partition chromatography set up (SCPE 250-BIO). A separation factor of 1.74 was achieved for α- and γ-tocopherol. Copyright © 2017 Elsevier B.V. All rights reserved.

Biphasic rattlesnake venom-induced thrombocytopenia.

PubMed

Offerman, Steven R; Barry, J David; Schneir, Aaron; Clark, Richard F

2003-04-01

Thrombocytopenia is a common occurrence in moderate to severe crotaline envenomation. The exact mechanism by which rattlesnake venom leads to thrombocytopenia is unclear, but aggressive treatment with crotaline-specific antivenom often leads to resolution of this disorder. Crotalinae Polyvalent Immune Fab (CroFab(TM), Protherics Inc., Nashville, TN) (crotaline Fab) is now available for the treatment of symptomatic rattlesnake envenomation. Although recurrence of thrombocytopenia has been reported in patients after envenomation treated with crotaline Fab, cases refractory to this therapy have not been described. We report a case of severe crotaline envenomation that appears to have exhibited two separate episodes of thrombocytopenia, only one of which responded to antivenom. The second, later phase was refractory to both crotaline Fab as well as traditional Antivenin (Crotalinae) Polyvalent (Wyeth-Ayerst Pharmaceuticals, Philadelphia, PA) (ACP). By reviewing the literature regarding venom-induced thrombocytopenia, we attempt to explain this "biphasic" phenomenon and the inability of crotaline Fab to reverse this toxic effect.

* Fabrication and Characterization of Biphasic Silk Fibroin Scaffolds for Tendon/Ligament-to-Bone Tissue Engineering.

PubMed

Font Tellado, Sònia; Bonani, Walter; Balmayor, Elizabeth R; Foehr, Peter; Motta, Antonella; Migliaresi, Claudio; van Griensven, Martijn

2017-08-01

Tissue engineering is an attractive strategy for tendon/ligament-to-bone interface repair. The structure and extracellular matrix composition of the interface are complex and allow for a gradual mechanical stress transfer between tendons/ligaments and bone. Thus, scaffolds mimicking the structural features of the native interface may be able to better support functional tissue regeneration. In this study, we fabricated biphasic silk fibroin scaffolds designed to mimic the gradient in collagen molecule alignment present at the interface. The scaffolds had two different pore alignments: anisotropic at the tendon/ligament side and isotropic at the bone side. Total porosity ranged from 50% to 80% and the majority of pores (80-90%) were <100-300 μm. Young's modulus varied from 689 to 1322 kPa depending on the type of construct. In addition, human adipose-derived mesenchymal stem cells were cultured on the scaffolds to evaluate the effect of pore morphology on cell proliferation and gene expression. Biphasic scaffolds supported cell attachment and influenced cytoskeleton organization depending on pore alignment. In addition, the gene expression of tendon/ligament, enthesis, and cartilage markers significantly changed depending on pore alignment in each region of the scaffolds. In conclusion, the biphasic scaffolds fabricated in this study show promising features for tendon/ligament-to-bone tissue engineering.

Evaluation of a Unique Defibrillation Unit with Dual-Vector Biphasic Waveform Capabilities: Towards a Miniaturized Defibrillator.

PubMed

Okamura, Hideo; Desimone, Christopher V; Killu, Ammar M; Gilles, Emily J; Tri, Jason; Asirvatham, Roshini; Ladewig, Dejae J; Suddendorf, Scott H; Powers, Joanne M; Wood-Wentz, Christina M; Gray, Peter D; Raymond, Douglas M; Savage, Shelley J; Savage, Walter T; Bruce, Charles J; Asirvatham, Samuel J; Friedman, Paul A

2017-02-01

Automated external defibrillators can provide life-saving therapies to treat ventricular fibrillation. We developed a prototype unit that can deliver a unique shock waveform produced by four independent capacitors that is delivered through two shock vectors, with the rationale of providing more robust shock pathways during emergent defibrillation. We describe the initial testing and feasibility of this unique defibrillation unit, features of which may enable downsizing of current defibrillator devices. We tested our defibrillation unit in four large animal models (two canine and two swine) under general anesthesia. Experimental defibrillation thresholds (DFT) were obtained by delivery of a unique waveform shock pulse via a dual-vector pathway with four defibrillation pads (placed across the chest). DFTs were measured and compared with those of a commercially available biphasic defibrillator (Zoll M series, Zoll Medical, Chelmsford, MA, USA) tested in two different vectors. Shocks were delivered after 10 seconds of stable ventricular fibrillation and the output characteristics and shock outcome recorded. Each defibrillation series used a step-down to failure protocol to define the defibrillation threshold. A total of 96 shocks were delivered during ventricular fibrillation in four large animals. In comparison to the Zoll M series, which delivered a single-vector, biphasic shock, the energy required for successful defibrillation using the unique dual-vector biphasic waveform did not differ significantly (P = 0.65). Our early findings support the feasibility of a unique external defibrillation unit using a dual-vector biphasic waveform approach. This warrants further study to leverage this unique concept and work toward a miniaturized, portable shock delivery system. © 2016 Wiley Periodicals, Inc.

A biphasic parameter estimation method for quantitative analysis of dynamic renal scintigraphic data

NASA Astrophysics Data System (ADS)

Koh, T. S.; Zhang, Jeff L.; Ong, C. K.; Shuter, B.

2006-06-01

Dynamic renal scintigraphy is an established method in nuclear medicine, commonly used for the assessment of renal function. In this paper, a biphasic model fitting method is proposed for simultaneous estimation of both vascular and parenchymal parameters from renal scintigraphic data. These parameters include the renal plasma flow, vascular and parenchymal mean transit times, and the glomerular extraction rate. Monte Carlo simulation was used to evaluate the stability and confidence of the parameter estimates obtained by the proposed biphasic method, before applying the method on actual patient study cases to compare with the conventional fitting approach and other established renal indices. The various parameter estimates obtained using the proposed method were found to be consistent with the respective pathologies of the study cases. The renal plasma flow and extraction rate estimated by the proposed method were in good agreement with those previously obtained using dynamic computed tomography and magnetic resonance imaging.

A randomised controlled trial of the effect of biphasic or monophasic waveform on the incidence and severity of cutaneous burns following external direct current cardioversion.

PubMed

Ambler, Jonathan J S; Deakin, Charles D

2006-12-01

Cutaneous burns are a common cause of morbidity following direct current (DC) cardioversion. We designed a prospective randomised double-blinded controlled study to determine the effect of biphasic or monophasic waveform on the pain and inflammation occurring after elective cardioversion. One hundred and thirty nine patients undergoing elective DC cardioversion were randomised to receive monophasic (HP Codemaster XL; 100, 200, 300, 360, and 360 J) or biphasic (Welch Allyn-MRL PIC defibrillator; 70, 100, 150, 200, and 300 J) waveforms. Two hours after DC cardioversion, skin temperature, erythema index and sensory threshold to light and sharp touch was measured at the centre and edge of paddle sites. Visual analogue pain score (VAS) was recorded at 2 and 24 h. There was significantly less pain following biphasic cardioversion as assessed by VAS at both 2 h (p < 0.001; 95% confidence intervals of difference of medians (CI) 0.2-0.8 cm) and 24 h (p = 0.004; 95% CI 0.0-0.4 cm). There was significantly less erythema in patients receiving biphasic cardioversion at the edge of the sternal site (p = 0.046; 95% CI 0.41-4.5). There was no difference in any other variable at any site between biphasic and monophasic cardioversion. The use of a biphasic waveform for DC cardioversion reduces the inflammation and pain of burns as measured by erythema index and visual analogue scale.

Biphasic and monophasic repair: comparative implications for biologically equivalent dose calculations in pulsed dose rate brachytherapy of cervical carcinoma

PubMed Central

Millar, W T; Davidson, S E

2013-01-01

Objective: To consider the implications of the use of biphasic rather than monophasic repair in calculations of biologically-equivalent doses for pulsed-dose-rate brachytherapy of cervix carcinoma. Methods: Calculations are presented of pulsed-dose-rate (PDR) doses equivalent to former low-dose-rate (LDR) doses, using biphasic vs monophasic repair kinetics, both for cervical carcinoma and for the organ at risk (OAR), namely the rectum. The linear-quadratic modelling calculations included effects due to varying the dose per PDR cycle, the dose reduction factor for the OAR compared with Point A, the repair kinetics and the source strength. Results: When using the recommended 1 Gy per hourly PDR cycle, different LDR-equivalent PDR rectal doses were calculated depending on the choice of monophasic or biphasic repair kinetics pertaining to the rodent central nervous and skin systems. These differences virtually disappeared when the dose per hourly cycle was increased to 1.7 Gy. This made the LDR-equivalent PDR doses more robust and independent of the choice of repair kinetics and α/β ratios as a consequence of the described concept of extended equivalence. Conclusion: The use of biphasic and monophasic repair kinetics for optimised modelling of the effects on the OAR in PDR brachytherapy suggests that an optimised PDR protocol with the dose per hourly cycle nearest to 1.7 Gy could be used. Hence, the durations of the new PDR treatments would be similar to those of the former LDR treatments and not longer as currently prescribed. Advances in knowledge: Modelling calculations indicate that equivalent PDR protocols can be developed which are less dependent on the different α/β ratios and monophasic/biphasic kinetics usually attributed to normal and tumour tissues for treatment of cervical carcinoma. PMID:23934965

Evaluation of parallel milliliter-scale stirred-tank bioreactors for the study of biphasic whole-cell biocatalysis with ionic liquids.

PubMed

Dennewald, Danielle; Hortsch, Ralf; Weuster-Botz, Dirk

2012-01-01

As clear structure-activity relationships are still rare for ionic liquids, preliminary experiments are necessary for the process development of biphasic whole-cell processes involving these solvents. To reduce the time investment and the material costs, the process development of such biphasic reaction systems would profit from a small-scale high-throughput platform. Exemplarily, the reduction of 2-octanone to (R)-2-octanol by a recombinant Escherichia coli in a biphasic ionic liquid/water system was studied in a miniaturized stirred-tank bioreactor system allowing the parallel operation of up to 48 reactors at the mL-scale. The results were compared to those obtained in a 20-fold larger stirred-tank reactor. The maximum local energy dissipation was evaluated at the larger scale and compared to the data available for the small-scale reactors, to verify if similar mass transfer could be obtained at both scales. Thereafter, the reaction kinetics and final conversions reached in different reactions setups were analysed. The results were in good agreement between both scales for varying ionic liquids and for ionic liquid volume fractions up to 40%. The parallel bioreactor system can thus be used for the process development of the majority of biphasic reaction systems involving ionic liquids, reducing the time and resource investment during the process development of this type of applications. Copyright © 2011. Published by Elsevier B.V.

Acute exercise induces biphasic increase in respiratory mRNA in skeletal muscle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ikeda, Shin-ichi; Kizaki, Takako; Haga, Shukoh

2008-04-04

Peroxisome proliferator-activated receptor {gamma} coactivator-1{alpha} (PGC-1{alpha}) promotes the expression of oxidative enzymes in skeletal muscle. We hypothesized that activation of the p38 MAPK (mitogen-activated protein kinase) in response to exercise was associated with exercise-induced PGC-1{alpha} and respiratory enzymes expression and aimed to demonstrate this under the physiological level. We subjected mice to a single bout of treadmill running and found that the exercise induced a biphasic increase in the expression of respiratory enzymes mRNA. The second phase of the increase was accompanied by an increase in PGC-1{alpha} protein, but the other was not. Administration of SB203580 (SB), an inhibitor ofmore » p38 MAPK, suppressed the increase in PGC-1{alpha} expression and respiratory enzymes mRNA in both phases. These data suggest that p38 MAPK is associated with the exercise-induced expression of PGC-1{alpha} and biphasic increase in respiratory enzyme mRNAs in mouse skeletal muscle under physiological conditions.« less

Occurrence of amylose-lipid complexes in teff and maize starch biphasic pastes.

PubMed

Wokadala, Obiro Cuthbert; Ray, Suprakas Sinha; Emmambux, Mohammad Naushad

2012-09-01

The occurrence of amylose-lipid complexes was determined in maize and teff starch biphasic pastes i.e. peak viscosity pastes at short and prolonged pasting times. Maize and teff starches were pasted for 11.5 and 130 min with or without added stearic acid followed by thermo-stable alpha-amylase hydrolysis in a rapid visco-analyzer. X-ray diffraction analysis of pastes before and residues after hydrolysis showed crystalline V-amylose diffraction patterns for the starches pasted for a prolonged time with added stearic acid while less distinct V-amylose patterns with non-complexed stearic acid peaks were observed with a short pasting time. Differential scanning calorimetry of pastes before and residues after paste hydrolysis showed that Type I amylose-lipid complexes were formed after pasting for the short duration with added stearic acid, while Type II complexes are formed after pasting for the prolonged time. The present research provides evidence that amylose-lipid complexes play an important role in starch biphasic pasting. Copyright © 2012 Elsevier Ltd. All rights reserved.

Injectable TEMPO-oxidized nanofibrillated cellulose/biphasic calcium phosphate hydrogel for bone regeneration.

PubMed

Safwat, Engie; Hassan, Mohammad L; Saniour, Sayed; Zaki, Dalia Yehia; Eldeftar, Mervat; Saba, Dalia; Zazou, Mohamed

2018-05-01

Nanofibrillated cellulose, obtained from rice straw agricultural wastes was used as a substrate for the preparation of a new injectable and mineralized hydrogel for bone regeneration. Tetramethyl pyridine oxyl (TEMPO) oxidized nanofibrillated cellulose, was mineralized through the incorporation of a prepared and characterized biphasic calcium phosphate at a fixed ratio of 50 wt%. The TEMPO-oxidized rice straw nanofibrillated cellulose was characterized using transmission electron microscopy, Fourier transform infrared, and carboxylic content determination. The injectability and viscosity of the prepared hydrogel were evaluated using universal testing machine and rheometer testing, respectively. Cytotoxicity and alkaline phosphatase level tests on osteoblast like-cells for in vitro assessment of the biocompatibility were investigated. Results revealed that the isolated rice straw nanofibrillated cellulose is a nanocomposite of the cellulose nanofibers and silica nanoparticles. Rheological properties of the tested materials are suitable for use as injectable material and of nontoxic effect on osteoblast-like cells, as revealed by the positive alkaline phosphate assay. However, nanofibrillated cellulose/ biphasic calcium phosphate hydrogel showed higher cytotoxicity and lower bioactivity test results when compared to that of nanofibrillated cellulose.

Origin and Correction of Magnetic Field Inhomogeneity at the Interface in Biphasic NMR Samples

PubMed Central

Martin, Bryan T.; Chingas, G. C.

2012-01-01

The use of susceptibility matching to minimize spectral distortion of biphasic samples layered in a standard 5 mm NMR tube is described. The approach uses magic angle spinning (MAS) to first extract chemical shift differences by suppressing bulk magnetization. Then, using biphasic coaxial samples, magnetic susceptibilities are matched by titration with a paramagnetic salt. The matched phases are then layered in a standard NMR tube where they can be shimmed and examined. Line widths of two distinct spectral lines, selected to characterize homogeneity in each phase, are simultaneously optimized. Two-dimensional distortion-free, slice-resolved spectra of an octanol/water system illustrate the method. These data are obtained using a 2D stepped-gradient pulse sequence devised for this application. Advantages of this sequence over slice-selective methods are that acquisition efficiency is increased and processing requires only conventional software. PMID:22459062

Effect of molecular weight of hyaluronic acid (HA) on viscoelasticity and particle texturing feel of HA dermal biphasic fillers.

PubMed

Chun, Cheolbyong; Lee, Deuk Yong; Kim, Jin-Tae; Kwon, Mi-Kyung; Kim, Young-Zu; Kim, Seok-Soon

2016-01-01

Hyaluronic acid (HA) dermal biphasic fillers are synthesized for their efficacy in correcting aesthetic defects such as wrinkles, scars and facial contouring defects. The fillers consist of crosslinked HA microspheres suspended in a noncrosslinked HA. To extend the duration of HAs within the dermis and obtain the particle texturing feel, HAs are crosslinked to obtain the suitable mechanical properties. Hyaluronic acid (HA) dermal biphasic fillers are prepared by mixing the crosslinked HA microspheres and the noncrosslinked HAs. The elastic modulus of the fillers increased with raising the volume fraction of the microspheres. The mechanical properties and the particle texturing feel of the fillers made from crosslinked HA (1058 kDa) microspheres suspended in noncrosslinked HA (1368 kDa) are successfully achieved, which are adequate for the fillers. Dermal biphasic HA fillers made from 1058 kDa exhibit suitable elastic moduli (211 to 420 Pa) and particle texturing feel (scale 7 ~ 9).

Steroid biotransformations in biphasic systems with Yarrowia lipolytica expressing human liver cytochrome P450 genes

PubMed Central

2012-01-01

Background Yarrowia lipolytica efficiently metabolizes and assimilates hydrophobic compounds such as n-alkanes and fatty acids. Efficient substrate uptake is enabled by naturally secreted emulsifiers and a modified cell surface hydrophobicity and protrusions formed by this yeast. We were examining the potential of recombinant Y. lipolytica as a biocatalyst for the oxidation of hardly soluble hydrophobic steroids. Furthermore, two-liquid biphasic culture systems were evaluated to increase substrate availability. While cells, together with water soluble nutrients, are maintained in the aqueous phase, substrates and most of the products are contained in a second water-immiscible organic solvent phase. Results For the first time we have co-expressed the human cytochromes P450 2D6 and 3A4 genes in Y. lipolytica together with human cytochrome P450 reductase (hCPR) or Y. lipolytica cytochrome P450 reductase (YlCPR). These whole-cell biocatalysts were used for the conversion of poorly soluble steroids in biphasic systems. Employing a biphasic system with the organic solvent and Y. lipolytica carbon source ethyl oleate for the whole-cell bioconversion of progesterone, the initial specific hydroxylation rate in a 1.5 L stirred tank bioreactor was further increased 2-fold. Furthermore, the product formation was significantly prolonged as compared to the aqueous system. Co-expression of the human CPR gene led to a 4-10-fold higher specific activity, compared to the co-overexpression of the native Y. lipolytica CPR gene. Multicopy transformants showed a 50-70-fold increase of activity as compared to single copy strains. Conclusions Alkane-assimilating yeast Y. lipolytica, coupled with the described expression strategies, demonstrated its high potential for biotransformations of hydrophobic substrates in two-liquid biphasic systems. Especially organic solvents which can be efficiently taken up and/or metabolized by the cell might enable more efficient bioconversion as compared

Clinical experience with biphasic insulin aspart in people with type 2 diabetes: Results from the Libya cohort of the A1chieve study.

PubMed

Hajjaji, Issam M; Sherif, Ibrahim; Elazrag, Aisha; Jaber, Suhair; Chakkarwar, Praful N; Eltabal, Salem

2013-11-01

The A1chieve, a multicentric (28 countries), 24-week, non-interventional study evaluated the safety and effectiveness of insulin detemir, biphasic insulin aspart and insulin aspart in people with T2DM (n = 66,726) in routine clinical care across four continents. Data was collected at baseline, at 12 weeks and at 24 weeks. This short communication presents the results for patients enrolled in biphasic insulin aspart sub group from Libya. A total of 179 patients were enrolled in the biphasic insulin aspart subgroup. All the patients were prior insulin users. At baseline glycaemic control was poor (mean HbA1c: 9.3%). After 24 weeks of treatment there was an improvement in HbA1c (-0.9%). Hypoglycaemic events reduced from 7.2 events/patient-year to 3.7 events/patient-year in 24 weeks. SADRs did not occur in any of the study patients. Starting or switching to biphasic insulin aspart was associated with improvement in glycaemic control with a low rate of hypoglycaemia.

Photochromism of 7-(N,N-diethylamino)-4'-hydroxyflavylium in a water-ionic liquid biphasic system.

PubMed

Pina, Fernando; Parola, A Jorge; Melo, Maria João; Laia, César A T; Afonso, Carlos A M

2007-04-28

Photochromism of trans-4-(N,N-diethylamino)-2,4'-dihydroxychalcone, with formation of the photoproduct 7-(N,N-diethylamino)-4'-hydroxyflavylium, is promoted in the ionic liquid phase of a water/[bmim][PF6] biphasic system.

Safety and effectiveness of biphasic insulin aspart 30 in people with type 2 diabetes switching from basal-bolus insulin regimens in the A1chieve study.

PubMed

Dieuzeide, Guillermo; Chuang, Lee-Ming; Almaghamsi, Abdulrahman; Zilov, Alexey; Chen, Jian-Wen; Lavalle-González, Fernando J

2014-07-01

Biphasic insulin aspart 30 allows fewer daily injections versus basal-bolus insulin regimens, which may improve adherence and treatment outcome. This sub-analysis of the observational A1chieve study assessed clinical safety and effectiveness of biphasic insulin aspart 30 in people with type 2 diabetes previously receiving basal-bolus insulin regimens. A1chieve was an international, open-label, 24-week study in people with type 2 diabetes starting/switching to biphasic insulin aspart 30, insulin detemir or insulin aspart. This sub-analysis assessed patients switching from insulin glargine- or neutral protamine Hagedorn insulin-based basal-bolus insulin regimens to biphasic insulin aspart 30. 1024 patients were included. At 24 weeks, glycated haemoglobin and fasting plasma glucose were significantly reduced from baseline in both cohorts (all p<0.001). The proportion reporting any hypoglycaemia, major hypoglycaemia or nocturnal hypoglycaemia was significantly reduced after 24 weeks (all p<0.05). No serious adverse drug reactions were reported. Both cohorts had significantly improved health-related quality of life (HRQoL; p<0.001). 24 weeks after switching from basal-bolus insulin regimens to biphasic insulin aspart 30, glycaemic control and HRQoL were significantly improved, and hypoglycaemia was significantly reduced. This suggests that people with type 2 diabetes inadequately controlled on basal-bolus insulin regimens can consider biphasic insulin aspart 30. Copyright © 2013 Primary Care Diabetes Europe. Published by Elsevier Ltd. All rights reserved.

Biphasic growth of orbital volume in Chinese children.

PubMed

Wei, Nan; Bi, Hua; Zhang, Bin; Li, Xue; Sun, Fengyuan; Qian, Xuehan

2017-09-01

The aim of this study was to map out the developmental curve of the orbital volume of Chinese children aged 1-15 years. CT scanning was performed on 109 children and the orbital volume, interlateral orbital rim distance (IORD), and extent of exophthalmos were measured on the CT images and plotted against age. The development of the orbit structure followed a biphasic pattern. The first growth phase was before 3 years and the second growth phase was between 7 years and 12 years of age. The growth speed in the first phase was about 3 times that of the second one (first vs second phase: 2.28 cm 3 /year vs 0.67 cm 3 /year for orbital volume, 5.01 mm/year vs 1.57 mm/year for IORD, 1.29 mm/year vs 0.42 mm/year for the exophthalmos). During development, there was no significant difference between the left and right orbits. There was no significant difference between boys and girls before 12 years of age. However, after 12 years of age, boys had significantly larger orbital volumes (22.16±2.28 cm 3 /year vs 18.57±1.16 cm 3 /year, p<0.001) and a greater IORD (96.29±3.18 mm/year vs 91.00±4.54 mm/year, p<0.001) than girls. In Chinese children, the development of orbital volume follows a biphasic pattern and a sex difference becomes significant after the age of 12 years. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Application of aqueous biphasic systems as strategy to purify tannase from Aspergillus tamarii URM 7115.

PubMed

de Sena, Amanda Reges; Barros Oliveira, Flávio Manoel; Campos Leite, Tonny Cley; Evaristo da Silva Nascimento, Talita Camila; Moreira, Keila Aparecida; de Assis, Sandra Aparecida

2017-10-21

The aims of the current study are to assess the influence of polyethylene glycol (PEG) concentration, molar mass, pH, and citrate concentrations on aqueous biphasic systems based on 2 4 factorial designs, as well as to check their capacity to purify tannase secreted by Aspergillus tamarii URM 7115. Tannase was produced through submerged fermentation at 26°C for 67 h in Czapeck-Dox modified broth and added with yeast extract and tannic acid. The factorial design was followed to assess the influence of PEG molar mass (M PEG 600; 4,000 and 8,000 g/ mol), and PEG (C PEG 20.0; 22.0 and 24.0% w/w) and citrate concentrations (C CIT 15.0, 17.5, and 20.0%, w/w), as well as of pH (6.0, 7.0, and 8.0) on the response variables; moreover, partition coefficient (K), yield (Y), and purification factor (PF) were analyzed. The most suitable parameters to purify tannase secreted by A. tamarii URM 7115 through a biphasic system were 600 (g/mol) M PEG , 24% (w/w) C PEG , 15% (w/w) C CIT at pH 6.0 and they resulted in 6.33 enzyme partition, 131.25% yield, 19.80 purification factor and 195.08 selectivity. Tannase secreted by A. tamarii URM 7115 purified through aqueous biphasic systems composed of PEG/citrate can be used for industrial purposes, since it presents suitable purification factor and yield.

A promising tritium breeding material: Nanostructured 2Li2TiO3-Li4SiO4 biphasic ceramic pebbles

NASA Astrophysics Data System (ADS)

Dang, Chen; Yang, Mao; Gong, Yichao; Feng, Lan; Wang, Hailiang; Shi, Yanli; Shi, Qiwu; Qi, Jianqi; Lu, Tiecheng

2018-03-01

As an advanced tritium breeder material for the fusion reactor blanket of the International Thermonuclear Experimental Reactor (ITER), Li2TiO3-Li4SiO4 biphasic ceramic has attracted widely attention due to its merits. In this paper, the uniform precursor powders were prepared by hydrothermal method, and nanostructured 2Li2TiO3-Li4SiO4 biphasic ceramic pebbles were fabricated by an indirect wet method at the first time. In addition, the composition dependence (x/y) of their microstructure characteristics and mechanical properties were investigated. The results indicated that the crush load of biphasic ceramic pebbles was better than that of single phase ceramic pebbles under identical conditions. The 2Li2TiO3-Li4SiO4 ceramic pebbles have good morphology, small grain size (90 nm), satisfactory crush load (37.8 N) and relative density (81.8 %T.D.), which could be a promising breeding material in the future fusion reactor.

Formation of a Fluorous/Organic Biphasic Supramolecular Octopus Assembly for Enhanced Porphyrin Phosphorescence in Air

DOE PAGES

Yang, Chi; Arvapally, Ravi K.; Tekarli, Sammer M.; ...

2015-03-03

The trinuclear triangle-shaped system [tris{3,5-bis(heptafluoropropyl)-1,2,4-triazolatosilver(I)}] (1) and the multi-armed square-shaped metalloporphyrin PtOEP or the free porphyrin base H2OEP serve as excellent octopus hosts (OEP=2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine). Coupling of the fluorous/organic molecular octopi 1 and H2OEP or PtOEP by strong quadrupole-quadrupole and metal- interactions affords the supramolecular assemblies [1PtOEP] or [1H(2)OEP] (2a), which feature nanoscopic cavities surrounding the upper triangular and lower square cores. The fluorous/organic biphasic configuration of [1PtOEP] leads to an increase in the phosphorescence of PtOEP under ambient conditions. Guest molecules can be included in the biphasic double-octopus assembly in three different site-selective modes.

Aqueous biphasic extraction of uranium and thorium from contaminated soils. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaiko, D.J.; Gartelmann, J.; Henriksen, J.L.

1995-07-01

The aqueous biphasic extraction (ABE) process for soil decontamination involves the selective partitioning of solutes and fine particulates between two immiscible aqueous phases. The biphase system is generated by the appropriate combination of a water-soluble polymer (e.g., polyethlene glycol) with an inorganic salt (e.g., sodium carbonate). Selective partitioning results in 99 to 99.5% of the soil being recovered in the cleaned-soil fraction, while only 0.5 to 1% is recovered in the contaminant concentrate. The ABE process is best suited to the recovery of ultrafine, refractory material from the silt and clay fractions of soils. During continuous countercurrent extraction tests withmore » soil samples from the Fernald Environmental Management Project site (Fernald, OH), particulate thorium was extracted and concentrated between 6- and 16-fold, while the uranium concentration was reduced from about 500 mg/kg to about 77 mg/kg. Carbonate leaching alone was able to reduce the uranium concentration only to 146 mg/kg. Preliminary estimates for treatment costs are approximately $160 per ton of dry soil. A detailed flowsheet of the ABE process is provided.« less

Method for separating water soluble organics from a process stream by aqueous biphasic extraction

DOEpatents

Chaiko, David J.; Mego, William A.

1999-01-01

A method for separating water-miscible organic species from a process stream by aqueous biphasic extraction is provided. An aqueous biphase system is generated by contacting a process stream comprised of water, salt, and organic species with an aqueous polymer solution. The organic species transfer from the salt-rich phase to the polymer-rich phase, and the phases are separated. Next, the polymer is recovered from the loaded polymer phase by selectively extracting the polymer into an organic phase at an elevated temperature, while the organic species remain in a substantially salt-free aqueous solution. Alternatively, the polymer is recovered from the loaded polymer by a temperature induced phase separation (cloud point extraction), whereby the polymer and the organic species separate into two distinct solutions. The method for separating water-miscible organic species is applicable to the treatment of industrial wastewater streams, including the extraction and recovery of complexed metal ions from salt solutions, organic contaminants from mineral processing streams, and colorants from spent dye baths.

Design and development of a low-cost biphasic charge-balanced functional electric stimulator and its clinical validation.

PubMed

Shendkar, Chandrashekhar; Lenka, Prasanna K; Biswas, Abhishek; Kumar, Ratnesh; Mahadevappa, Manjunatha

2015-10-01

Functional electric stimulators that produce near-ideal, charge-balanced biphasic stimulation waveforms with interphase delay are considered safer and more efficacious than conventional stimulators. An indigenously designed, low-cost, portable FES device named InStim is developed. It features a charge-balanced biphasic single channel. The authors present the complete design, mathematical analysis of the circuit and the clinical evaluation of the device. The developed circuit was tested on stroke patients affected by foot drop problems. It was tested both under laboratory conditions and in clinical settings. The key building blocks of this circuit are low dropout regulators, a DC-DC voltage booster and a single high-power current source OP-Amp with current-limiting capabilities. This allows the device to deliver high-voltage, constant current, biphasic pulses without the use of a bulky step-up transformer. The advantages of the proposed design over the currently existing devices include improved safety features (zero DC current, current-limiting mechanism and safe pulses), waveform morphology that causes less muscle fatigue, cost-effectiveness and compact power-efficient circuit design with minimal components. The device is also capable of producing appropriate ankle dorsiflexion in patients having foot drop problems of various Medical Research Council scale grades.

Ru-Catalyzed Estragole Isomerization under Homogeneous and Ionic Liquid Biphasic Conditions

PubMed Central

2017-01-01

The isomerization of estragole to trans-anethole is an important reaction and is industrially performed using an excess of NaOH or KOH in ethanol at high temperatures with very low selectivity. Simple Ru-based transition-metal complexes, under homogeneous, ionic liquid (IL)-supported (biphasic) and “solventless” conditions, can be used for this reaction. The selectivity of this reaction is more sensitive to the solvent/support used than the ligands associated with the metal catalyst. Thus, under the optimized reaction conditions, 100% conversion can be achieved in the estragole isomerization, using as little as 4 × 10–3 mol % (40 ppm) of [RuHCl(CO)(PPh3)3] in toluene, reflecting a total turnover number (TON) of 25 000 and turnover frequencies (TOFs) of up to 500 min–1 at 80 °C. Using a dimeric Ru precursor, [RuCl(μ-Cl)(η3:η3-C10H16)]2, in ethanol associated with P(OEt)3, a TON of 10 000 and a TOF of 125 min–1 are obtained with 100% conversion and 99% selectivity. These two Ru catalytic systems can be transposed to biphasic IL systems by using ionic-tagged P-ligands such as 1-(3-(diphenylphosphanyl)propyl)-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide immobilized in 1-(3-hydroxypropyl)-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl) imide with up to 99% selectivity and almost complete estragole conversion. However, the reaction is much slower than that performed under solventless or homogeneous conditions. The use of ionic-tagged ligands significantly reduces the Ru leaching to the organic phase, compared to that in reactions performed under homogeneous conditions, where the catalytic system loses catalytic performance after the second recycling. Detailed kinetic investigations of the reaction catalyzed by [RuHCl(CO)(PPh3)3] indicate that a simplified kinetic model (a monomolecular reversible first-order reaction) is adequate for fitting the homogeneous reaction at 80 °C and under biphasic conditions. However, the kinetics of

Dmp1 Null Mice Develop a Unique Osteoarthritis-like Phenotype

PubMed Central

Zhang, Qi; Lin, Shuxian; Liu, Ying; Yuan, Baozhi; Harris, Steph E; Feng, Jian Q.

2016-01-01

Patients with hypophosphatemia rickets (including DMP1 mutations) develop severe osteoarthritis (OA), although the mechanism is largely unknown. In this study, we first identified the expression of DMP1 in hypertrophic chondrocytes using immunohistochemistry (IHC) and X-gal analysis of Dmp1-knockout-lacZ-knockin heterozygous mice. Next, we characterized the OA-like phenotype in Dmp1 null mice from 7-week-old to one-year-old using multiple techniques, including X-ray, micro-CT, H&E staining, Goldner staining, scanning electronic microscopy, IHC assays, etc. We found a classical OA-like phenotype in Dmp1 null mice such as articular cartilage degradation, osteophyte formation, and subchondral osteosclerosis. These Dmp1 null mice also developed unique pathological changes, including a biphasic change in their articular cartilage from the initial expansion of hypertrophic chondrocytes at the age of 1-month to a quick diminished articular cartilage layer at the age of 3-months. Further, these null mice displayed severe enlarged knees and poorly formed bone with an expanded osteoid area. To address whether DMP1 plays a direct role in the articular cartilage, we deleted Dmp1 specifically in hypertrophic chondrocytes by crossing the Dmp1-loxP mice with Col X Cre mice. Interestingly, these conditional knockout mice didn't display notable defects in either the articular cartilage or the growth plate. Because of the hypophosphatemia remained in the entire life span of the Dmp1 null mice, we also investigated whether a high phosphate diet would improve the OA-like phenotype. A 8-week treatment of a high phosphate diet significantly rescued the OA-like defect in Dmp1 null mice, supporting the critical role of phosphate homeostasis in maintaining the healthy joint morphology and function. Taken together, this study demonstrates a unique OA-like phenotype in Dmp1 null mice, but a lack of the direct impact of DMP1 on chondrogenesis. Instead, the regulation of phosphate homeostasis

Fixed-energy biphasic waveform defibrillation in a pediatric model of cardiac arrest and resuscitation.

PubMed

Tang, Wanchun; Weil, Max Harry; Jorgenson, Dawn; Klouche, Kada; Morgan, Carl; Yu, Ting; Sun, Shijie; Snyder, David

2002-12-01

For adults, 150-J fixed-energy, impedance-compensating biphasic truncated exponential (ICBTE) shocks are now effectively used in automated defibrillators. However, the high energy levels delivered by adult automated defibrillators preclude their use for pediatric patients. Accordingly, we investigated a method by which adult automated defibrillators may be adapted to deliver a 50-J ICBTE shock for pediatric defibrillation. Prospective, randomized study. A university-affiliated research institution. Domestic piglets. We initially investigated four groups of anesthetized mechanically ventilated piglets weighing 3.8, 7.5, 15, and 25 kg. Ventricular fibrillation was induced with an AC current delivered to the right ventricular endocardium. After 7 mins of untreated ventricular fibrillation, a conventional manual defibrillator was used to deliver up to three 50-J ICBTE shocks. If ventricular fibrillation was not reversed, a 1-min interval of precordial compression preceded a second sequence of up to three shocks. The protocol was repeated until spontaneous circulation was restored, or for a total of 15 mins. In a second set of experiments, we evaluated a 150-J biphasic adult automated defibrillator that was operated in conjunction with energy-reducing electrodes such as to deliver 50-J shocks. The same resuscitation protocol was then exercised on piglets weighing 3.7, 13.5, and 24.2 kg. All animals were successfully resuscitated. Postresuscitation hemodynamic and myocardial function quickly returned to baseline values in both experimental groups, and all animals survived. An adaptation of a 150-J biphasic adult automated defibrillator in which energy-reducing electrodes delivered 50-J shocks successfully resuscitated animals ranging from 3.7 to 25 kg without compromise of postresuscitation myocardial function or survival.

Partitioning of mercury in aqueous biphasic systems and on ABEC resins.

PubMed

Rogers, R D; Griffin, S T

1998-06-26

Poly(ethylene glycol)-based aqueous biphasic systems (PEG-ABS) can be utilized to separate and recover metal ions in environmental and hydrometallurgical applications. A concurrent study was conducted comparing the partitioning of mercury between aqueous layers in an ABS [Me-PEG-5000/(NH4)2SO4] and partitioning of mercury from aqueous solutions to aqueous biphasic extraction chromatographic (ABEC-5000) resins. In ammonium sulfate solutions, mercury partitions to the salt-rich phase in ABS, but by using halide ion extractants, mercury will partition to the PEG-rich phase after formation of a chloro, bromo or iodo complex. The efficacy of the extractant increases in the order Cl-

Muscle biopsies from human muscle diseases with myopathic pathology reveal common alterations in mitochondrial function.

PubMed

Sunitha, Balaraju; Gayathri, Narayanappa; Kumar, Manish; Keshava Prasad, Thottethodi Subrahmanya; Nalini, Atchayaram; Padmanabhan, Balasundaram; Srinivas Bharath, Muchukunte Mukunda

2016-07-01

Muscle diseases are clinically and genetically heterogeneous and manifest as dystrophic, inflammatory and myopathic pathologies, among others. Our previous study on the cardiotoxin mouse model of myodegeneration and inflammation linked muscle pathology with mitochondrial damage and oxidative stress. In this study, we investigated whether human muscle diseases display mitochondrial changes. Muscle biopsies from muscle disease patients, represented by dysferlinopathy (dysfy) (dystrophic pathology; n = 43), polymyositis (PM) (inflammatory pathology; n = 24), and distal myopathy with rimmed vacuoles (DMRV) (distal myopathy; n = 31) were analyzed. Mitochondrial damage (ragged blue and COX-deficient fibers) was revealed in dysfy, PM, and DMRV cases by enzyme histochemistry (SDH and COX-SDH), electron microscopy (vacuolation and altered cristae) and biochemical assays (significantly increased ADP/ATP ratio). Proteomic analysis of muscle mitochondria from all three muscle diseases by isobaric tag for relative and absolute quantitation labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated down-regulation of electron transport chain (ETC) complex subunits, assembly factors and Krebs cycle enzymes. Interestingly, 80 of the under-expressed proteins were common among the three pathologies. Assay of ETC and Krebs cycle enzyme activities validated the MS data. Mitochondrial proteins from muscle pathologies also displayed higher tryptophan (Trp) oxidation and the same was corroborated in the cardiotoxin model. Molecular modeling predicted Trp oxidation to alter the local structure of mitochondrial proteins. Our data highlight mitochondrial alterations in muscle pathologies, represented by morphological changes, altered mitochondrial proteome and protein oxidation, thereby establishing the role of mitochondrial damage in human muscle diseases. We investigated whether human muscle diseases display mitochondrial changes. Muscle biopsies

A randomized controlled trial of efficacy and ST change following use of the Welch-Allyn MRL PIC biphasic waveform versus damped sine monophasic waveform for external DC cardioversion.

PubMed

Ambler, Jonathan J S; Deakin, Charles D

2006-11-01

Biphasic waveforms have similar or greater efficacy at cardioverting atrial and ventricular arrhythmias at lower energy levels than monophasic waveforms, and cause less ST depression following defibrillation of ventricular fibrillation. No studies have investigated this effect on ST change with atrial arrhythmias. We studied the efficacy of the Welch Allyn-MRL PIC biphasic defibrillator. One hundred and thirty-nine patients undergoing elective DC cardioversion for atrial arrhythmias were randomised to cardioversion by monophasic (Hewlett Packard Codemaster XL; 100, 200, 300, 360 and 360J) or biphasic (Welch Allyn-MRL PIC; 70, 100, 150, 200 and 300J) defibrillator. We analysed success of cardioversion after 0 and 30min, cumulative energy, number of shocks and energy at successful cardioversion. The ST change in the recorded electrocardiogram was measured at 15s after all shocks using electronic callipers. Immediately after cardioversion 59/68 (86.8%) of the monophasic group versus 56/60 (93.3%) of the biphasic group were in sinus rhythm. Of the monophasic group, 55/67 (82.1%) remained in sinus rhythm at 30min versus 53/58 (91.4%) of the biphasic group. These differences were not significant at 0min (P=0.35) or 30min (P=0.21). The biphasic group required significantly fewer shocks (P=0.006), less cumulative energy (P<0.0001) and required lower total energy for successful cardioversion (P<0.0001). Of the 102 patients with electrocardiogram recordings suitable for analysis, ST segment change was greater in the monophasic group (P=0.037). The Welch Allyn-MRL biphasic waveform for DC cardioversion results in fewer shocks, with less cumulative energy delivered and less post shock ST change than with a Hewlett Packard Codemaster XL damped sine wave monophasic waveform.

Average current is better than peak current as therapeutic dosage for biphasic waveforms in a ventricular fibrillation pig model of cardiac arrest.

PubMed

Chen, Bihua; Yu, Tao; Ristagno, Giuseppe; Quan, Weilun; Li, Yongqin

2014-10-01

Defibrillation current has been shown to be a clinically more relevant dosing unit than energy. However, the effects of average and peak current in determining shock outcome are still undetermined. The aim of this study was to investigate the relationship between average current, peak current and defibrillation success when different biphasic waveforms were employed. Ventricular fibrillation (VF) was electrically induced in 22 domestic male pigs. Animals were then randomized to receive defibrillation using one of two different biphasic waveforms. A grouped up-and-down defibrillation threshold-testing protocol was used to maintain the average success rate of 50% in the neighborhood. In 14 animals (Study A), defibrillations were accomplished with either biphasic truncated exponential (BTE) or rectilinear biphasic waveforms. In eight animals (Study B), shocks were delivered using two BTE waveforms that had identical peak current but different waveform durations. Both average and peak currents were associated with defibrillation success when BTE and rectilinear waveforms were investigated. However, when pathway impedance was less than 90Ω for the BTE waveform, bivariate correlation coefficient was 0.36 (p=0.001) for the average current, but only 0.21 (p=0.06) for the peak current in Study A. In Study B, a high defibrillation success (67.9% vs. 38.8%, p<0.001) was observed when the waveform delivered more average current (14.9±2.1A vs. 13.5±1.7A, p<0.001) while keeping the peak current unchanged. In this porcine model of VF, average current was better than peak current to be an adequate parameter to describe the therapeutic dosage when biphasic defibrillation waveforms were used. The institutional protocol number: P0805. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Superabsorbent biphasic system based on poly(lactic acid) and poly(acrylic acid)

NASA Astrophysics Data System (ADS)

Sartore, Luciana; Pandini, Stefano; Baldi, Francesco; Bignotti, Fabio

2016-05-01

In this research work, biocomposites based on crosslinked particles of poly(acrylic acid), commonly used as superabsorbent polymer (SAP), and poly-L-lactic acid (PLLA) were developed to elucidate the role of the filler (i.e., polymeric crosslinked particles) on the overall physico-mechanical behavior and to obtain superabsorbent thermoplastic products. Samples prepared by melt-blending of components in different ratios showed a biphasic system with a regular distribution of particles, with diameter ranging from 5 to 10 μm, within the PLLA polymeric matrix. The polymeric biphasic system, coded PLASA i.e. superabsorbent poly(lactic acid), showed excellent swelling properties, demonstrating that cross-linked particles retain their superabsorbent ability, as in their free counterparts, even if distributed in a thermoplastic polymeric matrix. The thermal characteristics of the biocomposites evidence enhanced thermal stability in comparison with neat PLLA and also mechanical properties are markedly modified by addition of crosslinked particles which induce regular stiffening effect. Furthermore, in aqueous environments the particles swell and are leached from PLLA matrix generating very high porosity. These new open-pore PLLA foams, produced in absence of organic solvents and chemical foaming agents, with good physico-mechanical properties appear very promising for several applications, for instance in tissue engineering for scaffold production.

Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis.

PubMed

Ferguson, Alison C; Pearce, Simon; Band, Leah R; Yang, Caiyun; Ferjentsikova, Ivana; King, John; Yuan, Zheng; Zhang, Dabing; Wilson, Zoe A

2017-01-01

Viable pollen is essential for plant reproduction and crop yield. Its production requires coordinated expression at specific stages during anther development, involving early meiosis-associated events and late pollen wall formation. The ABORTED MICROSPORES (AMS) transcription factor is a master regulator of sporopollenin biosynthesis, secretion and pollen wall formation in Arabidopsis. Here we show that it has complex regulation and additional essential roles earlier in pollen formation. An inducible-AMS reporter was created for functional rescue, protein expression pattern analysis, and to distinguish between direct and indirect targets. Mathematical modelling was used to create regulatory networks based on wild-type RNA and protein expression. Dual activity of AMS was defined by biphasic protein expression in anther tapetal cells, with an initial peak around pollen meiosis and then later during pollen wall development. Direct AMS-regulated targets exhibit temporal regulation, indicating that additional factors are associated with their regulation. We demonstrate that AMS biphasic expression is essential for pollen development, and defines distinct functional activities during early and late pollen development. Mathematical modelling suggests that AMS may competitively form a protein complex with other tapetum-expressed transcription factors, and that biphasic regulation is due to repression of upstream regulators and promotion of AMS protein degradation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Development of a discriminative biphasic in vitro dissolution test and correlation with in vivo pharmacokinetic studies for differently formulated racecadotril granules.

PubMed

Deng, Jia; Staufenbiel, Sven; Hao, Shilei; Wang, Bochu; Dashevskiy, Andriy; Bodmeier, Roland

2017-06-10

The purpose of this study was to discriminate the release behavior from three differently formulated racecadotril (BCS II) granules and to establish an in vitro-in vivo correlation. Three granule formulations of the lipophilic drug were prepared with equivalent composition but prepared with different manufacturing processes (dry granulation, wet granulation with or without binder). In vitro release of the three granules was investigated using a biphasic dissolution system (phosphate buffer pH6.8 and octanol) and compared to the conventional single phase USP II dissolution test performed under sink and non-sink conditions. In vivo studies with each granule formulation were performed in rats. Interestingly, the granule formulations exhibited pronouncedly different behavior in the different dissolution systems depending on different wetting and dissolution conditions. Single phase USP II dissolution tests lacked discrimination. In contrast, remarkable discrimination between the granule formulations was observed in the octanol phase of biphasic dissolution system with a rank order of release from granules prepared by wet granulation with binder>wet granulation without binder>dry granulation. This release order correlated well with the wettability of these granules. An excellent correlation was also established between in vitro release in the octanol phase of the biphasic test and in vivo data (R 2 =0.999). Compared to conventional dissolution methods, the biphasic method provides great potential to discriminate between only minor formulation and process changes within the same dosage form for poorly soluble drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

Biphasic effects of alcohol as a function of circadian phase.

PubMed

Van Reen, Eliza; Rupp, Tracy L; Acebo, Christine; Seifer, Ronald; Carskadon, Mary A

2013-01-01

To assess how alcohol affects multiple sleep latency tests (MSLT) and subjective measures of stimulation/sedation when alcohol is given at different circadian phases. Twenty-seven healthy young adults (age 21-26 yr) were studied. Double-blind placebo and alcohol (vodka tonic targeting 0.05 g% concentration) beverages were each administered three times during the 20-h forced desynchrony protocol. Sleep latency tests and Biphasic Effects of Alcohol Scale (BAES) were administered on each forced desynchrony day. The outcome variables for this study include sleep onset latency (SOL) and stimulation and sedation value (from the BAES). Each outcome variable was associated with the ascending or descending limb of the breath alcohol concentration (BrAC) curve and assigned a circadian phase within a 90° bin. BrAC confirmed targeted maximal levels. Only outcome variables associated with the ascending and descending limb of the alcohol curve were analyzed for this article. Alcohol administered at a circadian time associated with greatest sleepiness showed longer SOL compared with placebo when measured on the ascending limb of the BrAC curve. We also found longer SOL with alcohol on the ascending limb of the BrAC curve in a circadian bin that favors greatest alertness. We observed shorter SOLs on the descending limb of the BrAC curve, but with no circadian phase interaction. The subjective data were partially consistent with the objective data. The physiologic findings in this study support the biphasic stimulating and sedating properties of alcohol, but limit the effect to specific circadian times.

Accounting for phase drifts in SSVEP-based BCIs by means of biphasic stimulation.

PubMed

Wu, Hung-Yi; Lee, Po-Lei; Chang, Hsiang-Chih; Hsieh, Jen-Chuen

2011-05-01

This study proposes a novel biphasic stimulation technique to solve the issue of phase drifts in steady-state visual evoked potential (SSVEPs) in phase-tagged systems. Phase calibration was embedded in stimulus sequences using a biphasic flicker, which is driven by a sequence with alternating reference and phase-shift states. Nine subjects were recruited to participate in off-line and online tests. Signals were bandpass filtered and segmented by trigger signals into reference and phase-shift epochs. Frequency components of SSVEP in the reference and phase-shift epochs were extracted using the Fourier method with a 50% overlapped sliding window. The real and imaginary parts of the SSVEP frequency components were organized into complex vectors in each epoch. Hotelling's t-square test was used to determine the significances of nonzero mean vectors. The rejection of noisy data segments and the validation of gaze detections were made based on p values. The phase difference between the valid mean vectors of reference and phase-shift epochs was used to identify user's gazed targets in this system. Data showed an average information transfer rate of 44.55 and 38.21 bits/min in off-line and online tests, respectively. © 2011 IEEE

Application of a Three-Dimensional Poroelastic BEM to Modeling the Biphasic Mechanics of Cell-Matrix Interactions in Articular Cartilage (REVISION)

PubMed Central

Haider, Mansoor A.; Guilak, Farshid

2009-01-01

Articular cartilage exhibits viscoelasticity in response to mechanical loading that is well described using biphasic or poroelastic continuum models. To date, boundary element methods (BEMs) have not been employed in modeling biphasic tissue mechanics. A three dimensional direct poroelastic BEM, formulated in the Laplace transform domain, is applied to modeling stress relaxation in cartilage. Macroscopic stress relaxation of a poroelastic cylinder in uni-axial confined compression is simulated and validated against a theoretical solution. Microscopic cell deformation due to poroelastic stress relaxation is also modeled. An extended Laplace inversion method is employed to accurately represent mechanical responses in the time domain. PMID:19851478

Application of a Three-Dimensional Poroelastic BEM to Modeling the Biphasic Mechanics of Cell-Matrix Interactions in Articular Cartilage (REVISION).

PubMed

Haider, Mansoor A; Guilak, Farshid

2007-06-15

Articular cartilage exhibits viscoelasticity in response to mechanical loading that is well described using biphasic or poroelastic continuum models. To date, boundary element methods (BEMs) have not been employed in modeling biphasic tissue mechanics. A three dimensional direct poroelastic BEM, formulated in the Laplace transform domain, is applied to modeling stress relaxation in cartilage. Macroscopic stress relaxation of a poroelastic cylinder in uni-axial confined compression is simulated and validated against a theoretical solution. Microscopic cell deformation due to poroelastic stress relaxation is also modeled. An extended Laplace inversion method is employed to accurately represent mechanical responses in the time domain.

Characterizing liquid redistribution in a biphasic vibrating vocal fold using finite element analysis.

PubMed

Kvit, Anton A; Devine, Erin E; Jiang, Jack J; Vamos, Andrew C; Tao, Chao

2015-05-01

Vocal fold tissue is biphasic and consists of a solid extracellular matrix skeleton swelled with interstitial fluid. Interactions between the liquid and solid impact the material properties and stress response of the tissue. The objective of this study was to model the movement of liquid during vocal fold vibration and to estimate the volume of liquid accumulation and stress experienced by the tissue near the anterior-posterior midline, where benign lesions are observed to form. A three-dimensional biphasic finite element model of a single vocal fold was built to solve for the liquid velocity, pore pressure, and von Mises stress during and just after vibration using the commercial finite element software COMSOL Multiphysics (Version 4.3a, 2013, Structural Mechanics and Subsurface Flow Modules). Vibration was induced by applying direct load pressures to the subglottal and intraglottal surfaces. Pressure ranges, frequency, and material parameters were chosen based on those reported in the literature. Postprocessing included liquid velocity, pore pressure, and von Mises stress calculations as well as the frequency-stress and amplitude-stress relationships. Resulting time-averaged velocity vectors during vibration indicated liquid movement toward the midline of the fold, as well as upward movement in the inferior-superior direction. Pore pressure and von Misses stresses were higher in this region just after vibration. A linear relationship was found between the amplitude and pore pressure, whereas a nonlinear relationship was found between the frequency and pore pressure. Although this study had certain computational simplifications, it is the first biphasic finite element model to use a realistic geometry and demonstrate the ability to characterize liquid movement due to vibration. Results indicate that there is a significant amount of liquid that accumulates at the midline; however, the role of this accumulation still requires investigation. Further investigation of

Characterizing liquid redistribution in a biphasic vibrating vocal fold using finite element analysis

PubMed Central

Kvit, Anton A.; Devine, Erin E.; Vamos, Andrew C.; Tao, Chao; Jiang, Jack J.

2015-01-01

OBJECTIVE Vocal fold tissue is biphasic and consists of a solid extracellular matric skeleton swelled with interstitial fluid. Interactions between the liquid and solid impact the material properties and stress response of the tissue. The objective of this study was to model the movement of liquid during vocal fold vibration and estimate the volume of liquid accumulation and stress experienced by the tissue near the anterior-posterior midline, where benign lesions are observed to form. METHODS A three-dimensional biphasic finite element model of a single vocal fold was built to solve for the liquid velocity, pore pressure, and von Mises stress during and just after vibration using the commercial finite element software COMSOL Multiphysics (Version 4.3a, 2013, Structural Mechanics and Subsurface Flow Modules). Vibration was induced by applying direct-load pressures to the subglottal and intraglottal surfaces. Pressure ranges, frequency and material parameters were chosen based on those reported in the literature. Post-processing included liquid velocity, pore pressure and von Mises stress calculations, as well as the frequency-stress and amplitude-stress relationships. RESULTS Resulting time-averaged velocity vectors during vibration indicated liquid movement towards the midline of the fold, as upwards movement in the inferior-superior direction. Pore pressure and von Misses stresses were higher in this region just following vibration. A linear relationship was found between the amplitude and pore pressure, while a nonlinear relationship was found between the frequency and pore pressure. CONCLUSIONS While this study had certain computational simplifications, it is the first biphasic finite element model to employ a realistic geometry and demonstrated the ability to characterize liquid movement due to vibration. Results indicate that there is a significant amount of liquid that accumulates at the midline, however the role of this accumulation still requires

Biphasic investigation of contact mechanics in natural human hips during activities.

PubMed

Li, Junyan; Hua, Xijin; Jin, Zhongmin; Fisher, John; Wilcox, Ruth K

2014-06-01

The aim of this study was to determine the cartilage contact mechanics and the associated fluid pressurisation of the hip joint under eight daily activities, using a three-dimensional finite element hip model with biphasic cartilage layers and generic geometries. Loads with spatial and temporal variations were applied over time and the time-dependent performance of the hip cartilage during walking was also evaluated. It was found that the fluid support ratio was over 90% during the majority of the cycles for all the eight activities. A reduced fluid support ratio was observed for the time at which the contact region slid towards the interior edge of the acetabular cartilage, but these occurred when the absolute level of the peak contact stress was minimal. Over 10 cycles of gait, the peak contact stress and peak fluid pressure remained constant, but a faster process of fluid exudation was observed for the interior edge region of the acetabular cartilage. The results demonstrate the excellent function of the hip cartilage within which the solid matrix is prevented from high levels of stress during activities owing to the load shared by fluid pressurisation. The findings are important in gaining a better understanding of the hip function during daily activities, as well as the pathology of hip degeneration and potential for future interventions. They provide a basis for future subject-specific biphasic investigations of hip performance during activities. © IMechE 2014.

Biphasic investigation of contact mechanics in natural human hips during activities

PubMed Central

Hua, Xijin; Jin, Zhongmin; Fisher, John; Wilcox, Ruth K

2014-01-01

The aim of this study was to determine the cartilage contact mechanics and the associated fluid pressurisation of the hip joint under eight daily activities, using a three-dimensional finite element hip model with biphasic cartilage layers and generic geometries. Loads with spatial and temporal variations were applied over time and the time-dependent performance of the hip cartilage during walking was also evaluated. It was found that the fluid support ratio was over 90% during the majority of the cycles for all the eight activities. A reduced fluid support ratio was observed for the time at which the contact region slid towards the interior edge of the acetabular cartilage, but these occurred when the absolute level of the peak contact stress was minimal. Over 10 cycles of gait, the peak contact stress and peak fluid pressure remained constant, but a faster process of fluid exudation was observed for the interior edge region of the acetabular cartilage. The results demonstrate the excellent function of the hip cartilage within which the solid matrix is prevented from high levels of stress during activities owing to the load shared by fluid pressurisation. The findings are important in gaining a better understanding of the hip function during daily activities, as well as the pathology of hip degeneration and potential for future interventions. They provide a basis for future subject-specific biphasic investigations of hip performance during activities. PMID:24898443

Myopathic changes in murine skeletal muscle lacking synemin

PubMed Central

García-Pelagio, Karla P.; Muriel, Joaquin; O'Neill, Andrea; Desmond, Patrick F.; Lovering, Richard M.; Lund, Linda; Bond, Meredith

2015-01-01

Diseases of striated muscle linked to intermediate filament (IF) proteins are associated with defects in the organization of the contractile apparatus and its links to costameres, which connect the sarcomeres to the cell membrane. Here we study the role in skeletal muscle of synemin, a type IV IF protein, by examining mice null for synemin (synm-null). Synm-null mice have a mild skeletal muscle phenotype. Tibialis anterior (TA) muscles show a significant decrease in mean fiber diameter, a decrease in twitch and tetanic force, and an increase in susceptibility to injury caused by lengthening contractions. Organization of proteins associated with the contractile apparatus and costameres is not significantly altered in the synm-null. Elastimetry of the sarcolemma and associated contractile apparatus in extensor digitorum longus myofibers reveals a reduction in tension consistent with an increase in sarcolemmal deformability. Although fatigue after repeated isometric contractions is more marked in TA muscles of synm-null mice, the ability of the mice to run uphill on a treadmill is similar to controls. Our results suggest that synemin contributes to linkage between costameres and the contractile apparatus and that the absence of synemin results in decreased fiber size and increased sarcolemmal deformability and susceptibility to injury. Thus synemin plays a moderate but distinct role in fast twitch skeletal muscle. PMID:25567810

Application of a biphasic test for characterization of in vitro drug release of immediate release formulations of celecoxib and its relevance to in vivo absorption.

PubMed

Shi, Yi; Gao, Ping; Gong, Yuchuan; Ping, Haili

2010-10-04

A biphasic in vitro test method was used to examine release profiles of a poorly soluble model drug, celecoxib (CEB), from its immediate release formulations. Three formulations of CEB were investigated in this study, including a commercial Celebrex capsule, a solution formulation (containing cosolvent and surfactant) and a supersaturatable self-emulsifying drug delivery system (S-SEDDS). The biphasic test system consisted of an aqueous buffer and a water-immiscible organic solvent (e.g., octanol) with the use of both USP II and IV apparatuses. The aqueous phase provided a nonsink dissolution medium for CEB, while the octanol phase acted as a sink for CEB partitioning. For comparison, CEB concentration-time profiles of these formulations in the aqueous medium under either a sink condition or a nonsink condition were also explored. CEB release profiles of these formulations observed in the aqueous medium from either the sink condition test, the nonsink condition test, or the biphasic test have little relevance to the pharmacokinetic observations (e.g., AUC, C(max)) in human subjects. In contrast, a rank order correlation among the three CEB formulations is obtained between the in vitro AUC values of CEB from the octanol phase up to t = 2 h and the in vivo mean AUC (or C(max)) values. As the biphasic test permits a rapid removal of drug from the aqueous phase by partitioning into the organic phase, the amount of drug in the organic phase represents the amount of drug accumulated in systemic circulation in vivo. This hypothesis provides the scientific rationale for the rank order relationship among these CEB formulations between their CEB concentrations in the organic phase and the relative AUC or C(max). In addition, the biphasic test method permits differentiation and discrimination of key attributes among the three different CEB formulations. This work demonstrates that the biphasic in vitro test method appears to be useful as a tool in evaluating performance of

Metabolic and miRNA Profiling of TMV Infected Plants Reveals Biphasic Temporal Changes

PubMed Central

Bazzini, Ariel A.; Manacorda, Carlos A.; Tohge, Takayuki; Conti, Gabriela; Rodriguez, Maria C.; Nunes-Nesi, Adriano; Villanueva, Sofía; Fernie, Alisdair R.; Carrari, Fernando; Asurmendi, Sebastian

2011-01-01

Plant viral infections induce changes including gene expression and metabolic components. Identification of metabolites and microRNAs (miRNAs) differing in abundance along infection may provide a broad view of the pathways involved in signaling and defense that orchestrate and execute the response in plant-pathogen interactions. We used a systemic approach by applying both liquid and gas chromatography coupled to mass spectrometry to determine the relative level of metabolites across the viral infection, together with a miRs profiling using a micro-array based procedure. Systemic changes in metabolites were characterized by a biphasic response after infection. The first phase, detected at one dpi, evidenced the action of a systemic signal since no virus was detected systemically. Several of the metabolites increased at this stage were hormone-related. miRs profiling after infection also revealed a biphasic alteration, showing miRs alteration at 5 dpi where no virus was detected systemically and a late phase correlating with virus accumulation. Correlation analyses revealed a massive increase in the density of correlation networks after infection indicating a complex reprogramming of the regulatory pathways, either in response to the plant defense mechanism or to the virus infection itself. Our data propose the involvement of a systemic signaling on early miRs alteration. PMID:22174812

Exocyst sec5 regulates exocytosis of newcomer insulin granules underlying biphasic insulin secretion.

PubMed

Xie, Li; Zhu, Dan; Kang, Youhou; Liang, Tao; He, Yu; Gaisano, Herbert Y

2013-01-01

The exocyst complex subunit Sec5 is a downstream effector of RalA-GTPase which promotes RalA-exocyst interactions and exocyst assembly, serving to tether secretory granules to docking sites on the plasma membrane. We recently reported that RalA regulates biphasic insulin secretion in pancreatic islet β cells in part by tethering insulin secretory granules to Ca(2+) channels to assist excitosome assembly. Here, we assessed β cell exocytosis by patch clamp membrane capacitance measurement and total internal reflection fluorescence microscopy to investigate the role of Sec5 in regulating insulin secretion. Sec5 is present in human and rodent islet β cells, localized to insulin granules. Sec5 protein depletion in rat INS-1 cells inhibited depolarization-induced release of primed insulin granules from both readily-releasable pool and mobilization from the reserve pool. This reduction in insulin exocytosis was attributed mainly to reduction in recruitment and exocytosis of newcomer insulin granules that undergo minimal docking time at the plasma membrane, but which encompassed a larger portion of biphasic glucose stimulated insulin secretion. Sec5 protein knockdown had little effect on predocked granules, unless vigorously stimulated by KCl depolarization. Taken together, newcomer insulin granules in β cells are more sensitive than predocked granules to Sec5 regulation.

A Physicochemically Optimized and Neuroconductive Biphasic Nerve Guidance Conduit for Peripheral Nerve Repair.

PubMed

Ryan, Alan J; Lackington, William A; Hibbitts, Alan J; Matheson, Austyn; Alekseeva, Tijna; Stejskalova, Anna; Roche, Phoebe; O'Brien, Fergal J

2017-12-01

Clinically available hollow nerve guidance conduits (NGCs) have had limited success in treating large peripheral nerve injuries. This study aims to develop a biphasic NGC combining a physicochemically optimized collagen outer conduit to bridge the transected nerve, and a neuroconductive hyaluronic acid-based luminal filler to support regeneration. The outer conduit is mechanically optimized by manipulating crosslinking and collagen density, allowing the engineering of a high wall permeability to mitigate the risk of neuroma formation, while also maintaining physiologically relevant stiffness and enzymatic degradation tuned to coincide with regeneration rates. Freeze-drying is used to seamlessly integrate the luminal filler into the conduit, creating a longitudinally aligned pore microarchitecture. The luminal stiffness is modulated to support Schwann cells, with laminin incorporation further enhancing bioactivity by improving cell attachment and metabolic activity. Additionally, this biphasic NGC is shown to support neurogenesis and gliogenesis of neural progenitor cells and axonal outgrowth from dorsal root ganglia. These findings highlight the paradigm that a successful NGC requires the concerted optimization of both a mechanical support phase capable of bridging a nerve defect and a neuroconductive phase with an architecture capable of supporting both Schwann cells and neurons in order to achieve functional regenerative outcome. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biphasic fermentation is an efficient strategy for the overproduction of δ-endotoxin from Bacillus thuringiensis.

PubMed

Jisha, Veloorvalappil Narayanan; Smitha, Robinson Babysarojam; Priji, Prakasan; Sajith, Sreedharan; Benjamin, Sailas

2015-02-01

This study illustrates a biphasic solid-state fermentation (SSF) strategy for the overproduction of δ-endotoxin from Bacillus thuringiensis subsp. kurstaki (Btk) and also purification of δ-endotoxin from the solid-fermented medium. The fermentation strategy had two phases (biphasic); i.e., the first short phase was semisolid state (12 h), and the remaining long phase was strict SSF. To achieve the biphasic SSF, after 12 h (150 rpm, 37 °C) fermentation of the medium [Luria-Bertani (LB) supplemented with 30 % (w/v) raw soybean flour (phase I)], the supernatant in it was completely centrifuged out (1,000 × g, 10 min) aseptically for harvesting the extracellular enzymes as by-product. The resultant wet solid matter without free-flowing liquid but with embedded Btk was incubated 60 h more (phase II) for enhancing δ-endotoxin production at static condition (37 °C). Coupled with this, δ-endotoxin was purified by the modified phase separation method, and its purity was physically confirmed by both staining and microscopic techniques. The maximum δ-endotoxin yield from solid medium (48 h) was 15.8 mg/mL (recovery was 55-59 %) LB-equivalent, while that of LB control (recovery was 95 %) was only 0.43 mg/mL (72 h), i.e., thus, in comparison, 36.74-fold more yield in solid medium obtained by 24 h less gestation period. The purified crystal proteins showed apparent molecular weights (MWs) of 45, 35, and 6 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Briefly, this unique study physically demonstrates how Btk δ-endotoxin is purified (95-99 % purity) from solid-fermented matter for the first time, coupled with its overproduction at the expense of only 21.5 % higher production cost.

Lignocellulose fractionation into furfural and glucose by AlCl3-catalyzed DES/MIBK biphasic pretreatment.

PubMed

Wang, Zhi-Kun; Shen, Xiao-Jun; Chen, Jun-Jie; Jiang, Ying-Qiu; Hu, Zhi-Yan; Wang, Xing; Liu, Li

2018-06-01

Herein, an efficient DES/MIBK biphasic pretreatment system for preparation of furfural and fermentable glucose from lignocellulose was developed with AlCl 3 as catalysis. The low-cost and renewable DES (Choline chloride-Oxalic acid) served not only as a Brønsted acid catalyst, but also as a pretreatment solvent in present work, and MIBK as an extracting reagent which can increase the yield of furfural in DES phase. The effects of this biphasic pretreatment on the furfural yield and saccharification of the lignocellulose before and after pretreatment were explored using HPLC, HAPEC, FT-IR, XRD and SEM. Under the best pretreatment condition (at 140 °C for 90 min), furfural could be obtained in 70.3% yield and 80.8% of the pretreated lignocellulose was saccharified, which was 8.4 times higher than that of the raw lignocellulose without pretreatment. In a word, this pretreatment system can be considered as a potential technique for efficient valorization of lignocellulose for production of furfural and fermentable glucose. Copyright © 2018. Published by Elsevier B.V.

Online Epileptic Seizure Prediction Using Wavelet-Based Bi-Phase Correlation of Electrical Signals Tomography.

PubMed

Vahabi, Zahra; Amirfattahi, Rasoul; Shayegh, Farzaneh; Ghassemi, Fahimeh

2015-09-01

Considerable efforts have been made in order to predict seizures. Among these methods, the ones that quantify synchronization between brain areas, are the most important methods. However, to date, a practically acceptable result has not been reported. In this paper, we use a synchronization measurement method that is derived according to the ability of bi-spectrum in determining the nonlinear properties of a system. In this method, first, temporal variation of the bi-spectrum of different channels of electro cardiography (ECoG) signals are obtained via an extended wavelet-based time-frequency analysis method; then, to compare different channels, the bi-phase correlation measure is introduced. Since, in this way, the temporal variation of the amount of nonlinear coupling between brain regions, which have not been considered yet, are taken into account, results are more reliable than the conventional phase-synchronization measures. It is shown that, for 21 patients of FSPEEG database, bi-phase correlation can discriminate the pre-ictal and ictal states, with very low false positive rates (FPRs) (average: 0.078/h) and high sensitivity (100%). However, the proposed seizure predictor still cannot significantly overcome the random predictor for all patients.

Electronic and structural characteristics of zinc-blende wurtzite biphasic homostructure GaN nanowires

DOE PAGES

Jacobs, Benjamin W.; Ayres, Virginia M.; Petkov, Mihail P.; ...

2007-04-07

Here, we report a new biphasic crystalline wurtzite/zinc-blende homostructure in gallium nitride nanowires. Cathodoluminescence was used to quantitatively measure the wurtzite and zinc-blende band gaps. High-resolution transmission electron microscopy was used to identify distinct wurtzite and zinc-blende crystalline phases within single nanowires through the use of selected area electron diffraction, electron dispersive spectroscopy, electron energy loss spectroscopy, and fast Fourier transform techniques. A mechanism for growth is identified.

Electronic and structural characteristics of zinc-blende wurtzite biphasic homostructure GaN nanowires.

PubMed

Jacobs, Benjamin W; Ayres, Virginia M; Petkov, Mihail P; Halpern, Joshua B; He, Maoqi; Baczewski, Andrew D; McElroy, Kaylee; Crimp, Martin A; Zhang, Jiaming; Shaw, Harry C

2007-05-01

We report a new biphasic crystalline wurtzite/zinc-blende homostructure in gallium nitride nanowires. Cathodoluminescence was used to quantitatively measure the wurtzite and zinc-blende band gaps. High-resolution transmission electron microscopy was used to identify distinct wurtzite and zinc-blende crystalline phases within single nanowires through the use of selected area electron diffraction, electron dispersive spectroscopy, electron energy loss spectroscopy, and fast Fourier transform techniques. A mechanism for growth is identified.

Acute Biphasic Effects of Ayahuasca

PubMed Central

Schenberg, Eduardo Ekman; Alexandre, João Felipe Morel; Filev, Renato; Cravo, Andre Mascioli; Sato, João Ricardo; Muthukumaraswamy, Suresh D.; Yonamine, Maurício; Waguespack, Marian; Lomnicka, Izabela; Barker, Steven A.; da Silveira, Dartiu Xavier

2015-01-01

Ritual use of ayahuasca, an amazonian Amerindian medicine turned sacrament in syncretic religions in Brazil, is rapidly growing around the world. Because of this internationalization, a comprehensive understanding of the pharmacological mechanisms of action of the brew and the neural correlates of the modified states of consciousness it induces is important. Employing a combination of electroencephalogram (EEG) recordings and quantification of ayahuasca's compounds and their metabolites in the systemic circulation we found ayahuasca to induce a biphasic effect in the brain. This effect was composed of reduced power in the alpha band (8–13 Hz) after 50 minutes from ingestion of the brew and increased slow- and fast-gamma power (30–50 and 50–100 Hz, respectively) between 75 and 125 minutes. Alpha power reductions were mostly located at left parieto-occipital cortex, slow-gamma power increase was observed at left centro-parieto-occipital, left fronto-temporal and right frontal cortices while fast-gamma increases were significant at left centro-parieto-occipital, left fronto-temporal, right frontal and right parieto-occipital cortices. These effects were significantly associated with circulating levels of ayahuasca’s chemical compounds, mostly N,N-dimethyltryptamine (DMT), harmine, harmaline and tetrahydroharmine and some of their metabolites. An interpretation based on a cognitive and emotional framework relevant to the ritual use of ayahuasca, as well as it's potential therapeutic effects is offered. PMID:26421727

Acute Biphasic Effects of Ayahuasca.

PubMed

Schenberg, Eduardo Ekman; Alexandre, João Felipe Morel; Filev, Renato; Cravo, Andre Mascioli; Sato, João Ricardo; Muthukumaraswamy, Suresh D; Yonamine, Maurício; Waguespack, Marian; Lomnicka, Izabela; Barker, Steven A; da Silveira, Dartiu Xavier

2015-01-01

Ritual use of ayahuasca, an amazonian Amerindian medicine turned sacrament in syncretic religions in Brazil, is rapidly growing around the world. Because of this internationalization, a comprehensive understanding of the pharmacological mechanisms of action of the brew and the neural correlates of the modified states of consciousness it induces is important. Employing a combination of electroencephalogram (EEG) recordings and quantification of ayahuasca's compounds and their metabolites in the systemic circulation we found ayahuasca to induce a biphasic effect in the brain. This effect was composed of reduced power in the alpha band (8-13 Hz) after 50 minutes from ingestion of the brew and increased slow- and fast-gamma power (30-50 and 50-100 Hz, respectively) between 75 and 125 minutes. Alpha power reductions were mostly located at left parieto-occipital cortex, slow-gamma power increase was observed at left centro-parieto-occipital, left fronto-temporal and right frontal cortices while fast-gamma increases were significant at left centro-parieto-occipital, left fronto-temporal, right frontal and right parieto-occipital cortices. These effects were significantly associated with circulating levels of ayahuasca's chemical compounds, mostly N,N-dimethyltryptamine (DMT), harmine, harmaline and tetrahydroharmine and some of their metabolites. An interpretation based on a cognitive and emotional framework relevant to the ritual use of ayahuasca, as well as it's potential therapeutic effects is offered.

Evolution of a mini-scale biphasic dissolution model: Impact of model parameters on partitioning of dissolved API and modelling of in vivo-relevant kinetics.

PubMed

Locher, Kathrin; Borghardt, Jens M; Frank, Kerstin J; Kloft, Charlotte; Wagner, Karl G

2016-08-01

Biphasic dissolution models are proposed to have good predictive power for the in vivo absorption. The aim of this study was to improve our previously introduced mini-scale dissolution model to mimic in vivo situations more realistically and to increase the robustness of the experimental model. Six dissolved APIs (BCS II) were tested applying the improved mini-scale biphasic dissolution model (miBIdi-pH-II). The influence of experimental model parameters including various excipients, API concentrations, dual paddle and its rotation speed was investigated. The kinetics in the biphasic model was described applying a one- and four-compartment pharmacokinetic (PK) model. The improved biphasic dissolution model was robust related to differing APIs and excipient concentrations. The dual paddle guaranteed homogenous mixing in both phases; the optimal rotation speed was 25 and 75rpm for the aqueous and the octanol phase, respectively. A one-compartment PK model adequately characterised the data of fully dissolved APIs. A four-compartment PK model best quantified dissolution, precipitation, and partitioning also of undissolved amounts due to realistic pH profiles. The improved dissolution model is a powerful tool for investigating the interplay between dissolution, precipitation and partitioning of various poorly soluble APIs (BCS II). In vivo-relevant PK parameters could be estimated applying respective PK models. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of low-energy versus high-energy biphasic defibrillation shocks following prolonged ventricular fibrillation.

PubMed

Walcott, Gregory P; Melnick, Sharon B; Killingsworth, Cheryl R; Ideker, Raymond E

2010-01-01

Since the initial development of the defibrillator, there has been concern that, while delivery of a large electric shock would stop fibrillation, it would also cause damage to the heart. This concern has been raised again with the development of the biphasic defibrillator. To compare defibrillation efficacy, postshock cardiac function, and troponin I levels following 150-J and 360-J shocks. Nineteen swine were anesthetized with isoflurane and instrumented with pressure catheters in the left ventricle, aorta, and right atrium. The animals were fibrillated for 6 minutes, followed by defibrillation with either low-energy (n = 8) or high-energy (n = 11) shocks. After defibrillation, chest compressions were initiated and continued until return of spontaneous circulation (ROSC). Epinephrine, 0.01 mg/kg every 3 minutes, was given for arterial blood pressure < 50 mmHg. Hemodynamic parameters were recorded for four hours. Transthoracic echocardiography was performed and troponin I levels were measured at baseline and four hours following ventricular fibrillation (VF). Survival rates at four hours were not different between the two groups (low-energy, 5 of 8; high-energy, 7 of 11). Results for arterial blood pressure, positive dP/dt (first derivative of pressure measured over time, a measure of left ventricular contractility), and negative dP/dt at the time of lowest arterial blood pressure (ABP) following ROSC were not different between the two groups (p = not significant [NS]), but were lower than at baseline. All hemodynamic measures returned to baseline by four hours. Ejection fractions, stroke volumes, and cardiac outputs were not different between the two groups at four hours. Troponin I levels at four hours were not different between the two groups (12 +/- 11 ng/mL versus 21 +/- 26 ng/mL, p = NS) but were higher at four hours than at baseline (19 +/- 19 ng/mL versus 0.8 +/- 0.5 ng/mL, p < 0.05, groups combined). Biphasic 360-J shocks do not cause more cardiac damage

"Washing-out" ionic liquids from polyethylene glycol to form aqueous biphasic systems.

PubMed

Tomé, Luciana I N; Pereira, Jorge F B; Rogers, Robin D; Freire, Mara G; Gomes, José R B; Coutinho, João A P

2014-02-14

The molecular-level mechanisms behind the formation of aqueous biphasic systems (ABS) composed of ionic liquids (ILs) and polymers are hitherto not completely understood. For the first time, it is herein shown that polymer-IL-based ABS are a result of a "washing-out" phenomenon, and not of a salting-out effect of the IL over the polymer as assumed in the past few years. Novel evidence is herein provided by experimental results combined with molecular dynamics (MD) simulations and density functional theory (DFT) calculations.

Controlled and reversible induction of differentiation and activation of adult human hepatocytes by a biphasic culture technique

PubMed Central

Auth, Marcus K.H.; Boost, Kim A.; Leckel, Kerstin; Beecken, Wolf-Dietrich; Engl, Tobias; Jonas, Dietger; Oppermann, Elsie; Hilgard, Philip; Markus, Bernd H.; Bechstein, Wolf-Otto; Blaheta, Roman A.

2005-01-01

AIM: Clinical application of human hepatocytes (HC) is hampered by the progressive loss of growth and differentiation in vitro. The object of the study was to evaluate the effect of a biphasic culture technique on expression and activation of growth factor receptors and differentiation of human adult HC. METHODS: Isolated HC were sequentially cultured in a hormone enriched differentiation medium (DM) containing nicotinamide, insulin, transferrin, selenium, and dexame-thasone or activation medium (AM) containing hepatocyte growth factor (HGF), epidermal growth factor (EGF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). Expression, distribution and activation of the HC receptors (MET and EGFR) and the pattern of characteristic cytokeratin (CK) filaments were measured by fluorometry, confocal microscopy and Western blotting. RESULTS: In the biphasic culture system, HC underwent repeated cycles of activation (characterized by expression and activation of growth factor receptors) and re-differentiation (illustrated by distribution of typical filaments CK-18 but low or absent expression of CK-19). In AM increased expression of MET and EGFR was associated with receptor translocation into the cytoplasm and induction of atypical CK-19. In DM low expression of MET and EGFR was localized on the cell membrane and CK-19 was reduced. Receptor phosphorylation required embedding of HC in collagen type I gel. CONCLUSION: Control and reversible modulation of growth factor receptor activation of mature human HC can be accomplished in vitro, when defined signals from the extracellular matrix and sequential growth stimuli are provided. The biphasic technique helps overcome de-differentiation, which occurs during continuous stimulation by means of growth factors. PMID:15810072

Controlled and reversible induction of differentiation and activation of adult human hepatocytes by a biphasic culture technique.

PubMed

Auth, Marcus-K H; Boost, Kim A; Leckel, Kerstin; Beecken, Wolf-Dietrich; Engl, Tobias; Jonas, Dietger; Oppermann, Elsie; Hilgard, Philip; Markus, Bernd H; Bechstein, Wolf-Otto; Blaheta, Roman A

2005-04-14

Clinical application of human hepatocytes (HC) is hampered by the progressive loss of growth and differentiation in vitro. The object of the study was to evaluate the effect of a biphasic culture technique on expression and activation of growth factor receptors and differentiation of human adult HC. Isolated HC were sequentially cultured in a hormone enriched differentiation medium (DM) containing nicotinamide, insulin, transferrin, selenium, and dexame-thasone or activation medium (AM) containing hepatocyte growth factor (HGF), epidermal growth factor (EGF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). Expression, distribution and activation of the HC receptors (MET and EGFR) and the pattern of characteristic cytokeratin (CK) filaments were measured by fluorometry, confocal microscopy and Western blotting. In the biphasic culture system, HC underwent repeated cycles of activation (characterized by expression and activation of growth factor receptors) and re-differentiation (illustrated by distribution of typical filaments CK-18 but low or absent expression of CK-19). In AM increased expression of MET and EGFR was associated with receptor translocation into the cytoplasm and induction of atypical CK-19. In DM low expression of MET and EGFR was localized on the cell membrane and CK-19 was reduced. Receptor phosphorylation required embedding of HC in collagen type I gel. Control and reversible modulation of growth factor receptor activation of mature human HC can be accomplished in vitro, when defined signals from the extracellular matrix and sequential growth stimuli are provided. The biphasic technique helps overcome de-differentiation, which occurs during continuous stimulation by means of growth factors.

Toward Highly Efficient Electrocatalyst for Li-O2 Batteries Using Biphasic N-Doping Cobalt@Graphene Multiple-Capsule Heterostructures.

PubMed

Tan, Guoqiang; Chong, Lina; Amine, Rachid; Lu, Jun; Liu, Cong; Yuan, Yifei; Wen, Jianguo; He, Kun; Bi, Xuanxuan; Guo, Yuanyuan; Wang, Hsien-Hau; Shahbazian-Yassar, Reza; Al Hallaj, Said; Miller, Dean J; Liu, Dijia; Amine, Khalil

2017-05-10

For the promotion of lithium-oxygen batteries available for practical applications, the development of advanced cathode catalysts with low-cost, high activity, and stable structural properties is demanded. Such development is rooted on certain intelligent catalyst-electrode design that fundamentally facilitates electronic and ionic transport and improves oxygen diffusivity in a porous environment. Here we design a biphasic nitrogen-doped cobalt@graphene multiple-capsule heterostructure, combined with a flexible, stable porous electrode architecture, and apply it as promising cathodes for lithium-oxygen cells. The biphasic nitrogen-doping feature improves the electric conductivity and catalytic activity; the multiple-nanocapsule configuration makes high/uniform electroactive zones possible; furthermore, the colander-like porous electrode facilitates the oxygen diffusion, catalytic reaction, and stable deposition of discharge products. As a result, the electrode exhibits much improved electrocatalytic properties associated with unique morphologies of electrochemically grown lithium peroxides.

Charge-balanced biphasic electrical stimulation inhibits neurite extension of spiral ganglion neurons.

PubMed

Shen, Na; Liang, Qiong; Liu, Yuehong; Lai, Bin; Li, Wen; Wang, Zhengmin; Li, Shufeng

2016-06-15

Intracochlear application of exogenous or transgenic neurotrophins, such as neurotrophin-3 (NT-3) and brain derived neurotrophic factor (BDNF), could promote the resprouting of spiral ganglion neuron (SGN) neurites in deafened animals. These resprouting neurites might reduce the gap between cochlear implant electrodes and their targeting SGNs, allowing for an improvement of spatial resolution of electrical stimulation. This study is to investigate the impact of electrical stimulation employed in CI on the extension of resprouting SGN neurites. We established an in vitro model including the devices delivering charge-balanced biphasic electrical stimulation, and spiral ganglion (SG) dissociated culture treated with BDNF and NT-3. After electrical stimulation with varying durations and intensities, we quantified neurite lengths and Schwann cell densities in SG cultures. Stimulations that were greater than 50μA or longer than 8h significantly decreased SG neurite length. Schwann cell density under 100μA electrical stimulation for 48h was significantly lower compared to that in non-stimulated group. These electrical stimulation-induced decreases of neurite extension and Schwann cell density were attenuated by various types of voltage-dependent calcium channel (VDCC) blockers, or completely prevented by their combination, cadmium or calcium-free medium. Our study suggested that charge-balanced biphasic electrical stimulation inhibited the extension of resprouting SGN neurites and decreased Schwann cell density in vitro. Calcium influx through multiple types of VDCCs was involved in the electrical stimulation-induced inhibition. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Direct transformation of xylan-type hemicelluloses to furfural via SnCl₄ catalysts in aqueous and biphasic systems.

PubMed

Wang, Wenju; Ren, Junli; Li, Huiling; Deng, Aojie; Sun, Runcang

2015-05-01

Direct catalytic transformation of xylan-type hemicelluloses to furfural in the aqueous system and the biphasic system were comparatively investigated under mild conditions. Screening of several promising chlorides for conversion of beech xylan in the aqueous system revealed the Lewis acid SnCl4 was the most effective catalyst. Comparing to the single aqueous system, the bio-based 2-methyltetrahydrofuran (2-MTHF)/H2O biphasic system was more conducive to the synthesis of furfural, in which the highest furfural yield of 78.1% was achieved by using SnCl4 as catalysts under the optimized reaction conditions (150°C, 120 min). Additionally, the influences of xylan-type hemicelluloses with different chemical and structural features from beech, corncob and bagasse on the furfural production were studied. It was found that furfural yield to some extent was determined by the xylose content in hemicelluloses and also had relationships with the molecular weight of hemicelluloses and the degree of crystallization. Copyright © 2015 Elsevier Ltd. All rights reserved.

In vitro testing of calcium phosphate (HA, TCP, and biphasic HA-TCP) whiskers.

PubMed

Jalota, Sahil; Bhaduri, Sarit B; Tas, A Cuneyt

2006-09-01

Calcium phosphate [single-phase hydroxyapatite (HA, Ca(10)(PO(4))(6)(OH)(2)), single-phase tricalcium phosphate (beta-TCP, Ca(3)(PO(4))(2)), and biphasic HA-TCP] whiskers were formed by using a novel microwave-assisted molten salt mediated process. Aqueous solutions containing NaNO(3), HNO(3), Ca(NO(3))(2) x 4H(2)O, and KH(2)PO(4) (with or without urea) were used as starting reagents. These solutions were irradiated in a household microwave oven for 5 min. As-recovered precursors were then simply stirred in water at room temperature for 1 h to obtain the whiskers of the desired calcium phosphate (CaP) bioceramics. These whiskers were evaluated, respectively, in vitro by (1) soaking those in synthetic body fluid (SBF) solutions at 37 degrees C for one week, and (2) performing cell attachment and total protein assay tests on the neat whiskers by using a mouse osteoblast cell line (7F2). beta-TCP, HA, and HA-TCP biphasic whiskers were all found to possess apatite-inducing ability when soaked in SBF. SBF-soaked whiskers were found to have BET surface areas ranging from 45 to 112 m(2)/g. Although the osteoblast viability and protein concentrations were found to be the highest on the neat HA whiskers, cells were attached and proliferated on all the whiskers.

Short-term effectiveness of bi-phase oscillatory waves versus hyperthermia for isolated long head biceps tendinopathy

PubMed Central

Oliva, Francesco; Via, Alessio Giai; Rossi, Silvio

2011-01-01

Summary Introduction: Long head biceps (LHB) tendinopathy is a common cause of anterior shoulder pain. Isolated LHB pathology is most common among younger people who practise overhead sports. The authors conducted a short-term prospective randomised study to test the effectiveness of two different methods for the treatment of isolated LHB tendinopathy: biphasic oscillatory waves and hyperthermia. Study design: The study is a prospective randomised study (Level II). Material and methods: The authors identified 20 patients who had clinical and ultrasound (US) evidence of LHB tendinopathy. No patient was a high-level athlete. The patients were randomly assigned to two groups. Group A (10 patients) was treated with bi-phasic oscillatory waves, while Group B received hyperthermia. During the treatment period, no other electromedical therapy, injections with corticosteroids, oral analgesics or nonsteroidal anti-inflammatory drugs were allowed. All the patients were assessed at baseline (T0), immediately after the end of the treatment period (T1) and 6 months after the end of treatment (T2) using a visual analogic scale (VAS) and Constant-Murley Score (CMS). Furthermore, all patients underwent US examinations at T0 and at T1. All the US examinations were performed by the same radiologist. Results: The VAS scores showed a highly statistically significant reduction of pain at T1 both in Group A (65%; p=0,004) and in Group B (50%; p=0,0002). The CMS also showed a statistically significant improvement between the pre-intervention, the post-treatment and the short-term follow-up in both groups. In addition, the peritendinous fluid evident on US examination at T0 was no longer present in all cases at T1. Conclusion: These findings suggest that both bi-phasic oscillatory waves and hyperthermia are able to relieve pain in patients with isolated LHB tendinopathy. This is a Class II level of evidence. PMID:23738257

Toward highly efficient electrocatalyst for Li–O 2 batteries using biphasic N-doping cobalt@graphene multiple-capsule heterostructures

DOE PAGES

Tan, Guoqiang; Chong, Lina; Amine, Rachid; ...

2017-04-12

To promote lithium-oxygen batteries available for practical applications, the development of advanced cathode catalysts with low-cost, high activity and stable structural properties is demanded. Such development is rooted on certain intelligent catalyst-electrode design that fundamentally facilitates electronic and ionic transport, and improves oxygen diffusivity in a porous environment. Here we design a biphasic nitrogen-doped cobalt@graphene multiple-capsule heterostructure, combined with a flexible, stable porous electrode architecture, and apply it as promising cathodes for lithium-oxygen cells. The biphasic nitrogen-doping feature improves the electric conductivity and catalytic activity; the multiple-nanocapsule configuration makes high/uniform electro-active zones possible; furthermore, the colander-like porous electrode facilitates themore » oxygen diffusion, catalytic reaction, and stable deposition of discharge products. Finally, the electrode exhibits much improved electrocatalytic properties associated with unique morphologies of electrochemically grown lithium peroxides.« less

Toward Highly Efficient Electrocatalyst for Li–O 2 Batteries Using Biphasic N-Doping Cobalt@Graphene Multiple-Capsule Heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Guoqiang; Chong, Lina; Amine, Rachid

For the promotion of lithium oxygen batteries available for :practical applications, the development of advanced cathode catalysts with low-high activity, and stable structural properties is demanded. Such development is rooted on certain intelligent catalyst-electrode design that fundamentally facilitates electronic and ionic transport and improves oxygen diffusivity in a porous environment. Here we design a biphasic nitrogen-doped cobalt@grapbene Multiple-capsule heterostructure, combined with a flexible, stable porous electrode architecture, and apply it as promising cathodes for lithium oxygen cells. 'The biphasic nitrogen-doping feature improves the electric conductivity and catalytic activity; the multiple-nanocapsule configuration makes high/uniform electroactive zones possible; furthermore the colander-like porousmore » electrode facilitates the oxygen diffusion, catalytic reaction,and stable deposition of discharge products. As a result, the electrode exhibits much improved electrocatalytic properties associated with unique morphologies of electrochemically grown lithium peroxides.« less

Toward highly efficient electrocatalyst for Li–O 2 batteries using biphasic N-doping cobalt@graphene multiple-capsule heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Guoqiang; Chong, Lina; Amine, Rachid

To promote lithium-oxygen batteries available for practical applications, the development of advanced cathode catalysts with low-cost, high activity and stable structural properties is demanded. Such development is rooted on certain intelligent catalyst-electrode design that fundamentally facilitates electronic and ionic transport, and improves oxygen diffusivity in a porous environment. Here we design a biphasic nitrogen-doped cobalt@graphene multiple-capsule heterostructure, combined with a flexible, stable porous electrode architecture, and apply it as promising cathodes for lithium-oxygen cells. The biphasic nitrogen-doping feature improves the electric conductivity and catalytic activity; the multiple-nanocapsule configuration makes high/uniform electro-active zones possible; furthermore, the colander-like porous electrode facilitates themore » oxygen diffusion, catalytic reaction, and stable deposition of discharge products. Finally, the electrode exhibits much improved electrocatalytic properties associated with unique morphologies of electrochemically grown lithium peroxides.« less

Management of postprandial glucose: Recommended targets and treatment with biphasic insulin.

PubMed

Liebl, Andreas

2016-12-01

Increases in glycaemia, particularly following meals, have been independently associated with diabetes complications, most notably cardiovascular disease. Control of postprandial plasma glucose (PPG) therefore plays an important role in diabetes management. International diabetes guidelines acknowledge the value of PPG monitoring yet place relatively little emphasis on PPG control. This article considers the impact of suboptimal PPG control and current recommendations with regard to management of PPG. Specific consideration is given to the role of biphasic insulins, one of the treatment options recognised by the International Diabetes Federation as preferentially lowering PPG levels. Copyright © 2016 Primary Care Diabetes Europe. Published by Elsevier Ltd. All rights reserved.

Biphasic Role of Chondroitin Sulfate in Cardiac Differentiation of Embryonic Stem Cells through Inhibition of Wnt/β-Catenin Signaling

PubMed Central

Prinz, Robert D.; Willis, Catherine M.; van Kuppevelt, Toin H.; Klüppel, Michael

2014-01-01

The glycosaminoglycan chondroitin sulfate is a critical component of proteoglycans on the cell surface and in the extracellular matrix. As such, chondroitin sulfate side chains and the sulfation balance of chondroitin play important roles in the control of signaling pathways, and have a functional importance in human disease. In contrast, very little is known about the roles of chondroitin sulfate molecules and sulfation patterns during mammalian development and cell lineage specification. Here, we report a novel biphasic role of chondroitin sulfate in the specification of the cardiac cell lineage during embryonic stem cell differentiation through modulation of Wnt/beta-catenin signaling. Lineage marker analysis demonstrates that enzymatic elimination of endogenous chondroitin sulfates leads to defects specifically in cardiac differentiation. This is accompanied by a reduction in the number of beating cardiac foci. Mechanistically, we show that endogenous chondroitin sulfate controls cardiac differentiation in a temporal biphasic manner through inhibition of the Wnt/beta-catenin pathway, a known regulatory pathway for the cardiac lineage. Treatment with a specific exogenous chondroitin sulfate, CS-E, could mimic these biphasic effects on cardiac differentiation and Wnt/beta-catenin signaling. These results establish chondroitin sulfate and its sulfation balance as important regulators of cardiac cell lineage decisions through control of the Wnt/beta-catenin pathway. Our work suggests that targeting the chondroitin biosynthesis and sulfation machinery is a novel promising avenue in regenerative strategies after heart injury. PMID:24667694

Biphasic role of chondroitin sulfate in cardiac differentiation of embryonic stem cells through inhibition of Wnt/β-catenin signaling.

PubMed

Prinz, Robert D; Willis, Catherine M; van Kuppevelt, Toin H; Klüppel, Michael

2014-01-01

The glycosaminoglycan chondroitin sulfate is a critical component of proteoglycans on the cell surface and in the extracellular matrix. As such, chondroitin sulfate side chains and the sulfation balance of chondroitin play important roles in the control of signaling pathways, and have a functional importance in human disease. In contrast, very little is known about the roles of chondroitin sulfate molecules and sulfation patterns during mammalian development and cell lineage specification. Here, we report a novel biphasic role of chondroitin sulfate in the specification of the cardiac cell lineage during embryonic stem cell differentiation through modulation of Wnt/beta-catenin signaling. Lineage marker analysis demonstrates that enzymatic elimination of endogenous chondroitin sulfates leads to defects specifically in cardiac differentiation. This is accompanied by a reduction in the number of beating cardiac foci. Mechanistically, we show that endogenous chondroitin sulfate controls cardiac differentiation in a temporal biphasic manner through inhibition of the Wnt/beta-catenin pathway, a known regulatory pathway for the cardiac lineage. Treatment with a specific exogenous chondroitin sulfate, CS-E, could mimic these biphasic effects on cardiac differentiation and Wnt/beta-catenin signaling. These results establish chondroitin sulfate and its sulfation balance as important regulators of cardiac cell lineage decisions through control of the Wnt/beta-catenin pathway. Our work suggests that targeting the chondroitin biosynthesis and sulfation machinery is a novel promising avenue in regenerative strategies after heart injury.

Biphasic regulation of polymorphonuclear leukocyte spreading by polyphenolic compounds with pyrogallol moieties.

PubMed

Kori, Soichiro; Namiki, Hideo; Suzuki, Kingo

2009-09-01

Green tea polyphenols have been reported to have anti-inflammatory activities, although the molecular mechanisms responsible for this effect remain unclear. In the present study, we examined the effect of green tea extract and a variety of polyphenolic compounds on spreading of peripheral blood polymorphonuclear leukocytes (PMNs) over fibrinogen-coated surfaces. Green tea extract exerted a biphasic effect on PMN spreading; it induced or suppressed spreading at low and high concentrations, respectively. We also found that pyrogallol-bearing compounds have spreading induction activity. Among the compounds tested, tannic acid (TA) had the strongest activity; the concentrations required for induction of maximal spreading were 2 microM for TA, 200 microM for (-)-epigallocatechin gallate, and 2000 microM for the other active compounds. Furthermore, TA was the only compound showing a biphasic effect similar to that of green tea extract; TA at 20 or 200 microM suppressed spreading. The spreading-stimulatory signal was still latent during PMN exposure to TA at concentrations that inhibited spreading, because the pre-exposed PMNs underwent spreading when plated after removal of free TA by centrifugation. The spreading-inhibitory effect of TA at high concentrations overcame the induction of spreading by other stimuli, including phorbol 12-myristate 13-acetate, hydrogen peroxide, denatured fibrinogen surfaces, and naked plastic surfaces. These results suggest that TA as well as green tea extract is bi-functional, having pro-inflammatory and anti-inflammatory effects at low and high concentrations, respectively. Pharmacological use of TA may thus provide new strategies aimed at regulation of PMN spreading for control of inflammation.

Three-dimensional real-time imaging of bi-phasic flow through porous media

NASA Astrophysics Data System (ADS)

Sharma, Prerna; Aswathi, P.; Sane, Anit; Ghosh, Shankar; Bhattacharya, S.

2011-11-01

We present a scanning laser-sheet video imaging technique to image bi-phasic flow in three-dimensional porous media in real time with pore-scale spatial resolution, i.e., 35 μm and 500 μm for directions parallel and perpendicular to the flow, respectively. The technique is illustrated for the case of viscous fingering. Using suitable image processing protocols, both the morphology and the movement of the two-fluid interface, were quantitatively estimated. Furthermore, a macroscopic parameter such as the displacement efficiency obtained from a microscopic (pore-scale) analysis demonstrates the versatility and usefulness of the method.

Coenzyme Q10 reverses pathological phenotype and reduces apoptosis in familial CoQ10 deficiency.

PubMed

Di Giovanni, S; Mirabella, M; Spinazzola, A; Crociani, P; Silvestri, G; Broccolini, A; Tonali, P; Di Mauro, S; Servidei, S

2001-08-14

Two brothers with myopathic coenzyme Q10 (CoQ10) deficiency responded dramatically to CoQ10 supplementation. Muscle biopsies before therapy showed ragged-red fibers, lipid storage, and complex I + III and II + III deficiency. Approximately 30% of myofibers had multiple features of apoptosis. After 8 months of treatment, excessive lipid storage resolved, CoQ10 level normalized, mitochondrial enzymes increased, and proportion of fibers with TUNEL-positive nuclei decreased to 10%. The authors conclude that muscle CoQ10 deficiency can be corrected by supplementation of CoQ10, which appears to stimulate mitochondrial proliferation and to prevent apoptosis.

Anatase/rutile bi-phasic titanium dioxide nanoparticles for photocatalytic applications enhanced by nitrogen doping and platinum nano-islands.

PubMed

Bear, Joseph C; Gomez, Virginia; Kefallinos, Nikolaos S; McGettrick, James D; Barron, Andrew R; Dunnill, Charles W

2015-12-15

Titanium dioxide (TiO2) bi-phasic powders with individual particles containing an anatase and rutile hetero-junction have been prepared using a sequential layer sol-gel deposition technique to soluble substrates. Sequential thin films of rutile and subsequently anatase TiO2 were deposited onto sodium chloride substrates yielding extremely fragile composite layered discs that fractured into "Janus-like" like powders on substrate dissolution. Nitrogen doped and platinum sputtered analogues were also prepared, and analysed for photocatalytic potential using the photodegradation of Rhodamine B, a model organic pollutant under UV and visible light irradiation. The materials were characterised using X-ray diffraction, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy, Raman spectroscopy and scanning electron microscopy. This paper sheds light on the relationship between anatase and rutile materials when in direct contact and demonstrates a robust method for the synthesis of bi-phasic nanoparticles, ostensibly of any two materials, for photocatalytic reactions or otherwise. Copyright © 2015 Elsevier Inc. All rights reserved.

Fabrication of nano structural biphasic materials from phosphogypsum waste and their in vitro applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohamed, Khaled R., E-mail: Kh_rezk966@yahoo.com; Mousa, Sahar M.; Inorganic Chemistry Department, National Research Centre, Dokki, P.O. Box 12622, 11787 Cairo

2014-02-01

Graphical abstract: (a) Schema of the process, (b) TEM of nano particles of biphasic materials and (c) SEM of post-immersion. - Highlights: • Ratio of HA and β-TCP phases were controlled by thermal treatment. • HA partially decomposed into β-TCP with other bioactive phases. • Calcined HA at 900 °C is the best for the bioactivity behavior. - Abstract: In this study, a novel process of preparing biphasic calcium phosphate (BCP) is proposed. Also its bioactivity for the utilization of the prepared BCP as a biomaterial is studied. A mixture of calcium hydroxyapatite (HAP) and tricalcium phosphate (β-TCP) could bemore » obtained by thermal treatment of HAP which was previously prepared from phosphogypsum (PG) waste. The chemical and phase composition, morphology and particle size of prepared samples was characterized by X-ray diffraction (XRD), Infrared spectroscopy (IR), Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM). The bioactivity was investigated by soaking of the calcined samples in simulated body fluid (SBF). Results confirmed that the calcination temperatures played an important role in the formation of calcium phosphate (CP) materials. XRD results indicated that HAP was partially decomposed into β-TCP. The in vitro data confirmed that the calcined HAP forming BCP besides other phases such as pyrophosphate and silica are bioactive materials. Therefore, BCP will be used as good biomaterials for medical applications.« less

Catalytic conversion of corncob and corncob pretreatment hydrolysate to furfural in a biphasic system with addition of sodium chloride.

PubMed

Qing, Qing; Guo, Qi; Zhou, Linlin; Wan, Yilun; Xu, Youqing; Ji, Huilong; Gao, Xiaohang; Zhang, Yue

2017-02-01

Catalytic conversion of corncob pretreatment hydrolysate and raw corncob into furfural in a modified biphasic system by SO 4 2- /SnO 2 - MMT solid catalyst has been developed. The influence of the organic solvent type, organic to water phase ratio, sodium chloride concentration, reaction temperature and time on the furfural production were comparatively evaluated. The results showed that furfural yields of 81.7% and 66.1% were achieved at 190°C for 15mins and 190°C for 20mins, respectively, for corncob pretreatment hydrolysate and raw corncob by this solid catalyst. The solid catalyst used in this study exhibited good stability and high efficiency applied in the modified biphasic system in addition to excellent recyclability. The proposed catalytic system displayed high performance for catalytic conversion of lignocellulosic biomass into important platform chemicals and has great potential in industrial application. Copyright © 2016 Elsevier Ltd. All rights reserved.

Trophic Ecology of Benthic Marine Invertebrates with Bi-Phasic Life Cycles: What Are We Still Missing?

PubMed

Calado, Ricardo; Leal, Miguel Costa

2015-01-01

The study of trophic ecology of benthic marine invertebrates with bi-phasic life cycles is critical to understand the mechanisms shaping population dynamics. Moreover, global climate change is impacting the marine environment at an unprecedented level, which promotes trophic mismatches that affect the phenology of these species and, ultimately, act as drivers of ecological and evolutionary change. Assessing the trophic ecology of marine invertebrates is critical to understanding maternal investment, larval survival to metamorphosis, post-metamorphic performance, resource partitioning and trophic cascades. Tools already available to assess the trophic ecology of marine invertebrates, including visual observation, gut content analysis, food concentration, trophic markers, stable isotopes and molecular genetics, are reviewed and their main advantages and disadvantages for qualitative and quantitative approaches are discussed. The challenges to perform the partitioning of ingestion, digestion and assimilation are discussed together with different approaches to address each of these processes for short- and long-term fingerprinting. Future directions for research on the trophic ecology of benthic marine invertebrates with bi-phasic life cycles are discussed with emphasis on five guidelines that will allow for systematic study and comparative meta-analysis to address important unresolved questions. © 2015 Elsevier Ltd. All rights reserved.

Injectable glycosaminoglycan-protein nano-complex in semi-interpenetrating networks: A biphasic hydrogel for hyaline cartilage regeneration.

PubMed

Radhakrishnan, Janani; Subramanian, Anuradha; Sethuraman, Swaminathan

2017-11-01

Articular hyaline cartilage regeneration remains challenging due to its less intrinsic reparability. The study develops injectable biphasic semi-interpenetrating polymer networks (SIPN) hydrogel impregnated with chondroitin sulfate (ChS) nanoparticles for functional cartilage restoration. ChS loaded zein nanoparticles (∼150nm) prepared by polyelectrolyte-protein complexation were interspersed into injectable SIPNs developed by blending alginate with poly(vinyl alcohol) and calcium crosslinking. The hydrogel exhibited interconnected porous microstructure (39.9±5.8μm pore diameter, 57.7±5.9% porosity), 92% swellability and >350Pa elastic modulus. Primary chondrocytes compatibility, chondrocyte-matrix interaction with cell-cell clustering and spheroidal morphology was demonstrated in ChS loaded hydrogel and long-term (42days) proliferation was also determined. Higher fold expression of cartilage-specific genes sox9, aggrecan and collagen-II was observed in ChS loaded hydrogel while exhibiting poor expression of collagen-I. Immunoblotting of aggregan and collagen II demonstrate favorable positive influence of ChS on chondrocytes. Thus, the injectable biphasic SIPNs could be promising composition-mimetic substitute for cartilage restoration at irregular defects. Copyright © 2017 Elsevier Ltd. All rights reserved.

INVESTIGATION OF AQUEOUS BIPHASIC SYSTEMS FOR THE SEPARATIONS OF LIGNINS FROM CELLULOSE IN THE PAPER PULPING PROCESS. (R826732)

EPA Science Inventory

In efforts to apply a polymer-based aqueous biphasic system (ABS) extraction to the paper pulping process, the study of the distribution of various lignin and cellulosic fractions in ABS and the effects of temperature on system composition and solute partitioning have been inv...

Biphasic cultivation strategy to avoid Epo-Fc aggregation and optimize protein expression.

PubMed

Kaisermayer, Christian; Reinhart, David; Gili, Andreas; Chang, Martina; Aberg, Per-Mikael; Castan, Andreas; Kunert, Renate

2016-06-10

In biphasic cultivations, the culture conditions are initially kept at an optimum for rapid cell growth and biomass accumulation. In the second phase, the culture is shifted to conditions ensuring maximum specific protein production and the protein quality required. The influence of specific culture parameters is cell line dependent and their impact on product quality needs to be investigated. In this study, a biphasic cultivation strategy for a Chinese hamster ovary (CHO) cell line expressing an erythropoietin fusion protein (Epo-Fc) was developed. Cultures were run in batch mode and after an initial growth phase, cultivation temperature and pH were shifted. Applying a DoE (Design of Experiments) approach, a fractional factorial design was used to systematically evaluate the influence of cultivation temperature and pH as well as their synergistic effect on cell growth as well as on recombinant protein production and aggregation. All three responses were influenced by the cultivation temperature. Additionally, an interaction between pH and temperature was found to be related to protein aggregation. Compared with the initial standard conditions of 37°C and pH 7.05, a parameter shift to low temperature and acidic pH resulted in a decrease in the aggregate fraction from 75% to less than 1%. Furthermore, the synergistic effect of temperature and pH substantially lowered the cell-specific rates of glucose and glutamine consumption as well as lactate and ammonium production. The optimized culture conditions also led to an increase of the cell-specific rates of recombinant Epo-Fc production, thus resulting in a more economic bioprocess. Copyright © 2016. Published by Elsevier B.V.

Development of a biphasic dissolution test for Deferasirox dispersible tablets and its application in establishing an in vitro-in vivo correlation.

PubMed

Al Durdunji, Amal; AlKhatib, Hatim S; Al-Ghazawi, Mutasim

2016-05-01

In a biphasic dissolution medium, the integration of the in vitro dissolution of a drug in an aqueous phase and its subsequent partitioning into an organic phase is hypothesized to simulate the in vivo drug absorption. Such a methodology is expected to improve the probability of achieving a successful in vitro-in vivo correlation. Dissolution of Dispersible tablets of Deferasirox, a biopharmaceutics classification system type II compound, was studied in a biphasic dissolution medium using a flow-through dissolution apparatus coupled to a paddle apparatus. The experimental parameters associated with dissolution were optimized to discriminate between Deferasirox dispersible tablets of different formulations. The dissolution profiles obtained from this system were subsequently used to construct a level A in vitro-in vivo correlation. Copyright © 2016 Elsevier B.V. All rights reserved.

Biphasic interactions between a cationic dendrimer and actin.

PubMed

Ruenraroengsak, Pakatip; Florence, Alexander T

2010-12-01

Gene delivery systems face the problem not only of the route toward the cell and tissues in question, but also of the molecularly crowded environment of both the cytoplasm and the nucleus itself. One of the physical barriers in the cytoplasm for diffusing nanoparticles is an actin network. Here, we describe the finding that a self-fluorescent sixth generation cationic dendrimer (6 nm in diameter) interacts reversibly and possibly electrostatically with actin filaments in vitro. Not only does this interaction slow the diffusion of the dendrimer but it also affects actin polymerization in a biphasic manner. At low concentrations the dendrimer behaves like a G-binding actin protein, retarding actin polymerization, whereas at high concentrations the dendrimer acts as a nucleating protein accelerating the polymerization. Thus in vivo the diffusion of a dendrimer carrier such as this has both physical and chemical elements: by decreasing polymerization it might accelerate its own transport, and by enhancing actin polymerization retard it. This finding suggests that such a dendrimer may have a role as an anticancer agent through its inhibitory effect on actin polymerization.

A biphasic model for bleeding in soft tissue

NASA Astrophysics Data System (ADS)

Chang, Yi-Jui; Chong, Kwitae; Eldredge, Jeff D.; Teran, Joseph; Benharash, Peyman; Dutson, Erik

2017-11-01

The modeling of blood passing through soft tissues in the body is important for medical applications. The current study aims to capture the effect of tissue swelling and the transport of blood under bleeding or hemorrhaging conditions. The soft tissue is considered as a non-static poro-hyperelastic material with liquid-filled voids. A biphasic formulation effectively, a generalization of Darcy's law-is utilized, treating the phases as occupying fractions of the same volume. The interaction between phases is captured through a Stokes-like friction force on their relative velocities and a pressure that penalizes deviations from volume fractions summing to unity. The soft tissue is modeled as a hyperelastic material with a typical J-shaped stress-strain curve, while blood is considered as a Newtonian fluid. The method of Smoothed Particle Hydrodynamics is used to discretize the conservation equations based on the ease of treating free surfaces in the liquid. Simulations of swelling under acute hemorrhage and of draining under gravity and compression will be demonstrated. Ongoing progress in modeling of organ tissues under injuries and surgical conditions will be discussed.

Satellite cell senescence underlies myopathy in a mouse model of limb-girdle muscular dystrophy 2H

PubMed Central

Kudryashova, Elena; Kramerova, Irina; Spencer, Melissa J.

2012-01-01

Mutations in the E3 ubiquitin ligase tripartite motif-containing 32 (TRIM32) are responsible for the disease limb-girdle muscular dystrophy 2H (LGMD2H). Previously, we generated Trim32 knockout mice (Trim32–/– mice) and showed that they display a myopathic phenotype accompanied by neurogenic features. Here, we used these mice to investigate the muscle-specific defects arising from the absence of TRIM32, which underlie the myopathic phenotype. Using 2 models of induced atrophy, we showed that TRIM32 is dispensable for muscle atrophy. Conversely, TRIM32 was necessary for muscle regrowth after atrophy. Furthermore, TRIM32-deficient primary myoblasts underwent premature senescence and impaired myogenesis due to accumulation of PIAS4, an E3 SUMO ligase and TRIM32 substrate that was previously shown to be associated with senescence. Premature senescence of myoblasts was also observed in vivo in an atrophy/regrowth model. Trim32–/– muscles had substantially fewer activated satellite cells, increased PIAS4 levels, and growth failure compared with wild-type muscles. Moreover, Trim32–/– muscles exhibited features of premature sarcopenia, such as selective type II fast fiber atrophy. These results imply that premature senescence of muscle satellite cells is an underlying pathogenic feature of LGMD2H and reveal what we believe to be a new mechanism of muscular dystrophy associated with reductions in available satellite cells and premature sarcopenia. PMID:22505452

Activated microglia in acute encephalopathy with biphasic seizures and late reduced diffusion.

PubMed

Fujita, Yuji; Takanashi, Jun-Ichi; Takei, Haruka; Ota, Setsuo; Fujii, Katsunori; Sakuma, Hiroshi; Hayashi, Masaharu

2016-07-15

Acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) is the most common subtype of infectious pediatric encephalopathy in Japan. The exact pathogenesis of and the best therapeutic strategy for AESD are uncertain. We firstly performed a brain biopsy in a 2-year-old boy with AESD associated with RS viral infection, which revealed activated ameoboid microglia accumulation around degenerated neuron, and astrogliosis in the affected cortex. Glutamate released from activated microglia may play an important role in the pathogenesis of AESD, which is compatible with the previous report of magnetic resonance spectroscopy showing elevated glutamate. Copyright © 2016 Elsevier B.V. All rights reserved.

A biphasic approach for the study of lift generation in soft porous media

NASA Astrophysics Data System (ADS)

Wu, Qianhong; Santhanam, Sridhar; Nathan, Rungun; Wang, Qiuyun

2017-04-01

Lift generation in highly compressible porous media under rapid compression continues to be an important topic in porous media flow. Although significant progress has been made, how to model different lifting forces during the compression process remains unclear. This is mainly because the input parameters of the existing theoretical studies, including the Darcy permeability of the porous media and the viscous damping coefficient of its solid phase, were manually adjusted so as to match the experimental data. In the current paper, we report a biphasic approach to experimentally and theoretically treat this limitation. Synthetic fibrous porous materials, whose permeability were precisely measured, were subsequently exposed to sudden impacts using a porous-walled cylinder-piston apparatus. The obtained time-dependent compression of the porous media, along with the permeability data, was applied in two different theoretical models to predict the pore pressure generation, a plug flow model and a consolidation model [Q. Wu et al., J. Fluid Mech. 542, 281 (2005a)]. Comparison between the theory and the experiments on the pore pressure distribution proved the validity of the consolidation model. Furthermore, a viscoelastic model, containing a nonlinear spring in conjunction with a linear viscoelastic generalized Maxwell mechanical module, was developed to characterize the solid phase lifting force. The model matched the experimental data very well. The paper presented herein, as one of the series studies on this topic, provides an important biphasic approach to characterize different forces that contribute to the lift generation in a soft porous medium under rapid compression.

Comparison between FEBio and Abaqus for biphasic contact problems.

PubMed

Meng, Qingen; Jin, Zhongmin; Fisher, John; Wilcox, Ruth

2013-09-01

Articular cartilage plays an important role in the function of diarthrodial joints. Computational methods have been used to study the biphasic mechanics of cartilage, and Abaqus has been one of the most widely used commercial software packages for this purpose. A newly developed open-source finite element solver, FEBio, has been developed specifically for biomechanical applications. The aim of this study was to undertake a direct comparison between FEBio and Abaqus for some practical contact problems involving cartilage. Three model types, representing a porous flat-ended indentation test, a spherical-ended indentation test, and a conceptual natural joint contact model, were compared. In addition, a parameter sensitivity study was also performed for the spherical-ended indentation test to investigate the effects of changes in the input material properties on the model outputs, using both FEBio and Abaqus. Excellent agreement was found between FEBio and Abaqus for all of the model types and across the range of material properties that were investigated.

Comparison between FEBio and Abaqus for biphasic contact problems

PubMed Central

Jin, Zhongmin; Fisher, John; Wilcox, Ruth

2013-01-01

Articular cartilage plays an important role in the function of diarthrodial joints. Computational methods have been used to study the biphasic mechanics of cartilage, and Abaqus has been one of the most widely used commercial software packages for this purpose. A newly developed open-source finite element solver, FEBio, has been developed specifically for biomechanical applications. The aim of this study was to undertake a direct comparison between FEBio and Abaqus for some practical contact problems involving cartilage. Three model types, representing a porous flat-ended indentation test, a spherical-ended indentation test, and a conceptual natural joint contact model, were compared. In addition, a parameter sensitivity study was also performed for the spherical-ended indentation test to investigate the effects of changes in the input material properties on the model outputs, using both FEBio and Abaqus. Excellent agreement was found between FEBio and Abaqus for all of the model types and across the range of material properties that were investigated. PMID:23804955

Probing the limit of magnesium uptake by β-tricalcium phosphate in biphasic mixtures formed from calcium deficient apatites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, P. Nandha; Mishra, Sandeep K.; Kannan, S., E-mail: para_kanna@yahoo.com

2015-11-15

A series of magnesium doped non-stoichiometric calcium deficient apatites were synthesized through an aqueous precipitation route. The resultant structural changes during heat treatment were investigated by X-ray diffraction, Raman and FT-IR spectroscopy and Rietveld refinement. The results confirmed the formation of biphasic mixtures comprising Ca{sub 10}(PO{sub 4}){sub 6}(OH){sub 2} and β-Ca{sub 3}(PO{sub 4}){sub 2} after heat treatment at 1000 °C with the preferential occupancy of Mg{sup 2+} at the crystal lattice of β-Ca{sub 3}(PO{sub 4}){sub 2}. The concentration of Mg{sup 2+} uptake in β-Ca{sub 3}(PO{sub 4}){sub 2} is limited till reaching the stoichiometric ratio of (Ca+Mg)/P=1.67 and beyond this stoichiometricmore » value [(Ca+Mg)/P>1.67], Mg{sup 2+} precipitates as Mg(OH){sub 2} and thereafter gets converted to MgO during heat treatment. Any kind of Mg{sup 2+} uptake in the crystal lattice of Ca{sub 10}(PO{sub 4}){sub 6}(OH){sub 2} is discarded from the investigation. - Highlights: • Aqueous co-precipitation of calcium deficient apatites with excess magnesium (Mg{sup 2+}) additions. • Heat treatments beyond 800 °C results in the formation of biphasic apatite mixtures. • Mg{sup 2+} gets accommodated at the β-Ca{sub 3}(PO{sub 4}){sub 2} lattice of biphasic mixtures. • Mg{sup 2+} additions exceeding stoichiometric value (Ca/P>1.67) results in its formation as MgO. • Mg{sup 2+} occupancy at β-Ca{sub 3}(PO{sub 4}){sub 2} lattice delays its allotropic conversion α-Ca{sub 3}(PO{sub 4}){sub 2} till 1350 °C.« less

Biphasic voltage-dependent inactivation of human NaV 1.3, 1.6 and 1.7 Na+ channels expressed in rodent insulin-secreting cells.

PubMed

Godazgar, Mahdieh; Zhang, Quan; Chibalina, Margarita V; Rorsman, Patrik

2018-05-01

Na + current inactivation is biphasic in insulin-secreting cells, proceeding with two voltage dependences that are half-maximal at ∼-100 mV and -60 mV. Inactivation of voltage-gated Na + (Na V ) channels occurs at ∼30 mV more negative voltages in insulin-secreting Ins1 and primary β-cells than in HEK, CHO or glucagon-secreting αTC1-6 cells. The difference in inactivation between Ins1 and non-β-cells persists in the inside-out patch configuration, discounting an involvement of a diffusible factor. In Ins1 cells and primary β-cells, but not in HEK cells, inactivation of a single Na V subtype is biphasic and follows two voltage dependences separated by 30-40 mV. We propose that Na V channels adopt different inactivation behaviours depending on the local membrane environment. Pancreatic β-cells are equipped with voltage-gated Na + channels that undergo biphasic voltage-dependent steady-state inactivation. A small Na + current component (10-15%) inactivates over physiological membrane potentials and contributes to action potential firing. However, the major Na + channel component is completely inactivated at -90 to -80 mV and is therefore inactive in the β-cell. It has been proposed that the biphasic inactivation reflects the contribution of different Na V α-subunits. We tested this possibility by expression of TTX-resistant variants of the Na V subunits found in β-cells (Na V 1.3, Na V 1.6 and Na V 1.7) in insulin-secreting Ins1 cells and in non-β-cells (including HEK and CHO cells). We found that all Na V subunits inactivated at 20-30 mV more negative membrane potentials in Ins1 cells than in HEK or CHO cells. The more negative inactivation in Ins1 cells does not involve a diffusible intracellular factor because the difference between Ins1 and CHO persisted after excision of the membrane. Na V 1.7 inactivated at 15--20 mV more negative membrane potentials than Na V 1.3 and Na V 1.6 in Ins1 cells but this small difference is insufficient to solely

Biphasic pulses enhance bleomycin efficacy in a spontaneous canine genital tumor model of chemoresistance: Sticker sarcoma

PubMed Central

Spugnini , Enrico P; Dotsinsky , Ivan; Mudrov , Nikolay; Citro , Gennaro; D'Avino , Alfredo; Baldi , Alfonso

2008-01-01

Sticker's sarcoma (also known as transmissible venereal tumor) is a horizontally transmitted neoplasm of the dog, that is passed with coitus. It is a locally aggressive tumor with a low tendency to metastatic spread. The most common locations are the genitals, the nose, the perianal area. Standard treatment consists with chemotherapy with vincristine, however other therapies such as, cryotherapy, immunotherapy or, in selected cases, radiation therapy, have been reported. In this article we describe the outcome of a small cohort of canine patients, with chemotherapy resistant transmissible venereal tumor (TVT), treated with bleomycin selectively driven by trains of biphasic pulses (electrochemotherapy). Three canine patients, with refractory TVT, entered the study and received two sessions of ECT under sedation. The pets had local injection of bleomycin at the concentration of 1.5 mg/ml and five minutes after the chemotherapy, trains of 8 biphasic electric pulses lasting 50 + 50 μs each, with 1 ms interpulse intervals, were delivered by means of modified caliper or, for difficult districts, through paired needle electrode. All the patients responded to the treatment and are still in remission at different times. Electrochemotherapy appears as a safe and efficacious modality for the treatment of TVT and warrants further investigations. PMID:18980687

Biphasic effect of citral, a flavoring and scenting agent, on spatial learning and memory in rats.

PubMed

Yang, Zheqiong; Xi, Jinlei; Li, Jihong; Qu, Wen

2009-10-01

Although some central effects of citral have been reported, cognitive effects on spatial memory have not been investigated. The evidence showed that citral can regulate the synthesis of retinoic acid (RA), which exerts a vital function in the development and maintenance of spatial memory. In this study, we applied Morris water maze to test the effect of citral on animals' spatial learning and memory. To elucidate the mechanism of this effect, we also measured the retinoic acid concentration in rats' hippocampus by high performance liquid chromatography (HPLC). Our data implied biphasic effects of citral. The low dose (0.1 mg/kg) of citral improved the spatial learning capability, and enhanced the spatial reference memory of rats, whereas the high dose (1.0 mg/kg) was like to produce the opposite effects. Meanwhile, the low dose of citral increased the hippocampal retinoic acid concentration, while the high dose decreased it. Due to the quick elimination and non-bioaccumulation in the body, effects of citral on spatial memory in this study seemed to be indirect actions. The change in hippocampal retinoic acid concentration induced by different doses of citral might be responsible for the biphasic effect of citral on spatial learning and memory.

Bi-phasic regulation of glycogen content in astrocytes via Cav-1/PTEN/PI3K/AKT/GSK-3β pathway by fluoxetine.

PubMed

Bai, Qiufang; Song, Dan; Gu, Li; Verkhratsky, Alexei; Peng, Liang

2017-04-01

Here, we present the data indicating that chronic treatment with fluoxetine regulates Cav-1/PTEN/PI3K/AKT/GSK-3β signalling pathway and glycogen content in primary cultures of astrocytes with bi-phasic concentration dependence. At lower concentrations, fluoxetine downregulates gene expression of Cav-1, decreases membrane content of PTEN, increases activity of PI3K/AKT, and elevates GSK-3β phosphorylation thus suppressing its activity. At higher concentrations, fluoxetine acts in an inverse fashion. As expected, fluoxetine at lower concentrations increased while at higher concentrations decreased glycogen content in astrocytes. Our findings indicate that bi-phasic regulation of glycogen content via Cav-1/PTEN/PI3K/AKT/GSK-3β pathway by fluoxetine may be responsible for both therapeutic and side effects of the drug.

Frequent biphasic cellular responses of permanent fish cell cultures to deoxynivalenol (DON)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pietsch, Constanze, E-mail: constanze.pietsch@unibas.ch; Bucheli, Thomas D.; Wettstein, Felix E.

Contamination of animal feed with mycotoxins is a major problem for fish feed mainly due to usage of contaminated ingredients for production and inappropriate storage of feed. The use of cereals for fish food production further increases the risk of a potential contamination. Potential contaminants include the mycotoxin deoxynivalenol (DON) which is synthesized by globally distributed fungi of the genus Fusarium. The toxicity of DON is well recognized in mammals. In this study, we confirm cytotoxic effects of DON in established permanent fish cell lines. We demonstrate that DON is capable of influencing the metabolic activity and cell viability inmore » fish cells as determined by different assays to indicate possible cellular targets of this toxin. Evaluation of cell viability by measurement of membrane integrity, mitochondrial activity and lysosomal function after 24 h of exposure of fish cell lines to DON at a concentration range of 0-3000 ng ml{sup -1} shows a biphasic effect on cells although differences in sensitivity occur. The cell lines derived from rainbow trout are particularly sensitive to DON. The focus of this study lies, furthermore, on the effects of DON at different concentrations on production of reactive oxygen species (ROS) in the different fish cell lines. The results show that DON mainly reduces ROS production in all cell lines that were used. Thus, our comparative investigations reveal that the fish cell lines show distinct species-related endpoint sensitivities that also depend on the type of tissue from which the cells were derived and the severity of exposure. - Highlights: > DON uptake by cells is not extensive. > All fish cell lines are sensitive to DON. > DON is most cytotoxic to rainbow trout cells. > Biphasic cellular responses were frequently observed. > Our results are similar to studies on mammalian cell lines.« less

The expanding phenotype of mitochondrial myopathy.

PubMed

DiMauro, Salvatore; Gurgel-Giannetti, Juliana

2005-10-01

Our understanding of mitochondrial diseases (defined restrictively as defects in the mitochondrial respiratory chain) continues to progress apace. In this review we provide an update of information regarding disorders that predominantly or exclusively affect skeletal muscle. Most recently described mitochondrial myopathies are due to defects in nuclear DNA, including coenzyme Q10 deficiency, and mutations in genes that control mitochondrial DNA (mtDNA) abundance and structure such as POLG and TK2. Barth syndrome, an X-linked recessive mitochondrial myopathy/cardiopathy, is associated with altered lipid composition of the inner mitochondrial membrane, but a putative secondary impairment of the respiratory chain remains to be documented. Concerning the 'other genome', the role played by mutations in protein encoding genes of mtDNA in causing isolated myopathies has been confirmed. It has also been confirmed that mutations in tRNA genes of mtDNA can cause predominantly myopathic syndromes and - contrary to conventional wisdom - these mutations can be homoplasmic. Defects in the mitochondrial respiratory chain impair energy production and almost invariably involve skeletal muscle, causing exercise intolerance, myalgia, cramps, or fixed weakness, which often affects extraocular muscles and results in droopy eyelids (ptosis) and progressive external ophthalmoplegia.

Neutron Polarization Analysis for Biphasic Solvent Extraction Systems

DOE PAGES

Motokawa, Ryuhei; Endo, Hitoshi; Nagao, Michihiro; ...

2016-06-16

Here we performed neutron polarization analysis (NPA) of extracted organic phases containing complexes, comprised of Zr(NO 3) 4 and tri-n-butyl phosphate, which enabled decomposition of the intensity distribution of small-angle neutron scattering (SANS) into the coherent and incoherent scattering components. The coherent scattering intensity, containing structural information, and the incoherent scattering compete over a wide range of magnitude of scattering vector, q, specifically when q is larger than q* ≈ 1/R g, where R g is the radius of gyration of scatterer. Therefore, it is important to determine the incoherent scattering intensity exactly to perform an accurate structural analysis frommore » SANS data when R g is small, such as the aforementioned extracted coordination species. Although NPA is the best method for evaluating the incoherent scattering component for accurately determining the coherent scattering in SANS, this method is not used frequently in SANS data analysis because it is technically challenging. In this study, we successfully demonstrated that experimental determination of the incoherent scattering using NPA is suitable for sample systems containing a small scatterer with a weak coherent scattering intensity, such as extracted complexes in biphasic solvent extraction systems.« less

The Role of Magnesium Ion Substituted Biphasic Calcium Phosphate Spherical Micro-Scaffolds in Osteogenic Differentiation of Human Adipose Tissue-Derived Mesenchymal Stem Cells.

PubMed

Kim, Dong-Hyun; Shin, Keun-Koo; Jung, Jin Sup; Chun, Ho Hwan; Park, Seong Soo; Lee, Jong Kook; Park, Hong-Chae; Yoon, Seog-Young

2015-08-01

This study was investigated the role of magnesium (Mg2+) ion substituted biphasic calcium phosphate (Mg-BCP) spherical micro-scaffolds in osteogenic differentiation of human adipose tissue-derived mesenchymal stem cells (hAT-MSCs). Mg-BCP micro-scaffolds with spherical morphology were successfully prepared using in situ co-precipitation and spray drying atomization process. The in vitro cell proliferation and differentiation of hAT-MSCs were determined up to day 14. After in vitro biological tests, Mg-BCP micro-scaffolds with hAT-MSCs showed more enhanced osteogenicity than pure hAT-MSCs as control group by unique biodegradation of TCP phase and influence of substituted Mg2+ ion in biphasic nanostructure. Therefore, these results suggest that Mg-BCP micro-scaffolds promote osteogenic differentiation of hAT-MSCs.

Clinical features of the myasthenic syndrome arising from mutations in GMPPB.

PubMed

Rodríguez Cruz, Pedro M; Belaya, Katsiaryna; Basiri, Keivan; Sedghi, Maryam; Farrugia, Maria Elena; Holton, Janice L; Liu, Wei Wei; Maxwell, Susan; Petty, Richard; Walls, Timothy J; Kennett, Robin; Pitt, Matthew; Sarkozy, Anna; Parton, Matt; Lochmüller, Hanns; Muntoni, Francesco; Palace, Jacqueline; Beeson, David

2016-08-01

Congenital myasthenic syndrome (CMS) due to mutations in GMPPB has recently been reported confirming the importance of glycosylation for the integrity of neuromuscular transmission. Review of case notes of patients with mutations in GMPPB to identify the associated clinical, neurophysiological, pathological and laboratory features. In addition, serum creatine kinase (CK) levels within the Oxford CMS cohort were retrospectively analysed to assess its usefulness in the differential diagnosis of this new entity. All patients had prominent limb-girdle weakness with minimal or absent craniobulbar manifestations. Presentation was delayed beyond infancy with proximal muscle weakness and most patients recall poor performance in sports during childhood. Neurophysiology showed abnormal neuromuscular transmission only in the affected muscles and myopathic changes. Muscle biopsy showed dystrophic features and reduced α-dystroglycan glycosylation. In addition, myopathic changes were present on muscle MRI. CK was significantly increased in serum compared to other CMS subtypes. Patients were responsive to pyridostigimine alone or combined with 3,4-diaminopyridine and/or salbutamol. Patients with GMPPB-CMS have phenotypic features aligned with CMS subtypes harbouring mutations within the early stages of the glycosylation pathway. Additional features shared with the dystroglycanopathies include myopathic features, raised CK levels and variable mild cognitive delay. This syndrome underlines that CMS can occur in the absence of classic myasthenic manifestations such as ptosis and ophthalmoplegia or facial weakness, and links myasthenic disorders with dystroglycanopathies. This report should facilitate the recognition of this disorder, which is likely to be underdiagnosed and can benefit from symptomatic treatment. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

In vitro biphasic dissolution tests and their suitability for establishing in vitro-in vivo correlations: A historical review.

PubMed

Pestieau, Aude; Evrard, Brigitte

2017-05-01

For many decades, one of the most critical issues in the pharmaceutical industry has been the poor solubility of some drugs. Indeed, a prerequisite for drug absorption is the presence of dissolved drug at the absorption site and this can be challenging for compounds with low aqueous solubility such as BCS class II (low solubility, high permeability) and IV (low solubility, low permeability) compounds. If the development of oral delivery formulations of these compounds is frequently challenging to formulation scientists in the pharmaceutical industry, the in vitro evaluation of these new formulations is also a great challenge. One alternative approach to overcome the problems encountered with conventional dissolution methods is the use of biphasic dissolution systems. This review provides an overview of the origin and the evolution over time of the biphasic systems and the growing interest among scientists regarding their suitability for establishing in vitro-in vivo correlations. The evolution of these systems and their applications from the 1960s to the present day, such as in system variants and improvements, analysis of complex formulations, discriminatory power, bio-relevance, precipitation and supersaturation visualization, etc. will be discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Biphasic oxidation of oxy-hemoglobin in bloodstains.

PubMed

Bremmer, Rolf H; de Bruin, Daniel M; de Joode, Maarten; Buma, Wybren Jan; van Leeuwen, Ton G; Aalders, Maurice C G

2011-01-01

In forensic science, age determination of bloodstains can be crucial in reconstructing crimes. Upon exiting the body, bloodstains transit from bright red to dark brown, which is attributed to oxidation of oxy-hemoglobin (HbO(2)) to met-hemoglobin (met-Hb) and hemichrome (HC). The fractions of HbO(2), met-Hb and HC in a bloodstain can be used for age determination of bloodstains. In this study, we further analyze the conversion of HbO(2) to met-Hb and HC, and determine the effect of temperature and humidity on the conversion rates. The fractions of HbO(2), met-Hb and HC in a bloodstain, as determined by quantitative analysis of optical reflectance spectra (450-800 nm), were measured as function of age, temperature and humidity. Additionally, Optical Coherence Tomography around 1300 nm was used to confirm quantitative spectral analysis approach. The oxidation rate of HbO(2) in bloodstains is biphasic. At first, the oxidation of HbO(2) is rapid, but slows down after a few hours. These oxidation rates are strongly temperature dependent. However, the oxidation of HbO(2) seems to be independent of humidity, whereas the transition of met-Hb into HC strongly depends on humidity. Knowledge of these decay rates is indispensable for translating laboratory results into forensic practice, and to enable bloodstain age determination on the crime scene.

Stability of a jet in confined pressure-driven biphasic flows at low reynolds numbers.

PubMed

Guillot, Pierre; Colin, Annie; Utada, Andrew S; Ajdari, Armand

2007-09-07

Motivated by its importance for microfluidic applications, we study the stability of jets formed by pressure-driven concentric biphasic flows in cylindrical capillaries. The specificity of this variant of the classical Rayleigh-Plateau instability is the role of the geometry which imposes confinement and Poiseuille flow profiles. We experimentally evidence a transition between situations where the flow takes the form of a jet and regimes where drops are produced. We describe this as the transition from convective to absolute instability, within a simple linear analysis using lubrication theory for flows at low Reynolds number, and reach remarkable agreement with the data.

Process boundaries of irreversible scCO2 -assisted phase separation in biphasic whole-cell biocatalysis.

PubMed

Brandenbusch, Christoph; Glonke, Sebastian; Collins, Jonathan; Hoffrogge, Raimund; Grunwald, Klaudia; Bühler, Bruno; Schmid, Andreas; Sadowski, Gabriele

2015-11-01

The formation of stable emulsions in biphasic biotransformations catalyzed by microbial cells turned out to be a major hurdle for industrial implementation. Recently, a cost-effective and efficient downstream processing approach, using supercritical carbon dioxide (scCO2 ) for both irreversible emulsion destabilization (enabling complete phase separation within minutes of emulsion treatment) and product purification via extraction has been proposed by Brandenbusch et al. (2010). One of the key factors for a further development and scale-up of the approach is the understanding of the mechanism underlying scCO2 -assisted phase separation. A systematic approach was applied within this work to investigate the various factors influencing phase separation during scCO2 treatment (that is pressure, exposure of the cells to CO2 , and changes of cell surface properties). It was shown that cell toxification and cell disrupture are not responsible for emulsion destabilization. Proteins from the aqueous phase partially adsorb to cells present at the aqueous-organic interface, causing hydrophobic cell surface characteristics, and thus contribute to emulsion stabilization. By investigating the change in cell-surface hydrophobicity of these cells during CO2 treatment, it was found that a combination of catastrophic phase inversion and desorption of proteins from the cell surface is responsible for irreversible scCO2 mediated phase separation. These findings are essential for the definition of process windows for scCO2 -assisted phase separation in biphasic whole-cell biocatalysis. © 2015 Wiley Periodicals, Inc.

A feasible process for furfural production from the pre-hydrolysis liquor of corncob via biochar catalysts in a new biphasic system.

PubMed

Deng, Aojie; Lin, Qixuan; Yan, Yuhuan; Li, Huiling; Ren, Junli; Liu, Chuanfu; Sun, Runcang

2016-09-01

A feasible approach was developed to produce furfural from the pre-hydrolysis liquor of corncob via biochar catalysts as the solid acid catalyst in a new biphasic system with dichloromethane (DCM) as the organic phase and the concentrated pre-hydrolysis liquor (CPHL) containing NaCl as the aqueous phase. The biochar catalyst possessing many acidity groups (SO3H, COOH and phenolic OH groups) was prepared by the carbonization and sulfonation process of the corncob hydrolyzed residue. The influence of the catalytic condition on furfural yield and selectivity was comparatively studied. It was found that 81.14% furfural yield and 83.0% furfural selectivity were obtained from CPHL containing 5wt% xylose using this biochar catalyst in the CPHL-NaCl/DCM biphasic system at 170°C for 60min. In addition, with the regeneration process, this catalyst displayed the high performance and excellent recyclability. Copyright © 2016 Elsevier Ltd. All rights reserved.

Alendronate-Eluting Biphasic Calcium Phosphate (BCP) Scaffolds Stimulate Osteogenic Differentiation

PubMed Central

Kim, Sung Eun; Lee, Deok-Won; Kang, Eun Young; Jeong, Won Jae; Lee, Boram; Jeong, Myeong Seon; Kim, Hak Jun; Park, Kyeongsoon; Song, Hae-Ryong

2015-01-01

Biphasic calcium phosphate (BCP) scaffolds have been widely used in orthopedic and dental fields as osteoconductive bone substitutes. However, BCP scaffolds are not satisfactory for the stimulation of osteogenic differentiation and maturation. To enhance osteogenic differentiation, we prepared alendronate- (ALN-) eluting BCP scaffolds. The coating of ALN on BCP scaffolds was confirmed by scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDS), and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). An in vitro release study showed that release of ALN from ALN-eluting BCP scaffolds was sustained for up to 28 days. In vitro results revealed that MG-63 cells grown on ALN-eluting BCP scaffolds exhibited increased ALP activity and calcium deposition and upregulated gene expression of Runx2, ALP, OCN, and OPN compared with the BCP scaffold alone. Therefore, this study suggests that ALN-eluting BCP scaffolds have the potential to effectively stimulate osteogenic differentiation. PMID:26221587

In situ synthesis of magnesium-substituted biphasic calcium phosphate and in vitro biodegradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Tae-Wan; Lee, Hyeong-Shin; Kim, Dong-Hyun

Highlights: ► Mg–BCP were successfully prepared through in situ aqueous co-precipitation method. ► The amount of β-TCP phase was changed with the magnesium substitution level. ► The substitution of magnesium led to a decrease in the unit cell volume. ► Mg–BCP could be able to develop a new apatite phase on the surface faster than BCP. -- Abstract: In situ preparation of magnesium (Mg) substituted biphasic calcium phosphate (BCP) of hydroxyapatite (HAp)/β-tricalcium phosphate (β-TCP) were carried out through aqueous co-precipitation method. The concentrations of added magnesium were varied with the calcium in order to obtain constant (Ca + Mg)/P ratiosmore » of 1.602. X-ray diffraction (XRD) and Fourier transformed infrared (FTIR) spectroscopy were used to characterize the structure of synthesized magnesium substituted BCP powders. The results have shown that substitution of magnesium in the calcium deficient apatites revealed the formation of biphasic mixtures of different HAp/β-TCP ratios after heating at 1000 °C. The ratios of the formation of phase mixtures were dependent on the content of magnesium. After immersing in Hanks’ balanced salt solution (HBSS) for 1 week, 1 wt% magnesium substituted BCP powders were degraded and precipitation started to be formed with small granules consisting of number of flake-like crystal onto the surface of synthesized powders. On the other hand, in the case of pure BCP powders, the formation of new precipitates was detected after immersion in HBSS for 2 weeks. On the basis of these results, magnesium substituted BCP could be able to develop a new apatite phase on the surface in contact with physiological fluids faster than BCP does. In addition, the retention time to produce the new apatite phase in implantation operation for the BCP powder could be controlled by the amount of magnesium substitution.« less

Sodium lauryl sulfate impedes drug release from zinc-crosslinked alginate beads: switching from enteric coating release into biphasic profiles.

PubMed

Taha, Mutasem O; Nasser, Wissam; Ardakani, Adel; Alkhatib, Hatim S

2008-02-28

The aim of this research is to investigate the effects of sodium lauryl sulfate (SLS) on ionotropically cross-linked alginate beads. Different levels of SLS were mixed with sodium alginate and chlorpheniramine maleate (as loaded model drug). The resulting viscous solutions were dropped onto aqueous solutions of zinc or calcium ions for ionotropic curing. The generated beads were assessed by their drug releasing profiles, infrared and differential scanning colorimetery (DSC) traits. SLS was found to exert profound concentration-dependent impacts on the characteristics of zinc-crosslinked alginate beads such that moderate modifications in the levels of SLS switched drug release from enteric coating-like behavior to a biphasic release modifiable to sustained-release by the addition of minute amounts of xanthan gum. Calcium cross-linking failed to reproduce the same behavior, probably due to the mainly ionic nature of calcium-carboxylate bonds compared to the coordinate character of their zinc-carboxylate counterparts. Apparently, moderate levels of SLS repel water penetration into the beads, and therefore minimize chlorpheniramine release. However, higher SLS levels seem to discourage polymeric cross-linking and therefore allow biphasic drug release.

Regulation of the demographic structure in isomorphic biphasic life cycles at the spatial fine scale.

PubMed

Vieira, Vasco Manuel Nobre de Carvalho da Silva; Mateus, Marcos Duarte

2014-01-01

Isomorphic biphasic algal life cycles often occur in the environment at ploidy abundance ratios (Haploid:Diploid) different from 1. Its spatial variability occurs within populations related to intertidal height and hydrodynamic stress, possibly reflecting the niche partitioning driven by their diverging adaptation to the environment argued necessary for their prevalence (evolutionary stability). Demographic models based in matrix algebra were developed to investigate which vital rates may efficiently generate an H:D variability at a fine spatial resolution. It was also taken into account time variation and type of life strategy. Ploidy dissimilarities in fecundity rates set an H:D spatial structure miss-fitting the ploidy fitness ratio. The same happened with ploidy dissimilarities in ramet growth whenever reproductive output dominated the population demography. Only through ploidy dissimilarities in looping rates (stasis, breakage and clonal growth) did the life cycle respond to a spatially heterogeneous environment efficiently creating a niche partition. Marginal locations were more sensitive than central locations. Related results have been obtained experimentally and numerically for widely different life cycles from the plant and animal kingdoms. Spore dispersal smoothed the effects of ploidy dissimilarities in fertility and enhanced the effects of ploidy dissimilarities looping rates. Ploidy dissimilarities in spore dispersal could also create the necessary niche partition, both over the space and time dimensions, even in spatial homogeneous environments and without the need for conditional differentiation of the ramets. Fine scale spatial variability may be the key for the prevalence of isomorphic biphasic life cycles, which has been neglected so far.

Regulation of the Demographic Structure in Isomorphic Biphasic Life Cycles at the Spatial Fine Scale

PubMed Central

Vieira, Vasco Manuel Nobre de Carvalho da Silva; Mateus, Marcos Duarte

2014-01-01

Isomorphic biphasic algal life cycles often occur in the environment at ploidy abundance ratios (Haploid:Diploid) different from 1. Its spatial variability occurs within populations related to intertidal height and hydrodynamic stress, possibly reflecting the niche partitioning driven by their diverging adaptation to the environment argued necessary for their prevalence (evolutionary stability). Demographic models based in matrix algebra were developed to investigate which vital rates may efficiently generate an H:D variability at a fine spatial resolution. It was also taken into account time variation and type of life strategy. Ploidy dissimilarities in fecundity rates set an H:D spatial structure miss-fitting the ploidy fitness ratio. The same happened with ploidy dissimilarities in ramet growth whenever reproductive output dominated the population demography. Only through ploidy dissimilarities in looping rates (stasis, breakage and clonal growth) did the life cycle respond to a spatially heterogeneous environment efficiently creating a niche partition. Marginal locations were more sensitive than central locations. Related results have been obtained experimentally and numerically for widely different life cycles from the plant and animal kingdoms. Spore dispersal smoothed the effects of ploidy dissimilarities in fertility and enhanced the effects of ploidy dissimilarities looping rates. Ploidy dissimilarities in spore dispersal could also create the necessary niche partition, both over the space and time dimensions, even in spatial homogeneous environments and without the need for conditional differentiation of the ramets. Fine scale spatial variability may be the key for the prevalence of isomorphic biphasic life cycles, which has been neglected so far. PMID:24658603

Effect of Ganoderma lucidum on pollen-induced biphasic nasal blockage in a guinea pig model of allergic rhinitis.

PubMed

Mizutani, Nobuaki; Nabe, Takeshi; Shimazu, Masaji; Yoshino, Shin; Kohno, Shigekatsu

2012-03-01

Ganoderma lucidum (GL), an oriental medical mushroom, has been used in Asia for the prevention and treatment of a variety of diseases. However, the effect of GL on allergic rhinitis has not been well defined. The current study describes the inhibitory effect of GL on the biphasic nasal blockage and nasal hyperresponsiveness induced by repeated antigen challenge in a guinea pig model of allergic rhinitis. Intranasally sensitized guinea pigs were repeatedly challenged by inhalation of Japanese cedar pollen once every week. Ganoderma lucidum was orally administered once daily for 8 weeks from the time before the first challenge. The treatment with GL dose-dependently inhibited the early and late phase nasal blockage at the fifth to ninth antigen challenges. Furthermore, nasal hyperresponsiveness to intranasally applied leukotriene D₄ on 2 days after the eighth antigen challenge was also inhibited by the treatment with GL. However, Cry j 1-specific IgE antibody production was not affected by the treatment. In conclusion, we demonstrated that the pollen-induced biphasic nasal blockage and nasal hyperresponsiveness were suppressed by the daily treatment with GL in the guinea pig model of allergic rhinitis. These results suggest that GL may be a useful therapeutic drug for treating patients with allergic rhinitis. Copyright © 2011 John Wiley & Sons, Ltd.

Augmenting in vitro osteogenesis of a glycine-arginine-glycine-aspartic-conjugated oxidized alginate-gelatin-biphasic calcium phosphate hydrogel composite and in vivo bone biogenesis through stem cell delivery.

PubMed

Linh, Nguyen Tb; Paul, Kallyanashis; Kim, Boram; Lee, Byong-Taek

2016-11-01

A functionally modified peptide-conjugated hydrogel system was fabricated with oxidized alginate/gelatin loaded with biphasic calcium phosphate to improve its biocompatibility and functionality. Sodium alginate was treated by controlled oxidation to transform the cis-diol group into an aldehyde group in a controlled manner, which was then conjugated to the amine terminus of glycine-arginine-glycine-aspartic. Oxidized alginate glycine-arginine-glycine-aspartic was then combined with gelatin-loaded biphasic calcium phosphate to form a hydrogel of composite oxidized alginate/gelatin/biphasic calcium phosphate that displayed enhanced human adipose stem cell adhesion, spreading and differentiation. 1 H nuclear magnetic resonance and electron spectroscopy for chemical analysis confirmed that the glycine-arginine-glycine-aspartic was successfully grafted to the oxidized alginate. Co-delivery of glycine-arginine-glycine-aspartic and human adipose stem cell in a hydrogel matrix was studied with the results indicating that hydrogel incorporated modified with glycine-arginine-glycine-aspartic and seeded with human adipose stem cell enhanced osteogenesis in vitro and bone formation in vivo. © The Author(s) 2016.

Evolution of the optimum bidirectional (+/- biphasic) wave for defibrillation.

PubMed

Geddes, L A; Havel, W

2000-01-01

Introduction of the asymmetric bidirectional (+/- biphasic) current waveform has made it possible to achieve ventricular defibrillation with less energy and current than are needed with a unidirectional (monophasic) waveform. The symmetrical bidirectional (sinusoidal) waveform was used for the first human-heart defibrillation. Subsequent studies employed the underdamped and overdamped sine waves, then the trapezoidal (monophasic) wave. Studies were then undertaken to investigate the benefit of adding a second identical and inverted wave; little success rewarded these efforts until it was discovered that the second inverted wave needed to be much less in amplitude to lower the threshold for defibrillation. However, there is no physiologic theory that explains the mechanism of action of the bidirectional wave, nor does any theory predict the optimum amplitude and time dimensions for the second inverted wave. The authors analyze the research that shows that the threshold defibrillation energy is lowest when the charge in the second, inverted phase is slightly more than a third of that in the first phase. An ion-flux, spatial-K+ summation hypothesis is presented that shows the effect on myocardial cells of adding the second inverted current pulse.

[Genotype/phenotype correlation in autism: genetic models and phenotypic characterization].

PubMed

Bonnet-Brilhault, F

2011-02-01

Autism spectrum disorders are a class of conditions categorized by communication problems, ritualistic behaviors, and deficits in social behaviors. This class of disorders merges a heterogeneous group of neurodevelopmental disorders regarding some phenotypic and probably physiopathological aspects. Genetic basis is well admitted, however, considering phenotypic and genotypic heterogeneity, correspondences between genotype and phenotype have yet to be established. To better identify such correspondences, genetic models have to be identified and phenotypic markers have to be characterized. Recent insights show that a variety of genetic mechanisms may be involved in autism spectrum disorders, i.e. single gene disorders, copy number variations and polygenic mechanisms. These current genetic models are described. Regarding clinical aspects, several approaches can be used in genetic studies. Nosographical approach, especially with the concept of autism spectrum disorders, merges a large group of disorders with clinical heterogeneity and may fail to identify clear genotype/phenotype correlations. Dimensional approach referred in genetic studies to the notion of "Broad Autism Phenotype" related to a constellation of language, personality, and social-behavioral features present in relatives that mirror the symptom domains of autism, but are much milder in expression. Studies of this broad autism phenotype may provide a potentially important complementary approach for detecting the genes involved in these domains. However, control population used in those studies need to be well characterized too. Identification of endophenotypes seems to offer more promising results. Endophenotypes, which are supposed to be more proximal markers of gene action in the same biological pathway, linking genes and complex clinical symptoms, are thought to be less genetically complex than the broader disease phenotype, indexing a limited aspect of genetic risk for the disorder as a whole. However

HYDROSTATIC PRESSURIZATION AND DEPLETION OF TRAPPED LUBRICANT POOL DURING CREEP CONTACT OF A RIPPLED INDENTER AGAINST A BIPHASIC ARTICULAR CARTILAGE LAYER

PubMed Central

Soltz, Michael A.; Basalo, Ines M.; Ateshian, Gerard A.

2010-01-01

This study presents an analysis of the contact of a rippled rigid impermeable indenter against a cartilage layer, which represents a first simulation of the contact of rough cartilage surfaces with lubricant entrapment. Cartilage was modeled with the biphasic theory for hydrated soft tissues, to account for fluid flow into or out of the lubricant pool. The findings of this study demonstrate that under contact creep, the trapped lubricant pool gets depleted within a time period on the order of seconds or minutes as a result of lubricant flow into the articular cartilage. Prior to depletion, hydrostatic fluid load across the contact interface may be enhanced by the presence of the trapped lubricant pool, depending on the initial geometry of the lubricant pool. According to friction models based on the biphasic nature of the tissue, this enhancement in fluid load support produces a smaller minimum friction coefficient than would otherwise be predicted without a lubricant pool. The results of this study support the hypothesis that trapped lubricant decreases the initial friction coefficient following load application, independently of squeeze-film lubrication effects. PMID:14618917

Biphasic effects of substance P on respiratory activity and respiration-related neurones in ventrolateral medulla in the neonatal rat brainstem in vitro.

PubMed

Shvarev, Y N; Lagercrantz, H; Yamamoto, Y

2002-01-01

The effects of substance P (SP) on respiratory activity in the brainstem-spinal cord preparation from neonatal rats (0-4 days old) were investigated. The respiratory activity was recorded from C4 ventral roots and intracellularly from three types of respiration-related neurones, i.e. pre-inspiratory (or biphasic E), three subtypes of inspiratory; expiratory and tonic neurones in the ventrolateral medulla (VLM). After the onset of SP bath application (10 nM-1 microM) a dose-dependent decline of burst rate (by 48%) occurred, followed by a weaker dose-dependent increase (by 17.5%) in burst rate. The biphasic effect of SP on inspiratory burst rate was associated with sustained membrane depolarization (in a range of 0.5-13 mV) of respiration-related and tonic neurones. There were no significant changes in membrane resistance in any type of neurones when SP was applied alone or when synaptic transmission was blocked with tetrodotoxin (TTX). The initial depolarization was associated with an increase in inspiratory drive potential (by 25%) as well as in bursting time (by 65%) and membrane excitability in inspiratory and pre-inspiratory neurones, which corresponded to the decrease in burst rate (C4 activity). The spiking frequency of expiratory and tonic neurones was also increased (by 36 and 48%). This activation was followed by restoration of the synaptic drive potential and bursting time in inspiratory and to a less extent in pre-inspiratory neurones, which corresponded to the increase in burst rate. The discharge frequency of expiratory and tonic neurones also decreased to control values. This phase followed the peak membrane depolarization. At the peak depolarization, SP reduced the amplitude of the action potential by 4-8% in all types of neurones. Our results suggest that SP exerts a general excitatory effect on respiration-related neurones and synaptic coupling within the respiratory network in the VLM. The transient changes in neuronal activity in the VLM may

Biphasic insulin-releasing effect of BTS 67 582 in rats.

PubMed

Storey, D A; Bailey, C J

1998-12-01

BTS 67 582 (1,1-dimethyl-2(2-morpholinophenyl)guanidine fumarate) is being developed as a short-acting anti-diabetic insulin secretagogue. The effect of BTS 67 582 on the phasic pattern of insulin release was assessed in anaesthetized normal rats by measuring arterial plasma insulin concentrations while arterial glucose concentrations were fixed at 6, 8.5 and 12.5 mM. Intravenous BTS 67 582 (10 mg kg(-1)) induced an immediate but transient increase in insulin concentrations which declined by 10 min (first phase). This was followed by a smaller but sustained increase in insulin concentrations (second phase). The increment from basal to peak insulin release (0-2 min) was independent of glucose, but the first phase was maintained for longer and the second phase was greater at the highest concentration of glucose (12.5 mM). BTS 67 582 also extended the first-phase insulin response to a standard intravenous glucose challenge and enhanced the rate of glucose disappearance by approximately 12%. Thus BTS 67 582 causes biphasic stimulation of insulin release and augments the insulin-releasing effect of glucose.

Carrageenan-induced mouse paw oedema is biphasic, age-weight dependent and displays differential nitric oxide cyclooxygenase-2 expression

PubMed Central

Posadas, Inmaculada; Bucci, Mariarosaria; Roviezzo, Fiorentina; Rossi, Antonietta; Parente, Luca; Sautebin, Lidia; Cirino, Giuseppe

2004-01-01

Injection of carrageenan 1% (50 μl) in the mouse paw causes a biphasic response: an early inflammatory response that lasts 6 h and a second late response that peaks at 72 h, declining at 96 h. Only mice 7- or 8-week old, weighing 32–34 g, displayed a consistent response in both phases. In 8-week-old mice, myeloperoxidase (MPO) levels are significantly elevated in the early phase at 6 h and reach their maximum at 24 h to decline to basal value at 48 h. Nitrate+nitrite (NOx) levels in the paw are maximal after 2 h and slowly decline thereafter in contrast to prostaglandin E2 levels that peak in the second phase at the 72 h point. Western blot analysis showed that inducible nitric oxide synthase (iNOS) is detectable at 6 h and cyclooxygenase 2 (COX-2) at 24 h point, respectively. Analysis of endothelial nitric oxide synthase (eNOS), iNOS and COX-2 expression at 6 and 24 h in 3–8-week-old mice demonstrated that both eNOS and iNOS expressions are dependent upon the age–weight of mice, as opposite to COX-2 that is present only in the second phase of the oedema and is not linked to mouse age–weight. Subplantar injection of carrageenan to C57BL/6J causes a biphasic oedema that is significantly reduced by about 20% when compared to CD1 mice. Interestingly, in these mice, iNOS expression is absent up to 6 h, as opposite to CD1, and becomes detectable at the 24 h point. Cyclooxygenase (COX-1) expression is upregulated between 4 and 24 h after carrageenan injection, whereas in CD1 mice COX-1 remains unchanged after irritant agent injection. MPO levels are maximal at the 24 h point and they are significantly lower, at 6 h point, than MPO levels detected in CD1 mice. In conclusion, mouse paw oedema is biphasic and age-weight dependent. The present results are the first report on the differential expressions of eNOS, iNOS, COX-1 and COX-2 in response to carrageenan injection in the two phases of the mouse paw oedema. PMID:15155540

Use of biphase-coded pulses for wideband data storage in time-domain optical memories.

PubMed

Shen, X A; Kachru, R

1993-06-10

We demonstrate that temporally long laser pulses with appropriate phase modulation can replace either temporally brief or frequency-chirped pulses in a time-domain optical memory to store and retrieve information. A 1.65-µs-long write pulse was biphase modulated according to the 13-bit Barker code for storing multiple bits of optical data into a Pr(3+):YAlO(3) crystal, and the stored information was later recalled faithfully by using a read pulse that was identical to the write pulse. Our results further show that the stored data cannot be retrieved faithfully if mismatched write and read pulses are used. This finding opens up the possibility of designing encrypted optical memories for secure data storage.

Randomized, Blinded Pilot Testing of Nonconventional Stimulation Patterns and Shapes in Parkinson's Disease and Essential Tremor: Evidence for Further Evaluating Narrow and Biphasic Pulses

PubMed Central

Akbar, Umer; Raike, Robert S.; Hack, Nawaz; Hess, Christopher W.; Skinner, Jared; Martinez‐Ramirez, Daniel; DeJesus, Sol

2016-01-01

Objectives Evidence suggests that nonconventional programming may improve deep brain stimulation (DBS) therapy for movement disorders. The primary objective was to assess feasibility of testing the tolerability of several nonconventional settings in Parkinson's disease (PD) and essential tremor (ET) subjects in a single office visit. Secondary objectives were to explore for potential efficacy signals and to assess the energy demand on the implantable pulse‐generators (IPGs). Materials and Methods A custom firmware (FW) application was developed and acutely uploaded to the IPGs of eight PD and three ET subjects, allowing delivery of several nonconventional DBS settings, including narrow pulse widths, square biphasic pulses, and irregular pulse patterns. Standard clinical rating scales and several objective measures were used to compare motor outcomes with sham, clinically‐optimal and nonconventional settings. Blinded and randomized testing was conducted in a traditional office setting. Results Overall, the nonconventional settings were well tolerated. Under these conditions it was also possible to detect clinically‐relevant differences in DBS responses using clinical rating scales but not objective measures. Compared to the clinically‐optimal settings, some nonconventional settings appeared to offer similar benefit (e.g., narrow pulse widths) and others lesser benefit. Moreover, the results suggest that square biphasic pulses may deliver greater benefit. No unexpected IPG efficiency disadvantages were associated with delivering nonconventional settings. Conclusions It is feasible to acutely screen nonconventional DBS settings using controlled study designs in traditional office settings. Simple IPG FW upgrades may provide more DBS programming options for optimizing therapy. Potential advantages of narrow and biphasic pulses deserve follow up. PMID:27000764

A biphasic oxidation of alcohols to aldehydes and ketones using a simplified packed-bed microreactor

PubMed Central

Bogdan, Andrew

2009-01-01

Summary We demonstrate the preparation and characterization of a simplified packed-bed microreactor using an immobilized TEMPO catalyst shown to oxidize primary and secondary alcohols via the biphasic Anelli-Montanari protocol. Oxidations occurred in high yields with great stability over time. We observed that plugs of aqueous oxidant and organic alcohol entered the reactor as plugs but merged into an emulsion on the packed-bed. The emulsion coalesced into larger plugs upon exiting the reactor, leaving the organic product separate from the aqueous by-products. Furthermore, the microreactor oxidized a wide range of alcohols and remained active in excess of 100 trials without showing any loss of catalytic activity. PMID:19478910

A novel low-energy electrotherapy that terminates ventricular tachycardia with lower energy than a biphasic shock when antitachycardia pacing fails.

PubMed

Janardhan, Ajit H; Li, Wenwen; Fedorov, Vadim V; Yeung, Michael; Wallendorf, Michael J; Schuessler, Richard B; Efimov, Igor R

2012-12-11

The authors sought to develop a low-energy electrotherapy that terminates ventricular tachycardia (VT) when antitachycardia pacing (ATP) fails. High-energy implantable cardioverter-defibrillator (ICD) shocks are associated with device failure, significant morbidity, and increased mortality. A low-energy alternative to ICD shocks is desirable. Myocardial infarction was created in 25 dogs. Sustained, monomorphic VT was induced by programmed stimulation. Defibrillation electrodes were placed in the right ventricular apex, and coronary sinus and left ventricular epicardium. If ATP failed to terminate sustained VT, the defibrillation thresholds (DFTs) of standard versus experimental electrotherapies were measured. Sustained VT ranged from 276 to 438 beats/min (mean 339 beats/min). The right ventricular-coronary sinus shock vector had lower impedance than the right ventricular-left ventricular patch (54.4 ± 18.1 Ω versus 109.8 ± 16.9 Ω; p < 0.001). A single shock required between 0.3 ± 0.2 J to 5.9 ± 2.5 J (mean 2.64 ± 3.22 J; p = 0.008) to terminate VT, and varied depending upon the phase of the VT cycle in which it was delivered. By contrast, multiple shocks delivered within 1 VT cycle length were not phase dependent and achieved lower DFT compared with a single shock (0.13 ± 0.09 J for 3 shocks, 0.08 ± 0.04 J for 5 shocks, and 0.09 ± 0.07 J for 7 shocks; p < 0.001). Finally, a multistage electrotherapy (MSE) achieved significantly lower DFT compared with a single biphasic shock (0.03 ± 0.05 J versus 2.37 ± 1.20 J; respectively, p < 0.001). At a peak shock amplitude of 20 V, MSE achieved 91.3% of terminations versus 10.5% for a biphasic shock (p < 0.001). MSE achieved a major reduction in DFT compared with a single biphasic shock for ATP-refractory monomorphic VT, and represents a novel electrotherapy to reduce high-energy ICD shocks. Copyright © 2012 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Biphasic influence of dexamethasone exposure on embryonic vertebrate skeleton development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Xin; Chen, Jian-long; Ma, Zheng-lai

slightly increased in mesenchymal cell mass treated by low concentration of Dex. Mmp-13 expression was obviously up-regulated by Dex in both mesenchymal cells and primary chondrocyte cultures. And Col10a1 expression was also increased by Dex exposure in chondrocyte. In summary, we have revealed that different concentrations of Dex exposure during early gestation could exert a biphasic effect on vertebrate skeletal development. - Highlights: • Chick embryos occurred shortening of the long bone following Dex exposure. • Dex suppressed chondrocytes proliferation and promoted apoptosis. • Dex exposure decreased ALP production and up-regulated Runx-2 and Mmp-13. • Dex exhibited biphasic effects on chondrogenic proliferation and nodule formation. • The hypertrophy and ossification were accelerated by Dex both in vivo and in vitro.« less

Design and hydraulic characteristics of a field-scale bi-phasic bioretention rain garden system for storm water management.

PubMed

Yang, H; Florence, D C; McCoy, E L; Dick, W A; Grewal, P S

2009-01-01

A field-scale bioretention rain garden system was constructed using a novel bi-phasic (i.e. sequence of anaerobic to aerobic) concept for improving retention and removal of storm water runoff pollutants. Hydraulic tests with bromide tracer and simulated runoff pollutants (nitrate-N, phosphate-P, Cu, Pb, and Zn) were performed in the system under a simulated continuous rainfall. The objectives of the tests were (1) to determine hydraulic characteristics of the system, and (2) to evaluate the movement of runoff pollutants through the system. For the 180 mm/24 h rainfall, the bi-phasic bioretention system effectively reduced both peak flow (approximately 70%) and runoff volume (approximately 42%). The breakthrough curves (BTCs) of bromide tracer suggest that the transport pattern of the system is similar to dispersed plug flow under this large runoff event. The BTCs of bromide showed mean 10% and 90% breakthrough times of 5.7 h and 12.5 h, respectively. Under the continuous rainfall, a significantly different transport pattern was found between each runoff pollutant. Nitrate-N was easily transported through the system with potential leaching risk from the initial soil medium, whereas phosphate-P and metals were significantly retained indicating sorption-mediated transport. These findings support the importance of hydraulics, in combination with the soil medium, when creating bioretention systems for bioremediation that are effective for various rainfall sizes and intervals.

A new injectable biphasic hydrogel based on partially hydrolyzed polyacrylamide and nano hydroxyapatite, crosslinked with chromium acetate, as scaffold for cartilage regeneration

NASA Astrophysics Data System (ADS)

Koushki, N.; Tavassoli, H.; Katbab, A. A.; Katbab, P.; Bonakdar, S.

2015-05-01

Polymer scaffolds are applied in the field of tissue engineering as three dimensional structures to organize cells and present stimuli to direct generation of a desired damaged tissue. In situ gelling scaffolds have attracted great attentions, as they are structurally similar to the extra cellular matrix (ECM). In the present work, attempts have been made to design and fabricate a new injectable and crosslinkable biphasic hydrogel based on partially hydrolyzed polyacrylamide (HPAM), chromium acetate as crosslink agent and nanocrystalline hydroxyapatite (nHAp) as reinforcing and bioactive agent for repair and regeneration of damaged cartilage. The distinct characteristic of HPAM is the presence of carboxylate anion groups on its backbone which allows to engineer the structure of the hydrogel for the desired bioactivity with appropriate cells differentiation towards both soft and hard (bone) tissues. The synthesized hydrogel exhibited bifunctional behavior which was derived by its biphasic structure in which one phase was loaded with nano hydroxyapatite to provide integration capability by subchondral bones and fix the hydrogel at cartilage defect without a need for suturing. The other phase differentiates the rabbit adipogenic mesenchymal stem cells (MSCs) towards soft tissue. Rheomechanical spectrometry (RMS) was employed to study the kinetic of the gelation including induction time and rate, as well as to measure the ultimate elastic modulus of the optimum crosslinked hydrogel. Surface tension measurement was also performed to tailor the surface characteristics of the gels. In vitro culturing of the cells inside the crosslinked hydrogel revealed high viability and high differentiation of the encapsulated rabbit stem cells, providing that the chromium acetate level was kept below 0.2 wt%. Based on the obtained results, the designed and fabricated biphasic hydrogel exhibited high potential as carrier for the stem cells for cartilage tissue engineering application

Topical hindpaw application of L-menthol decreases responsiveness to heat with biphasic effects on cold sensitivity of rat lumbar dorsal horn neurons

PubMed Central

Klein, Amanda H.; Sawyer, Carolyn M.; Takechi, Kenichi; Davoodi, Auva; Ivanov, Margaret A.; Carstens, Mirela Iodi; Carstens, E

2012-01-01

Menthol is used in pharmaceutical applications because of its desired cooling and analgesic properties. The neural mechanism by which topical application of menthol decreases heat pain is not fully understood. We investigated the effects of topical menthol application on lumbar dorsal horn wide dynamic range and nociceptive-specific neuronal responses to noxious heat and cooling of glaborous hindpaw cutaneous receptive fields. Menthol increased thresholds for responses to noxious heat in a concentration-dependent manner. Menthol had a biphasic effect on cold-evoked responses, reducing the threshold (to warmer temperatures) at a low (1%) concentration and increasing threshold and reducing response magnitude at high (10, 40%) concentrations. Menthol had little effect on responses to innocuous or noxious mechanical stimuli, ruling out a local anesthetic action. Application of 40% menthol to the contralateral hindpaw tended to reduce responses to cooling and noxious heat, suggesting a weak heterosegmental inhibitory effect. These results indicate that menthol has an analgesic effect on heat sensitivity of nociceptive dorsal horn neurons, as well as biphasic effects on cold sensitivity, consistent with previous behavioral observations. PMID:22687951

Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity.

PubMed

Wagner, Andreas

2014-02-18

Novel phenotypes can originate either through mutations in existing genotypes or through phenotypic plasticity, the ability of one genotype to form multiple phenotypes. From molecules to organisms, plasticity is a ubiquitous feature of life, and a potential source of exaptations, adaptive traits that originated for nonadaptive reasons. Another ubiquitous feature is robustness to mutations, although it is unknown whether such robustness helps or hinders the origin of new phenotypes through plasticity. RNA is ideal to address this question, because it shows extensive plasticity in its secondary structure phenotypes, a consequence of their continual folding and unfolding, and these phenotypes have important biological functions. Moreover, RNA is to some extent robust to mutations. This robustness structures RNA genotype space into myriad connected networks of genotypes with the same phenotype, and it influences the dynamics of evolving populations on a genotype network. In this study I show that both effects help accelerate the exploration of novel phenotypes through plasticity. My observations are based on many RNA molecules sampled at random from RNA sequence space, and on 30 biological RNA molecules. They are thus not only a generic feature of RNA sequence space but are relevant for the molecular evolution of biological RNA. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biphasic microreactor for efficient membrane protein pretreatment with a combination of formic acid assisted solubilization, on-column pH adjustment, reduction, alkylation, and tryptic digestion.

PubMed

Zhao, Qun; Liang, Yu; Yuan, Huiming; Sui, Zhigang; Wu, Qi; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

2013-09-17

Combining good dissolving ability of formic acid (FA) for membrane proteins and excellent complementary retention behavior of proteins on strong cation exchange (SCX) and strong anion exchange (SAX) materials, a biphasic microreactor was established to pretreat membrane proteins at microgram and even nanogram levels. With membrane proteins solubilized by FA, all of the proteomics sample processing procedures, including protein preconcentration, pH adjustment, reduction, and alkylation, as well as tryptic digestion, were integrated into an "SCX-SAX" biphasic capillary column. To evaluate the performance of the developed microreactor, a mixture of bovine serum albumin, myoglobin, and cytochrome c was pretreated. Compared with the results obtained by the traditional in-solution process, the peptide recovery (93% vs 83%) and analysis throughput (3.5 vs 14 h) were obviously improved. The microreactor was further applied for the pretreatment of 14 μg of membrane proteins extracted from rat cerebellums, and 416 integral membrane proteins (IMPs) (43% of total protein groups) and 103 transmembrane peptides were identified by two-dimensional nanoliquid chromatography-electrospray ionization tandem mass spectrometry (2D nano-LC-ESI-MS/MS) in triplicate analysis. With the starting sample preparation amount decreased to as low as 50 ng, 64 IMPs and 17 transmembrane peptides were identified confidently, while those obtained by the traditional in-solution method were 10 and 1, respectively. All these results demonstrated that such an "SCX-SAX" based biphasic microreactor could offer a promising tool for the pretreatment of trace membrane proteins with high efficiency and throughput.

[Biphasic ceramic wedge and plate fixation with locked adjustable screws for open wedge tibial osteotomy].

PubMed

Lavallé, F; Pascal-Mousselard, H; Rouvillain, J L; Ribeyre, D; Delattre, O; Catonné, Y

2004-10-01

The aim of this radiological study was to evaluate the use of a biphasic ceramic wedge combined with plate fixation with locked adjustable screws for open wedge tibial osteotomy. Twenty-six consecutive patients (27 knees) underwent surgery between December 1999 and March 2002 to establish a normal lower-limb axis. The series included 6 women and 20 men, mean age 50 years (16 right knees and 11 left knees). Partial weight-bearing with crutches was allowed on day 1. A standard radiological assessment was performed on day 1, 90, and 360 (plain AP and lateral stance films of the knee). A pangonogram was performed before surgery and at day 360. Presence of a lateral metaphyseal space, development of peripheral cortical bridges, and osteointegration of the bone substitute-bone interface were evaluated used to assess bone healing. The medial tibial angle between the line tangent to the tibial plateau and the anatomic axis of the tibia (beta) was evaluated to assess preservation of postoperative correction. The HKA angle was determined. Three patients were lost to follow-up and 23 patients (24 knees) were retained for analysis. At last follow-up, presence of peripheral cortical bridges and complete filling of the lateral metaphyseal space demonstrated bone healing in all patients. Good quality osteointegration was achieved since 21 knees did not present an interface between the bone substitute and native bone (homogeneous transition zone). The beta angle was unchanged for 23 knees. A normal axis was observed in patients (16 knees) postoperatively. Use of a biphasic ceramic wedge in combination with plate fixation with locked adjustable screws is a reliable option for open wedge tibial osteotomy. The bone substitute fills the gap well. Tolerance and integration are optimal. Bone healing is achieved. Plate fixation with protected weight bearing appears to be a solid assembly, maintaining these corrections.

Square biphasic pulse deep brain stimulation for essential tremor: The BiP tremor study.

PubMed

De Jesus, Sol; Almeida, Leonardo; Shahgholi, Leili; Martinez-Ramirez, Daniel; Roper, Jaimie; Hass, Chris J; Akbar, Umer; Wagle Shukla, Aparna; Raike, Robert S; Okun, Michael S

2018-01-01

Conventional deep brain stimulation (DBS) utilizes regular, high frequency pulses to treat medication-refractory symptoms in essential tremor (ET). Modifications of DBS pulse shape to achieve improved effectiveness is a promising approach. The current study assessed the safety, tolerability and effectiveness of square biphasic pulse shaping as an alternative to conventional ET DBS. This pilot study compared biphasic pulses (BiP) versus conventional DBS pulses (ClinDBS). Eleven ET subjects with clinically optimized ventralis intermedius nucleus DBS were enrolled. Objective measures were obtained over 3 h while ON BiP stimulation. There was observed benefit in the Fahn-Tolosa Tremor Rating Scale (TRS) for BiP conditions when compared to the DBS off condition and to ClinDBS setting. Total TRS scores during the DBS OFF condition (28.5 IQR = 24.5-35.25) were significantly higher than the other time points. Following active DBS, TRS improved to (20 IQR = 13.8-24.3) at ClinDBS setting and to (16.5 IQR = 12-20.75) at the 3 h period ON BiP stimulation (p = 0.001). Accelerometer recordings revealed improvement in tremor at rest (χ 2  = 16.1, p = 0.006), posture (χ 2  = 15.9, p = 0.007) and with action (χ 2  = 32.1, p=<0.001) when comparing median total scores at ClinDBS and OFF DBS conditions to 3 h ON BiP stimulation. There were no adverse effects and gait was not impacted. BiP was safe, tolerable and effective on the tremor symptoms when tested up to 3 h. This study demonstrated the feasibility of applying a novel DBS waveform in the clinic setting. Larger prospective studies with longer clinical follow-up will be required. Copyright © 2017. Published by Elsevier Ltd.

Assessing composition and structure of soft biphasic media from Kelvin-Voigt fractional derivative model parameters

NASA Astrophysics Data System (ADS)

Zhang, Hongmei; Wang, Yue; Fatemi, Mostafa; Insana, Michael F.

2017-03-01

Kelvin-Voigt fractional derivative (KVFD) model parameters have been used to describe viscoelastic properties of soft tissues. However, translating model parameters into a concise set of intrinsic mechanical properties related to tissue composition and structure remains challenging. This paper begins by exploring these relationships using a biphasic emulsion materials with known composition. Mechanical properties are measured by analyzing data from two indentation techniques—ramp-stress relaxation and load-unload hysteresis tests. Material composition is predictably correlated with viscoelastic model parameters. Model parameters estimated from the tests reveal that elastic modulus E 0 closely approximates the shear modulus for pure gelatin. Fractional-order parameter α and time constant τ vary monotonically with the volume fraction of the material’s fluid component. α characterizes medium fluidity and the rate of energy dissipation, and τ is a viscous time constant. Numerical simulations suggest that the viscous coefficient η is proportional to the energy lost during quasi-static force-displacement cycles, E A . The slope of E A versus η is determined by α and the applied indentation ramp time T r. Experimental measurements from phantom and ex vivo liver data show close agreement with theoretical predictions of the η -{{E}A} relation. The relative error is less than 20% for emulsions 22% for liver. We find that KVFD model parameters form a concise features space for biphasic medium characterization that described time-varying mechanical properties. The experimental work was carried out at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Methodological development, including numerical simulation and all data analysis, were carried out at the school of Life Science and Technology, Xi’an JiaoTong University, 710049, China.

Phenotypic switching in bacteria

NASA Astrophysics Data System (ADS)

Merrin, Jack

Living matter is a non-equilibrium system in which many components work in parallel to perpetuate themselves through a fluctuating environment. Physiological states or functionalities revealed by a particular environment are called phenotypes. Transitions between phenotypes may occur either spontaneously or via interaction with the environment. Even in the same environment, genetically identical bacteria can exhibit different phenotypes of a continuous or discrete nature. In this thesis, we pursued three lines of investigation into discrete phenotypic heterogeneity in bacterial populations: the quantitative characterization of the so-called bacterial persistence, a theoretical model of phenotypic switching based on those measurements, and the design of artificial genetic networks which implement this model. Persistence is the phenotype of a subpopulation of bacteria with a reduced sensitivity to antibiotics. We developed a microfluidic apparatus, which allowed us to monitor the growth rates of individual cells while applying repeated cycles of antibiotic treatments. We were able to identify distinct phenotypes (normal and persistent) and characterize the stochastic transitions between them. We also found that phenotypic heterogeneity was present prior to any environmental cue such as antibiotic exposure. Motivated by the experiments with persisters, we formulated a theoretical model describing the dynamic behavior of several discrete phenotypes in a periodically varying environment. This theoretical framework allowed us to quantitatively predict the fitness of dynamic populations and to compare survival strategies according to environmental time-symmetries. These calculations suggested that persistence is a strategy used by bacterial populations to adapt to fluctuating environments. Knowledge of the phenotypic transition rates for persistence may provide statistical information about the typical environments of bacteria. We also describe a design of artificial

Randomized, Blinded Pilot Testing of Nonconventional Stimulation Patterns and Shapes in Parkinson's Disease and Essential Tremor: Evidence for Further Evaluating Narrow and Biphasic Pulses.

PubMed

Akbar, Umer; Raike, Robert S; Hack, Nawaz; Hess, Christopher W; Skinner, Jared; Martinez-Ramirez, Daniel; DeJesus, Sol; Okun, Michael S

2016-06-01

Evidence suggests that nonconventional programming may improve deep brain stimulation (DBS) therapy for movement disorders. The primary objective was to assess feasibility of testing the tolerability of several nonconventional settings in Parkinson's disease (PD) and essential tremor (ET) subjects in a single office visit. Secondary objectives were to explore for potential efficacy signals and to assess the energy demand on the implantable pulse-generators (IPGs). A custom firmware (FW) application was developed and acutely uploaded to the IPGs of eight PD and three ET subjects, allowing delivery of several nonconventional DBS settings, including narrow pulse widths, square biphasic pulses, and irregular pulse patterns. Standard clinical rating scales and several objective measures were used to compare motor outcomes with sham, clinically-optimal and nonconventional settings. Blinded and randomized testing was conducted in a traditional office setting. Overall, the nonconventional settings were well tolerated. Under these conditions it was also possible to detect clinically-relevant differences in DBS responses using clinical rating scales but not objective measures. Compared to the clinically-optimal settings, some nonconventional settings appeared to offer similar benefit (e.g., narrow pulse widths) and others lesser benefit. Moreover, the results suggest that square biphasic pulses may deliver greater benefit. No unexpected IPG efficiency disadvantages were associated with delivering nonconventional settings. It is feasible to acutely screen nonconventional DBS settings using controlled study designs in traditional office settings. Simple IPG FW upgrades may provide more DBS programming options for optimizing therapy. Potential advantages of narrow and biphasic pulses deserve follow up. © 2016 The Authors. Neuromodulation: Technology at the Neural Interface published by Wiley Periodicals, Inc. on behalf of International Neuromodulation Society.

Serum and cerebrospinal fluid levels of visinin-like protein-1 in acute encephalopathy with biphasic seizures and late reduced diffusion.

PubMed

Hasegawa, Shunji; Matsushige, Takeshi; Inoue, Hirofumi; Takahara, Midori; Kajimoto, Madoka; Momonaka, Hiroshi; Oka, Momoko; Isumi, Hiroshi; Emi, Sakie; Hayashi, Megumi; Ichiyama, Takashi

2014-08-01

Acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) has recently been recognized as an encephalopathy subtype. Typical clinical symptoms of AESD are biphasic seizures, and MRI findings show reduced subcortical diffusion during clustering seizures with unconsciousness after the acute phase. Visinin-like protein-1 (VILIP-1) is a recently discovered protein that is abundant in the central nervous system, and some reports have shown that VILIP-1 may be a prognostic biomarker of conditions such as Alzheimer's disease, stroke, and brain injury. However, there have been no reports regarding serum and cerebrospinal fluid (CSF) levels of VILIP-1 in patients with AESD. We measured the serum and CSF levels of VILIP-1 in patients with AESD, and compared the levels to those in patients with prolonged febrile seizures (FS). Both serum and CSF levels of VILIP-1 were significantly higher in patients with AESD than in patients with prolonged FS. Serum and CSF VILIP-1 levels were normal on day 1 of AESD. Our results suggest that both serum and CSF levels of VILIP-1 may be one of predictive markers of AESD. Copyright © 2013 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

A Novel Low-Energy Electrotherapy That Terminates Ventricular Tachycardia With Lower Energy than a Biphasic Shock When Anti-Tachycardia Pacing Fails

PubMed Central

Janardhan, Ajit H.; Li, Wenwen; Fedorov, Vadim V.; Yeung, Michael; Wallendorf, Michael J.; Schuessler, Richard B.; Efimov, Igor R.

2015-01-01

Objectives To develop a low-energy electrotherapy that terminates ventricular tachycardia (VT) when anti-tachycardia pacing (ATP) fails. Background High-energy ICD shocks are associated with device failure, significant morbidity and increased mortality. A low-energy alternative to ICD shocks is desirable. Methods Myocardial infarction (MI) was created in 25 dogs. Sustained, monomorphic VT was induced by programmed stimulation. Defibrillation electrodes were placed in the RV apex, and coronary sinus (CS) and LV epicardium (LVP). If ATP failed to terminate sustained VT, the defibrillation thresholds (DFTs) of standard versus experimental electrotherapies were measured. Results Sustained VT ranged from 276–438 bpm (mean 339 bpm). The RV-CS shock vector had lower impedance than RV-LVP (54.4±18.1 Ω versus 109.8±16.9, Ω p<0.001). A single shock required between 0.3±0.2 J to 5.9±2.5 J (mean 2.64±3.22 J; p=0.008) to terminate VT, and varied depending upon the phase of the VT cycle at which it was delivered. In contrast, multiple shocks delivered within 1 VT cycle length were not phase-dependent and achieved lower DFT compared to a single shock (0.13±0.09 J for 3 shocks, 0.08±0.04 J for 5 shocks, 0.09±0.07 J for 7 shocks; p<0.001). Finally, a multi-stage electrotherapy (MSE) achieved significantly lower DFT compared to a single biphasic shock (0.03±0.05 J versus 2.37±1.20 J, respectively, p<0.001). At a peak shock amplitude of 20 V, MSE achieved 91.3% of terminations versus 10.5% for a biphasic shock (p<0.001). Conclusions MSE achieved a major reduction in DFT compared to a single biphasic shock for ATP-refractory monomorphic VT, and represents a novel electrotherapy to reduce high-energy ICD shocks. PMID:23141483

A flow reactor setup for photochemistry of biphasic gas/liquid reactions

PubMed Central

Schachtner, Josef; Bayer, Patrick

2016-01-01

Summary A home-built microreactor system for light-mediated biphasic gas/liquid reactions was assembled from simple commercial components. This paper describes in full detail the nature and function of the required building elements, the assembly of parts, and the tuning and interdependencies of the most important reactor and reaction parameters. Unlike many commercial thin-film and microchannel reactors, the described set-up operates residence times of up to 30 min which cover the typical rates of many organic reactions. The tubular microreactor was successfully applied to the photooxygenation of hydrocarbons (Schenck ene reaction). Major emphasis was laid on the realization of a constant and highly reproducible gas/liquid slug flow and the effective illumination by an appropriate light source. The optimized set of conditions enabled the shortening of reaction times by more than 99% with equal chemoselectivities. The modular home-made flow reactor can serve as a prototype model for the continuous operation of various other reactions at light/liquid/gas interfaces in student, research, and industrial laboratories. PMID:27829887

Antibacterial activity evaluation of bioactive glass and biphasic calcium phosphate nanopowders mixtures

NASA Astrophysics Data System (ADS)

Nazemi, Zahra; Mehdikhani-Nahrkhalaji, Mehdi; Haghbin-Nazarpak, Masoumeh; Staji, Hamid; Kalani, Mohammad Mehdi

2016-12-01

The aim of this work was to evaluate the antibacterial activity of bioactive glass (BG) and biphasic calcium phosphate (BCP) nanopowders mixtures for the first time. 37S BG and BCP (50% HA-50% β-TCP) nanopowders were prepared via sol-gel technique. Characterization techniques such as X-ray diffraction, scanning electron microscopy, transition electron microscopy, and X-ray fluorescent. The antibacterial activity was studied using Escherichia coli and Salmonella typhi as gram-negative, and Staphylococcus aureus as gram-positive bacteria. The antibacterial effect of BG, BCP nanopowders, and their mixtures was evaluated at different concentrations. The 37S BG nanopowders showed minimum bactericidal concentration at 25 mg/ml. At broth concentrations below 300 mg/ml, BCP showed no antibacterial activity. BCP and BG nanopowders mixture (M2) with 60/40 ratio of BCP/BG showed noticeable antibacterial effect. It was concluded that BCP and 37S BG nanopowders mixture could be used as a good candidate for dental and orthopedic applications.

DEL phenotype.

PubMed

Kwon, Dong H; Sandler, S G; Flegel, Willy A

2017-09-01

DEL red blood cells (RBCs) type as D- by routine serologic methods and are transfused routinely, without being identified as expressing a very weak D antigen, to D- recipients. DEL RBCs are detected only by adsorption and elution of anti-D or by molecular methods. Most DEL phenotypes have been reported in population studies conducted in East Asia, although DEL phenotypes have been detected also among Caucasian individuals. Approximately 98 percent of DEL phenotypes in East Asians are associated with the RHD*DEL1 or RHD*01EL.01 allele. The prevalence of DEL phenotypes has been reported among D- Han Chinese (30%), Japanese (28%), and Korean (17%) populations. The prevalence of DEL phenotypes is significantly lower among D- Caucasian populations (0.1%). Among the 3-5 percent of African individuals who are D-, there are no reports of the DEL phenotype. Case reports from East Asia indicate that transfusion of DEL RBCs to D- recipients has been associated with D alloimmunization. East Asian immigrants constitute 2.1 percent of the 318.9 million persons residing in the United States, and an estimated 2.8 percent are blood donors. Using these statistics, we estimate that 68-683 units of DEL RBCs from donors of East Asian ancestry are transfused as D- annually in the United States. Given the reports from East Asia of D alloimmunization attributed to transfusion of DEL RBCs, one would expect an occasional report of D alloimmunization in the United States following transfusion of DEL RBCs to a D- recipient. If such cases do occur, the most likely reason that they are not detected is the absence of active post-transfusion monitoring for formation of anti-D.

Biphase Cobalt-Manganese Oxide with High Capacity and Rate Performance for Aqueous Sodium-Ion Electrochemical Energy Storage

DOE PAGES

Shan, Xiaoqiang; Charles, Daniel S.; Xu, Wenqian; ...

2017-11-22

Manganese-based metal oxide electrode materials are of great importance in electrochemical energy storage for their favorable redox behavior, low cost and environmental-friendliness. However, their storage capacity and cycle life in aqueous Na-ion electrolytes is not satisfactory. In this paper, we report the development of a bi-phase cobalt-manganese oxide (Co-Mn-O) nanostructured electrode material, comprised of a layered MnO 2.H 2O birnessite phase and a (Co 0.83Mn 0.13Va 0.04)tetra(Co 0.38Mn 1.62) octaO 3.72 (Va: vacancy; tetra: tetrahedral sites; octa: octahedral sites) spinel phase, verified by neutron total scattering and pair distribution function analyses. The bi-phase Co-Mn-O material demonstrates an excellent storage capacitymore » towards Na-ions in an aqueous electrolyte (121 mA h g -1 at a scan rate of 1 mV s -1 in the half-cell and 81 mA h g -1 at a current density of 2 A g -1 after 5000 cycles in full-cells), as well as high rate performance (57 mA h g -1 a rate of 360 C). Electro-kinetic analysis and in situ X-ray diffraction measurements further confirm that the synergistic interaction between the spinel and layered phases, as well as the vacancy of the tetrahedral sites of spinel phase, contribute to the improved capacity and rate performance of the Co-Mn-O material by facilitating both diffusion-limited redox and capacitive charge storage processes.« less

TSDC and impedance spectroscopy measurements on hydroxyapatite, β-tricalcium phosphate and hydroxyapatite/β-tricalcium phosphate biphasic bioceramics

NASA Astrophysics Data System (ADS)

Prezas, P. R.; Melo, B. M. G.; Costa, L. C.; Valente, M. A.; Lança, M. C.; Ventura, J. M. G.; Pinto, L. F. V.; Graça, M. P. F.

2017-12-01

Bone grafting and surgical interventions related with orthopaedic disorders consist in a big business, generating large revenues worldwide every year. There is a need to replace the biomaterials that currently still dominate this market, i.e., autografts and allografts, due to their disadvantages, such as limited availability, need for additional surgeries and diseases transmission possibilities. The most promising replacement materials are biomaterials with bioactive properties, such as the calcium phosphate-based bioceramics group. The bioactivity of these materials, i.e., the rate at which they promote the growth and directly bond with the new host biological bone, can be enhanced through their electrical polarization. In the present work, the electrical polarization features of pure hydroxyapatite (Hap), pure β-tricalcium phosphate (β-TCP) and biphasic hydroxyapatite/β-tricalcium phosphate composites (HTCP) were analyzed by measuring thermally stimulated depolarization currents (TSDC). The samples were thermoelectrically polarized at 500 °C under a DC electric field with a magnitude of 5 kV/cm. The biphasic samples were also polarized under electric fields with different magnitudes: 2, 3, 4 and 5 kV/cm. Additionally, the depolarization processes detected in the TSDC measurements were correlated with dielectric relaxation processes observed in impedance spectroscopy (IS) measurements. The results indicate that the β-TCP crystalline phase has a considerable higher ability to store electrical charge compared with the Hap phase. This indicates that it has a suitable composition and structure for ionic conduction and establishment of a large electric charge density, providing great potential for orthopaedic applications.

Biphase Cobalt-Manganese Oxide with High Capacity and Rate Performance for Aqueous Sodium-Ion Electrochemical Energy Storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shan, Xiaoqiang; Charles, Daniel S.; Xu, Wenqian

Manganese-based metal oxide electrode materials are of great importance in electrochemical energy storage for their favorable redox behavior, low cost and environmental-friendliness. However, their storage capacity and cycle life in aqueous Na-ion electrolytes is not satisfactory. In this paper, we report the development of a bi-phase cobalt-manganese oxide (Co-Mn-O) nanostructured electrode material, comprised of a layered MnO 2.H 2O birnessite phase and a (Co 0.83Mn 0.13Va 0.04)tetra(Co 0.38Mn 1.62) octaO 3.72 (Va: vacancy; tetra: tetrahedral sites; octa: octahedral sites) spinel phase, verified by neutron total scattering and pair distribution function analyses. The bi-phase Co-Mn-O material demonstrates an excellent storage capacitymore » towards Na-ions in an aqueous electrolyte (121 mA h g -1 at a scan rate of 1 mV s -1 in the half-cell and 81 mA h g -1 at a current density of 2 A g -1 after 5000 cycles in full-cells), as well as high rate performance (57 mA h g -1 a rate of 360 C). Electro-kinetic analysis and in situ X-ray diffraction measurements further confirm that the synergistic interaction between the spinel and layered phases, as well as the vacancy of the tetrahedral sites of spinel phase, contribute to the improved capacity and rate performance of the Co-Mn-O material by facilitating both diffusion-limited redox and capacitive charge storage processes.« less

Cofilin 1-Mediated Biphasic F-Actin Dynamics of Neuronal Cells Affect Herpes Simplex Virus 1 Infection and Replication

PubMed Central

Xiang, Yangfei; Zheng, Kai; Ju, Huaiqiang; Wang, Shaoxiang; Pei, Ying; Ding, Weichao; Chen, Zhenping; Wang, Qiaoli; Qiu, Xianxiu; Zhong, Meigong; Zeng, Fanli; Ren, Zhe; Qian, Chuiwen; Liu, Ge

2012-01-01

Herpes simplex virus 1 (HSV-1) invades the nervous system and causes pathological changes. In this study, we defined the remodeling of F-actin and its possible mechanisms during HSV-1 infection of neuronal cells. HSV-1 infection enhanced the formation of F-actin-based structures in the early stage of infection, which was followed by a continuous decrease in F-actin during the later stages of infection. The disruption of F-actin dynamics by chemical inhibitors significantly reduced the efficiency of viral infection and intracellular HSV-1 replication. The active form of the actin-depolymerizing factor cofilin 1 was found to increase at an early stage of infection and then to continuously decrease in a manner that corresponded to the remodeling pattern of F-actin, suggesting that cofilin 1 may be involved in the biphasic F-actin dynamics induced by HSV-1 infection. Knockdown of cofilin 1 impaired HSV-1-induced F-actin assembly during early infection and inhibited viral entry; however, overexpression of cofilin 1 did not affect F-actin assembly or viral entry during early infection but decreased intracellular viral reproduction efficiently. Our results, for the first time, demonstrated the biphasic F-actin dynamics in HSV-1 neuronal infection and confirmed the association of F-actin with the changes in the expression and activity of cofilin 1. These results may provide insight into the mechanism by which HSV-1 productively infects neuronal cells and causes pathogenesis. PMID:22623803

Mouse phenotyping.

PubMed

Fuchs, Helmut; Gailus-Durner, Valérie; Adler, Thure; Aguilar-Pimentel, Juan Antonio; Becker, Lore; Calzada-Wack, Julia; Da Silva-Buttkus, Patricia; Neff, Frauke; Götz, Alexander; Hans, Wolfgang; Hölter, Sabine M; Horsch, Marion; Kastenmüller, Gabi; Kemter, Elisabeth; Lengger, Christoph; Maier, Holger; Matloka, Mikolaj; Möller, Gabriele; Naton, Beatrix; Prehn, Cornelia; Puk, Oliver; Rácz, Ildikó; Rathkolb, Birgit; Römisch-Margl, Werner; Rozman, Jan; Wang-Sattler, Rui; Schrewe, Anja; Stöger, Claudia; Tost, Monica; Adamski, Jerzy; Aigner, Bernhard; Beckers, Johannes; Behrendt, Heidrun; Busch, Dirk H; Esposito, Irene; Graw, Jochen; Illig, Thomas; Ivandic, Boris; Klingenspor, Martin; Klopstock, Thomas; Kremmer, Elisabeth; Mempel, Martin; Neschen, Susanne; Ollert, Markus; Schulz, Holger; Suhre, Karsten; Wolf, Eckhard; Wurst, Wolfgang; Zimmer, Andreas; Hrabě de Angelis, Martin

2011-02-01

Model organisms like the mouse are important tools to learn more about gene function in man. Within the last 20 years many mutant mouse lines have been generated by different methods such as ENU mutagenesis, constitutive and conditional knock-out approaches, knock-down, introduction of human genes, and knock-in techniques, thus creating models which mimic human conditions. Due to pleiotropic effects, one gene may have different functions in different organ systems or time points during development. Therefore mutant mouse lines have to be phenotyped comprehensively in a highly standardized manner to enable the detection of phenotypes which might otherwise remain hidden. The German Mouse Clinic (GMC) has been established at the Helmholtz Zentrum München as a phenotyping platform with open access to the scientific community (www.mousclinic.de; [1]). The GMC is a member of the EUMODIC consortium which created the European standard workflow EMPReSSslim for the systemic phenotyping of mouse models (http://www.eumodic.org/[2]). Copyright © 2010 Elsevier Inc. All rights reserved.

A novel P450-initiated biphasic process for sustainable biodegradation of benzo[a]pyrene in soil under nutrient-sufficient conditions by the white rot fungus Phanerochaete chrysosporium

PubMed Central

Bhattacharya, Sukanta S.; Syed, Khajamohiddin; Shann, Jodi; Yadav, Jagjit S.

2013-01-01

High molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) such as benzo[a]pyrene (BaP) are resistant to biodegradation in soil. Conventionally, white rot fungus Phanerochaete chrysosporium has been investigated for HMW-PAH degradation in soil primarily using nutrient-deficient (ligninolytic) conditions, albeit with limited and non-sustainable biodegradation outcomes. In this study, we report development of an alternative novel biphasic process initiated under nutrient-sufficient (non-ligninolytic) culture conditions, by employing an advanced experimental design strategy. During the initial nutrient-sufficient non-ligninolytic phase (16 days), the process showed upregulation (3.6-and 22.3-fold, respectively) of two key PAH-oxidizing P450 monooxygenases pc2 (CYP63A2) and pah4 (CYP5136A3) and formation of typical P450-hydroxylated metabolite. This along with abrogation (84.9%) of BaP degradation activity in response to a P450-specific inhibitor implied key role of these monooxygenases. The subsequent phase triggered on continued incubation (to 25 days) switched the process from non-ligninolytic to ligninolytic resulting in a significantly higher net degradation (91.6% as against 67.4% in the control nutrient-limited set) of BaP with concomitant de novo ligninolytic enzyme expression making it a biphasic process yielding improved sustainable bioremediation of PAH-contaminated soil. To our knowledge this is the first report on development of such biphasic process for bioremediation application of a white rot fungus. PMID:24051002

Onset of white striping and progression into wooden breast as defined by myopathic changes underlying Pectoralis major growth. Estimation of growth parameters as predictors for stage of myopathy progression.

PubMed

Griffin, Jacqueline Reedy; Moraes, Luis; Wick, Macdonald; Lilburn, Michael Snell

2018-02-01

The broiler industry has incurred significant economic losses due to two muscle myopathies, white striping (WS) and wooden breast (WB), affecting the Pectoralis major (P. major) of commercial broilers. The present study documented macroscopic changes occurring with age/growth in the P. major and P. minor muscles of commercial broilers from day 2 through day 46 (n = 27/day). Distinct myopathic aberrations observed in both breast muscles corresponded to the onset of WB. These distinct morphological changes were used as determinants in developing a ranking system, defining the ontogeny of WB as the following four stages: (1) WS, (2) petechial epimysium haemorrhages, (3) intramuscular haemorrhages and (4) ischaemia. A cumulative logit proportional odds model was used to relate the rank probabilities with the following growth parameters: body weight, P. major and P. minor weight/yield/length/width/depth. The best-fit model included P. major length/width/depth, P. minor width, P. major and P. minor yield as predictors for rank. Increasing P. major depth, P. minor width and P. major yield increased the odds of falling into higher ranks (more severe myopathy). Conversely, increasing P. major length, P. major width and P. minor yield increased the odds of falling into smaller ranks (less severe myopathy). This study describes the macroscopic changes associated with WB ontogeny in the development of a ranking system and the contribution of growth parameters in the determination of rank (WB severity). Results suggest that physical measurements inherent to selection for high-yielding broiler genotypes are contributing to the occurrence and severity of WS and WB.

Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis.

PubMed

Harper, Marc; Gronenberg, Luisa; Liao, James; Lee, Christopher

2014-01-01

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. We combine an experimental design for detecting independent genetic causes of a phenotype with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome.

Asthma phenotypes in childhood.

PubMed

Reddy, Monica B; Covar, Ronina A

2016-04-01

This review describes the literature over the past 18 months that evaluated childhood asthma phenotypes, highlighting the key aspects of these studies, and comparing these studies to previous ones in this area. Recent studies on asthma phenotypes have identified new phenotypes on the basis of statistical analyses (using cluster analysis and latent class analysis methodology) and have evaluated the outcomes and associated risk factors of previously established early childhood asthma phenotypes that are based on asthma onset and patterns of wheezing illness. There have also been investigations focusing on immunologic, physiologic, and genetic correlates of various phenotypes, as well as identification of subphenotypes of severe childhood asthma. Childhood asthma remains a heterogeneous condition, and investigations into these various presentations, risk factors, and outcomes are important since they can offer therapeutic and prognostic relevance. Further investigation into the immunopathology and genetic basis underlying childhood phenotypes is important so therapy can be tailored accordingly.

Micromechanical model of biphasic biomaterials with internal adhesion: Application to nanocellulose hydrogel composites.

PubMed

Bonilla, Mauricio R; Lopez-Sanchez, P; Gidley, M J; Stokes, J R

2016-01-01

The mechanical properties of hydrated biomaterials are non-recoverable upon unconfined compression if adhesion occurs between the structural components in the material upon fluid loss and apparent plastic behaviour. We explore these micromechanical phenomena by introducing an aggregation force and a critical yield pressure into the constitutive biphasic formulation for transversely isotropic tissues. The underlying hypothesis is that continual fluid pressure build-up during compression temporarily supresses aggregation. Once compression stops and the pressure falls below some critical value, internal aggregation occurs over a time scale comparable to the poroelastic time. We demonstrate this model by predicting the mechanical response of bacterial nanocellulose hydrogel composites, which are promising biomaterials and a structural mimetic for the plant cell wall. Cross-linking of cellulose by xyloglucan creates an extensional resistance and substantially increases the compressive modulus under large compression and densification. In comparison, incorporating non-crosslinking arabinoxylan into the hydrogel has little effect on its mechanics at the strain rates investigated. These results assist in elucidating the mechanical role of these polysaccharides in the complex plant cell wall structure. They also suggest xyloglucan is a suitable candidate to tailor the stiffness of nanocellulose hydrogels in biomaterial design, which includes modulating cell-adhesion in tissue engineering applications. The model and overall approach may be utilised to characterise and design a myriad of biomaterials and mammalian tissues, particularly those with a fibrillar structure. The mechanical properties of hydrated biomaterials can be non-recoverable upon compression due to increased adhesion occurring between the structural components in the material. Cellulose-hemicellulose composite hydrogels constitute a classical example of this phenomenon, since fibres can freely re-orient and

The ethyl acetate fraction of a methanolic extract of unripe noni (Morinda citrifolia Linn.) fruit exhibits a biphasic effect on the dopaminergic system in mice

PubMed Central

Pandy, Vijayapandi; Narasingam, Megala; Vijeepallam, Kamini; Mohan, Syam; Mani, Vasudevan; Mohamed, Zahurin

2017-01-01

In earlier ex vivo studies, we reported the biphasic effect of a methanolic extract of unripe Morinda citrifolia fruit (MMC) on dopamine-induced contractility in isolated rat vas deferens preparations. The present in vivo study was designed and undertaken to further explore our earlier ex vivo findings. This study examined the effect of the ethyl acetate fraction of a methanolic extract of unripe Morinda citrifolia Linn. fruit (EA-MMC; 5–100 mg/kg, p.o.) on the dopaminergic system using mouse models of apomorphine-induced climbing time and climbing behavior, methamphetamine-induced stereotypy (sniffing, biting, gnawing, and licking) and haloperidol-induced catalepsy using the bar test. Acute treatment with EA-MMC at a low dose (25 mg/kg, p.o.) significantly attenuated the apomorphine-induced climbing time and climbing behavior in mice. Similarly, EA-MMC (5 and 10 mg/kg, p.o.) significantly inhibited methamphetamine-induced stereotyped behavior in mice. These results demonstrated that the antidopaminergic effect of EA-MMC was observed at relatively lower doses (<25 mg/kg, p.o.). On the other hand, EA-MMC showed dopaminergic agonistic activity at a high dose (3,000 mg/kg, p.o.), which was evident from alleviation of haloperidol (a dopamine D2 blocker)-induced catalepsy in mice. Therefore, it is concluded that EA-MMC might possess a biphasic effect on the dopaminergic system, i.e., an antagonistic effect at lower doses (<25 mg/kg, p.o.) and an agonistic effect at higher doses (>1,000 mg/kg, p.o.). However, further receptor-ligand binding assays are necessary to confirm the biphasic effects of M. citrifolia fruit on the dopaminergic system. PMID:28450692

The ethyl acetate fraction of a methanolic extract of unripe noni (Morinda citrifolia Linn.) fruit exhibits a biphasic effect on the dopaminergic system in mice.

PubMed

Pandy, Vijayapandi; Narasingam, Megala; Vijeepallam, Kamini; Mohan, Syam; Mani, Vasudevan; Mohamed, Zahurin

2017-08-05

In earlier ex vivo studies, we reported the biphasic effect of a methanolic extract of unripe Morinda citrifolia fruit (MMC) on dopamine-induced contractility in isolated rat vas deferens preparations. The present in vivo study was designed and undertaken to further explore our earlier ex vivo findings. This study examined the effect of the ethyl acetate fraction of a methanolic extract of unripe Morinda citrifolia Linn. fruit (EA-MMC; 5-100 mg/kg, p.o.) on the dopaminergic system using mouse models of apomorphine-induced climbing time and climbing behavior, methamphetamine-induced stereotypy (sniffing, biting, gnawing, and licking) and haloperidol-induced catalepsy using the bar test. Acute treatment with EA-MMC at a low dose (25 mg/kg, p.o.) significantly attenuated the apomorphine-induced climbing time and climbing behavior in mice. Similarly, EA-MMC (5 and 10 mg/kg, p.o.) significantly inhibited methamphetamine-induced stereotyped behavior in mice. These results demonstrated that the antidopaminergic effect of EA-MMC was observed at relatively lower doses (<25 mg/kg, p.o.). On the other hand, EA-MMC showed dopaminergic agonistic activity at a high dose (3,000 mg/kg, p.o.), which was evident from alleviation of haloperidol (a dopamine D 2 blocker)-induced catalepsy in mice. Therefore, it is concluded that EA-MMC might possess a biphasic effect on the dopaminergic system, i.e., an antagonistic effect at lower doses (<25 mg/kg, p.o.) and an agonistic effect at higher doses (>1,000 mg/kg, p.o.). However, further receptor-ligand binding assays are necessary to confirm the biphasic effects of M. citrifolia fruit on the dopaminergic system.

Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

PubMed Central

Adissu, Hibret A.; Estabel, Jeanne; Sunter, David; Tuck, Elizabeth; Hooks, Yvette; Carragher, Damian M.; Clarke, Kay; Karp, Natasha A.; Project, Sanger Mouse Genetics; Newbigging, Susan; Jones, Nora; Morikawa, Lily; White, Jacqueline K.; McKerlie, Colin

2014-01-01

The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice. PMID:24652767

Abnormalities in intracellular calcium regulation and contractile function in myocardium from dogs with pacing-induced heart failure

NASA Technical Reports Server (NTRS)

Perreault, C. L.; Shannon, R. P.; Komamura, K.; Vatner, S. F.; Morgan, J. P.

1992-01-01

24 d of rapid ventricular pacing induced dilated cardiomyopathy with both systolic and diastolic dysfunction in conscious, chronically instrumented dogs. We studied mechanical properties and intracellular calcium (Ca2+i) transients of trabeculae carneae isolated from 15 control dogs (n = 32) and 11 dogs with pacing-induced cardiac failure (n = 26). Muscles were stretched to maximum length at 30 degrees C and stimulated at 0.33 Hz; a subset (n = 17 control, n = 17 myopathic) was loaded with the [Ca2+]i indicator aequorin. Peak tension was depressed in the myopathic muscles, even in the presence of maximally effective (i.e., 16 mM) [Ca2+] in the perfusate. However, peak [Ca2+]i was similar (0.80 +/- 0.13 vs. 0.71 +/- 0.05 microM; [Ca2+]o = 2.5 mM), suggesting that a decrease in Cai2+ availability was not responsible for the decreased contractility. The time for decline from the peak of the Cai2+ transient was prolonged in the myopathic group, which correlated with prolongation of isometric contraction and relaxation. However, similar end-diastolic [Ca2+]i was achieved in both groups (0.29 +/- 0.05 vs. 0.31 +/- 0.02 microM), indicating that Cai2+ homeostasis can be maintained in myopathic hearts. The inotropic response of the myopathic muscles to milrinone was depressed compared with the controls. However, when cAMP production was stimulated by pretreatment with forskolin, the response of the myopathic muscles to milrinone was improved. Our findings provide direct evidence that abnormal [Ca2+]i handling is an important cause of contractile dysfunction in dogs with pacing-induced heart failure and suggest that deficient production of cAMP may be an important cause of these changes in excitation-contraction coupling.

Traumatic head injury mimicking acute encephalopathy with biphasic seizures and late reduced diffusion.

PubMed

Inoue, Hirofumi; Hasegawa, Shunji; Kajimoto, Madoka; Matsushige, Takeshi; Ichiyama, Takashi

2014-10-01

Many studies have reported acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) associated with viral infection at onset, but few studies have reported AESD without infection. We report the case of a 9-month-old boy who had a clinical course mimicking AESD after a traffic accident. The traffic accident caused a mild subdural hematoma without neurological abnormalities on admission. The boy became unconscious on the second day, and he was diagnosed with non-convulsive status epilepticus on the third day. Diffusion-weighted imaging showed reduced water diffusion in the subcortical white matter. On laboratory analysis interleukin (IL)-6 was elevated in the cerebrospinal fluid (CSF), but not in the serum. He had severe neurological sequelae with mental retardation, spastic tetraplegia, and epilepsy. We suggest that brain damage mimicking AESD was caused by the traffic accident and the prolonged seizure during infancy. © 2014 Japan Pediatric Society.

Biphasic rapamycin effects in lymphoma and carcinoma treatment

PubMed Central

Liu, Yang; Pandeswara, Srilakshmi; Dao, Vinh; Padrón, Álvaro; Drerup, Justin M.; Lao, Shunhua; Liu, Aijie; Hurez, Vincent; Curiel, Tyler J.

2017-01-01

mTOR drives tumor growth but also supports T cell function, rendering the applications of mTOR inhibitors complex especially in T cell malignancies. Here we studied the effects of the mTOR inhibitor rapamycin in mouse EL4 T cell lymphoma. Typical pharmacologic rapamycin (1–8 mg/kg) significantly reduced tumor burden via direct suppression of tumor cell proliferation and improved survival in EL4 challenge independent of anti-tumor immunity. Denileukin diftitox (DD)-mediated depletion of regulatory T cells significantly slowed EL4 growth in vivo in a T cell-dependent fashion. However, typical rapamycin inhibited T cell activation and tumor infiltration in vivo and failed to boost DD treatment effects. Low dose rapamycin (LD, 75 μg/kg) increased potentially beneficial CD44hiCD62L+ CD8+ central memory T cells in EL4 challenge, but without clinical benefit. LD rapamycin significantly enhanced DD treatment efficacy, but DD plus LD rapamycin treatment effects were independent of anti-tumor immunity. Instead, rapamycin up-regulated EL4 IL-2 receptor in vitro and in vivo, facilitating direct DD tumor cell killing. LD rapamycin augmented DD efficacy against B16 melanoma and a human B cell lymphoma, but not against human Jurkat T cell lymphoma or ID8agg ovarian cancer cells. Treatment effects correlated with IL-2R expression, but mechanisms in some tumors were not fully defined. Overall, our data define a distinct, biphasic mechanisms of action of mTOR inhibition at doses that are clinically exploitable, including in T cell lymphomas. PMID:27737881

Appraisal of the sensitising potential of orally and dermally administered mercaptobenzothiazole by a biphasic protocol of the local lymph node assay.

PubMed

Ahuja, Varun; Wanner, Reinhard; Platzek, Thomas; Stahlmann, Ralf

2009-10-01

Mercaptobenzothiazole (MBT) is used while manufacturing natural rubber products. Our study deals with assessing its allergenic potential following dermal and oral routes of exposure, using a biphasic local lymph node assay (LLNA). Female Balb/c mice were treated with MBT (dermally 3, 10, 30% concentrations in DMSO; orally 1, 10, 100 mg/kg doses in corn oil) on the back (dermal study) or through oral administration (oral study) on days 1-3 followed by auricular application of 3, 10 and 30% concentrations, respectively, on days 15-17. End points determined on day 19 included ear thickness, ear punch weight, lymph node weight, lymph node cell count, and lymphocyte subpopulations (CD4+, CD8+, CD45+). After dermal application of 3% or 10% solution, a significant increase in cell count and lymph node weight along with significant decrease in CD8+ cells was observed. After initial oral administration of 1 mg/kg, we noticed a significant amplification in cell count. Following oral administration of 10 mg/kg, we observed a similar increase in cell count and lymph node weight. The results of our study show that the modified biphasic LLNA protocol can be used to study the sensitising potential of a compound also following the oral route of exposure.

Mutations in the satellite cell gene MEGF10 cause a recessive congenital myopathy with minicores.

PubMed

Boyden, Steven E; Mahoney, Lane J; Kawahara, Genri; Myers, Jennifer A; Mitsuhashi, Satomi; Estrella, Elicia A; Duncan, Anna R; Dey, Friederike; DeChene, Elizabeth T; Blasko-Goehringer, Jessica M; Bönnemann, Carsten G; Darras, Basil T; Mendell, Jerry R; Lidov, Hart G W; Nishino, Ichizo; Beggs, Alan H; Kunkel, Louis M; Kang, Peter B

2012-05-01

We ascertained a nuclear family in which three of four siblings were affected with an unclassified autosomal recessive myopathy characterized by severe weakness, respiratory impairment, scoliosis, joint contractures, and an unusual combination of dystrophic and myopathic features on muscle biopsy. Whole genome sequence from one affected subject was filtered using linkage data and variant databases. A single gene, MEGF10, contained nonsynonymous mutations that co-segregated with the phenotype. Affected subjects were compound heterozygous for missense mutations c.976T > C (p.C326R) and c.2320T > C (p.C774R). Screening the MEGF10 open reading frame in 190 patients with genetically unexplained myopathies revealed a heterozygous mutation, c.211C > T (p.R71W), in one additional subject with a similar clinical and histological presentation as the discovery family. All three mutations were absent from at least 645 genotyped unaffected control subjects. MEGF10 contains 17 atypical epidermal growth factor-like domains, each of which contains eight cysteine residues that likely form disulfide bonds. Both the p.C326R and p.C774R mutations alter one of these residues, which are completely conserved in vertebrates. Previous work showed that murine Megf10 is required for preserving the undifferentiated, proliferative potential of satellite cells, myogenic precursors that regenerate skeletal muscle in response to injury or disease. Here, knockdown of megf10 in zebrafish by four different morpholinos resulted in abnormal phenotypes including unhatched eggs, curved tails, impaired motility, and disorganized muscle tissue, corroborating the pathogenicity of the human mutations. Our data establish the importance of MEGF10 in human skeletal muscle and suggest satellite cell dysfunction as a novel myopathic mechanism.

Facile preparation of biphasic-induced magnetic icariin-loaded composite microcapsules by automated in situ click technology.

PubMed

Pan, Panpan; Chen, Jingdi; Fan, Tiantang; Hu, Yimin; Wu, Tao; Zhang, Qiqing

2016-04-01

This research aims to prepare the biphasic-induced magnetic composite microcapsules (BIMCM) as a promising environmental stimuli-responsive delivery vehicle to dispose the problem of drug burst effect. The paper presented a novel automated in situ click technology of magnetic chitosan/nano hydroxyapatite (CS/nHA) microcapsules. Fe3O4 magnetic nanoparticles (MNP) and nHA were simultaneously in situ crystallized by one-step process. Icariin (ICA), a plant-derived flavonol glycoside, was combined to study drug release properties of BIMCM. BIMCM were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and Thermal gravimetric analysis/Differential Scanning Calorimetry(TGA/DSC) in order to reveal their component and surface morphology as well as the role of the in situ generated Fe3O4 MNP and nHA. The magnetic test showed the BIMCM were super-paramagnetic. Both in situ generated Fe3O4 MNP and nHA serve as stable inorganic crosslinkers in BIMCM to form many intermolecular crosslinkages for the movability of the CS chains. This makes ICA loaded microcapsules take on a sustained release behavior and results in the self-adjusting of surface morphology, decreasing of swelling and degradation rates. In addition, in vitro tests were systematically carried out to examine the biocompatibility of the microcapsules by MTT test, Wright-Giemsa dying assay and AO/EB fluorescent staining method. These results demonstrated that successful introduction of the in situ click Fe3O4 MNP provided an alternative strategy because of magnetic sensitivity and sustained release. As such, the novel ICA loaded biphasic-induced magnetic CS/nHA/MNP microcapsules are expected to find potential applications in drug delivery system for bone repair. Copyright © 2015 Elsevier B.V. All rights reserved.

New biphasic solvent system based on cyclopentyl methyl ether for the purification of a non-polar synthetic peptide by pH-zone refining centrifugal partition chromatography.

PubMed

Amarouche, Nassima; Boudesocque, Leslie; Borie, Nicolas; Giraud, Matthieu; Forni, Luciano; Butte, Alessandro; Edwards, Florence; Renault, Jean-Hugues

2014-06-01

A new type 1 ternary biphasic system composed of cyclopentyl methyl ether, dimethylformamide and water was developed, characterized and successfully used for the purification of a lipophilic, protected peptide by pH-zone refining centrifugal partition chromatography. The protected peptide is an 8-mer, key intermediate in bivalirudin (Angiomax®) synthesis and shows a very low solubility in the solvents usually used in liquid chromatography. All ionic groups, except the N-terminal end of the peptide, are protected by a benzyl group. The purification of this peptide was achieved with a purity of about 99.04% and a recovery of 94% using the new ternary biphasic system cyclopentyl methyl ether/dimethylformamide/water (49:40:11, v/v) in the descending pH-zone refining mode with triethylamine (28 mM) as the retainer and methanesulfonic acid (18 mM) as the eluter. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The thermal stability of hydroxyapatite in biphasic calcium phosphate ceramics.

PubMed

Nilen, R W N; Richter, P W

2008-04-01

Biphasic calcium phosphate ceramics (BCP) comprising a mix of non-resorbable hydroxyapatite (HA) and resorbable beta-tricalcium phosphate (beta-TCP) are particularly suitable materials for synthetic bone substitute applications. In this study, HA synthesised by solid state reaction was mechanically mixed with beta-TCP, then sintered to form a suite of BCP materials with a wide range of HA/beta-TCP phase content ratios. The influence of sintering temperature and composition on the HA thermal stability was quantified by X-ray diffraction (XRD). The pre-sinter beta-TCP content was found to strongly affect the post-sinter HA/beta-TCP ratio by promoting the thermal decomposition of HA to beta-TCP, even at sintering temperatures as low as 850 degrees C. For BCP material with pre-sinter HA/beta-TCP = 40/60 wt%, approximately 80% of the HA decomposed to beta-TCP during sintering at 1000 degrees C. Furthermore, the HA content appeared to influence the reverse transformation of alpha-TCP to beta-TCP expected upon gradual cooling from sintering temperatures greater than 1125 degrees C. Because the HA/beta-TCP ratio dominantly determines the rate and extent of BCP resorption in vivo, the possible thermal decomposition of HA during BCP synthesis must be considered, particularly if high temperature treatments are involved.

Longitudinal study of the effects of chronic hypothyroidism on skeletal muscle in dogs.

PubMed

Rossmeisl, John H; Duncan, Robert B; Inzana, Karen D; Panciera, David L; Shelton, G Diane

2009-07-01

To study the effects of experimentally induced hypothyroidism on skeletal muscle and characterize any observed myopathic abnormalities in dogs. 9 female, adult mixed-breed dogs; 6 with hypothyroidism induced with irradiation with 131 iodine and 3 untreated control dogs. Clinical examinations were performed monthly. Electromyographic examinations; measurement of plasma creatine kinase, alanine aminotransferase, aspartate aminotransferase, lactate, and lactate dehydrogenase isoenzyme activities; and skeletal muscle morphologic-morphometric examinations were performed prior to and every 6 months for 18 months after induction of hypothyroidism. Baseline, 6-month, and 18-month assessments of plasma, urine, and skeletal muscle carnitine concentrations were also performed. Hypothyroid dogs developed electromyographic and morphologic evidence of myopathy by 6 months after treatment, which persisted throughout the study, although these changes were subclinical at all times. Hypothyroid myopathy was associated with significant increases in plasma creatine kinase, aspartate aminotransferase, and lactate dehydrogenase 5 isoenzyme activities and was characterized by nemaline rod inclusions, substantial and progressive predominance of type I myofibers, decrease in mean type II fiber area, subsarcolemmal accumulations of abnormal mitochondria, and myofiber degeneration. Chronic hypothyroidism was associated with substantial depletion in skeletal muscle free carnitine. Chronic, experimentally induced hypothyroidism resulted in substantial but subclinical phenotypic myopathic changes indicative of altered muscle energy metabolism and depletion of skeletal muscle carnitine. These abnormalities may contribute to nonspecific clinical signs, such as lethargy and exercise intolerance, often reported in hypothyroid dogs.

Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

PubMed

Paredes, João A; Zhou, Xiaoshan; Höglund, Stefan; Karlsson, Anna

2013-01-01

Loss of thymidine kinase 2 (TK2) causes a heterogeneous myopathic form of mitochondrial DNA (mtDNA) depletion syndrome (MDS) in humans that predominantly affects skeletal muscle tissue. In mice, TK2 deficiency also affects several tissues in addition to skeletal muscle, including brain, heart, adipose tissue, kidneys and causes death about 3 weeks after birth. We analysed skeletal muscle and heart muscle tissues of Tk2 knockout mice at postnatal development phase and observed that TK2 deficient pups grew slower and their skeletal muscles appeared significantly underdeveloped, whereas heart was close to normal in size. Both tissues showed mtDNA depletion and mitochondria with altered ultrastructure, as revealed by transmission electron microscopy. Gene expression microarray analysis showed a strong down-regulation of genes involved in cell cycle and cell proliferation in both tissues, suggesting a lower pool of undifferentiated proliferating cells. Analysis of isolated primary myoblasts from Tk2 knockout mice showed slow proliferation, less ability to differentiate and signs of premature senescence, even in absence of mtDNA depletion. Our data demonstrate that TK2 deficiency disturbs myogenic progenitor cells function in postnatal skeletal muscle and we propose this as one of the causes of underdeveloped phenotype and myopathic characteristic of the TK2 deficient mice, in addition to the progressive mtDNA depletion, mitochondrial damage and respiratory chain deficiency in post-mitotic differentiated tissue.

Gene Expression Deregulation in Postnatal Skeletal Muscle of TK2 Deficient Mice Reveals a Lower Pool of Proliferating Myogenic Progenitor Cells

PubMed Central

Paredes, João A.; Zhou, Xiaoshan; Höglund, Stefan; Karlsson, Anna

2013-01-01

Loss of thymidine kinase 2 (TK2) causes a heterogeneous myopathic form of mitochondrial DNA (mtDNA) depletion syndrome (MDS) in humans that predominantly affects skeletal muscle tissue. In mice, TK2 deficiency also affects several tissues in addition to skeletal muscle, including brain, heart, adipose tissue, kidneys and causes death about 3 weeks after birth. We analysed skeletal muscle and heart muscle tissues of Tk2 knockout mice at postnatal development phase and observed that TK2 deficient pups grew slower and their skeletal muscles appeared significantly underdeveloped, whereas heart was close to normal in size. Both tissues showed mtDNA depletion and mitochondria with altered ultrastructure, as revealed by transmission electron microscopy. Gene expression microarray analysis showed a strong down-regulation of genes involved in cell cycle and cell proliferation in both tissues, suggesting a lower pool of undifferentiated proliferating cells. Analysis of isolated primary myoblasts from Tk2 knockout mice showed slow proliferation, less ability to differentiate and signs of premature senescence, even in absence of mtDNA depletion. Our data demonstrate that TK2 deficiency disturbs myogenic progenitor cells function in postnatal skeletal muscle and we propose this as one of the causes of underdeveloped phenotype and myopathic characteristic of the TK2 deficient mice, in addition to the progressive mtDNA depletion, mitochondrial damage and respiratory chain deficiency in post-mitotic differentiated tissue. PMID:23341978

The Molecular Basis of Muscular Dystrophy in the mdx Mouse: A Point Mutation

NASA Astrophysics Data System (ADS)

Sicinski, Piotr; Geng, Yan; Ryder-Cook, Allan S.; Barnard, Eric A.; Darlison, Mark G.; Barnard, Pene J.

1989-06-01

The mdx mouse is an X-linked myopathic mutant, an animal model for human Duchenne muscular dystrophy. In both mouse and man the mutations lie within the dystrophin gene, but the phenotypic differences of the disease in the two species confer much interest on the molecular basis of the mdx mutation. The complementary DNA for mouse dystrophin has been cloned, and the sequence has been used in the polymerase chain reaction to amplify normal and mdx dystrophin transcripts in the area of the mdx mutation. Sequence analysis of the amplification products showed that the mdx mouse has a single base substitution within an exon, which causes premature termination of the polypeptide chain.

Multivariate Analysis of Genotype-Phenotype Association.

PubMed

Mitteroecker, Philipp; Cheverud, James M; Pavlicev, Mihaela

2016-04-01

With the advent of modern imaging and measurement technology, complex phenotypes are increasingly represented by large numbers of measurements, which may not bear biological meaning one by one. For such multivariate phenotypes, studying the pairwise associations between all measurements and all alleles is highly inefficient and prevents insight into the genetic pattern underlying the observed phenotypes. We present a new method for identifying patterns of allelic variation (genetic latent variables) that are maximally associated-in terms of effect size-with patterns of phenotypic variation (phenotypic latent variables). This multivariate genotype-phenotype mapping (MGP) separates phenotypic features under strong genetic control from less genetically determined features and thus permits an analysis of the multivariate structure of genotype-phenotype association, including its dimensionality and the clustering of genetic and phenotypic variables within this association. Different variants of MGP maximize different measures of genotype-phenotype association: genetic effect, genetic variance, or heritability. In an application to a mouse sample, scored for 353 SNPs and 11 phenotypic traits, the first dimension of genetic and phenotypic latent variables accounted for >70% of genetic variation present in all 11 measurements; 43% of variation in this phenotypic pattern was explained by the corresponding genetic latent variable. The first three dimensions together sufficed to account for almost 90% of genetic variation in the measurements and for all the interpretable genotype-phenotype association. Each dimension can be tested as a whole against the hypothesis of no association, thereby reducing the number of statistical tests from 7766 to 3-the maximal number of meaningful independent tests. Important alleles can be selected based on their effect size (additive or nonadditive effect on the phenotypic latent variable). This low dimensionality of the genotype-phenotype map

Facile synthesis and photocatalytic activity of bi-phase dispersible Cu-ZnO hybrid nanoparticles

NASA Astrophysics Data System (ADS)

Liu, Xiao; Liu, HongLing; Zhang, WenXing; Li, XueMei; Fang, Ning; Wang, XianHong; Wu, JunHua

2015-04-01

Bi-phase dispersible Cu-ZnO hybrid nanoparticles were synthesized by one-pot non-aqueous nanoemulsion with the use of poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEO-PPO-PEO) as the surfactant. The transmission electron microscopy (TEM) and X-ray diffraction (XRD) show high crystallinity of the Cu-ZnO hybrid nanoparticles and an average particle size of ~19.4 nm. The ultraviolet-visible light absorbance spectrometry (UV-vis) and photoluminescence spectrophotometry (PL) demonstrate well dispersibility and excellent optical performance of Cu-ZnO hybrid nanoparticles both in organic and aqueous solvent. The X-ray photoelectron spectroscopy (XPS) confirms Cu1+ and Cu2+ in ZnO. The observation using Sudan red (III) as probe molecule reveals that the Cu-ZnO hybrid nanoparticles possess enhanced photocatalytic activity and stability which are promising for potential applications in photocatalysis.

A novel syndrome of Klippel-Feil anomaly, myopathy, and characteristic facies is linked to a null mutation in MYO18B.

PubMed

Alazami, Anas M; Kentab, Amal Y; Faqeih, Eissa; Mohamed, Jawahir Y; Alkhalidi, Hisham; Hijazi, Hadia; Alkuraya, Fowzan S

2015-06-01

Klippel-Feil anomaly (KFA) can be seen in a number of syndromes. We describe an apparently novel syndromic association with KFA. Clinical phenotyping of two consanguineous families followed by combined autozygome/exome analysis. Two patients from two apparently unrelated families shared a strikingly similar phenotype characterised by KFA, myopathy, mild short stature, microcephaly, and distinctive facies. They shared a single founder autozygous interval in which whole exome sequencing revealed a truncating mutation in MYO18B. There was virtually complete loss of the transcript in peripheral blood, indicative of nonsense-mediated decay. Electron microscopy of muscle confirms abnormal myosin filaments with accompanying myopathic changes. Deficiency of MYO18B is linked to a novel developmental disorder which combines KFA with myopathy. This suggests a widespread developmental role for this gene in humans, as observed for its murine ortholog. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Changes in biphasic electrode impedance with protein adsorption and cell growth

PubMed Central

Newbold, Carrie; Richardson, Rachael; Millard, Rodney; Huang, Christie; Milojevic, Dusan; Shepherd, Robert; Cowan, Robert

2012-01-01

This study was undertaken to assess the contribution of protein adsorption and cell growth to increases in electrode impedance that occur immediately following implantation of cochlear implant electrodes and other neural stimulation devices. An in vitro model of the electrode-tissue interface was used. Radiolabelled albumin in phosphate buffered saline was added to planar gold electrodes and electrode impedance measured using a charge-balanced biphasic current pulse. The polarisation impedance component increased with protein adsorption, while no change to access resistance was observed. The maximum level of protein adsorbed was measured at 0.5 μg/cm2, indicating a tightly packed monolayer of albumin molecules on the gold electrode and resin substrate. Three cell types were grown over the electrodes, macrophage cell line J774, dissociated fibroblasts and epithelial cell line MDCK, all of which created a significant increase in electrode impedance. As cell cover over electrodes increased, there was a corresponding increase in the initial rise in voltage, suggesting cell cover mainly contributes to the access resistance of the electrodes. Only a small increase in the polarisation component of impedance was seen with cell cover. PMID:20841637

The Human Phenotype Ontology in 2017

PubMed Central

Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie; Aymé, Ségolène; Baynam, Gareth; Bello, Susan M.; Boerkoel, Cornelius F.; Boycott, Kym M.; Brudno, Michael; Buske, Orion J.; Chinnery, Patrick F.; Cipriani, Valentina; Connell, Laureen E.; Dawkins, Hugh J.S.; DeMare, Laura E.; Devereau, Andrew D.; de Vries, Bert B.A.; Firth, Helen V.; Freson, Kathleen; Greene, Daniel; Hamosh, Ada; Helbig, Ingo; Hum, Courtney; Jähn, Johanna A.; James, Roger; Krause, Roland; F. Laulederkind, Stanley J.; Lochmüller, Hanns; Lyon, Gholson J.; Ogishima, Soichi; Olry, Annie; Ouwehand, Willem H.; Pontikos, Nikolas; Rath, Ana; Schaefer, Franz; Scott, Richard H.; Segal, Michael; Sergouniotis, Panagiotis I.; Sever, Richard; Smith, Cynthia L.; Straub, Volker; Thompson, Rachel; Turner, Catherine; Turro, Ernest; Veltman, Marijcke W.M.; Vulliamy, Tom; Yu, Jing; von Ziegenweidt, Julie; Zankl, Andreas; Züchner, Stephan; Zemojtel, Tomasz; Jacobsen, Julius O.B.; Groza, Tudor; Smedley, Damian; Mungall, Christopher J.; Haendel, Melissa; Robinson, Peter N.

2017-01-01

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology. PMID:27899602

The Human Phenotype Ontology in 2017

DOE PAGES

Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; ...

2016-11-24

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical softwaremore » tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.« less

Computational Approaches to Phenotyping

PubMed Central

Lussier, Yves A.; Liu, Yang

2007-01-01

The recent completion of the Human Genome Project has made possible a high-throughput “systems approach” for accelerating the elucidation of molecular underpinnings of human diseases, and subsequent derivation of molecular-based strategies to more effectively prevent, diagnose, and treat these diseases. Although altered phenotypes are among the most reliable manifestations of altered gene functions, research using systematic analysis of phenotype relationships to study human biology is still in its infancy. This article focuses on the emerging field of high-throughput phenotyping (HTP) phenomics research, which aims to capitalize on novel high-throughput computation and informatics technology developments to derive genomewide molecular networks of genotype–phenotype associations, or “phenomic associations.” The HTP phenomics research field faces the challenge of technological research and development to generate novel tools in computation and informatics that will allow researchers to amass, access, integrate, organize, and manage phenotypic databases across species and enable genomewide analysis to associate phenotypic information with genomic data at different scales of biology. Key state-of-the-art technological advancements critical for HTP phenomics research are covered in this review. In particular, we highlight the power of computational approaches to conduct large-scale phenomics studies. PMID:17202287

Study on biphasic material model and mechanical analysis of knee joint cartilage

NASA Astrophysics Data System (ADS)

Nakatani, A.; Sakashita, A.

2008-02-01

A material model of articular cartilage is formulated, and fundamental problems are analyzed. The soft tissue is assumed to comprise two phases: solid and fluid. The biphasic theory proposed by Spilker and Suh (1990) to deal with such materials is reviewed, and some new additional analyses are carried out on the basis of this theory. Assuming the elasticity for the solid phase and introducing the pressure, which is defined by the product of the volume change and penalty coefficient, it is shown that the viscoelastic property of the soft tissue can be reproduced. A preferable solution is obtained for the solid phase by using the reduction integral, even if a high-order interpolation function is used. However, the high-order element cannot satisfactorily capture the velocity distribution of fluids. The pressure distribution is studied by assuming the change in the surface characteristics of the cartilage tissue with the progress of osteoarthritis. The pressure is strongly related to the lubrication conditions, i.e., perfect lubrication, perfect adhesion, and partial adhesion.

Advanced phenotyping and phenotype data analysis for the study of plant growth and development

PubMed Central

Rahaman, Md. Matiur; Chen, Dijun; Gillani, Zeeshan; Klukas, Christian; Chen, Ming

2015-01-01

Due to an increase in the consumption of food, feed, fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to breed high yielding crops that can adapt to the future climate changes, particularly in developing countries. To solve these global challenges, novel approaches are required to identify quantitative phenotypes and to explain the genetic basis of agriculturally important traits. These advances will facilitate the screening of germplasm with high performance characteristics in resource-limited environments. Recently, plant phenomics has offered and integrated a suite of new technologies, and we are on a path to improve the description of complex plant phenotypes. High-throughput phenotyping platforms have also been developed that capture phenotype data from plants in a non-destructive manner. In this review, we discuss recent developments of high-throughput plant phenotyping infrastructure including imaging techniques and corresponding principles for phenotype data analysis. PMID:26322060

Advanced phenotyping and phenotype data analysis for the study of plant growth and development.

PubMed

Rahaman, Md Matiur; Chen, Dijun; Gillani, Zeeshan; Klukas, Christian; Chen, Ming

2015-01-01

Due to an increase in the consumption of food, feed, fuel and to meet global food security needs for the rapidly growing human population, there is a necessity to breed high yielding crops that can adapt to the future climate changes, particularly in developing countries. To solve these global challenges, novel approaches are required to identify quantitative phenotypes and to explain the genetic basis of agriculturally important traits. These advances will facilitate the screening of germplasm with high performance characteristics in resource-limited environments. Recently, plant phenomics has offered and integrated a suite of new technologies, and we are on a path to improve the description of complex plant phenotypes. High-throughput phenotyping platforms have also been developed that capture phenotype data from plants in a non-destructive manner. In this review, we discuss recent developments of high-throughput plant phenotyping infrastructure including imaging techniques and corresponding principles for phenotype data analysis.

A boundary-integral representation for biphasic mixture theory, with application to the post-capillary glycocalyx

PubMed Central

Sumets, P. P.; Cater, J. E.; Long, D. S.; Clarke, R. J.

2015-01-01

We describe a new boundary-integral representation for biphasic mixture theory, which allows us to efficiently solve certain elastohydrodynamic–mobility problems using boundary element methods. We apply this formulation to model the motion of a rigid particle through a microtube which has non-uniform wall shape, is filled with a viscous Newtonian fluid, and is lined with a thin poroelastic layer. This is relevant to scenarios such as the transport of small rigid cells (such as neutrophils) through microvessels that are lined with an endothelial glycocalyx layer (EGL). In this context, we examine the impact of geometry upon some recently reported phenomena, including the creation of viscous eddies, fluid flux into the EGL, as well as the role of the EGL in transmitting mechanical signals to the underlying endothelial cells. PMID:26345494

Interoperability between phenotype and anatomy ontologies.

PubMed

Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

2010-12-15

Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

Biphasic Rapamycin Effects in Lymphoma and Carcinoma Treatment.

PubMed

Liu, Yang; Pandeswara, Srilakshmi; Dao, Vinh; Padrón, Álvaro; Drerup, Justin M; Lao, Shunhua; Liu, Aijie; Hurez, Vincent; Curiel, Tyler J

2017-01-15

mTOR drives tumor growth but also supports T-cell function, rendering the applications of mTOR inhibitors complex especially in T-cell malignancies. Here, we studied the effects of the mTOR inhibitor rapamycin in mouse EL4 T-cell lymphoma. Typical pharmacologic rapamycin (1-8 mg/kg) significantly reduced tumor burden via direct suppression of tumor cell proliferation and improved survival in EL4 challenge independent of antitumor immunity. Denileukin diftitox (DD)-mediated depletion of regulatory T cells significantly slowed EL4 growth in vivo in a T-cell-dependent fashion. However, typical rapamycin inhibited T-cell activation and tumor infiltration in vivo and failed to boost DD treatment effects. Low-dose (LD) rapamycin (75 μg/kg) increased potentially beneficial CD44hiCD62L + CD8 + central memory T cells in EL4 challenge, but without clinical benefit. LD rapamycin significantly enhanced DD treatment efficacy, but DD plus LD rapamycin treatment effects were independent of antitumor immunity. Instead, rapamycin upregulated EL4 IL2 receptor in vitro and in vivo, facilitating direct DD tumor cell killing. LD rapamycin augmented DD efficacy against B16 melanoma and a human B-cell lymphoma, but not against human Jurkat T-cell lymphoma or ID8agg ovarian cancer cells. Treatment effects correlated with IL2R expression, but mechanisms in some tumors were not fully defined. Overall, our data define a distinct, biphasic mechanisms of action of mTOR inhibition at doses that are clinically exploitable, including in T-cell lymphomas. Cancer Res; 77(2); 520-31. ©2016 AACR. ©2016 American Association for Cancer Research.

EHR Big Data Deep Phenotyping

PubMed Central

Lenert, L.; Lopez-Campos, G.

2014-01-01

Summary Objectives Given the quickening speed of discovery of variant disease drivers from combined patient genotype and phenotype data, the objective is to provide methodology using big data technology to support the definition of deep phenotypes in medical records. Methods As the vast stores of genomic information increase with next generation sequencing, the importance of deep phenotyping increases. The growth of genomic data and adoption of Electronic Health Records (EHR) in medicine provides a unique opportunity to integrate phenotype and genotype data into medical records. The method by which collections of clinical findings and other health related data are leveraged to form meaningful phenotypes is an active area of research. Longitudinal data stored in EHRs provide a wealth of information that can be used to construct phenotypes of patients. We focus on a practical problem around data integration for deep phenotype identification within EHR data. The use of big data approaches are described that enable scalable markup of EHR events that can be used for semantic and temporal similarity analysis to support the identification of phenotype and genotype relationships. Conclusions Stead and colleagues’ 2005 concept of using light standards to increase the productivity of software systems by riding on the wave of hardware/processing power is described as a harbinger for designing future healthcare systems. The big data solution, using flexible markup, provides a route to improved utilization of processing power for organizing patient records in genotype and phenotype research. PMID:25123744

The Barrett's Gland in Phenotype Space.

PubMed

McDonald, Stuart A C; Graham, Trevor A; Lavery, Danielle L; Wright, Nicholas A; Jansen, Marnix

2015-01-01

Barrett's esophagus is characterized by the erosive replacement of esophageal squamous epithelium by a range of metaplastic glandular phenotypes. These glandular phenotypes likely change over time, and their distribution varies along the Barrett's segment. Although much recent work has addressed Barrett's esophagus from the genomic viewpoint-its genotype space- the fact that the phenotype of Barrett's esophagus is nonstatic points to conversion between phenotypes and suggests that Barrett's esophagus also exists in phenotype space . Here we explore this latter concept, investigating the scope of glandular phenotypes in Barrett's esophagus and how they exist in physical and temporal space as well as their evolution and their life history. We conclude that individual Barrett's glands are clonal units; because of this important fact, we propose that it is the Barrett's gland that is the unit of selection in phenotypic and indeed neoplastic progression. Transition between metaplastic phenotypes may be governed by neutral drift akin to niche turnover in normal and dysplastic niches. In consequence, the phenotype of Barrett's glands assumes considerable importance, and we make a strong plea for the integration of the Barrett's gland in both genotype and phenotype space in future work.

A rolling phenotype in Crohn's disease.

PubMed

Irwin, James; Ferguson, Emma; Simms, Lisa A; Hanigan, Katherine; Carbonnel, Franck; Radford-Smith, Graham

2017-01-01

The Montreal classification of disease behaviour in Crohn's disease describes progression of disease towards a stricturing and penetrating phenotype. In the present paper, we propose an alternative representation of the long-term course of Crohn's disease complications, the rolling phenotype. As is commonly observed in clinical practice, this definition allows progression to a more severe phenotype (stricturing, penetrating) but also, regression to a less severe behaviour (inflammatory, or remission) over time. All patients diagnosed with Crohn's Disease between 01/01/1994 and 01/03/2008, managed at a single centre and observed for a minimum of 5 years, had development and resolution of all complications recorded. A rolling phenotype was defined at each time point based on all observed complications in the three years prior to the time point. Phenotype was defined as B1, B2, B3, or B23 (penetrating and stenotic). The progression over time of the rolling phenotype was compared to that of the cumulative Montreal phenotype. 305 patients were observed a median of 10.0 (Intraquartile range 7.3-13.7) years. Longitudinal progression of rolling phenotype demonstrated a consistent proportion of patients with B1 (70%), B2 (20%), B3 (5%) and B23 (5%) phenotypes. These proportions were observed regardless of initial phenotype. In contrast, the cumulative Montreal phenotype progressed towards a more severe phenotype with time (B1 (39%), B2 (26%), B3(35%) at 10 years). A rolling phenotype provides an alternative view of the longitudinal burden of intra-abdominal complications in Crohn's disease. From this viewpoint, 70% of patients have durable freedom from complication over time (>3 years).

Involvement of α-, γ- and δ-Tocopherol Isomers from
Pumpkin (Cucurbita pepo L.) Seed Oil or Oil Mixtures in
the Biphasic DPPH˙ Disappearance Kinetics

PubMed Central

Broznić, Dalibor; Milin, Čedomila

2016-01-01

Summary The antioxidant activity of three types of pumpkin seed oil or oil mixtures (cold- -pressed, produced from roasted seed paste and salad) produced in the northern part of Croatia and the kinetics of their behaviour as free radical scavengers were investigated using DPPH˙. In addition, the involvement of oil tocopherol isomers (α-, γ- and δ-) in different steps of DPPH˙ disappearance and their impact on the rate of reaction were analysed. The kinetics of DPPH˙ disappearance is a two-step process. In the first step, rapid disappearance of DPPH˙ occurs during the first 11 min of the reaction, depending on the oil type, followed by a slower decline in the second step. To describe DPPH˙ disappearance kinetics, six mathematical models (mono- and biphasic) were tested. Our findings showed that γ- and δ-tocopherols affected DPPH˙ disappearance during the first step, and α-tocopherol in the second step of the reaction. Moreover, α-tocopherol demonstrated 30 times higher antioxidant activity than γ- and δ-tocopherols. The results indicated the biphasic double-exponential behaviour of DPPH˙ disappearance in oil samples, due to the complexity of reactions that involve different tocopherol isomers and proceed through different chemical pathways. PMID:27904410

Involvement of α-, γ- and δ-Tocopherol Isomers from
Pumpkin (Cucurbita pepo L.) Seed Oil or Oil Mixtures in
the Biphasic DPPH˙ Disappearance Kinetics.

PubMed

Broznić, Dalibor; Jurešić, Gordana Čanadi; Milin, Čedomila

2016-06-01

The antioxidant activity of three types of pumpkin seed oil or oil mixtures (cold- -pressed, produced from roasted seed paste and salad) produced in the northern part of Croatia and the kinetics of their behaviour as free radical scavengers were investigated using DPPH˙. In addition, the involvement of oil tocopherol isomers (α-, γ- and δ-) in different steps of DPPH˙ disappearance and their impact on the rate of reaction were analysed. The kinetics of DPPH˙ disappearance is a two-step process. In the first step, rapid disappearance of DPPH˙ occurs during the first 11 min of the reaction, depending on the oil type, followed by a slower decline in the second step. To describe DPPH˙ disappearance kinetics, six mathematical models (mono- and biphasic) were tested. Our findings showed that γ- and δ-tocopherols affected DPPH˙ disappearance during the first step, and α-tocopherol in the second step of the reaction. Moreover, α-tocopherol demonstrated 30 times higher antioxidant activity than γ- and δ-tocopherols. The results indicated the biphasic double-exponential behaviour of DPPH˙ disappearance in oil samples, due to the complexity of reactions that involve different tocopherol isomers and proceed through different chemical pathways.

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

PubMed

Lee, Jessica J Y; Gottlieb, Michael M; Lever, Jake; Jones, Steven J M; Blau, Nenad; van Karnebeek, Clara D M; Wasserman, Wyeth W

2018-05-01

Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze phenotypes. Such methods have allowed phenotypic data to be widely used in medical applications, from assisting clinical diagnoses to prioritizing genomic diagnoses. To channel the benefits of phenomics into the field of inborn errors of metabolism (IEM), we have recently launched IEMbase, an expert-curated knowledgebase of IEM and their disease-characterizing phenotypes. While our efforts with IEMbase have realized benefits, taking full advantage of phenomics requires a comprehensive curation of IEM phenotypes in core phenomics projects, which is dependent upon contributions from the IEM clinical and research community. Here, we assess the inclusion of IEM biochemical phenotypes in a core phenomics project, the Human Phenotype Ontology. We then demonstrate the utility of biochemical phenotypes using a text-based phenomics method to predict gene-disease relationships, showing that the prediction of IEM genes is significantly better using biochemical rather than clinical profiles. The findings herein provide a motivating goal for the IEM community to expand the computationally accessible descriptions of biochemical phenotypes associated with IEM in phenomics resources.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

PubMed Central

Köhler, Sebastian; Doelken, Sandra C.; Mungall, Christopher J.; Bauer, Sebastian; Firth, Helen V.; Bailleul-Forestier, Isabelle; Black, Graeme C. M.; Brown, Danielle L.; Brudno, Michael; Campbell, Jennifer; FitzPatrick, David R.; Eppig, Janan T.; Jackson, Andrew P.; Freson, Kathleen; Girdea, Marta; Helbig, Ingo; Hurst, Jane A.; Jähn, Johanna; Jackson, Laird G.; Kelly, Anne M.; Ledbetter, David H.; Mansour, Sahar; Martin, Christa L.; Moss, Celia; Mumford, Andrew; Ouwehand, Willem H.; Park, Soo-Mi; Riggs, Erin Rooney; Scott, Richard H.; Sisodiya, Sanjay; Vooren, Steven Van; Wapner, Ronald J.; Wilkie, Andrew O. M.; Wright, Caroline F.; Vulto-van Silfhout, Anneke T.; de Leeuw, Nicole; de Vries, Bert B. A.; Washingthon, Nicole L.; Smith, Cynthia L.; Westerfield, Monte; Schofield, Paul; Ruef, Barbara J.; Gkoutos, Georgios V.; Haendel, Melissa; Smedley, Damian; Lewis, Suzanna E.; Robinson, Peter N.

2014-01-01

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. PMID:24217912

Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication

PubMed Central

Garciarena, Carolina D.; Malik, Akif; Swietach, Pawel; Moreno, Alonso P.; Vaughan-Jones, Richard D.

2018-01-01

Most mammalian cells can intercommunicate via connexin-assembled, gap-junctional channels. To regulate signal transmission, connexin (Cx) channel permeability must respond dynamically to physiological and pathophysiological stimuli. One key stimulus is intracellular pH (pHi), which is modulated by a tissue’s metabolic and perfusion status. Our understanding of the molecular mechanism of H+ gating of Cx43 channels—the major isoform in the heart and brain—is incomplete. To interrogate the effects of acidic and alkaline pHi on Cx43 channels, we combined voltage-clamp electrophysiology with pHi imaging and photolytic H+ uncaging, performed over a range of pHi values. We demonstrate that Cx43 channels expressed in HeLa or N2a cell pairs are gated biphasically by pHi via a process that consists of activation by H+ ions at alkaline pHi and inhibition at more acidic pHi. For Cx43 channel–mediated solute/ion transmission, the ensemble of these effects produces a pHi optimum, near resting pHi. By using Cx43 mutants, we demonstrate that alkaline gating involves cysteine residues of the C terminus and is independent of motifs previously implicated in acidic gating. Thus, we present a molecular mechanism by which cytoplasmic acid–base chemistry fine tunes intercellular communication and establishes conditions for the optimal transmission of solutes and signals in tissues, such as the heart and brain.—Garciarena, C. D., Malik, A., Swietach, P., Moreno, A. P., Vaughan-Jones, R. D. Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication. PMID:29183963

Biphasic dose-dependent effect of lithium chloride on survival of human hormone-dependent breast cancer cells (MCF-7).

PubMed

Suganthi, Muralidharan; Sangeetha, Gopalakrishnan; Gayathri, Govindaraj; Ravi Sankar, Bhaskaran

2012-12-01

Lithium, the first element of Group I in the periodic system, is used to treat bipolar psychiatric disorders. Lithium chloride (LiCl) is a selective inhibitor of glycogen synthase kinase-3β (GSK-3β), a serine/threonine kinase that regulates many cellular processes, in addition to its role in the regulation of glycogen synthase. GSK-3β is emerged as a promising drug target for various neurological diseases, type-2 diabetes, cancer, and inflammation. Several works have demonstrated that lithium can either inhibit or stimulate growth of normal and cancer cells. Hence, the present study is focused to analyze the underlying mechanisms that dictate the biphasic oncogenic properties of LiCl. In the current study, we have investigated the dose-dependent effects of LiCl on human breast cancer cells (MCF-7) by assessing the consequences on cytotoxicity and protein expressions of signaling molecules crucial for the maintenance of cell survival. The results showed breast cancer cells respond in a diverse manner to LiCl, i.e., at lower concentrations (1, 5, and 10 mM), LiCl induces cell survival by inhibiting apoptosis through regulation of GSK-3β, caspase-2, Bax, and cleaved caspase-7 and by activating anti-apoptotic proteins (Akt, β-catenin, Bcl-2, and cyclin D1). In contrast, at high concentrations (50 and 100 mM), it induces apoptosis by reversing these effects. Moreover, LiCl also alters the sodium and potassium levels thereby altering the membrane potential of MCF-7 cells. Thus it is inferred that LiCl exerts a dose-dependent biphasic effect on breast cancer cells (MCF-7) by altering the apoptotic/anti-apoptotic balance.

Leaf-Cutter Ant Fungus Gardens Are Biphasic Mixed Microbial Bioreactors That Convert Plant Biomass to Polyols with Biotechnological Applications

PubMed Central

Somera, Alexandre F.; Lima, Adriel M.; dos Santos-Neto, Álvaro J.; Lanças, Fernando M.

2015-01-01

Leaf-cutter ants use plant matter to culture the obligate mutualistic basidiomycete Leucoagaricus gongylophorus. This fungus mediates ant nutrition on plant resources. Furthermore, other microbes living in the fungus garden might also contribute to plant digestion. The fungus garden comprises a young sector with recently incorporated leaf fragments and an old sector with partially digested plant matter. Here, we show that the young and old sectors of the grass-cutter Atta bisphaerica fungus garden operate as a biphasic solid-state mixed fermenting system. An initial plant digestion phase occurred in the young sector in the fungus garden periphery, with prevailing hemicellulose and starch degradation into arabinose, mannose, xylose, and glucose. These products support fast microbial growth but were mostly converted into four polyols. Three polyols, mannitol, arabitol, and inositol, were secreted by L. gongylophorus, and a fourth polyol, sorbitol, was likely secreted by another, unidentified, microbe. A second plant digestion phase occurred in the old sector, located in the fungus garden core, comprising stocks of microbial biomass growing slowly on monosaccharides and polyols. This biphasic operation was efficient in mediating symbiotic nutrition on plant matter: the microbes, accounting for 4% of the fungus garden biomass, converted plant matter biomass into monosaccharides and polyols, which were completely consumed by the resident ants and microbes. However, when consumption was inhibited through laboratory manipulation, most of the plant polysaccharides were degraded, products rapidly accumulated, and yields could be preferentially switched between polyols and monosaccharides. This feature might be useful in biotechnology. PMID:25911490

Structural and mechanical characterization of boron doped biphasic calcium phosphate produced by wet chemical method and subsequent thermal treatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albayrak, Onder, E-mail: albayrakonder@mersin.edu.tr

In the current study, boron doped biphasic calcium phosphate bioceramics consisting of a mixture of boron doped hydroxyapatite (BHA) and beta tricalcium phosphate (β-TCP) of varying BHA/β-TCP ratios were obtained after sintering stage. The effects of varying boron contents and different sintering temperatures on the BHA/β-TCP ratios and on the sinterability of the final products were investigated. Particle sizes and morphologies of the obtained precipitates were determined using SEM. XRD and FTIR investigation were conducted to detect the boron formation in the structure of HA and quantitative analysis was performed to determine the BHA/β-TCP ratio before and after sintering stage.more » In order to determine the sinterability of the obtained powders, pellets were prepared and sintered; the rates of densification were calculated and obtained results were correlated by SEM images. Also Vickers microhardness values of the sintered samples were determined. The experimental results verified that boron doped hydroxyapatite powders were obtained after sintering stage and the structure consists of a mixture of BHA and β-TCP. As the boron content used in the precipitation stage increases, β-TCP content of the BHA/β-TCP ratio increases but sinterability, density and microhardness deteriorate. As the sintering temperature increases, β-TCP content, density and microhardness of the samples increase and sinterability improves. - Highlights: • This is the first paper about boron doped biphasic calcium phosphate bioceramics. • Boron doping affects the structural and mechanical properties. • BHA/β-TCP ratio can be adjustable with boron content and sintering temperature.« less

Leaf-cutter ant fungus gardens are biphasic mixed microbial bioreactors that convert plant biomass to polyols with biotechnological applications.

PubMed

Somera, Alexandre F; Lima, Adriel M; Dos Santos-Neto, Álvaro J; Lanças, Fernando M; Bacci, Maurício

2015-07-01

Leaf-cutter ants use plant matter to culture the obligate mutualistic basidiomycete Leucoagaricus gongylophorus. This fungus mediates ant nutrition on plant resources. Furthermore, other microbes living in the fungus garden might also contribute to plant digestion. The fungus garden comprises a young sector with recently incorporated leaf fragments and an old sector with partially digested plant matter. Here, we show that the young and old sectors of the grass-cutter Atta bisphaerica fungus garden operate as a biphasic solid-state mixed fermenting system. An initial plant digestion phase occurred in the young sector in the fungus garden periphery, with prevailing hemicellulose and starch degradation into arabinose, mannose, xylose, and glucose. These products support fast microbial growth but were mostly converted into four polyols. Three polyols, mannitol, arabitol, and inositol, were secreted by L. gongylophorus, and a fourth polyol, sorbitol, was likely secreted by another, unidentified, microbe. A second plant digestion phase occurred in the old sector, located in the fungus garden core, comprising stocks of microbial biomass growing slowly on monosaccharides and polyols. This biphasic operation was efficient in mediating symbiotic nutrition on plant matter: the microbes, accounting for 4% of the fungus garden biomass, converted plant matter biomass into monosaccharides and polyols, which were completely consumed by the resident ants and microbes. However, when consumption was inhibited through laboratory manipulation, most of the plant polysaccharides were degraded, products rapidly accumulated, and yields could be preferentially switched between polyols and monosaccharides. This feature might be useful in biotechnology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Towards improving phenotype representation in OWL

PubMed Central

2012-01-01

Background Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. Methods We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. Results In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. Conclusion Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions. PMID:23046625

Childhood asthma-predictive phenotype.

PubMed

Guilbert, Theresa W; Mauger, David T; Lemanske, Robert F

2014-01-01

Wheezing is a fairly common symptom in early childhood, but only some of these toddlers will experience continued wheezing symptoms in later childhood. The definition of the asthma-predictive phenotype is in children with frequent, recurrent wheezing in early life who have risk factors associated with the continuation of asthma symptoms in later life. Several asthma-predictive phenotypes were developed retrospectively based on large, longitudinal cohort studies; however, it can be difficult to differentiate these phenotypes clinically as the expression of symptoms, and risk factors can change with time. Genetic, environmental, developmental, and host factors and their interactions may contribute to the development, severity, and persistence of the asthma phenotype over time. Key characteristics that distinguish the childhood asthma-predictive phenotype include the following: male sex; a history of wheezing, with lower respiratory tract infections; history of parental asthma; history of atopic dermatitis; eosinophilia; early sensitization to food or aeroallergens; or lower lung function in early life. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Serial computed tomography and magnetic resonance imaging findings of biphasic acute hemorrhagic leukoencephalitis localized to the brain stem and cerebellum.

PubMed

Lee, Nyoung Keun; Lee, Byung Hoon; Hwang, Yoon Joon; Kim, Su Young; Lee, Ji Young; Joo, Mee

2011-04-01

Acute hemorrhagic leukoencephalitis (AHL) is a rare and usually fatal disease characterized by an acute onset of neurological abnormalities. We describe the case of a 37-year-old man with biphasic AHL with a focus on the rare involvement of the brain stem and cerebellum. Initial computed tomography (CT) and magnetic resonance imaging revealed two hemorrhagic foci in the left middle cerebellar peduncle. After 15 days multifocal hematomas in the contralateral cerebellar hemisphere were imaged using CT. The pathological diagnosis was AHL. Following high-dose steroid treatment, the patient recovered with minor neurological sequelae.

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology.

PubMed

Masino, Aaron J; Dechene, Elizabeth T; Dulik, Matthew C; Wilkens, Alisha; Spinner, Nancy B; Krantz, Ian D; Pennington, Jeffrey W; Robinson, Peter N; White, Peter S

2014-07-21

Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype. To assist interpretation, we implemented an algorithm that ranks a given set of genes relative to patient phenotype. The algorithm orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing the patient. Phenotypic descriptor terms are taken from the Human Phenotype Ontology (HPO) and semantic similarity is derived from each term's information content. Model validation was performed via simulation and with clinical data. We simulated 33 Mendelian diseases with 100 patients per disease. We modeled clinical conditions by adding noise and imprecision, i.e. phenotypic terms unrelated to the disease and terms less specific than the actual disease terms. We ranked the causative gene against all 2488 HPO annotated genes. The median causative gene rank was 1 for the optimal and noise cases, 12 for the imprecision case, and 60 for the imprecision with noise case. Additionally, we examined a clinical cohort of subjects with hearing impairment. The disease gene median rank was 22. However, when also considering the patient's exome data and filtering non-exomic and common variants, the median rank improved to 3. Semantic similarity can rank a causative gene highly within a gene list relative to patient phenotype characteristics, provided that imprecision is mitigated. The clinical case results suggest that phenotype rank combined with variant analysis provides significant improvement over the individual approaches. We expect that this combined prioritization approach may increase accuracy and decrease effort for

Aqueous biphasic systems in the separation of food colorants.

PubMed

Santos, João H P M; Capela, Emanuel V; Boal-Palheiros, Isabel; Coutinho, João A P; Freire, Mara G; Ventura, Sónia P M

2018-04-25

Aqueous biphasic systems (ABS) composed of polypropylene glycol and carbohydrates, two benign substances are proposed to separate two food colorants (E122 and E133). ABS are promising extractive platforms, particularly for biomolecules, due to their aqueous and mild nature (pH and temperature), reduced environmental impact and processing costs. Another major aspect considered, particularly useful in downstream processing, is the "tuning" ability for the extraction and purification of these systems by a proper choice of the ABS components. In this work, our intention is to show the concept of ABS as an alternative and volatile organic solvent-free tool to separate two different biomolecules in a simple way, so simple that teachers can effectively adopt it in their classes to explain the concept of bioseparation processes. Informative documents and general information about the preparation of binodal curves and their use in the partition of biomolecules is available in this work to be used by teachers in their classes. In this sense, the students use different carbohydrates to build ABS, then study the partition of two food color dyes (synthetic origin), thus evaluating their ability on the separation of both food colorants. Through these experiments, the students get acquainted with ABS, learn how to determine solubility curves and perform extraction procedures using colorant food additives, that can also be applied in the extraction of various (bio)molecules. © 2018 by The International Union of Biochemistry and Molecular Biology, 2018. © 2018 The International Union of Biochemistry and Molecular Biology.

Aerosol Particle Interfacial Thermodynamics and Phase Partitioning Measurements Using Biphasic Microfluidics

NASA Astrophysics Data System (ADS)

Dutcher, Cari; Metcalf, Andrew

2015-03-01

Secondary organic aerosol particles are nearly ubiquitous in the atmosphere and yet there remain large uncertainties in their formation processes and ambient properties. These particles are complex microenvironments, which can contain multiple interfaces due to internal aqueous-organic phase partitioning and to the external liquid-vapor surface. Interfacial properties affect the ambient aerosol morphology, or internal structure of the particle, which in turn can affect the way a particle interacts with an environment of condensable clusters and organic vapors. To improve our ability to accurately predict ambient aerosol morphology, we must improve our knowledge of aerosol interfaces and their interactions with the ambient environment. Unfortunately, many techniques employed to measure interfacial properties do so in bulk solutions or in the presence of a ternary (e.g. solid) phase. In this talk, a novel method using biphasic microscale flows will be introduced for generating, trapping, and perturbing complex interfaces at atmospherically relevant conditions. These microfluidic experiments utilize high-speed imaging to monitor interfacial phenomena at the microscale and are performed with phase contrast and fluorescence microscopy on a temperature-controlled inverted microscope stage. From these experiments, interfacial thermodynamic properties such as surface or interfacial tension, rheological properties such as interfacial moduli, and kinetic properties such as mass transfer coefficients can be measured or inferred.

Seizure characteristics of epilepsy in childhood after acute encephalopathy with biphasic seizures and late reduced diffusion.

PubMed

Ito, Yuji; Natsume, Jun; Kidokoro, Hiroyuki; Ishihara, Naoko; Azuma, Yoshiteru; Tsuji, Takeshi; Okumura, Akihisa; Kubota, Tetsuo; Ando, Naoki; Saitoh, Shinji; Miura, Kiyokuni; Negoro, Tamiko; Watanabe, Kazuyoshi; Kojima, Seiji

2015-08-01

The aim of this study was to clarify characteristics of post-encephalopathic epilepsy (PEE) in children after acute encephalopathy with biphasic seizures and late reduced diffusion (AESD), paying particular attention to precise diagnosis of seizure types. Among 262 children with acute encephalopathy/encephalitis registered in a database of the Tokai Pediatric Neurology Society between 2005 and 2012, 44 were diagnosed with AESD according to the clinical course and magnetic resonance imaging (MRI) findings and were included in this study. Medical records were reviewed to investigate clinical data, MRI findings, neurologic outcomes, and presence or absence of PEE. Seizure types of PEE were determined by both clinical observation by pediatric neurologists and ictal video-electroencephalography (EEG) recordings. Of the 44 patients after AESD, 10 (23%) had PEE. The period between the onset of encephalopathy and PEE ranged from 2 to 39 months (median 8.5 months). Cognitive impairment was more severe in patients with PEE than in those without. Biphasic seizures and status epilepticus during the acute phase of encephalopathy did not influence the risk of PEE. The most common seizure type of PEE on clinical observation was focal seizures (n = 5), followed by epileptic spasms (n = 4), myoclonic seizures (n = 3), and tonic seizures (n = 2). In six patients with PEE, seizures were induced by sudden unexpected sounds. Seizure types confirmed by ictal video-EEG recordings were epileptic spasms and focal seizures with frontal onset, and all focal seizures were startle seizures induced by sudden acoustic stimulation. Intractable daily seizures remain in six patients with PEE. We demonstrate seizure characteristics of PEE in children after AESD. Epileptic spasms and startle focal seizures are common seizure types. The specific seizure types may be determined by the pattern of diffuse subcortical white matter injury in AESD and age-dependent reorganization of the brain

Neurobehavioral phenotype in Prader-Willi syndrome.

PubMed

Whittington, Joyce; Holland, Anthony

2010-11-15

The focus of this article is on the lifetime development of people with Prader-Willi syndrome (PWS) and specifically on the neurobehavioral phenotype. We consider studies of this aspect of the phenotype (the "behavioral phenotype" of the syndrome) that have confirmed that there are specific behaviors and psychiatric disorders, the propensities to which are increased in those with PWS, and cannot be accounted for by other variables such as IQ or adaptive behavior. Beginning with a description of what is observed in people with PWS, we review the evolving PWS phenotype and consider how some aspects of the phenotype might be best explained, and how this complex phenotype may relate to the equally complex genotype. We then consider in more detail some of the neurobehavioral aspects of the phenotype listed above that raise the greatest management problems for parents and carers. © 2010 Wiley-Liss, Inc.

Biphasic targeting and cleavage furrow ingression directed by the tail of a myosin II

PubMed Central

Fang, Xiaodong; Luo, Jianying; Nishihama, Ryuichi; Wloka, Carsten; Dravis, Christopher; Travaglia, Mirko; Iwase, Masayuki; Vallen, Elizabeth A.

2010-01-01

Cytokinesis in animal and fungal cells utilizes a contractile actomyosin ring (AMR). However, how myosin II is targeted to the division site and promotes AMR assembly, and how the AMR coordinates with membrane trafficking during cytokinesis, remains poorly understood. Here we show that Myo1 is a two-headed myosin II in Saccharomyces cerevisiae, and that Myo1 localizes to the division site via two distinct targeting signals in its tail that act sequentially during the cell cycle. Before cytokinesis, Myo1 localization depends on the septin-binding protein Bni5. During cytokinesis, Myo1 localization depends on the IQGAP Iqg1. We also show that the Myo1 tail is sufficient for promoting the assembly of a “headless” AMR, which guides membrane deposition and extracellular matrix remodeling at the division site. Our study establishes a biphasic targeting mechanism for myosin II and highlights an underappreciated role of the AMR in cytokinesis beyond force generation. PMID:21173112

Integration process of fermentation and liquid biphasic flotation for lipase separation from Burkholderia cepacia.

PubMed

Sankaran, Revathy; Show, Pau Loke; Lee, Sze Ying; Yap, Yee Jiun; Ling, Tau Chuan

2018-02-01

Liquid Biphasic Flotation (LBF) is an advanced recovery method that has been effectively applied for biomolecules extraction. The objective of this investigation is to incorporate the fermentation and extraction process of lipase from Burkholderia cepacia using flotation system. Initial study was conducted to compare the performance of bacteria growth and lipase production using flotation and shaker system. From the results obtained, bacteria shows quicker growth and high lipase yield via flotation system. Integration process for lipase separation was investigated and the result showed high efficiency reaching 92.29% and yield of 95.73%. Upscaling of the flotation system exhibited consistent result with the lab-scale which are 89.53% efficiency and 93.82% yield. The combination of upstream and downstream processes in a single system enables the acceleration of product formation, improves the product yield and facilitates downstream processing. This integration system demonstrated its potential for biomolecules fermentation and separation that possibly open new opportunities for industrial production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Amplification of a bi-phase shift-key modulated signal by a mm-wave FEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prosnitz, D.; Scharlemann, E.T.; Sheaffer, M.K.

Bi-phase shift keying (BPSK) is a modulation scheme used in communications and radar in which the phase of a transmitted rf signal is switched in a coded pattern between discrete values differing by {pi} radians. The transmitted information rate (in communications) or resolution (in imaging radar) depends on the rate at which the transmitted signal can be modulated. Modulation rates of greater than 1 GHz are generally desired. Although the instantaneous gain bandwidth of a mm-wave FEL amplifier can be much greater than 10 GHz, slippage may limit the BPSK modulation rate that can be amplified. Qualitative slippage arguments wouldmore » limit the modulation rate to relatively low values; nevertheless, simulations with a time-dependent FEL code (GINGER) indicate that rates of 2 GHz or more are amplified without much loss in modulation integrity. In this paper we describe the effects of slippage in the simulations and discuss the limits of simple arguments.« less

Quantifying Cartilage Contact Modulus, Tension Modulus, and Permeability With Hertzian Biphasic Creep

PubMed Central

Moore, A. C.; DeLucca, J. F.; Elliott, D. M.; Burris, D. L.

2016-01-01

This paper describes a new method, based on a recent analytical model (Hertzian biphasic theory (HBT)), to simultaneously quantify cartilage contact modulus, tension modulus, and permeability. Standard Hertzian creep measurements were performed on 13 osteochondral samples from three mature bovine stifles. Each creep dataset was fit for material properties using HBT. A subset of the dataset (N = 4) was also fit using Oyen's method and FEBio, an open-source finite element package designed for soft tissue mechanics. The HBT method demonstrated statistically significant sensitivity to differences between cartilage from the tibial plateau and cartilage from the femoral condyle. Based on the four samples used for comparison, no statistically significant differences were detected between properties from the HBT and FEBio methods. While the finite element method is considered the gold standard for analyzing this type of contact, the expertise and time required to setup and solve can be prohibitive, especially for large datasets. The HBT method agreed quantitatively with FEBio but also offers ease of use by nonexperts, rapid solutions, and exceptional fit quality (R2 = 0.999 ± 0.001, N = 13). PMID:27536012

Emerging molecular phenotypes of asthma

PubMed Central

Ray, Anuradha; Oriss, Timothy B.

2014-01-01

Although asthma has long been considered a heterogeneous disease, attempts to define subgroups of asthma have been limited. In recent years, both clinical and statistical approaches have been utilized to better merge clinical characteristics, biology, and genetics. These combined characteristics have been used to define phenotypes of asthma, the observable characteristics of a patient determined by the interaction of genes and environment. Identification of consistent clinical phenotypes has now been reported across studies. Now the addition of various 'omics and identification of specific molecular pathways have moved the concept of clinical phenotypes toward the concept of molecular phenotypes. The importance of these molecular phenotypes is being confirmed through the integration of molecularly targeted biological therapies. Thus the global term asthma is poised to become obsolete, being replaced by terms that more specifically identify the pathology associated with the disease. PMID:25326577

Synthesis of a Ni2P/Ni12P5 bi-phase nanocomposite for the efficient catalytic reduction of 4-nitrophenol based on the unique n-n heterojunction effects.

PubMed

Tian, Feng-Yu; Hou, Dongfang; Zhang, Wei-Min; Qiao, Xiu-Qing; Li, Dong-Sheng

2017-10-24

A novel heterostructure catalyst of Ni 2 P/Ni 12 P 5 has been fabricated through a simple solvothermal method by modifying the molar ratio of the initial raw materials. The products are characterized by X-ray powder diffraction (XRD), field emission scanning electron microscopy (FE-SEM), high-resolution transmission electron microscopy (HRTEM), nitrogen adsorption and X-ray photoelectron spectroscopy (XPS). It is found that the two phases, Ni 2 P and Ni 12 P 5 , are interlaced with one another in the as-formed nanocomposite, resulting in more interfaces. The bi-phase catalyst exhibits a markedly enhanced catalytic activity in the reduction of 4-nitrophenol, as compared to that of single Ni 2 P or Ni 12 P 5 . The enhanced catalytic activity can be attributed to the unique n-n series effects, which result in the increased ease of electron transfer over the Ni 2 P/Ni 12 P 5 bi-phase catalyst.

The influence of size, clearance, cartilage properties, thickness and hemiarthroplasty on the contact mechanics of the hip joint with biphasic layers.

PubMed

Li, Junyan; Stewart, Todd D; Jin, Zhongmin; Wilcox, Ruth K; Fisher, John

2013-06-21

Computational models of the natural hip joint are needed to examine and optimise tissue sparing interventions where the natural cartilage remains part of the bearing surfaces. Although the importance of interstitial fluid pressurisation in the performance of cartilage has long been recognized, few studies have investigated the time dependent interstitial fluid pressurisation in a three dimensional natural hip joint model. The primary aim of this study was to develop a finite element model of the natural hip incorporating the biphasic cartilage layers that was capable of simulating the joint response over a prolonged physiological loading period. An initial set of sensitivity studies were also undertaken to investigate the influence of hip size, clearance, cartilage properties, thickness and hemiarthroplasty on the contact mechanics of the joint. The contact stress, contact area, fluid pressure and fluid support ratio were calculated and cross-compared between models with different parameters to evaluate their influence. It was found that the model predictions for the period soon after loading were sensitive to the hip size, clearance, cartilage aggregate modulus, thickness and hemiarthroplasty, while the time dependent behaviour over 3000s was influenced by the hip clearance and cartilage aggregate modulus, permeability, thickness and hemiarthroplasty. The modelling methods developed in this study provide a basic platform for biphasic simulation of the whole hip joint onto which more sophisticated material models or other input parameters could be added in the future. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

The influence of size, clearance, cartilage properties, thickness and hemiarthroplasty on the contact mechanics of the hip joint with biphasic layers☆

PubMed Central

Li, Junyan; Stewart, Todd D.; Jin, Zhongmin; Wilcox, Ruth K.; Fisher, John

2013-01-01

Computational models of the natural hip joint are needed to examine and optimise tissue sparing interventions where the natural cartilage remains part of the bearing surfaces. Although the importance of interstitial fluid pressurisation in the performance of cartilage has long been recognized, few studies have investigated the time dependent interstitial fluid pressurisation in a three dimensional natural hip joint model. The primary aim of this study was to develop a finite element model of the natural hip incorporating the biphasic cartilage layers that was capable of simulating the joint response over a prolonged physiological loading period. An initial set of sensitivity studies were also undertaken to investigate the influence of hip size, clearance, cartilage properties, thickness and hemiarthroplasty on the contact mechanics of the joint. The contact stress, contact area, fluid pressure and fluid support ratio were calculated and cross-compared between models with different parameters to evaluate their influence. It was found that the model predictions for the period soon after loading were sensitive to the hip size, clearance, cartilage aggregate modulus, thickness and hemiarthroplasty, while the time dependent behaviour over 3000 s was influenced by the hip clearance and cartilage aggregate modulus, permeability, thickness and hemiarthroplasty. The modelling methods developed in this study provide a basic platform for biphasic simulation of the whole hip joint onto which more sophisticated material models or other input parameters could be added in the future. PMID:23664238

Coevolutionary dynamics of phenotypic diversity and contingent cooperation

PubMed Central

Wang, Long

2017-01-01

Phenotypic diversity is considered beneficial to the evolution of contingent cooperation, in which cooperators channel their help preferentially towards others of similar phenotypes. However, it remains largely unclear how phenotypic variation arises in the first place and thus leads to the construction of phenotypic complexity. Here we propose a mathematical model to study the coevolutionary dynamics of phenotypic diversity and contingent cooperation. Unlike previous models, our model does not assume any prescribed level of phenotypic diversity, but rather lets it be an evolvable trait. Each individual expresses one phenotype at a time and only the phenotypes expressed are visible to others. Moreover, individuals can differ in their potential of phenotypic variation, which is characterized by the number of distinct phenotypes they can randomly switch to. Each individual incurs a cost proportional to the number of potentially expressible phenotypes so as to retain phenotypic variation and expression. Our results show that phenotypic diversity coevolves with contingent cooperation under a wide range of conditions and that there exists an optimal level of phenotypic diversity best promoting contingent cooperation. It pays for contingent cooperators to elevate their potential of phenotypic variation, thereby increasing their opportunities of establishing cooperation via novel phenotypes, as these new phenotypes serve as secret tags that are difficult for defector to discover and chase after. We also find that evolved high levels of phenotypic diversity can occasionally collapse due to the invasion of defector mutants, suggesting that cooperation and phenotypic diversity can mutually reinforce each other. Thus, our results provide new insights into better understanding the coevolution of cooperation and phenotypic diversity. PMID:28141806

Highly efficient conversion of terpenoid biomass to jet-fuel range cycloalkanes in a biphasic tandem catalytic process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaokun; Li, Teng; Tang, Kan

2017-06-12

The demand for bio-jet fuels to reduce carbon emissions is increasing substantially in the aviation sector, while the scarcity of high-density jet fuel components limits the use of bio-jet fuels in high-performance aircrafts compared with conventional jet fuels. In this paper, we report a novel biphasic tandem catalytic process (biTCP) for synthesizing cycloalkanes from renewable terpenoid biomass, such as 1,8-cineole. Multistep tandem reactions, including C–O ring opening by hydrolysis, dehydration, and hydrogenation, were carried out in the “one-pot” biTCP. 1,8-Cineole was efficiently converted to p-menthane at high yields (>99%) in the biTCP under mild reaction conditions. Finally, the catalytic reactionmore » mechanism is discussed.« less

The digital revolution in phenotyping

PubMed Central

Oellrich, Anika; Collier, Nigel; Groza, Tudor; Rebholz-Schuhmann, Dietrich; Shah, Nigam; Bodenreider, Olivier; Boland, Mary Regina; Georgiev, Ivo; Liu, Hongfang; Livingston, Kevin; Luna, Augustin; Mallon, Ann-Marie; Manda, Prashanti; Robinson, Peter N.; Rustici, Gabriella; Simon, Michelle; Wang, Liqin; Winnenburg, Rainer; Dumontier, Michel

2016-01-01

Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support ‘bench to bedside’ efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions. To achieve this ambitious goal, a digital revolution is ongoing that enables the encoding of data in computer-readable formats and the data storage in specialized repositories, ready for integration, enabling translational research. While phenome research is an ongoing endeavor, the true potential hidden in the currently available data still needs to be unlocked, offering exciting opportunities for the forthcoming years. Here, we provide insights into the state-of-the-art in digital phenotyping, by means of representing, acquiring and analyzing phenotype data. In addition, we provide visions of this field for future research work that could enable better applications of phenotype data. PMID:26420780

An overview of a cohort of South African patients with mitochondrial disorders.

PubMed

Smuts, Izelle; Louw, Roan; du Toit, Hanli; Klopper, Brenda; Mienie, Lodewyk J; van der Westhuizen, Francois H

2010-12-01

Mitochondrial disorders are frequently encountered inherited diseases characterized by unexplained multisystem involvement with a chronic, intermittent, or progressive nature. The objective of this paper is to describe the profile of patients with mitochondrial disorders in South Africa. Patients with possible mitochondrial disorders were accessed over 10 years. Analyses for respiratory chain and pyruvate dehydrogenase complex enzymes were performed on muscle. A diagnosis of a mitochondrial disorder was accepted only if an enzyme activity was deficient. Sixty-three patients were diagnosed with a mitochondrial disorder, including 40 African, 20 Caucasian, one mixed ancestry, and two Indian patients. The most important findings were the difference between African patients and other ethnicities: respiratory chain enzyme complexes CI+III or CII+III deficiencies were found in 52.5% of African patients, being of statistical significance (p value = 0.0061). They also presented predominantly with myopathy (p value = 0.0018); the male:female ratio was 1:1.2. Twenty-five (62.5%) African patients presented with varying degrees of a myopathy accompanied by a myopathic face, high palate, and scoliosis. Fourteen of these 25 also had ptosis and/or progressive external ophthalmoplegia. No patients of other ethnicities presented with this specific myopathic phenotype. Caucasian patients (16/20) presented predominantly with central nervous system involvement. Of the South African pediatric neurology patients, Africans are more likely to present with myopathy and CII+III deficiency, and Caucasian patients are more likely to present with encephalopathy or encephalomyopathy.

Homozygous deletion in MYL9 expands the molecular basis of megacystis-microcolon-intestinal hypoperistalsis syndrome.

PubMed

Moreno, Carolina Araujo; Sobreira, Nara; Pugh, Elizabeth; Zhang, Peng; Steel, Gary; Torres, Fábio Rossi; Cavalcanti, Denise Pontes

2018-05-01

Megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIHS) is a severe disease characterized by functional obstruction in the urinary and gastrointestinal tract. The molecular basis of this condition started to be defined recently, and the genes related to the syndrome (ACTG2-heterozygous variant in sporadic cases; and MYH11 (myosin heavy chain 11), LMOD1 (leiomodin 1) and MYLK (myosin light chain (MLC) kinase)-autosomal recessive inheritance), encode proteins involved in the smooth muscle contraction, supporting a myopathic basis for the disease. In the present article, we described a family with two affected siblings with MMIHS born to consanguineous parents and the molecular investigation performed to define the genetic etiology. Previous whole exome sequencing of the affected child and parents did not identify a candidate gene for the disease in this family, but now we present a reanalysis of the data that led to the identification of a homozygous deletion encompassing the last exon of MYL9 (myosin regulatory light chain 9) in the affected individual. MYL9 gene encodes a regulatory myosin MLC and the phosphorylation of this protein is a crucial step in the contraction process of smooth muscle cell. Despite the absence of human or animal phenotype related to MYL9, a cause-effect relationship between MYL9 and the MMIHS seems biologically plausible. The present study reveals a strong candidate gene for autosomal recessive forms of MMIHS, expanding the molecular basis of this disease and reinforces the myopathic basis of this condition.

A Study of BMP-2-Loaded Bipotential Electrolytic Complex around a Biphasic Calcium Phosphate-Derived (BCP) Scaffold for Repair of Large Segmental Bone Defect

PubMed Central

Paul, Kallyanashis; Padalhin, Andrew R.; Linh, Nguyen Thuy Ba; Kim, Boram; Sarkar, Swapan Kumar; Lee, Byong Taek

2016-01-01

A bipotential polyelectrolyte complex with biphasic calcium phosphate (BCP) powder dispersion provides an excellent option for protein adsorption and cell attachment and can facilitate enhanced bone regeneration. Application of the bipotential polyelectrolyte complex embedded in a spongy scaffold for faster healing of large segmental bone defects (LSBD) can be a promising endeavor in tissue engineering application. In the present study, a hollow scaffold suitable for segmental long bone replacement was fabricated by the sponge replica method applying the microwave sintering process. The fabricated scaffold was coated with calcium alginate at the shell surface, and genipin-crosslinked chitosan with biphasic calcium phosphate (BCP) dispersion was loaded at the central hollow core. The chitosan core was subsequently loaded with BMP-2. The electrolytic complex was characterized using SEM, porosity measurement, FTIR spectroscopy and BMP-2 release for 30 days. In vitro studies such as MTT, live/dead, cell proliferation and cell differentiation were performed. The scaffold was implanted into a 12 mm critical size defect of a rabbit radius. The efficacy of this complex is evaluated through an in vivo study, one and two month post implantation. BV/TV ratio for BMP-2 loaded sample was (42±1.76) higher compared with hollow BCP scaffold (32±0.225). PMID:27711142

Biosynthesis of tert-butyl (3R,5S)-6-chloro-3,5-dihydroxyhexanoate by carbonyl reductase from Rhodosporidium toruloides in mono and biphasic media.

PubMed

Liu, Zhi-Qiang; Wu, Lin; Zheng, Ling; Wang, Wen-Zhong; Zhang, Xiao-Jian; Jin, Li-Qun; Zheng, Yu-Guo

2018-02-01

tert-Butyl (3R,5S)-6-chloro-3,5-dihydroxyhexanoate ((3R,5S)-CDHH) is the key intermediate for synthesis of atorvastatin and rosuvastatin. Carbonyl reductase exhibits excellent activity toward tert-butyl (S)-6-chloro-5-hydroxy-3-oxohexanoate ((S)-CHOH) to synthesize (3R,5S)-CDHH. In this study, a whole cell biosynthesis reaction system to produce (3R,5S)-CDHH was constructed in organic solvents. A solution of 10% (v/v) Tween-80 was introduced to the reaction system as a co-solvent, which greatly enhanced biotransformation process, giving 98.9% yield, >99% ee and 1.8-fold higher space time yield in 5 h bioconversion of 1 M (S)-CHOH, compared with 98.7% yield and >99% ee in 9 h bioconversion of a purely aqueous reaction system. Moreover, a water-octanol biphasic reaction system was built and 20% of octanol was added as reservoir of substrate resulting in 98% yield, >99% ee and 4.08 mmol L -1  h -1  g -1 (wet cell weight) space time yield. This study paved a way for the whole cell biosynthesis of (3R,5S)-CDHH in mono and biphasic media. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biphasic dose responses in biology, toxicology and medicine: accounting for their generalizability and quantitative features.

PubMed

Calabrese, Edward J

2013-11-01

The most common quantitative feature of the hormetic-biphasic dose response is its modest stimulatory response which at maximum is only 30-60% greater than control values, an observation that is consistently independent of biological model, level of organization (i.e., cell, organ or individual), endpoint measured, chemical/physical agent studied, or mechanism. This quantitative feature suggests an underlying "upstream" mechanism common across biological systems, therefore basic and general. Hormetic dose response relationships represent an estimate of the peak performance of integrative biological processes that are allometrically based. Hormetic responses reflect both direct stimulatory or overcompensation responses to damage induced by relatively low doses of chemical or physical agents. The integration of the hormetic dose response within an allometric framework provides, for the first time, an explanation for both the generality and the quantitative features of the hormetic dose response. Copyright © 2013 Elsevier Ltd. All rights reserved.

A new biphasic osteoinductive calcium composite material with a negative Zeta potential for bone augmentation

PubMed Central

Smeets, Ralf; Kolk, Andreas; Gerressen, Marcus; Driemel, Oliver; Maciejewski, Oliver; Hermanns-Sachweh, Benita; Riediger, Dieter; Stein, Jamal M

2009-01-01

The aim of the present study was to analyze the osteogenic potential of a biphasic calcium composite material (BCC) with a negative surface charge for maxillary sinus floor augmentation. In a 61 year old patient, the BCC material was used in a bilateral sinus floor augmentation procedure. Six months postoperative, a bone sample was taken from the augmented regions before two titanium implants were inserted at each side. We analyzed bone neoformation by histology, bone density by computed tomography, and measured the activity of voltage-activated calcium currents of osteoblasts and surface charge effects. Control orthopantomograms were carried out five months after implant insertion. The BCC was biocompatible and replaced by new mineralized bone after being resorbed completely. The material demonstrated a negative surface charge (negative Zeta potential) which was found to be favorable for bone regeneration and osseointegration of dental implants. PMID:19523239

Genotype-phenotype associations in obesity dependent on definition of the obesity phenotype.

PubMed

Kring, Sofia Inez Iqbal; Larsen, Lesli Hingstrup; Holst, Claus; Toubro, Søren; Hansen, Torben; Astrup, Arne; Pedersen, Oluf; Sørensen, Thorkild I A

2008-01-01

In previous studies of associations of variants in the genes UCP2, UCP3, PPARG2, CART, GRL, MC4R, MKKS, SHP, GHRL, and MCHR1 with obesity, we have used a case-control approach with cases defined by a threshold for BMI. In the present study, we assess the association of seven abdominal, peripheral, and overall obesity phenotypes, which were analyzed quantitatively, and thirteen candidate gene polymorphisms in these ten genes in the same cohort. Obese Caucasian men (n = 234, BMI >or= 31.0 kg/m(2)) and a randomly sampled non-obese group (n = 323), originally identified at the draft board examinations, were re-examined at median ages of 47.0 or 49.0 years by anthropometry and DEXA scanning. Obesity phenotypes included BMI, fat body mass index, waist circumference, waist for given BMI, intra-abdominal adipose tissue, hip circumference and lower body fat mass (%). Using logistic regression models, we estimated the odds for defined genotypes (dominant or recessive genetic transmission) in relation to z-scores of the phenotypes. The minor (rare) allele for SHP 512G>C (rs6659176) was associated with increased hip circumference. The minor allele for UCP2 Ins45bp was associated with increased BMI, increased abdominal obesity, and increased hip circumference. The minor allele for UCP2 -866G>A (rs6593669) was associated with borderline increased fat body mass index. The minor allele for MCHR1 100213G>A (rs133072) was associated with reduced abdominal obesity. None of the other genotype-phenotype combinations showed appreciable associations. If replicated in independent studies with focus on the specific phenotypes, our explorative studies suggest significant associations between some candidate gene polymorphisms and distinct obesity phenotypes, predicting beneficial and detrimental effects, depending on compartments for body fat accumulation. Copyright 2008 S. Karger AG, Basel.

Long-term phenotypic evolution of bacteria.

PubMed

Plata, Germán; Henry, Christopher S; Vitkup, Dennis

2015-01-15

For many decades comparative analyses of protein sequences and structures have been used to investigate fundamental principles of molecular evolution. In contrast, relatively little is known about the long-term evolution of species' phenotypic and genetic properties. This represents an important gap in our understanding of evolution, as exactly these proprieties play key roles in natural selection and adaptation to diverse environments. Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. The observed average divergence trend, with approximately similar fractions of phenotypic properties changing per unit time, continues for billions of years. We experimentally confirm the predicted divergence trend using the phenotypic profiles of 40 diverse bacterial species across more than 60 growth conditions. Our analysis suggests that, at long evolutionary distances, gene essentiality is significantly more conserved than the ability to utilize different nutrients, while synthetic lethality is significantly less conserved. We also find that although a rapid phenotypic evolution is sometimes observed within the same species, a transition from high to low phenotypic similarity occurs primarily at the genus level.

Reading tarot cards.

PubMed

Edmunds, L Henry

2004-02-01

In some patients acute myocardial infarction and/or infarct expansion induces progressive left ventricular dilatation that eventually leads to heart failure and death. The five year mortality after onset of heart failure is 50%. Chronically stretched viable myocardium adjacent to or remote from an expanding infarction initiates a myopathic process that leads to progressive myocyte apoptosis and adverse postinfarction remodeling. Revascularization of stunned or hibernating myocardium restores contractility and benefits patients in heart failure; however, revascularization does not restore contractility to myopathic, remodeling myocardium. Contemporary operations for heart failure temporarily reduce ventricular wall stress, but fail to reverse stretch induced myocyte apoptosis, which may not be reversible. Logically, prevention of this myopathic process after acute infarction seems required to extend survival. It follows that surgeons should operate before adverse postinfarction left ventricular remodeling occurs, using new operations, rather than afterwards.

Investigation of the sensitising and cross-sensitising potential of textile dyes and beta-lactam antibiotics using a biphasic mice local lymph node assay.

PubMed

Ahuja, Varun; Schreiber, Clemens; Platzek, Thomas; Stahlmann, Ralf

2009-07-01

We used a modified protocol of the murine local lymph node assay (LLNA) to study the cross-sensitising potential of (a) textile dye disperse yellow 3 and its metabolite 2-amino-p-cresol, (b) two antibiotics, penicillin G and cefotiam. The test substances were applied in a biphasic manner, i.e. first on the shaved skin of the back followed by application on the dorsal side of the ears after 2 weeks. The end-points analysed included thickness and weight of an ear-biopsy, weight and cell number of the draining lymph node, and lymphocyte cell surface markers analysed by flow-cytometry. Disperse yellow 3 and its metabolite significantly altered the various end-points at both the tested concentrations (0.5 and 1%), thus demonstrating the sensitising potential of the two substances. The cross-sensitisation study showed significant modulation in the tested variables in the treated group as compared to the control, signifying cross-sensitisation potential of the two substances. Penicillin G and cefotiam showed significant changes in various end-points, pointing towards their sensitising potential. However, even at 50% concentration of the beta-lactams no significant change in any end-point indicating absence of cross-reactivity of the antibiotics was noticed. We conclude that a biphasic, modified protocol of the LLNA is a suitable approach to test for a cross-reactivity potential of two related compounds.

Biomechanical behaviour of a jawbone loaded with a prosthetic system supported by monophasic and biphasic implants.

PubMed

Inchingolo, F; Paracchini, L; DE Angelis, F; Cielo, A; Orefici, A; Spitaleri, D; Santacroce, L; Gheno, E; Palermo, A

2016-01-01

Modern implantology is based on the use of endosseous dental implants and on the study of osseointegration processes. The loss of marginal bone around a dental implant can be caused by many factors; the proper distribution of the masticatory loads is important and is closely dependent on the quality and quantity of bone tissue surrounding the implant. In fact, bone has the ability to adapt its microstructure, through processes of resorption and neoformation of new bone matrix, as a result of the mechanical stimuli that are generated during the chewing cycles. The purpose of this article is to redefine in a modern key and in light of current industrial and engineering technology, clinical and biomechanical concepts that characterize the monophasic implants, in order to assess proper use by evaluating the biomechanical differences with the biphasic implants.

Clustering high-dimensional mixed data to uncover sub-phenotypes: joint analysis of phenotypic and genotypic data.

PubMed

McParland, D; Phillips, C M; Brennan, L; Roche, H M; Gormley, I C

2017-12-10

The LIPGENE-SU.VI.MAX study, like many others, recorded high-dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the metabolic syndrome (MetS), a complex disorder that can lead to higher risk of type 2 diabetes and cardiovascular disease. Interest lies in clustering the LIPGENE-SU.VI.MAX participants into homogeneous groups or sub-phenotypes, by jointly considering their phenotypic and genotypic data, and in determining which variables are discriminatory. A novel latent variable model that elegantly accommodates high dimensional, mixed data is developed to cluster LIPGENE-SU.VI.MAX participants using a Bayesian finite mixture model. A computationally efficient variable selection algorithm is incorporated, estimation is via a Gibbs sampling algorithm and an approximate BIC-MCMC criterion is developed to select the optimal model. Two clusters or sub-phenotypes ('healthy' and 'at risk') are uncovered. A small subset of variables is deemed discriminatory, which notably includes phenotypic and genotypic variables, highlighting the need to jointly consider both factors. Further, 7 years after the LIPGENE-SU.VI.MAX data were collected, participants underwent further analysis to diagnose presence or absence of the MetS. The two uncovered sub-phenotypes strongly correspond to the 7-year follow-up disease classification, highlighting the role of phenotypic and genotypic factors in the MetS and emphasising the potential utility of the clustering approach in early screening. Additionally, the ability of the proposed approach to define the uncertainty in sub-phenotype membership at the participant level is synonymous with the concepts of precision medicine and nutrition. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Geographic atrophy phenotype identification by cluster analysis.

PubMed

Monés, Jordi; Biarnés, Marc

2018-03-01

To identify ocular phenotypes in patients with geographic atrophy secondary to age-related macular degeneration (GA) using a data-driven cluster analysis. This was a retrospective analysis of data from a prospective, natural history study of patients with GA who were followed for ≥6 months. Cluster analysis was used to identify subgroups within the population based on the presence of several phenotypic features: soft drusen, reticular pseudodrusen (RPD), primary foveal atrophy, increased fundus autofluorescence (FAF), greyish FAF appearance and subfoveal choroidal thickness (SFCT). A comparison of features between the subgroups was conducted, and a qualitative description of the new phenotypes was proposed. The atrophy growth rate between phenotypes was then compared. Data were analysed from 77 eyes of 77 patients with GA. Cluster analysis identified three groups: phenotype 1 was characterised by high soft drusen load, foveal atrophy and slow growth; phenotype 3 showed high RPD load, extrafoveal and greyish FAF appearance and thin SFCT; the characteristics of phenotype 2 were midway between phenotypes 1 and 3. Phenotypes differed in all measured features (p≤0.013), with decreases in the presence of soft drusen, foveal atrophy and SFCT seen from phenotypes 1 to 3 and corresponding increases in high RPD load, high FAF and greyish FAF appearance. Atrophy growth rate differed between phenotypes 1, 2 and 3 (0.63, 1.91 and 1.73 mm 2 /year, respectively, p=0.0005). Cluster analysis identified three distinct phenotypes in GA. One of them showed a particularly slow growth pattern. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

ABO blood group phenotype frequency estimation using molecular phenotyping in rhesus and cynomolgus macaques.

PubMed

Kanthaswamy, S; Ng, J; Oldt, R F; Valdivia, L; Houghton, P; Smith, D G

2017-11-01

A much larger sample (N = 2369) was used to evaluate a previously reported distribution of the A, AB and B blood group phenotypes in rhesus and cynomolgus macaques from six different regional populations. These samples, acquired from 15 different breeding and research facilities in the United States, were analyzed using a real-time quantitative polymerase chain reaction (qPCR) assay that targets single nucleotide polymorphisms (SNPs) responsible for the macaque A, B and AB phenotypes. The frequency distributions of blood group phenotypes of the two species differ significantly from each other and significant regional differentiation within the geographic ranges of each species was also observed. The B blood group phenotype was prevalent in rhesus macaques, especially those from India, while the frequencies of the A, B and AB phenotypes varied significantly among cynomolgus macaques from different geographic regions. The Mauritian cynomolgus macaques, despite having originated in Indonesia, showed significant (P ≪ .01) divergence from the Indonesian animals at the ABO blood group locus. Most Mauritian animals belonged to the B blood group while the Indonesian animals were mostly A. The close similarity in blood group frequency distributions between the Chinese rhesus and Indochinese cynomolgus macaques demonstrates that the introgression between these two species extends beyond the zone of intergradation in Indochina. This study underscores the importance of ABO blood group phenotyping of the domestic supply of macaques and their biospecimens. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Separation of no-carrier-added rhenium from bulk tantalum by the sodium malonate-PEG aqueous biphasic system.

PubMed

Dutta, Binita; Lahiri, Susanta; Tomar, B S

2014-02-01

The aqueous biphasic system (ABS) involving sodium malonate-polyethylene glycol (PEG) phases has been applied for the first time for separation of no-carrier-added (183)Re (T1/2=70 d) from α-particle irradiated bulk tantalum target. The various ABS conditions were applied for investigating the separation by varying pH, temperature, PEG-molecular weight, concentration of salt. The extraction pattern was hardly affected by change in pH and the molecular weight of PEG. One step separation of nca (183)Re from Ta was achieved at the optimal conditions of (i) 50% (w/w) PEG-4000-2 M sodium malonate, 40 °C and (ii) 50% (w/w) PEG-4000-3 M sodium malonate, room temperature (27 °C). © 2013 Published by Elsevier Ltd.

Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders.

PubMed

Andrews, Tallulah; Meader, Stephen; Vulto-van Silfhout, Anneke; Taylor, Avigail; Steinberg, Julia; Hehir-Kwa, Jayne; Pfundt, Rolph; de Leeuw, Nicole; de Vries, Bert B A; Webber, Caleb

2015-03-01

Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51%) groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i) this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii) that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects.

Delineation of C12orf65-related phenotypes: a genotype-phenotype relationship.

PubMed

Spiegel, Ronen; Mandel, Hanna; Saada, Ann; Lerer, Issy; Burger, Ayala; Shaag, Avraham; Shalev, Stavit A; Jabaly-Habib, Haneen; Goldsher, Dorit; Gomori, John M; Lossos, Alex; Elpeleg, Orly; Meiner, Vardiella

2014-08-01

C12orf65 participates in the process of mitochondrial translation and has been shown to be associated with a spectrum of phenotypes, including early onset optic atrophy, progressive encephalomyopathy, peripheral neuropathy, and spastic paraparesis.We used whole-genome homozygosity mapping as well as exome sequencing and targeted gene sequencing to identify novel C12orf65 disease-causing mutations in seven affected individuals originating from two consanguineous families. In four family members affected with childhood-onset optic atrophy accompanied by slowly progressive peripheral neuropathy and spastic paraparesis, we identified a homozygous frame shift mutation c.413_417 delAACAA, which predicts a truncated protein lacking the C-terminal portion. In the second family, we studied three affected individuals who presented with early onset optic atrophy, peripheral neuropathy, and spastic gait in addition to moderate intellectual disability. Muscle biopsy in two of the patients revealed decreased activities of the mitochondrial respiratory chain complexes I and IV. In these patients, we identified a homozygous splice mutation, g.21043 T>A (c.282+2 T>A) which leads to skipping of exon 2. Our study broadens the phenotypic spectrum of C12orf65 defects and highlights the triad of optic atrophy, axonal neuropathy and spastic paraparesis as its key clinical features. In addition, a clear genotype-phenotype correlation is anticipated in which deleterious mutations which disrupt the GGQ-containing domain in the first coding exon are expected to result in a more severe phenotype, whereas down-stream C-terminal mutations may result in a more favorable phenotype, typically lacking cognitive impairment.

Synthesis of bi-phase dispersible core-shell FeAu@ZnO magneto-opto-fluorescent nanoparticles

NASA Astrophysics Data System (ADS)

Li, Xue-Mei; Liu, Hong-Ling; Liu, Xiao; Fang, Ning; Wang, Xian-Hong; Wu, Jun-Hua

2015-11-01

Bi-phase dispersible core-shell FeAu@ZnO magneto-opto-fluorescent nanoparticles were synthesized by a modified nanoemulsion process using poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEO-PPO-PEO) as the surfactant. The morphology and crystal structure of the nanoparticles were studied by TEM/HRTEM and XRD. The nanoparticles manifest soft ferromagnetic and/or near superparamagnetic behavior with a small coercivity of ~19 Oe at room temperature. The corresponding magnetic hysteresis curves were elucidated by the modified Langevin equation. The FTIR study confirms the PEO-PPO-PEO molecules on the surface of the nanoparticles. The UV-vis and PL results reveal the well-behaved absorption bands including surface plasmon resonance and multiple visible fingerprint photoluminescent emissions of the nanoparticles dispersed in both hydrophilic and hydrophobic solvents. Moreover, the processes of solvent dispersion-collection of the nanoparticles were demonstrated for application readiness of such core-shell nanostructures.

Synthesis of bi-phase dispersible core-shell FeAu@ZnO magneto-opto-fluorescent nanoparticles

PubMed Central

Li, Xue-Mei; Liu, Hong-Ling; Liu, Xiao; Fang, Ning; Wang, Xian-Hong; Wu, Jun-Hua

2015-01-01

Bi-phase dispersible core-shell FeAu@ZnO magneto-opto-fluorescent nanoparticles were synthesized by a modified nanoemulsion process using poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEO-PPO-PEO) as the surfactant. The morphology and crystal structure of the nanoparticles were studied by TEM/HRTEM and XRD. The nanoparticles manifest soft ferromagnetic and/or near superparamagnetic behavior with a small coercivity of ~19 Oe at room temperature. The corresponding magnetic hysteresis curves were elucidated by the modified Langevin equation. The FTIR study confirms the PEO-PPO-PEO molecules on the surface of the nanoparticles. The UV-vis and PL results reveal the well-behaved absorption bands including surface plasmon resonance and multiple visible fingerprint photoluminescent emissions of the nanoparticles dispersed in both hydrophilic and hydrophobic solvents. Moreover, the processes of solvent dispersion-collection of the nanoparticles were demonstrated for application readiness of such core-shell nanostructures. PMID:26548369

Developmental mechanisms underlying variable, invariant and plastic phenotypes

PubMed Central

Abley, Katie; Locke, James C. W.; Leyser, H. M. Ottoline

2016-01-01

Background Discussions of phenotypic robustness often consider scenarios where invariant phenotypes are optimal and assume that developmental mechanisms have evolved to buffer the phenotypes of specific traits against stochastic and environmental perturbations. However, plastic plant phenotypes that vary between environments or variable phenotypes that vary stochastically within an environment may also be advantageous in some scenarios. Scope Here the conditions under which invariant, plastic and variable phenotypes of specific traits may confer a selective advantage in plants are examined. Drawing on work from microbes and multicellular organisms, the mechanisms that may give rise to each type of phenotype are discussed. Conclusion In contrast to the view of robustness as being the ability of a genotype to produce a single, invariant phenotype, changes in a phenotype in response to the environment, or phenotypic variability within an environment, may also be delivered consistently (i.e. robustly). Thus, for some plant traits, mechanisms have probably evolved to produce plasticity or variability in a reliable manner. PMID:27072645

Machine-learning phenotypic classification of bicuspid aortopathy.

PubMed

Wojnarski, Charles M; Roselli, Eric E; Idrees, Jay J; Zhu, Yuanjia; Carnes, Theresa A; Lowry, Ashley M; Collier, Patrick H; Griffin, Brian; Ehrlinger, John; Blackstone, Eugene H; Svensson, Lars G; Lytle, Bruce W

2018-02-01

Bicuspid aortic valves (BAV) are associated with incompletely characterized aortopathy. Our objectives were to identify distinct patterns of aortopathy using machine-learning methods and characterize their association with valve morphology and patient characteristics. We analyzed preoperative 3-dimensional computed tomography reconstructions for 656 patients with BAV undergoing ascending aorta surgery between January 2002 and January 2014. Unsupervised partitioning around medoids was used to cluster aortic dimensions. Group differences were identified using polytomous random forest analysis. Three distinct aneurysm phenotypes were identified: root (n = 83; 13%), with predominant dilatation at sinuses of Valsalva; ascending (n = 364; 55%), with supracoronary enlargement rarely extending past the brachiocephalic artery; and arch (n = 209; 32%), with aortic arch dilatation. The arch phenotype had the greatest association with right-noncoronary cusp fusion: 29%, versus 13% for ascending and 15% for root phenotypes (P < .0001). Severe valve regurgitation was most prevalent in root phenotype (57%), followed by ascending (34%) and arch phenotypes (25%; P < .0001). Aortic stenosis was most prevalent in arch phenotype (62%), followed by ascending (50%) and root phenotypes (28%; P < .0001). Patient age increased as the extent of aneurysm became more distal (root, 49 years; ascending, 53 years; arch, 57 years; P < .0001), and root phenotype was associated with greater male predominance compared with ascending and arch phenotypes (94%, 76%, and 70%, respectively; P < .0001). Phenotypes were visually recognizable with 94% accuracy. Three distinct phenotypes of bicuspid valve-associated aortopathy were identified using machine-learning methodology. Patient characteristics and valvular dysfunction vary by phenotype, suggesting that the location of aortic pathology may be related to the underlying pathophysiology of this disease. Copyright © 2017 The American

Biphasic activation of nuclear factor-κB and expression of p65 and c-Rel following traumatic neuronal injury.

PubMed

Zhang, Huasheng; Zhang, Dingding; Li, Hua; Yan, Huiying; Zhang, Zihuan; Zhou, Chenhui; Chen, Qiang; Ye, Zhennan; Hang, Chunhua

2018-06-01

The transcription factor nuclear factor-κB (NF-κB) has been shown to function as a key regulator of cell death or survival in neuronal cells. Previous studies indicate that the biphasic activation of NF-κB occurs following experimental neonatal hypoxia-ischemia and subarachnoid hemorrhage. However, the comprehensive understanding of NF-κB activity following traumatic brain injury (TBI) is incomplete. In the current study, an in vitro model of TBI was designed to investigate the NF-κB activity and expression of p65 and c-Rel subunits following traumatic neuronal injury. Primary cultured neurons were assigned to control and transected groups. NF-κB activity was detected by electrophoretic mobility shift assay. Western blotting and immunofluorescence were used to investigate the expression and distribution of p65 and c-Rel. Reverse transcription-quantitative polymerase chain reaction was performed to assess the downstream genes of NF-κB. Lactate dehydrogenase (LDH) quantification and trypan blue staining were used to estimate the neuronal injury. Double peaks of elevated NF-κB activity were observed at 1 and 24 h following transection. The expression levels of downstream genes exhibited similar changes. The protein levels of p65 also presented double peaks while c-Rel was elevated significantly in the late stage. The results of the trypan blue staining and LDH leakage assays indicated there was no sustained neuronal injury during the late peak of NF-κB activity. In conclusion, biphasic activation of NF-κB is induced following experimental traumatic neuronal injury. The elevation of p65 and c-Rel levels at different time periods suggests that within a single neuron, NF-κB may participate in different pathophysiological processes.

Acute encephalopathy with biphasic seizures and late reduced diffusion associated with staphylococcal toxic shock syndrome caused by burns.

PubMed

Yokochi, Takaoki; Sakanishi, Shinpei; Ishidou, Yuuki; Kawano, Go; Matsuishi, Toyojiro; Akita, Yukihiro; Obu, Keizo

2016-10-01

We report a case of acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) associated with toxic shock syndrome caused by burns. A one-year-old girl was admitted to our hospital for treatment of severe burns. On day 3, she exhibited a fever, generalized rash and multiple organ failure. She was diagnosed with toxic shock syndrome after burns. She had seizures with fever twice on the same day, followed by secondary seizures on day 8 and transient deterioration of the gross motor functions involved in sitting alone and rolling over. On day 9, MRI diffusion-weighted images showed bright tree appearance (BTA). We conclude that she developed AESD. Copyright © 2016 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

The Nature of Stable Insomnia Phenotypes

PubMed Central

Pillai, Vivek; Roth, Thomas; Drake, Christopher L.

2015-01-01

Study Objectives: We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Design: Longitudinal. Setting: Urban, community-based. Participants: Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). Interventions: None. Measurements and results: At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the “neither criterion” phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. Conclusions: By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With

High-throughput discovery of novel developmental phenotypes.

PubMed

Dickinson, Mary E; Flenniken, Ann M; Ji, Xiao; Teboul, Lydia; Wong, Michael D; White, Jacqueline K; Meehan, Terrence F; Weninger, Wolfgang J; Westerberg, Henrik; Adissu, Hibret; Baker, Candice N; Bower, Lynette; Brown, James M; Caddle, L Brianna; Chiani, Francesco; Clary, Dave; Cleak, James; Daly, Mark J; Denegre, James M; Doe, Brendan; Dolan, Mary E; Edie, Sarah M; Fuchs, Helmut; Gailus-Durner, Valerie; Galli, Antonella; Gambadoro, Alessia; Gallegos, Juan; Guo, Shiying; Horner, Neil R; Hsu, Chih-Wei; Johnson, Sara J; Kalaga, Sowmya; Keith, Lance C; Lanoue, Louise; Lawson, Thomas N; Lek, Monkol; Mark, Manuel; Marschall, Susan; Mason, Jeremy; McElwee, Melissa L; Newbigging, Susan; Nutter, Lauryl M J; Peterson, Kevin A; Ramirez-Solis, Ramiro; Rowland, Douglas J; Ryder, Edward; Samocha, Kaitlin E; Seavitt, John R; Selloum, Mohammed; Szoke-Kovacs, Zsombor; Tamura, Masaru; Trainor, Amanda G; Tudose, Ilinca; Wakana, Shigeharu; Warren, Jonathan; Wendling, Olivia; West, David B; Wong, Leeyean; Yoshiki, Atsushi; MacArthur, Daniel G; Tocchini-Valentini, Glauco P; Gao, Xiang; Flicek, Paul; Bradley, Allan; Skarnes, William C; Justice, Monica J; Parkinson, Helen E; Moore, Mark; Wells, Sara; Braun, Robert E; Svenson, Karen L; de Angelis, Martin Hrabe; Herault, Yann; Mohun, Tim; Mallon, Ann-Marie; Henkelman, R Mark; Brown, Steve D M; Adams, David J; Lloyd, K C Kent; McKerlie, Colin; Beaudet, Arthur L; Bućan, Maja; Murray, Stephen A

2016-09-22

Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.

High-throughput discovery of novel developmental phenotypes

PubMed Central

Dickinson, Mary E.; Flenniken, Ann M.; Ji, Xiao; Teboul, Lydia; Wong, Michael D.; White, Jacqueline K.; Meehan, Terrence F.; Weninger, Wolfgang J.; Westerberg, Henrik; Adissu, Hibret; Baker, Candice N.; Bower, Lynette; Brown, James M.; Caddle, L. Brianna; Chiani, Francesco; Clary, Dave; Cleak, James; Daly, Mark J.; Denegre, James M.; Doe, Brendan; Dolan, Mary E.; Edie, Sarah M.; Fuchs, Helmut; Gailus-Durner, Valerie; Galli, Antonella; Gambadoro, Alessia; Gallegos, Juan; Guo, Shiying; Horner, Neil R.; Hsu, Chih-wei; Johnson, Sara J.; Kalaga, Sowmya; Keith, Lance C.; Lanoue, Louise; Lawson, Thomas N.; Lek, Monkol; Mark, Manuel; Marschall, Susan; Mason, Jeremy; McElwee, Melissa L.; Newbigging, Susan; Nutter, Lauryl M.J.; Peterson, Kevin A.; Ramirez-Solis, Ramiro; Rowland, Douglas J.; Ryder, Edward; Samocha, Kaitlin E.; Seavitt, John R.; Selloum, Mohammed; Szoke-Kovacs, Zsombor; Tamura, Masaru; Trainor, Amanda G; Tudose, Ilinca; Wakana, Shigeharu; Warren, Jonathan; Wendling, Olivia; West, David B.; Wong, Leeyean; Yoshiki, Atsushi; MacArthur, Daniel G.; Tocchini-Valentini, Glauco P.; Gao, Xiang; Flicek, Paul; Bradley, Allan; Skarnes, William C.; Justice, Monica J.; Parkinson, Helen E.; Moore, Mark; Wells, Sara; Braun, Robert E.; Svenson, Karen L.; de Angelis, Martin Hrabe; Herault, Yann; Mohun, Tim; Mallon, Ann-Marie; Henkelman, R. Mark; Brown, Steve D.M.; Adams, David J.; Lloyd, K.C. Kent; McKerlie, Colin; Beaudet, Arthur L.; Bucan, Maja; Murray, Stephen A.

2016-01-01

Approximately one third of all mammalian genes are essential for life. Phenotypes resulting from mouse knockouts of these genes have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5000 knockout mouse lines, we have identified 410 lethal genes during the production of the first 1751 unique gene knockouts. Using a standardised phenotyping platform that incorporates high-resolution 3D imaging, we identified novel phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes identified in our screen, thus providing a novel dataset that facilitates prioritization and validation of mutations identified in clinical sequencing efforts. PMID:27626380

Temporal abstraction-based clinical phenotyping with Eureka!

PubMed

Post, Andrew R; Kurc, Tahsin; Willard, Richie; Rathod, Himanshu; Mansour, Michel; Pai, Akshatha Kalsanka; Torian, William M; Agravat, Sanjay; Sturm, Suzanne; Saltz, Joel H

2013-01-01

Temporal abstraction, a method for specifying and detecting temporal patterns in clinical databases, is very expressive and performs well, but it is difficult for clinical investigators and data analysts to understand. Such patterns are critical in phenotyping patients using their medical records in research and quality improvement. We have previously developed the Analytic Information Warehouse (AIW), which computes such phenotypes using temporal abstraction but requires software engineers to use. We have extended the AIW's web user interface, Eureka! Clinical Analytics, to support specifying phenotypes using an alternative model that we developed with clinical stakeholders. The software converts phenotypes from this model to that of temporal abstraction prior to data processing. The model can represent all phenotypes in a quality improvement project and a growing set of phenotypes in a multi-site research study. Phenotyping that is accessible to investigators and IT personnel may enable its broader adoption.

Laser engineered multilayer coating of biphasic calcium phosphate/titanium nanocomposite on metal substrates.

PubMed

Zhang, Martin Yi; Ye, Chang; Erasquin, Uriel Joseph; Huynh, Toan; Cai, Chengzhi; Cheng, Gary J

2011-02-01

In this work, laser coating of biphasic calcium phosphate/titanium (BCP/Ti) nanocomposite on Ti-6Al-4 V substrates was developed. A continuous wave neodymium-doped yttrium aluminium garnet (Nd:YAG) laser was used to form a robust multilayer of BCP/Ti nanocomposite starting from hydroxyapatite and titanium nanoparticles. In this process, low power coating is realized because of the strong laser-nanoparticle interaction and good sinterability of nanosized titanium. To guide the optimization of laser processing conditions for the coating process, a multiphysics model coupling electromagnetic module with heat transfer module was developed. This model was validated by laser coating experiments. Important features of the coated samples, including microstructures, chemical compositions, and interfacial bonding strength, were characterized. We found that a multilayer of BCP, consisting of 72% hydroxyapatite (HA) and 28% beta-tricalcium phosphate (β-TCP), and titanium nanocomposite was formed on Ti-6Al-4 V substrates. Significantly, the coating/substrate interfacial bonding strength was found to be two times higher than that of the commercial plasma sprayed coatings. Preliminary cell culture studies showed that the resultant BCP/Ti nanocomposite coating supported the adhesion and proliferation of osteoblast-like UMR-106 cells.

The nature of stable insomnia phenotypes.

PubMed

Pillai, Vivek; Roth, Thomas; Drake, Christopher L

2015-01-01

We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Longitudinal. Urban, community-based. Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). None. At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the 'neither criterion' phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With the exception of daytime sleepiness, few clinical differences are apparent across stable phenotypes. �

Phenex: ontological annotation of phenotypic diversity.

PubMed

Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

2010-05-05

Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

Geographically multifarious phenotypic divergence during speciation

PubMed Central

Gompert, Zachariah; Lucas, Lauren K; Nice, Chris C; Fordyce, James A; Alex Buerkle, C; Forister, Matthew L

2013-01-01

Speciation is an important evolutionary process that occurs when barriers to gene flow evolve between previously panmictic populations. Although individual barriers to gene flow have been studied extensively, we know relatively little regarding the number of barriers that isolate species or whether these barriers are polymorphic within species. Herein, we use a series of field and lab experiments to quantify phenotypic divergence and identify possible barriers to gene flow between the butterfly species Lycaeides idas and Lycaeides melissa. We found evidence that L. idas and L. melissa have diverged along multiple phenotypic axes. Specifically, we identified major phenotypic differences in female oviposition preference and diapause initiation, and more moderate divergence in mate preference. Multiple phenotypic differences might operate as barriers to gene flow, as shown by correlations between genetic distance and phenotypic divergence and patterns of phenotypic variation in admixed Lycaeides populations. Although some of these traits differed primarily between species (e.g., diapause initiation), several traits also varied among conspecific populations (e.g., male mate preference and oviposition preference). PMID:23532669

Novel Measurements of Aerosol Particle Interfaces Using Biphasic Microfluidics

NASA Astrophysics Data System (ADS)

Metcalf, A. R.; Dutcher, C. S.

2014-12-01

Secondary organic aerosol (SOA) particles are nearly ubiquitous in the atmosphere and yet there remains large uncertainties in their formation processes and ambient properties. These particles are complex microenvironments, which can contain multiple interfaces due to internal aqueous-organic phase partitioning and to the external liquid-vapor surface. These aerosol interfaces can profoundly affect the fate of condensable organic compounds emitted into the atmosphere by altering the way in which organic vapors interact with the ambient aerosol. Aerosol interfaces affect particle internal structure, species uptake, equilibrium partitioning, activation to cloud condensation or ice nuclei, and optical properties. For example, organic thin films can shield the core of the aerosol from the ambient environment, which may disrupt equilibrium partitioning and mass transfer. To improve our ability to accurately predict the fate of SOA in the atmosphere, we must improve our knowledge of aerosol interfaces and their interactions with the ambient environment. Few technologies exist to accurately probe aerosol interfaces at atmospherically-relevant conditions. In this talk, a novel method using biphasic microscale flows will be introduced for generating, trapping, and perturbing complex interfaces at atmospherically relevant conditions. These microfluidic experiments utilize high-speed imaging to monitor interfacial phenomena at the microscale and are performed with phase contrast and fluorescence microscopy on a temperature-controlled inverted microscope stage. From these experiments, interfacial thermodynamic properties such as surface tension, rheological properties such as interfacial moduli, and kinetic properties such as mass transfer coefficients can be measured or inferred. Chemical compositions of the liquid phases studied here span a range of viscosities and include electrolyte and water soluble organic acid species often observed in the atmosphere, such as mixtures

The differential view of genotype–phenotype relationships

PubMed Central

Orgogozo, Virginie; Morizot, Baptiste; Martin, Arnaud

2015-01-01

An integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. Here we re-emphasize the old standpoint that the genotype–phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. Here we show that the differential view of GP relationships is a useful explanatory framework in the context of pervasive pleiotropy, epistasis, and environmental effects. In such cases, it is relevant to view GP relationships as differences embedded into differences. Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes. PMID:26042146

Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature

PubMed Central

Ke, Junyuan; Ho, Joyce C; Ghosh, Joydeep; Wallace, Byron C

2018-01-01

Background Researchers are developing methods to automatically extract clinically relevant and useful patient characteristics from raw healthcare datasets. These characteristics, often capturing essential properties of patients with common medical conditions, are called computational phenotypes. Being generated by automated or semiautomated, data-driven methods, such potential phenotypes need to be validated as clinically meaningful (or not) before they are acceptable for use in decision making. Objective The objective of this study was to present Phenotype Instance Verification and Evaluation Tool (PIVET), a framework that uses co-occurrence analysis on an online corpus of publically available medical journal articles to build clinical relevance evidence sets for user-supplied phenotypes. PIVET adopts a conceptual framework similar to the pioneering prototype tool PheKnow-Cloud that was developed for the phenotype validation task. PIVET completely refactors each part of the PheKnow-Cloud pipeline to deliver vast improvements in speed without sacrificing the quality of the insights PheKnow-Cloud achieved. Methods PIVET leverages indexing in NoSQL databases to efficiently generate evidence sets. Specifically, PIVET uses a succinct representation of the phenotypes that corresponds to the index on the corpus database and an optimized co-occurrence algorithm inspired by the Aho-Corasick algorithm. We compare PIVET’s phenotype representation with PheKnow-Cloud’s by using PheKnow-Cloud’s experimental setup. In PIVET’s framework, we also introduce a statistical model trained on domain expert–verified phenotypes to automatically classify phenotypes as clinically relevant or not. Additionally, we show how the classification model can be used to examine user-supplied phenotypes in an online, rather than batch, manner. Results PIVET maintains the discriminative power of PheKnow-Cloud in terms of identifying clinically relevant phenotypes for the same corpus with

Finding Our Way through Phenotypes

PubMed Central

Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva; Anzaldo, Salvatore S.; Ashburner, Michael; Balhoff, James P.; Blackburn, David C.; Blake, Judith A.; Burleigh, J. Gordon; Chanet, Bruno; Cooper, Laurel D.; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T. Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E.; Dumontier, Michel; Franz, Nico M.; Friedrich, Frank; Gkoutos, George V.; Haendel, Melissa; Harmon, Luke J.; Hayamizu, Terry F.; He, Yongqun; Hines, Heather M.; Ibrahim, Nizar; Jackson, Laura M.; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J.; Le Novère, Nicolas; Lundberg, John G.; Macklin, James; Mast, Austin R.; Midford, Peter E.; Mikó, István; Mungall, Christopher J.; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J.; Richter, Stefan; Robinson, Peter N.; Ruttenberg, Alan; Schulz, Katja S.; Segerdell, Erik; Seltmann, Katja C.; Sharkey, Michael J.; Smith, Aaron D.; Smith, Barry; Specht, Chelsea D.; Squires, R. Burke; Thacker, Robert W.; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D.; Vogt, Lars; Wall, Christine E.; Walls, Ramona L.; Westerfeld, Monte; Wharton, Robert A.; Wirkner, Christian S.; Woolley, James B.; Yoder, Matthew J.; Zorn, Aaron M.; Mabee, Paula

2015-01-01

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. PMID:25562316

Finding our way through phenotypes.

PubMed

Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

2015-01-01

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Manganese Exposure and Cognition Across the Lifespan: Contemporary Review and Argument for Biphasic Dose-Response Health Effects

PubMed Central

Vollet, Kaitlin; Dietrich, Kim N.

2016-01-01

Manganese (Mn) is both an essential micronutrient and potential neurotoxicant. This dual role underlies a growing body of literature demonstrating that Mn exhibits a biphasic dose-response relationship with neurocognitive outcomes. We reviewed recent epidemiologic studies from 2007–2016 that investigated the relationship between Mn exposure and cognitive outcomes across the lifespan: early life, school-aged children, and adulthood. In total, 27 research articles were included in this review: 12 pediatric and 15 adult studies (10 occupational and five environmental exposures). The majority of these studies provided evidence of the negative effects of Mn exposure on cognition. The pediatric literature provides evidence that both high and low levels of Mn are negatively associated with intellectual development. Future Mn research should include examination of non-linear relationships and multiple neurotoxicants across the lifespan, and particularly during critical developmental windows. PMID:27722879

Analysis of 31-year-old patient with SYNGAP1 gene defect points to importance of variants in broader splice regions and reveals developmental trajectory of SYNGAP1-associated phenotype: case report.

PubMed

Prchalova, Darina; Havlovicova, Marketa; Sterbova, Katalin; Stranecky, Viktor; Hancarova, Miroslava; Sedlacek, Zdenek

2017-06-02

Whole exome sequencing is a powerful tool for the analysis of genetically heterogeneous conditions. The prioritization of variants identified often focuses on nonsense, frameshift and canonical splice site mutations, and highly deleterious missense variants, although other defects can also play a role. The definition of the phenotype range and course of rare genetic conditions requires long-term clinical follow-up of patients. We report an adult female patient with severe intellectual disability, severe speech delay, epilepsy, autistic features, aggressiveness, sleep problems, broad-based clumsy gait and constipation. Whole exome sequencing identified a de novo mutation in the SYNGAP1 gene. The variant was located in the broader splice donor region of intron 10 and replaced G by A at position +5 of the splice site. The variant was predicted in silico and shown experimentally to abolish the regular splice site and to activate a cryptic donor site within exon 10, causing frameshift and premature termination. The overall clinical picture of the patient corresponded well with the characteristic SYNGAP1-associated phenotype observed in previously reported patients. However, our patient was 31 years old which contrasted with most other published SYNGAP1 cases who were much younger. Our patient had a significant growth delay and microcephaly. Both features normalised later, although the head circumference stayed only slightly above the lower limit of the norm. The patient had a delayed puberty. Her cognitive and language performance remained at the level of a one-year-old child even in adulthood and showed a slow decline. Myopathic facial features and facial dysmorphism became more pronounced with age. Although the gait of the patient was unsteady in childhood, more severe gait problems developed in her teens. While the seizures remained well-controlled, her aggressive behaviour worsened with age and required extensive medication. The finding in our patient underscores

Emerging semantics to link phenotype and environment

PubMed Central

Bunker, Daniel E.; Buttigieg, Pier Luigi; Cooper, Laurel D.; Dahdul, Wasila M.; Domisch, Sami; Franz, Nico M.; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J.; Midford, Peter E.; Mungall, Christopher J.; Ramírez, Martín J.; Specht, Chelsea D.; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L.; White, Jeffrey W.; Zhang, Guanyang; Deans, Andrew R.; Huala, Eva; Lewis, Suzanna E.; Mabee, Paula M.

2015-01-01

Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments. PMID:26713234

Emerging semantics to link phenotype and environment.

PubMed

Thessen, Anne E; Bunker, Daniel E; Buttigieg, Pier Luigi; Cooper, Laurel D; Dahdul, Wasila M; Domisch, Sami; Franz, Nico M; Jaiswal, Pankaj; Lawrence-Dill, Carolyn J; Midford, Peter E; Mungall, Christopher J; Ramírez, Martín J; Specht, Chelsea D; Vogt, Lars; Vos, Rutger Aldo; Walls, Ramona L; White, Jeffrey W; Zhang, Guanyang; Deans, Andrew R; Huala, Eva; Lewis, Suzanna E; Mabee, Paula M

2015-01-01

Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity

PubMed Central

Murren, C J; Auld, J R; Callahan, H; Ghalambor, C K; Handelsman, C A; Heskel, M A; Kingsolver, J G; Maclean, H J; Masel, J; Maughan, H; Pfennig, D W; Relyea, R A; Seiter, S; Snell-Rood, E; Steiner, U K; Schlichting, C D

2015-01-01

Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently costly. In addition, we examine opportunities to offset costs of phenotypes through ontogeny, amelioration of phenotypic costs across environments, and the condition-dependent hypothesis. We propose avenues of further inquiry in the limits of plasticity using new and classic methods of ecological parameterization, phylogenetics and omics in the context of answering questions on the constraints of plasticity. Given plasticity's key role in coping with environmental change, approaches spanning the spectrum from applied to basic will greatly enrich our understanding of the evolution of plasticity and resolve our understanding of limits. PMID:25690179

Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature.

PubMed

Henderson, Jette; Ke, Junyuan; Ho, Joyce C; Ghosh, Joydeep; Wallace, Byron C

2018-05-04

Researchers are developing methods to automatically extract clinically relevant and useful patient characteristics from raw healthcare datasets. These characteristics, often capturing essential properties of patients with common medical conditions, are called computational phenotypes. Being generated by automated or semiautomated, data-driven methods, such potential phenotypes need to be validated as clinically meaningful (or not) before they are acceptable for use in decision making. The objective of this study was to present Phenotype Instance Verification and Evaluation Tool (PIVET), a framework that uses co-occurrence analysis on an online corpus of publically available medical journal articles to build clinical relevance evidence sets for user-supplied phenotypes. PIVET adopts a conceptual framework similar to the pioneering prototype tool PheKnow-Cloud that was developed for the phenotype validation task. PIVET completely refactors each part of the PheKnow-Cloud pipeline to deliver vast improvements in speed without sacrificing the quality of the insights PheKnow-Cloud achieved. PIVET leverages indexing in NoSQL databases to efficiently generate evidence sets. Specifically, PIVET uses a succinct representation of the phenotypes that corresponds to the index on the corpus database and an optimized co-occurrence algorithm inspired by the Aho-Corasick algorithm. We compare PIVET's phenotype representation with PheKnow-Cloud's by using PheKnow-Cloud's experimental setup. In PIVET's framework, we also introduce a statistical model trained on domain expert-verified phenotypes to automatically classify phenotypes as clinically relevant or not. Additionally, we show how the classification model can be used to examine user-supplied phenotypes in an online, rather than batch, manner. PIVET maintains the discriminative power of PheKnow-Cloud in terms of identifying clinically relevant phenotypes for the same corpus with which PheKnow-Cloud was originally developed, but

Cattle phenotypes can disguise their maternal ancestry.

PubMed

Srirattana, Kanokwan; McCosker, Kieren; Schatz, Tim; St John, Justin C

2017-06-26

Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments. A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P < 0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos

Federated Tensor Factorization for Computational Phenotyping

PubMed Central

Kim, Yejin; Sun, Jimeng; Yu, Hwanjo; Jiang, Xiaoqian

2017-01-01

Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospitals, in which direct patient-level data sharing is not possible (e.g., due to institutional policies). In this paper, we developed a novel solution to enable federated tensor factorization for computational phenotyping without sharing patient-level data. We developed secure data harmonization and federated computation procedures based on alternating direction method of multipliers (ADMM). Using this method, the multiple hospitals iteratively update tensors and transfer secure summarized information to a central server, and the server aggregates the information to generate phenotypes. We demonstrated with real medical datasets that our method resembles the centralized training model (based on combined datasets) in terms of accuracy and phenotypes discovery while respecting privacy. PMID:29071165

Distribution of phenotypes among Bacillus thuringiensis strains.

PubMed

Martin, Phyllis A W; Gundersen-Rindal, Dawn E; Blackburn, Michael B

2010-06-01

An extensive collection of Bacillus thuringiensis isolates from around the world were phenotypically profiled using standard biochemical tests. Six phenotypic traits occurred in 20-86% of the isolates and were useful in distinguishing isolates: production of urease (U; 20.5% of isolates), hydrolysis of esculin (E; 32.3% of isolates), acid production from salicin (A; 37.4% of isolates), acid production from sucrose (S; 34.0% of isolates), production of phospholipase C or lecithinase (L; 79.7% of isolates), and hydrolysis of starch (T; 85.8% of isolates). With the exception of acid production from salicin and hydrolysis of esculin, which were associated, the traits assorted independently. Of the 64 possible combinations of these six phenotypic characteristics, 15 combinations accounted for ca. 80% of all isolates, with the most common phenotype being TL (23.6% of isolates). Surprisingly, while the biochemical traits generally assorted independently, certain phenotypic traits associated with the parasporal crystal were correlated with certain combinations of biochemical traits. Crystals that remained attached to spores (which tended to be non-toxic to insects) were highly correlated with the phenotypes that included both L and S. Among the 15 most abundant phenotypes characterizing B. thuringiensis strains, amorphous crystals were associated with TLE, TL, T, and Ø (the absence of positive tested biochemical traits). Amorphous crystal types displayed a distinct bias toward toxicity to dipteran insects. Although all common phenotypes included B. thuringiensis isolates producing bipyramidal crystals toxic to lepidopteran insects, those with the highest abundance of these toxic crystals displayed phenotypes TLU, TLUA, TLUAE, and TLAE.

Emerging semantics to link phenotype and environment

DOE PAGES

Thessen, Anne E.; Bunker, Daniel E.; Buttigieg, Pier Luigi; ...

2015-12-14

Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies aremore » well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. Lastly, in this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.« less

Determining Multiple Sclerosis Phenotype from Electronic Medical Records.

PubMed

Nelson, Richard E; Butler, Jorie; LaFleur, Joanne; Knippenberg, Kristin; C Kamauu, Aaron W; DuVall, Scott L

2016-12-01

Multiple sclerosis (MS), a central nervous system disease in which nerve signals are disrupted by scarring and demyelination, is classified into phenotypes depending on the patterns of cognitive or physical impairment progression: relapsing-remitting MS (RRMS), primary-progressive MS (PPMS), secondary-progressive MS (SPMS), or progressive-relapsing MS (PRMS). The phenotype is important in managing the disease and determining appropriate treatment. The ICD-9-CM code 340.0 is uninformative about MS phenotype, which increases the difficulty of studying the effects of phenotype on disease. To identify MS phenotype using natural language processing (NLP) techniques on progress notes and other clinical text in the electronic medical record (EMR). Patients with at least 2 ICD-9-CM codes for MS (340.0) from 1999 through 2010 were identified from nationwide EMR data in the Department of Veterans Affairs. Clinical experts were interviewed for possible keywords and phrases denoting MS phenotype in order to develop a data dictionary for NLP. For each patient, NLP was used to search EMR clinical notes, since the first MS diagnosis date for these keywords and phrases. Presence of phenotype-related keywords and phrases were analyzed in context to remove mentions that were negated (e.g., "not relapsing-remitting") or unrelated to MS (e.g., "RR" meaning "respiratory rate"). One thousand mentions of MS phenotype were validated, and all records of 150 patients were reviewed for missed mentions. There were 7,756 MS patients identified by ICD-9-CM code 340.0. MS phenotype was identified for 2,854 (36.8%) patients, with 1,836 (64.3%) of those having just 1 phenotype mentioned in their EMR clinical notes: 1,118 (39.2%) RRMS, 325 (11.4%) PPMS, 374 (13.1%) SPMS, and 19 (0.7%) PRMS. A total of 747 patients (26.2%) had 2 phenotypes, the most common being 459 patients (16.1%) with RRMS and SPMS. A total of 213 patients (7.5%) had 3 phenotypes, and 58 patients (2.0%) had 4 phenotypes mentioned

Mechanism of biphasic charge recombination and accumulation in TiO2 mesoporous structured perovskite solar cells.

PubMed

Wang, Hao-Yi; Wang, Yi; Yu, Man; Han, Jun; Guo, Zhi-Xin; Ai, Xi-Cheng; Zhang, Jian-Ping; Qin, Yujun

2016-04-28

Organic-inorganic halide perovskite solar cells are becoming the next big thing in the photovoltaic field owing to their rapidly developing photoelectric conversion performance. Herein, mesoporous structured perovskite devices with various perovskite grain sizes are fabricated by a sequential dropping method, and the charge recombination dynamics is investigated by transient optical-electric measurements. All devices exhibit an overall power conversion efficiency around 15%. More importantly, a biphasic trap-limited charge recombination process is proposed and interpreted by taking into account the specific charge accumulation mechanism in perovskite solar cells. At low Fermi levels, photo-generated electrons predominately populate in the perovskite phase, while at high Fermi levels, most electrons occupy traps in mesoporous TiO2. As a result, the dynamics of charge recombination is, respectively, dominated by the perovskite phase and mesoporous TiO2 in these two cases. The present work would give a new perspective on the charge recombination process in meso-structured perovskite solar cells.

A fast quadrature-based numerical method for the continuous spectrum biphasic poroviscoelastic model of articular cartilage.

PubMed

Stuebner, Michael; Haider, Mansoor A

2010-06-18

A new and efficient method for numerical solution of the continuous spectrum biphasic poroviscoelastic (BPVE) model of articular cartilage is presented. Development of the method is based on a composite Gauss-Legendre quadrature approximation of the continuous spectrum relaxation function that leads to an exponential series representation. The separability property of the exponential terms in the series is exploited to develop a numerical scheme that can be reduced to an update rule requiring retention of the strain history at only the previous time step. The cost of the resulting temporal discretization scheme is O(N) for N time steps. Application and calibration of the method is illustrated in the context of a finite difference solution of the one-dimensional confined compression BPVE stress-relaxation problem. Accuracy of the numerical method is demonstrated by comparison to a theoretical Laplace transform solution for a range of viscoelastic relaxation times that are representative of articular cartilage. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Novel alginate biphasic scaffold for osteochondral regeneration: an in vivo evaluation in rabbit and sheep models.

PubMed

Filardo, Giuseppe; Perdisa, Francesco; Gelinsky, Michael; Despang, Florian; Fini, Milena; Marcacci, Maurilio; Parrilli, Anna Paola; Roffi, Alice; Salamanna, Francesca; Sartori, Maria; Schütz, Kathleen; Kon, Elizaveta

2018-05-26

Current therapeutic strategies for osteochondral restoration showed a limited regenerative potential. In fact, to promote the growth of articular cartilage and subchondral bone is a real challenge, due to the different functional and anatomical properties. To this purpose, alginate is a promising biomaterial for a scaffold-based approach, claiming optimal biocompatibility and good chondrogenic potential. A previously developed mineralized alginate scaffold was investigated in terms of the ability to support osteochondral regeneration both in a large and medium size animal model. The results were evaluated macroscopically and by microtomography, histology, histomorphometry, and immunohistochemical analysis. No evidence of adverse or inflammatory reactions was observed in both models, but limited subchondral bone formation was present, together with a slow scaffold resorption time.The implantation of this biphasic alginate scaffold provided partial osteochondral regeneration in the animal model. Further studies are needed to evaluate possible improvement in terms of osteochondral tissue regeneration for this biomaterial.

Decomposing phenotype descriptions for the human skeletal phenome.

PubMed

Groza, Tudor; Hunter, Jane; Zankl, Andreas

2013-01-01

Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. The intrinsic value and knowledge captured within such descriptions can only be expressed by taking advantage of their inner structure that implicitly combines qualities and anatomical entities. We present a meta-model (the Phenotype Fragment Ontology) and a processing pipeline that enable together the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome. We use this approach to showcase the usefulness of the generic concept of phenotype decomposition by performing an experimental study on all skeletal phenotype concepts defined in the Human Phenotype Ontology.

Redefining Aging in HIV Infection Using Phenotypes.

PubMed

Stoff, David M; Goodkin, Karl; Jeste, Dilip; Marquine, Maria

2017-10-01

This article critically reviews the utility of "phenotypes" as behavioral descriptors in aging/HIV research that inform biological underpinnings and treatment development. We adopt a phenotypic redefinition of aging conceptualized within a broader context of HIV infection and of aging. Phenotypes are defined as dimensions of behavior, closely related to fundamental mechanisms, and, thus, may be more informative than chronological age. Primary emphasis in this review is given to comorbid aging and cognitive aging, though other phenotypes (i.e., disability, frailty, accelerated aging, successful aging) are also discussed in relation to comorbid aging and cognitive aging. The main findings that emerged from this review are as follows: (1) the phenotypes, comorbid aging and cognitive aging, are distinct from each other, yet overlapping; (2) associative relationships are the rule in HIV for comorbid and cognitive aging phenotypes; and (3) HIV behavioral interventions for both comorbid aging and cognitive aging have been limited. Three paths for research progress are identified for phenotype-defined aging/HIV research (i.e., clinical and behavioral specification, biological mechanisms, intervention targets), and some important research questions are suggested within each of these research paths.

The Value of Phenotypes in Knee Osteoarthritis Research.

PubMed

Nelson, Fred R T

2018-01-01

Over the past decade, phenotypes have been used to help categorize knee osteoarthritis patients relative to being subject to disease, disease progression, and treatment response. A review of potential phenotype selection is now appropriate. The appeal of using phenotypes is that they most rely on simple physical examination, clinically routine imaging, and demographics. The purpose of this review is to describe the panoply of phenotypes that can be potentially used in osteoarthritis research. A search of PubMed was used singularly to review the literature on knee osteoarthritis phenotypes. Four phenotype assembly groups were based on physical features and noninvasive imaging. Demographics included metabolic syndrome (dyslipidemia, hypertension, obesity, and diabetes). Mechanical characteristics included joint morphology, alignment, the effect of injury, and past and present history. Associated musculoskeletal disorder characteristics included multiple joint involvement, spine disorders, neuromuscular diseases, and osteoporosis. With the knee as an organ, tissue characteristics were used to focus on synovium, meniscus, articular cartilage, patella fat pad, bone sclerosis, bone cysts, and location of pain. Many of these phenotype clusters require further validation studies. There is special emphasis on knee osteoarthritis phenotypes due to its predominance in osteoarthritic disorders and the variety of tissues in that joint. More research will be required to determine the most productive phenotypes for future studies. The selection and assignment of phenotypes will take on an increasing role in osteoarthritis research in the future.

Age is associated with asthma phenotypes.

PubMed

Ponte, Eduardo V; Lima, Aline; Almeida, Paula C A; de Jesus, Juliana P V; Lima, Valmar B; Scichilone, Nicola; Souza-Machado, Adelmir; Cruz, Álvaro A

2017-11-01

The relationship between age and asthma phenotypes is important as population is ageing, asthma is becoming common in older ages and recently developed treatments for asthma are guided by phenotypes. The aim of this study is to evaluate whether age is associated with specific asthma phenotypes. This is a cross-sectional study. We included subjects with asthma of varied degrees of severity. Subjects underwent spirometry, skin prick test to aeroallergens, answered the Asthma Control Questionnaire and had blood samples collected. We performed binary logistic regression analysis to evaluate whether age is associated with asthma phenotypes. We enrolled 868 subjects. In comparison with subjects ≤ 40 years, older subjects had high odds of irreversible airway obstruction (from 41 to 64 years, OR: 1.83 (95% CI: 1.32-2.54); ≥65 years, OR: 3.45 (2.12-5.60)) and severe asthma phenotypes (from 41 to 64 years, OR: 3.23 (2.26-4.62); ≥65 years, OR: 4.55 (2.39-8.67)). Older subjects had low odds of atopic (from 41 to 64 years, OR: 0.56 (0.39-0.79); ≥65 years, OR: 0.47 (0.27-0.84)) and eosinophilic phenotypes (from 41 to 64 years, OR: 0.63 (0.46-0.84); ≥65 years, OR: 0.39 (0.24-0.64)). Older subjects with asthma have low odds of atopic and eosinophilic phenotypes, whereas they present high odds of irreversible airway obstruction and severe asthma. © 2017 Asian Pacific Society of Respirology.

The Broad Autism Phenotype Questionnaire

ERIC Educational Resources Information Center

Hurley, Robert S. E.; Losh, Molly; Parlier, Morgan; Reznick, J. Steven; Piven, Joseph

2007-01-01

The broad autism phenotype (BAP) is a set of personality and language characteristics that reflect the phenotypic expression of the genetic liability to autism, in non-autistic relatives of autistic individuals. These characteristics are milder but qualitatively similar to the defining features of autism. A new instrument designed to measure the…

Mixed phenotype (T/B/myeloid) extramedullary blast crisis as an initial presentation of chronic myelogenous leukemia.

PubMed

Qing, Xin; Qing, Annie; Ji, Ping; French, Samuel W; Mason, Holli

2018-04-01

Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized by the Philadelphia (Ph) chromosome generated by the reciprocal translocation t(9,22)(q34;q11). The natural progression of the disease follows a biphasic or triphasic course. Most cases of CML are diagnosed in the chronic phase. Extramedullary blast crisis rarely occurs during the course of CML, and is extremely rare as the initial presentation of CML. Here, we report the case of a 32-year-old female with enlarged neck lymph nodes and fatigue. She was diagnosed with B-lymphoblastic leukemia/lymphoma with possible mixed phenotype (B/myeloid) by right neck lymph node biopsy at an outside hospital. However, review of her peripheral blood smear and her bone marrow aspirate and biopsy showed features consistent with CML, which was confirmed by PCR and karyotyping. An ultrasound-guided right cervical lymph node core biopsy showed a diffuse infiltrate of blasts, near totally replacing the normal lymph node tissue, admixed with some hematopoietic cells including megakaryocytes, erythroid precursors and maturing myeloid cells. By flow cytometry and immunohistochemistry, the blasts expressed CD2, cytoplasmic CD3, CD5, CD7, CD56, TdT, CD10 (weak, subset), CD19 (subset), CD79a, PAX-5 (subset), CD34, CD38, CD117 (subset), HLA-DR (subset), CD11b, CD13 (subset), CD33 (subset), and weak cytoplasmic myeloperoxidase, without co-expression of surface CD3, CD4, CD8, CD20, CD22, CD14, CD15, CD16 and CD64, consistent with blasts with mixed phenotype (T/B/myeloid). A diagnosis of extramedullary blast crisis of CML was made. Chromosomal analysis performed on the lymph node biopsy tissue revealed multiple numerical and structural abnormalities including the Ph chromosome (46-49,XX,add(1)(p34),add(3)(p25),add(5)(q13),-6,t(9;22)(q34;q11.2),+10,-15,add(17)(p11.2),+19, +der(22)t(9;22),+mar[cp8]). After completion of one cycle of combined chemotherapy plus dasatinib treatment, she was transferred to City of Hope

Computable visually observed phenotype ontological framework for plants

PubMed Central

2011-01-01

Background The ability to search for and precisely compare similar phenotypic appearances within and across species has vast potential in plant science and genetic research. The difficulty in doing so lies in the fact that many visual phenotypic data, especially visually observed phenotypes that often times cannot be directly measured quantitatively, are in the form of text annotations, and these descriptions are plagued by semantic ambiguity, heterogeneity, and low granularity. Though several bio-ontologies have been developed to standardize phenotypic (and genotypic) information and permit comparisons across species, these semantic issues persist and prevent precise analysis and retrieval of information. A framework suitable for the modeling and analysis of precise computable representations of such phenotypic appearances is needed. Results We have developed a new framework called the Computable Visually Observed Phenotype Ontological Framework for plants. This work provides a novel quantitative view of descriptions of plant phenotypes that leverages existing bio-ontologies and utilizes a computational approach to capture and represent domain knowledge in a machine-interpretable form. This is accomplished by means of a robust and accurate semantic mapping module that automatically maps high-level semantics to low-level measurements computed from phenotype imagery. The framework was applied to two different plant species with semantic rules mined and an ontology constructed. Rule quality was evaluated and showed high quality rules for most semantics. This framework also facilitates automatic annotation of phenotype images and can be adopted by different plant communities to aid in their research. Conclusions The Computable Visually Observed Phenotype Ontological Framework for plants has been developed for more efficient and accurate management of visually observed phenotypes, which play a significant role in plant genomics research. The uniqueness of this

Extraction of Biomolecules Using Phosphonium-Based Ionic Liquids + K3PO4 Aqueous Biphasic Systems

PubMed Central

Louros, Cláudia L. S.; Cláudio, Ana Filipa M.; Neves, Catarina M. S. S.; Freire, Mara G.; Marrucho, Isabel M.; Pauly, Jérôme; Coutinho, João A. P.

2010-01-01

Aqueous biphasic systems (ABS) provide an alternative and efficient approach for the extraction, recovery and purification of biomolecules through their partitioning between two liquid aqueous phases. In this work, the ability of hydrophilic phosphonium-based ionic liquids (ILs) to form ABS with aqueous K3PO4 solutions was evaluated for the first time. Ternary phase diagrams, and respective tie-lines and tie-lines length, formed by distinct phosphonium-based ILs, water, and K3PO4 at 298 K, were measured and are reported. The studied phosphonium-based ILs have shown to be more effective in promoting ABS compared to the imidazolium-based counterparts with similar anions. Moreover, the extractive capability of such systems was assessed for distinct biomolecules (including amino acids, food colourants and alkaloids). Densities and viscosities of both aqueous phases, at the mass fraction compositions used for the biomolecules extraction, were also determined. The evaluated IL-based ABS have been shown to be prospective extraction media, particularly for hydrophobic biomolecules, with several advantages over conventional polymer-inorganic salt ABS. PMID:20480041

Biphasic effect of Syzygium aromaticum flower bud on reproductive physiology of male mice.

PubMed

Mishra, R K; Singh, S K

2016-11-01

The flower buds of Syzygium aromaticum (clove) have been used for the treatment of male sexual disorders in indigenous medicines of Indian subcontinent. Therefore to evaluate the efficacy of Syzygium aromaticum on the male reproductive health, chronic oral exposure of aqueous extract of flower buds of Syzygium in three doses (15 mg, 30 mg and 60 mg kg -1 BW) were studied for a single spermatogenic cycle (35 days) in Parkes (P) strain mice. Lower dose (15 mg) of Syzygium aromaticum flower buds increased serum testosterone level and testicular hydroxysteroid dehydrogenase (HSD) activities and improved sperm motility, sperm morphology, secretory activity of epididymis and seminal vesicle, and number of litters per female. On the other hand, higher doses (30 and 60 mg) of the treatment adversely affected above parameters. Further, higher doses of the extract also had adverse effects on daily sperm production, 1C cell population and on histology of testis. In conclusion, Syzygium aromaticum flower buds extract exhibits biphasic effect on reproductive physiology of male mice. Lower dose of Syzygium aromaticum flower bud extract is androgenic in nature and may have a viable future as an indigenous sexual rejuvenator, while higher doses adversely affected functional physiology of reproductive organs. © 2016 Blackwell Verlag GmbH.

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

PubMed Central

Koscielny, Gautier; Yaikhom, Gagarine; Iyer, Vivek; Meehan, Terrence F.; Morgan, Hugh; Atienza-Herrero, Julian; Blake, Andrew; Chen, Chao-Kung; Easty, Richard; Di Fenza, Armida; Fiegel, Tanja; Grifiths, Mark; Horne, Alan; Karp, Natasha A.; Kurbatova, Natalja; Mason, Jeremy C.; Matthews, Peter; Oakley, Darren J.; Qazi, Asfand; Regnart, Jack; Retha, Ahmad; Santos, Luis A.; Sneddon, Duncan J.; Warren, Jonathan; Westerberg, Henrik; Wilson, Robert J.; Melvin, David G.; Smedley, Damian; Brown, Steve D. M.; Flicek, Paul; Skarnes, William C.; Mallon, Ann-Marie; Parkinson, Helen

2014-01-01

The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and standardized protocols for the experimentation, collection and dissemination of data. Dedicated ‘data wranglers’ work with each phenotyping center to collate data and perform quality control of data. An automated statistical analysis pipeline has been developed to identify knockout strains with a significant change in the phenotype parameters. Annotation with biomedical ontologies allows biologists and clinicians to easily find mouse strains with phenotypic traits relevant to their research. Data integration with other resources will provide insights into mammalian gene function and human disease. As phenotype data become available for every gene in the mouse, the IMPC web portal will become an invaluable tool for researchers studying the genetic contributions of genes to human diseases. PMID:24194600

Phenotypes of organ involvement in sarcoidosis.

PubMed

Schupp, Jonas Christian; Freitag-Wolf, Sandra; Bargagli, Elena; Mihailović-Vučinić, Violeta; Rottoli, Paola; Grubanovic, Aleksandar; Müller, Annegret; Jochens, Arne; Tittmann, Lukas; Schnerch, Jasmin; Olivieri, Carmela; Fischer, Annegret; Jovanovic, Dragana; Filipovic, Snežana; Videnovic-Ivanovic, Jelica; Bresser, Paul; Jonkers, René; O'Reilly, Kate; Ho, Ling-Pei; Gaede, Karoline I; Zabel, Peter; Dubaniewicz, Anna; Marshall, Ben; Kieszko, Robert; Milanowski, Janusz; Günther, Andreas; Weihrich, Anette; Petrek, Martin; Kolek, Vitezslav; Keane, Michael P; O'Beirne, Sarah; Donnelly, Seamas; Haraldsdottir, Sigridur Olina; Jorundsdottir, Kristin B; Costabel, Ulrich; Bonella, Francesco; Wallaert, Benoît; Grah, Christian; Peroš-Golubičić, Tatjana; Luisetti, Mauritio; Kadija, Zamir; Pabst, Stefan; Grohé, Christian; Strausz, János; Vašáková, Martina; Sterclova, Martina; Millar, Ann; Homolka, Jiří; Slováková, Alena; Kendrick, Yvonne; Crawshaw, Anjali; Wuyts, Wim; Spencer, Lisa; Pfeifer, Michael; Valeyre, Dominique; Poletti, Venerino; Wirtz, Hubertus; Prasse, Antje; Schreiber, Stefan; Krawczak, Michael; Müller-Quernheim, Joachim

2018-01-01

Sarcoidosis is a highly variable, systemic granulomatous disease of hitherto unknown aetiology. The GenPhenReSa (Genotype-Phenotype Relationship in Sarcoidosis) project represents a European multicentre study to investigate the influence of genotype on disease phenotypes in sarcoidosis.The baseline phenotype module of GenPhenReSa comprised 2163 Caucasian patients with sarcoidosis who were phenotyped at 31 study centres according to a standardised protocol.From this module, we found that patients with acute onset were mainly female, young and of Scadding type I or II. Female patients showed a significantly higher frequency of eye and skin involvement, and complained more of fatigue. Based on multidimensional correspondence analysis and subsequent cluster analysis, patients could be clearly stratified into five distinct, yet undescribed, subgroups according to predominant organ involvement: 1) abdominal organ involvement, 2) ocular-cardiac-cutaneous-central nervous system disease involvement, 3) musculoskeletal-cutaneous involvement, 4) pulmonary and intrathoracic lymph node involvement, and 5) extrapulmonary involvement.These five new clinical phenotypes will be useful to recruit homogenous cohorts in future biomedical studies. Copyright ©ERS 2018.

Electrolyte-stimulated biphasic dissolution profile and stability enhancement for tablets containing drug-polyelectrolyte complexes.

PubMed

Kindermann, Christoph; Matthée, Karin; Sievert, Frank; Breitkreutz, Jörg

2012-10-01

Recently introduced drug-polyelectrolyte complexes prepared by hot-melt extrusion should be processed to solid dosage forms with tailor-made release properties. Their potential of stability enhancement should be investigated. Milled hot-melt extruded naproxen-EUDRAGIT® E PO polyelectrolyte complexes were subsequently processed to double-layer tablets with varying complex loadings on a rotary-die press. Physicochemical interactions were studied under ICH guideline conditions and using the Gordon-Taylor equation. Sorption and desorption were determined to investigate the influence of moisture and temperature on the complex and related to stability tests under accelerated conditions. Naproxen release from the drug-polyelectrolyte complex is triggered by electrolyte concentration. Depending on the complex loading, phosphate buffer pH 6.8 stimulated a biphasic dissolution profile of the produced double-layer tablets: immediate release from the first layer with 65% loading and prolonged release from the second layer within 24 h (98.5% loading). XRPD patterns proved pseudopolymorphism for tablets containing the pure drug under common storage conditions whereas the drug-complex was stable in the amorphous state. Drug-polyelectrolyte complexes enable tailor-made dissolution profiles of solid dosage forms by electrolyte stimulation and increase stability under common storage conditions.

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

PubMed Central

Edmunds, Richard C.; Su, Baofeng; Balhoff, James P.; Eames, B. Frank; Dahdul, Wasila M.; Lapp, Hilmar; Lundberg, John G.; Vision, Todd J.; Dunham, Rex A.; Mabee, Paula M.; Westerfield, Monte

2016-01-01

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology. PMID:26500251

Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks

PubMed Central

Ronellenfitsch, Henrik; Lasser, Jana; Daly, Douglas C.; Katifori, Eleni

2015-01-01

The leaves of angiosperms contain highly complex venation networks consisting of recursively nested, hierarchically organized loops. We describe a new phenotypic trait of reticulate vascular networks based on the topology of the nested loops. This phenotypic trait encodes information orthogonal to widely used geometric phenotypic traits, and thus constitutes a new dimension in the leaf venation phenotypic space. We apply our metric to a database of 186 leaves and leaflets representing 137 species, predominantly from the Burseraceae family, revealing diverse topological network traits even within this single family. We show that topological information significantly improves identification of leaves from fragments by calculating a “leaf venation fingerprint” from topology and geometry. Further, we present a phenomenological model suggesting that the topological traits can be explained by noise effects unique to specimen during development of each leaf which leave their imprint on the final network. This work opens the path to new quantitative identification techniques for leaves which go beyond simple geometric traits such as vein density and is directly applicable to other planar or sub-planar networks such as blood vessels in the brain. PMID:26700471

Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems.

PubMed

Zhang, Hongkai; Torkamani, Ali; Jones, Teresa M; Ruiz, Diana I; Pons, Jaume; Lerner, Richard A

2011-08-16

Use of large combinatorial antibody libraries and next-generation sequencing of nucleic acids are two of the most powerful methods in modern molecular biology. The libraries are screened using the principles of evolutionary selection, albeit in real time, to enrich for members with a particular phenotype. This selective process necessarily results in the loss of information about less-fit molecules. On the other hand, sequencing of the library, by itself, gives information that is mostly unrelated to phenotype. If the two methods could be combined, the full potential of very large molecular libraries could be realized. Here we report the implementation of a phenotype-information-phenotype cycle that integrates information and gene recovery. After selection for phage-encoded antibodies that bind to targets expressed on the surface of Escherichia coli, the information content of the selected pool is obtained by pyrosequencing. Sequences that encode specific antibodies are identified by a bioinformatic analysis and recovered by a stringent affinity method that is uniquely suited for gene isolation from a highly degenerate collection of nucleic acids. This approach can be generalized for selection of antibodies against targets that are present as minor components of complex systems.

Enabling phenotypic big data with PheNorm.

PubMed

Yu, Sheng; Ma, Yumeng; Gronsbell, Jessica; Cai, Tianrun; Ananthakrishnan, Ashwin N; Gainer, Vivian S; Churchill, Susanne E; Szolovits, Peter; Murphy, Shawn N; Kohane, Isaac S; Liao, Katherine P; Cai, Tianxi

2018-01-01

Electronic health record (EHR)-based phenotyping infers whether a patient has a disease based on the information in his or her EHR. A human-annotated training set with gold-standard disease status labels is usually required to build an algorithm for phenotyping based on a set of predictive features. The time intensiveness of annotation and feature curation severely limits the ability to achieve high-throughput phenotyping. While previous studies have successfully automated feature curation, annotation remains a major bottleneck. In this paper, we present PheNorm, a phenotyping algorithm that does not require expert-labeled samples for training. The most predictive features, such as the number of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes or mentions of the target phenotype, are normalized to resemble a normal mixture distribution with high area under the receiver operating curve (AUC) for prediction. The transformed features are then denoised and combined into a score for accurate disease classification. We validated the accuracy of PheNorm with 4 phenotypes: coronary artery disease, rheumatoid arthritis, Crohn's disease, and ulcerative colitis. The AUCs of the PheNorm score reached 0.90, 0.94, 0.95, and 0.94 for the 4 phenotypes, respectively, which were comparable to the accuracy of supervised algorithms trained with sample sizes of 100-300, with no statistically significant difference. The accuracy of the PheNorm algorithms is on par with algorithms trained with annotated samples. PheNorm fully automates the generation of accurate phenotyping algorithms and demonstrates the capacity for EHR-driven annotations to scale to the next level - phenotypic big data. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Biphasic force response to iso-velocity stretch in airway smooth muscle.

PubMed

Norris, Brandon A; Lan, Bo; Wang, Lu; Pascoe, Christopher D; Swyngedouw, Nicholas E; Paré, Peter D; Seow, Chun Y

2015-10-01

Airway smooth muscle (ASM) in vivo is constantly subjected to oscillatory strain due to tidal breathing and deep inspirations. ASM contractility is known to be adversely affected by strains, especially those of large amplitudes. Based on the cross-bridge model of contraction, it is likely that strain impairs force generation by disrupting actomyosin cross-bridge interaction. There is also evidence that strain modulates muscle stiffness and force through induction of cytoskeletal remodeling. However, the molecular mechanism by which strain alters smooth muscle function is not entirely clear. Here, we examine the response of ASM to iso-velocity stretches to probe the components within the muscle preparation that give rise to different features in the force response. We found in ASM that force response to a ramp stretch showed a biphasic feature, with the initial phase associated with greater muscle stiffness compared with that in the later phase, and that the transition between the phases occurred at a critical strain of ∼3.3%. Only strains with amplitudes greater than the critical strain could lead to reduction in force and stiffness of the muscle in the subsequent stretches. The initial-phase stiffness was found to be linearly related to the degree of muscle activation, suggesting that the stiffness stems mainly from attached cross bridges. Both phases were affected by the degree of muscle activation and by inhibitors of myosin light-chain kinase, PKC, and Rho-kinase. Different responses due to different interventions suggest that cross-bridge and cytoskeletal stiffness is regulated differently by the kinases. Copyright © 2015 the American Physiological Society.

A Biphasic Change of Regional Blood Volume in the Frontal Cortex during Non-Rapid Eye Movement Sleep: A Near-Infrared Spectroscopy Study.

PubMed

Zhang, Zhongxing; Khatami, Ramin

2015-08-01

Current knowledge on hemodynamics in sleep is limited because available techniques do not allow continuous recordings and mainly focus on cerebral blood flow while neglecting other important parameters, such as blood volume (BV) and vasomotor activity. Observational study. Continuous measures of hemodynamics over the left forehead and biceps were performed using near-infrared spectroscopy (NIRS) during nocturnal polysomnography in 16 healthy participants in sleep laboratory. Temporal dynamics and mean values of cerebral and muscular oxygenated hemoglobin (HbO2), deoxygenated hemoglobin (HHb), and BV during different sleep stages were compared. A biphasic change of cerebral BV was observed which contrasted a monotonic increase of muscular BV during non-rapid eye movement sleep. A significant decrement in cerebral HbO2 and BV accompanied by an increase of HHb was recorded at sleep onset (Phase I). Prior to slow wave sleep (SWS) HbO2 and BV turned to increase whereas HHb began to decrease in subsequent Phase II suggested increased brain perfusion during SWS. The cerebral HbO2 slope correlated to BV slope in Phase I and II, but it only correlated to HHb slope in Phase II. The occurrence time of inflection points correlated to SWS latencies. Initial decrease of brain perfusion with decreased blood volume (BV) and oxygenated hemoglobin (HbO2) together with increasing muscular BV fit thermoregulation process at sleep onset. The uncorrelated and correlated slopes of HbO2 and deoxygenated hemoglobin indicate different mechanisms underlying the biphasic hemodynamic process in light sleep and slow wave sleep (SWS). In SWS, changes in vasomotor activity (i.e., increased vasodilatation) may mediate increasing cerebral and muscular BV. © 2015 Associated Professional Sleep Societies, LLC.

Association between transthoracic impedance and electrical cardioversion success with biphasic defibrillators: An analysis of 1055 shocks for atrial fibrillation and flutter.

PubMed

Sadek, Mouhannad M; Chaugai, Varsha; Cleland, Mark J; Zakutney, Timothy J; Birnie, David H; Ramirez, F Daniel

2018-03-13

The relevance of transthoracic impedance (TTI) to electrical cardioversion (ECV) success for atrial tachyarrhythmias when using biphasic waveform defibrillators is unknown. TTI is predictive of ECV success with contemporary defibrillators. De-identified data stored in biphasic defibrillator memory cards from ECV attempts for atrial fibrillation (AF) or atrial flutter (AFL) over a 2-year period at our center were evaluated. ECV success, defined as arrhythmia termination and ≥ 1 sinus beat, was adjudicated by 2 blinded cardiac electrophysiologists. The association between TTI and ECV success was assessed via Cochrane-Armitage trend and Spearman rank correlation tests, as well as simple and multivariable logistic regression. The influence of TTI on the number of shocks and on cumulative energy delivered per patient was also examined. 703 patients (593 with AF, 110 with AFL) receiving 1055 shocks were included. Last shock success was achieved in 88.0% and 98.2% of patients with AF and AFL, respectively. In patients with AF, TTI was positively associated with last shock failure (P trend  =0.019), the need for multiple shocks (P trend  <0.001), and cumulative energy delivered (ρ = 0.348; P < 0.001). After adjusting for first shock energy, 10-Ω increments in TTI were associated with odds ratios of 1.36 (95% CI: 1.24-1.49) and 1.22 (95% CI: 1.09-1.37) for first and last shock failure, respectively (P < 0.001 for both). Although contemporary defibrillators are designed to compensate for TTI, this variable continues to be associated with ECV failure in patients with AF. Strategies to lower TTI during ECV for AF may improve procedural success. © 2018 Wiley Periodicals, Inc.

The Impact of "Possible Patients" on Phenotyping Algorithms: Electronic Phenotype Algorithms Can Only Be Reproduced by Sharing Detailed Annotation Criteria.

PubMed

Kagawa, Rina; Kawazoe, Yoshimasa; Shinohara, Emiko; Imai, Takeshi; Ohe, Kazuhiko

2017-01-01

Phenotyping is an automated technique for identifying patients diagnosed with a particular disease based on electronic health records (EHRs). To evaluate phenotyping algorithms, which should be reproducible, the annotation of EHRs as a gold standard is critical. However, we have found that the different types of EHRs cannot be definitively annotated into CASEs or CONTROLs. The influence of such "possible patients" on phenotyping algorithms is unknown. To assess these issues, for four chronic diseases, we annotated EHRs by using information not directly referring to the diseases and developed two types of phenotyping algorithms for each disease. We confirmed that each disease included different types of possible patients. The performance of phenotyping algorithms differed depending on whether possible patients were considered as CASEs, and this was independent of the type of algorithms. Our results indicate that researchers must share annotation criteria for classifying the possible patients to reproduce phenotyping algorithms.

Quality Control Test for Sequence-Phenotype Assignments

PubMed Central

Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

2015-01-01

Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement.

PubMed

Cobb, Joshua N; Declerck, Genevieve; Greenberg, Anthony; Clark, Randy; McCouch, Susan

2013-04-01

More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers. Robust phenotyping systems are needed to characterize the full suite of genetic factors that contribute to quantitative phenotypic variation across cells, organs and tissues, developmental stages, years, environments, species and research programs. Next-generation phenotyping generates significantly more data than previously and requires novel data management, access and storage systems, increased use of ontologies to facilitate data integration, and new statistical tools for enhancing experimental design and extracting biologically meaningful signal from environmental and experimental noise. To ensure relevance, the implementation of efficient and informative phenotyping experiments also requires familiarity with diverse germplasm resources, population structures, and target populations of environments. Today, phenotyping is quickly emerging as the major operational bottleneck limiting the power of genetic analysis and genomic prediction. The challenge for the next generation of quantitative geneticists and plant breeders is not only to understand the genetic basis of complex trait variation, but also to use that knowledge to efficiently synthesize twenty-first century crop varieties.

[Phenotypic heterogeneity of chronic obstructive pulmonary disease].

PubMed

Garcia-Aymerich, Judith; Agustí, Alvar; Barberà, Joan A; Belda, José; Farrero, Eva; Ferrer, Antoni; Ferrer, Jaume; Gáldiz, Juan B; Gea, Joaquim; Gómez, Federico P; Monsó, Eduard; Morera, Josep; Roca, Josep; Sauleda, Jaume; Antó, Josep M

2009-03-01

A functional definition of chronic obstructive pulmonary disease (COPD) based on airflow limitation has largely dominated the field. However, a view has emerged that COPD involves a complex array of cellular, organic, functional, and clinical events, with a growing interest in disentangling the phenotypic heterogeneity of COPD. The present review is based on the opinion of the authors, who have extensive research experience in several aspects of COPD. The starting assumption of the review is that current knowledge on the pathophysiology and clinical features of COPD allows us to classify phenotypic information in terms of the following dimensions: respiratory symptoms and health status, acute exacerbations, lung function, structural changes, local and systemic inflammation, and systemic effects. Twenty-six phenotypic traits were identified and assigned to one of the 6 dimensions. For each dimension, a summary is provided of the best evidence on the relationships among phenotypic traits, in particular among those corresponding to different dimensions, and on the relationship between these traits and relevant events in the natural history of COPD. The information has been organized graphically into a phenotypic matrix where each cell representing a pair of phenotypic traits is linked to relevant references. The information provided has the potential to increase our understanding of the heterogeneity of COPD phenotypes and help us plan future studies on aspects that are as yet unexplored.

Clinical experience with insulin detemir, biphasic insulin aspart and insulin aspart in people with type 2 diabetes: Results from the Mumbai cohort of the A1chieve study.

PubMed

Talwalkar, P G; Gupta, Vishal; Kovil, Rajiv

2013-11-01

The A1chieve, a multicentric (28 countries), 24-week, non-interventional study evaluated the safety and effectiveness of insulin detemir, biphasic insulin aspart and insulin aspart in people with T2DM (n = 66,726) in routine clinical care across four continents. Data was collected at baseline, at 12 weeks and at 24 weeks. This short communication presents the results for patients enrolled from Mumbai, India. A total of 2112 patients were enrolled in the study. Four different insulin analogue regimens were used in the study. Patients had started on or were switched to biphasic insulin aspart (n = 1561), insulin detemir (n = 313), insulin aspart (n = 144), basal insulin plus insulin aspart (n = 53) and other insulin combinations (n = 41). At baseline glycaemic control was poor for both insulin naïve (mean HbA1c: 8.7%) and insulin user (mean HbA1c: 9.2%) groups. After 24 weeks of treatment, both the groups showed improvement in HbA1c (insulin naïve: -1.4%, insulin users: -1.8%). SADRs including major hypoglycaemic events or episodes did not occur in any of the study patients. Starting or switching to insulin analogues was associated with improvement in glycaemic control with a low rate of hypoglycaemia.

The Evolution of Phenotypic Switching in Subdivided Populations

PubMed Central

Carja, Oana; Liberman, Uri; Feldman, Marcus W.

2014-01-01

Stochastic switching is an example of phenotypic bet hedging, where offspring can express a phenotype different from that of their parents. Phenotypic switching is well documented in viruses, yeast, and bacteria and has been extensively studied when the selection pressures vary through time. However, there has been little work on the evolution of phenotypic switching under both spatially and temporally fluctuating selection pressures. Here we use a population genetic model to explore the interaction of temporal and spatial variation in determining the evolutionary dynamics of phenotypic switching. We find that the stable switching rate is mainly determined by the rate of environmental change and the migration rate. This stable rate is also a decreasing function of the recombination rate, although this is a weaker effect than those of either the period of environmental change or the migration rate. This study highlights the interplay of spatial and temporal environmental variability, offering new insights into how migration can influence the evolution of phenotypic switching rates, mutation rates, or other sources of phenotypic variation. PMID:24496012

Social cognition, social skill, and the broad autism phenotype.

PubMed

Sasson, Noah J; Nowlin, Rachel B; Pinkham, Amy E

2013-11-01

Social-cognitive deficits differentiate parents with the "broad autism phenotype" from non-broad autism phenotype parents more robustly than other neuropsychological features of autism, suggesting that this domain may be particularly informative for identifying genetic and brain processes associated with the phenotype. The current study examined whether the social-cognitive deficits associated with the broad autism phenotype extend to the general population and relate to reduced social skill. A total of 74 undergraduates completed the Broad Autism Phenotype Questionnaire, three standardized social-cognitive tasks, and a live social interaction with an unfamiliar research assistant. Social broad autism phenotype traits were significantly associated with deficits in social cognition and reduced social skill. In addition, the relationship between social broad autism phenotype traits and social skill was partially mediated by social cognition, suggesting that the reduced interpersonal ability associated with the broad autism phenotype occurs in part because of poorer social-cognitive ability. Together, these findings indicate that the impairments in social cognition and social skill that characterize autism spectrum disorder extend in milder forms to the broad autism phenotype in the general population and suggest a framework for understanding how social broad autism phenotype traits may manifest in diminished social ability.

Geographical variation in neonatal phenotype

PubMed Central

Leary, Sam; Fall, Caroline; Osmond, Clive; Lovel, Hermione; Campbell, Doris; Eriksson, Johan; Forrester, Terrence; Godfrey, Keith; Hill, Jacqui; Jie, Mi; Law, Catherine; Newby, Rachel; Robinson, Sian; Yajnik, Chittaranjan

2009-01-01

Background Recent studies have shown associations between size and body proportions at birth and health outcomes throughout the life cycle, but there are few data on how neonatal phenotype varies in different populations around the world. Methods Data from the UK, Finland, India, Sri Lanka, China, DR Congo, Nigeria and Jamaica (N=22 067) were used to characterise geographical differences in phenotype in singleton, liveborn newborns. Measurements included birthweight, placental weight, length, head, chest, abdominal and arm circumferences and skinfolds. Results Neonates in Europe were the largest, followed by Jamaica, East Asia (China), then Africa and South Asia. Birthweight varied widely (mean values 2730g to 3570g), but in contrast, head circumference was similar in all except China (markedly smaller). The main difference in body proportions between populations was the head to length ratio, with small heads relative to length in China and large heads relative to length in South Asia and Africa. Conclusions These marked geographical differences in neonatal phenotype need to be considered when investigating determinants of fetal growth, and optimal phenotype for short-term and long-term outcomes. PMID:16929412

Biphasic effect of alcohol intake on the development of fatty liver disease.

PubMed

Takahashi, Hirokazu; Ono, Masafumi; Hyogo, Hideyuki; Tsuji, Chika; Kitajima, Yoichiro; Ono, Naofumi; Eguchi, Takahisa; Fujimoto, Kazuma; Chayama, Kazuaki; Saibara, Toshiji; Anzai, Keizo; Eguchi, Yuichiro

2015-11-01

Fatty liver is an important clinical feature not only in alcoholic and non-alcoholic fatty liver diseases, but in other chronic liver diseases as well. Our aim was to elucidate the effect and relationship between habitual alcohol intake and obesity in the development of fatty liver disease. We enrolled 8,029 subjects undergoing abdominal ultrasonography with general medical examinations, and analyzed the factors associated with fatty liver based on daily alcohol intake, body mass index (BMI), and waist circumference. For fatty liver, BMI, waist circumference, total cholesterol, triglycerides, and fasting plasma glucose were significant and independent risk factors. Heavy alcohol intake (50 g/day) was a significant risk factor for fatty liver in women (odds ratio [OR], 3.35). Analysis based on the presence or absence of obesity revealed that moderate alcohol intake was a significant negative risk factor for fatty liver in both male and female obese (BMI ≥25 kg/m(2)) subjects (OR, 0.74 for non-obese and 0.39 for obese patients, respectively). Heavy alcohol intake was also a significant negative risk factor in obese males (0.62). In contrast, heavy alcohol intake was a risk factor in non-obese males (OR, 1.29) and in all females (OR, 2.22 for non-obese and 6.6 for obese patients, respectively). The influence of alcohol intake on fatty liver differed depending on the level of alcohol consumption, gender, and the presence of obesity, and showed biphasic effects.

Investigation of structural resorption behavior of biphasic bioceramics with help of gravimetry, μCT, SEM, and XRD.

PubMed

de Wild, Michael; Amacher, Fabienne; Bradbury, Christopher R; Molenberg, Aart

2016-04-01

Resorbable bone substitute materials are widely used for bone augmentation after tumor resection, parallel to implant placement, or in critical size bone defects. In this study, the structural dissolution of a biphasic calcium phosphate bone substitute material with a hydroxyapatite (HA)/tricalcium phosphate (β-TCP) ratio of 60/40 was investigated by repeatedly placing porous blocks in EDTA solution at 37 °C. At several time points, the blocks were investigated by SEM, µCT, and gravimetry. It was found that always complete 2-3 µm sized grains were removed from the structure and that the β-TCP is dissolved more rapidly. This selective dissolution of the β-TCP grains was confirmed by XRD measurements. The blocks were eroded from the outside toward the center. The structure remained mechanically stable because the central part showed a delayed degradation and because the slower dissolving HA grains preserved the integrity of the structure. © 2015 Wiley Periodicals, Inc.

The genotype-phenotype map of an evolving digital organism.

PubMed

Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

2017-02-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

The genotype-phenotype map of an evolving digital organism

PubMed Central

Zaman, Luis; Wagner, Andreas

2017-01-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable. PMID:28241039

Metabolomic phenotyping of a cloned pig model

PubMed Central

2011-01-01

Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6) by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals. PMID:21859467

Light-controlled biphasic current stimulator IC using CMOS image sensors for high-resolution retinal prosthesis and in vitro experimental results with rd1 mouse.

PubMed

Oh, Sungjin; Ahn, Jae-Hyun; Lee, Sangmin; Ko, Hyoungho; Seo, Jong Mo; Goo, Yong-Sook; Cho, Dong-il Dan

2015-01-01

Retinal prosthetic devices stimulate retinal nerve cells with electrical signals proportional to the incident light intensities. For a high-resolution retinal prosthesis, it is necessary to reduce the size of the stimulator pixels as much as possible, because the retinal nerve cells are concentrated in a small area of approximately 5 mm × 5 mm. In this paper, a miniaturized biphasic current stimulator integrated circuit is developed for subretinal stimulation and tested in vitro. The stimulator pixel is miniaturized by using a complementary metal-oxide-semiconductor (CMOS) image sensor composed of three transistors. Compared to a pixel that uses a four-transistor CMOS image sensor, this new design reduces the pixel size by 8.3%. The pixel size is further reduced by simplifying the stimulation-current generating circuit, which provides a 43.9% size reduction when compared to the design reported to be the most advanced version to date for subretinal stimulation. The proposed design is fabricated using a 0.35 μm bipolar-CMOS-DMOS process. Each pixel is designed to fit in a 50 μ m × 55 μm area, which theoretically allows implementing more than 5000 pixels in the 5 mm × 5 mm area. Experimental results show that a biphasic current in the range of 0 to 300 μA at 12 V can be generated as a function of incident light intensities. Results from in vitro experiments with rd1 mice indicate that the proposed method can be effectively used for retinal prosthesis with a high resolution.

Behavioural phenotypes predict disease susceptibility and infectiousness

PubMed Central

Araujo, Alessandra; Kirschman, Lucas

2016-01-01

Behavioural phenotypes may provide a means for identifying individuals that disproportionally contribute to disease spread and epizootic outbreaks. For example, bolder phenotypes may experience greater exposure and susceptibility to pathogenic infection because of distinct interactions with conspecifics and their environment. We tested the value of behavioural phenotypes in larval amphibians for predicting ranavirus transmission in experimental trials. We found that behavioural phenotypes characterized by latency-to-food and swimming profiles were predictive of disease susceptibility and infectiousness defined as the capacity of an infected host to transmit an infection by contacts. While viral shedding rates were positively associated with transmission, we also found an inverse relationship between contacts and infections. Together these results suggest intrinsic traits that influence behaviour and the quantity of pathogens shed during conspecific interactions may be an important contributor to ranavirus transmission. These results suggest that behavioural phenotypes provide a means to identify individuals more likely to spread disease and thus give insights into disease outbreaks that threaten wildlife and humans. PMID:27555652

Phenotypic characterization of glioblastoma identified through shape descriptors

NASA Astrophysics Data System (ADS)

Chaddad, Ahmad; Desrosiers, Christian; Toews, Matthew

2016-03-01

This paper proposes quantitatively describing the shape of glioblastoma (GBM) tissue phenotypes as a set of shape features derived from segmentations, for the purposes of discriminating between GBM phenotypes and monitoring tumor progression. GBM patients were identified from the Cancer Genome Atlas, and quantitative MR imaging data were obtained from the Cancer Imaging Archive. Three GBM tissue phenotypes are considered including necrosis, active tumor and edema/invasion. Volumetric tissue segmentations are obtained from registered T1˗weighted (T1˗WI) postcontrast and fluid-attenuated inversion recovery (FLAIR) MRI modalities. Shape features are computed from respective tissue phenotype segmentations, and a Kruskal-Wallis test was employed to select features capable of classification with a significance level of p < 0.05. Several classifier models are employed to distinguish phenotypes, where a leave-one-out cross-validation was performed. Eight features were found statistically significant for classifying GBM phenotypes with p <0.05, orientation is uninformative. Quantitative evaluations show the SVM results in the highest classification accuracy of 87.50%, sensitivity of 94.59% and specificity of 92.77%. In summary, the shape descriptors proposed in this work show high performance in predicting GBM tissue phenotypes. They are thus closely linked to morphological characteristics of GBM phenotypes and could potentially be used in a computer assisted labeling system.

Acute encephalopathy with biphasic seizures and late reduced diffusion associated with hemophagocytic syndrome.

PubMed

Tadokoro, Rieko; Okumura, Akihisa; Nakazawa, Tomoyuki; Hara, Satoshi; Yamakawa, Yoko; Kamata, Ayako; Kinoshita, Keiji; Obinata, Kaoru; Shimizu, Toshiaki

2010-06-01

We reported a girl with HHV-6 infection associated with both acute encephalopathy with biphasic seizures and late reduced diffusion, and hemophagocytic syndrome. She had a prolonged convulsion after a one-day history of febrile illness. Cerebrospinal fluid or brain CT showed no abnormalities on admission and her consciousness was recovered on the next day. However, a prolonged seizure and deterioration of consciousness appeared on the sixth day of illness. Diffusion-weighted images revealed marked reduction of water diffusion in the bilateral frontal areas. HHV-6 infection was virologically proven by polymerase chain reaction. She was treated with gamma-globulin, steroid pulse therapy, and brain hypothermia. In addition, decrease in white blood cells and platelet counts, and elevation of liver enzymes and ferritin were noted on the fourth day of illness. Hemophagocytic macrophages were revealed by bone marrow aspiration on the sixth day. Her hematological and blood chemistry abnormalities recovered gradually after steroid pulse therapy. An elevation of interleukin-6, -8, and -10, and tumor necrosis factor in the serum and that of interleukin-4, -6, and-8 in the cerebrospinal fluid were observed at the onset of a late seizure. These facts suggested that hypercytokinemia will be related to the pathogenesis of acute encephalopathy of our patient. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Formation of Biphasic Hydroxylapatite-Beta Magnesium Tricalcium Phosphate in Heat Treated Salmonid Vertebrae.

PubMed

Butler, Don H; Shahack-Gross, Ruth

2017-06-15

Ichthyoarchaeological evidence is uncommon at ancient hunter-gatherer sites from various regions and timeframes. This research contributes to the development of microarchaeological techniques useful for identifying fishing economies in situations where classifiable bones are unavailable. Specifically, traces of heat altered bone mineral in domestic hearths are expected to provide markers for discarded fish remains. We used a series of laboratory incineration experiments to characterize the mineralogy of burned salmonid vertebrae. Fourier transform infrared spectroscopy and x-ray diffraction distinguished the formation of beta magnesium tricalcium phosphate (βMgTCP) at temperatures as low as 600 °C. Bones from a sample of game mammals and birds did not form this phase at temperatures below 1,000 °C. We propose that this neoformed mineral can serve as a proxy for hunter-gatherer salmonid fishing when typical ichthyoarchaeological evidence is absent. Using Fourier transform infrared spectroscopy, it will be possible to rapidly and inexpensively determine the presence of βMgTCP in fragmentary burned bone remains associated with combustion features. The occurrence of βMgTCP in archaeological hearth features will offer a new means of further evaluating the temporal, geographic, and cultural scope of salmonid harvesting. We also acknowledge the value of biphasic hydroxylapatite-βMgTCP recovered from Atlantic salmon vertebrae as a bioceramic.

Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Ninning; Chistol, Gheorghe; Cui, Yuanbo

Multi-subunit ring-shaped ATPases are molecular motors that harness chemical free energy to perform vital mechanical tasks such as polypeptide translocation, DNA unwinding, and chromosome segregation. Previously we reported the intersubunit coordination and stepping behavior of the hexameric ring-shaped ATPase SpoIIIE (Liu et al., 2015). Here we use optical tweezers to characterize the motor’s mechanochemistry. Analysis of the motor response to external force at various nucleotide concentrations identifies phosphate release as the likely force-generating step. Analysis of SpoIIIE pausing indicates that pauses are off-pathway events. Characterization of SpoIIIE slipping behavior reveals that individual motor subunits engage DNA upon ATP binding. Furthermore,more » we find that SpoIIIE’s velocity exhibits an intriguing bi-phasic dependence on force. We hypothesize that this behavior is an adaptation of ultra-fast motors tasked with translocating DNA from which they must also remove DNA-bound protein roadblocks. Based on these results, we formulate a comprehensive mechanochemical model for SpoIIIE.« less

A formal model of asynchronous communication and its use in mechanically verifying a biphase mark protocol

NASA Technical Reports Server (NTRS)

Moore, J. Strother

1992-01-01

In this paper we present a formal model of asynchronous communication as a function in the Boyer-Moore logic. The function transforms the signal stream generated by one processor into the signal stream consumed by an independently clocked processor. This transformation 'blurs' edges and 'dilates' time due to differences in the phases and rates of the two clocks and the communications delay. The model can be used quantitatively to derive concrete performance bounds on asynchronous communications at ISO protocol level 1 (physical level). We develop part of the reusable formal theory that permits the convenient application of the model. We use the theory to show that a biphase mark protocol can be used to send messages of arbitrary length between two asynchronous processors. We study two versions of the protocol, a conventional one which uses cells of size 32 cycles and an unconventional one which uses cells of size 18. We conjecture that the protocol can be proved to work under our model for smaller cell sizes and more divergent clock rates but the proofs would be harder.

Kinetic modelling and microbial community assessment of anaerobic biphasic fixed film bioreactor treating distillery spent wash.

PubMed

Acharya, Bhavik K; Pathak, Hilor; Mohana, Sarayu; Shouche, Yogesh; Singh, Vasdev; Madamwar, Datta

2011-08-01

Anaerobic digestion, microbial community structure and kinetics were studied in a biphasic continuously fed, upflow anaerobic fixed film reactor treating high strength distillery wastewater. Treatment efficiency of the bioreactor was investigated at different hydraulic retention times (HRT) and organic loading rates (OLR 5-20 kg COD m⁻³ d⁻¹). Applying the modified Stover-Kincannon model to the reactor, the maximum removal rate constant (U(max)) and saturation value constant (K(B)) were found to be 2 kg m⁻³ d⁻¹ and 1.69 kg m⁻³ d⁻¹ respectively. Bacterial community structures of acidogenic and methanogenic reactors were assessed using culture-independent analyses. Sequencing of 16S rRNA genes exhibited a total of 123 distinct operational taxonomic units (OTUs) comprising 49 from acidogenic reactor and 74 (28 of eubacteria and 46 of archaea) from methanogenic reactor. The findings reveal the role of Lactobacillus sp. (Firmicutes) as dominant acid producing organisms in acidogenic reactor and Methanoculleus sp. (Euryarchaeotes) as foremost methanogens in methanogenic reactor. Copyright © 2011 Elsevier Ltd. All rights reserved.

Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE

DOE PAGES

Liu, Ninning; Chistol, Gheorghe; Cui, Yuanbo; ...

2018-03-05

Multi-subunit ring-shaped ATPases are molecular motors that harness chemical free energy to perform vital mechanical tasks such as polypeptide translocation, DNA unwinding, and chromosome segregation. Previously we reported the intersubunit coordination and stepping behavior of the hexameric ring-shaped ATPase SpoIIIE (Liu et al., 2015). Here we use optical tweezers to characterize the motor’s mechanochemistry. Analysis of the motor response to external force at various nucleotide concentrations identifies phosphate release as the likely force-generating step. Analysis of SpoIIIE pausing indicates that pauses are off-pathway events. Characterization of SpoIIIE slipping behavior reveals that individual motor subunits engage DNA upon ATP binding. Furthermore,more » we find that SpoIIIE’s velocity exhibits an intriguing bi-phasic dependence on force. We hypothesize that this behavior is an adaptation of ultra-fast motors tasked with translocating DNA from which they must also remove DNA-bound protein roadblocks. Based on these results, we formulate a comprehensive mechanochemical model for SpoIIIE.« less

Biphasic photoelectrochemical sensing strategy based on in situ formation of CdS quantum dots for highly sensitive detection of acetylcholinesterase activity and inhibition.

PubMed

Hou, Ting; Zhang, Lianfang; Sun, Xinzhi; Li, Feng

2016-01-15

Herein, we reported a facile and highly sensitive biphasic photoelectrochemical (PEC) sensing strategy based on enzymatic product-mediated in situ formation of CdS quantum dots (QDs), and assayed the activity and inhibition of acetylcholinesterase (AChE) in its optimal state. Upon the hydrolysis of acetylthiocholine catalyzed by AChE, the product thiocholine stabilizes the in situ formation of CdS QDs in homogenous solution. Due to the electrostatic attraction, the resulting tertiary amino group-functionalized CdS QDs are attached to the surface of the negatively charged indium tin oxide (ITO) electrode, generating significant PEC response upon illumination in the presence of electron donors. By taking full advantage of the in situ formation of CdS QDs in homogenous solution, this strategy is capable of detecting AChE activity and inhibition in its optimal state. A directly measured detection limit of 0.01mU/mL for AChE activity is obtained, which is superior to those obtained by some fluorescence methods. The inhibition of AChE activity by aldicarb is successfully detected, and the corresponding IC50 is determined to be 13μg/L. In addition to high sensitivity and good selectivity, this strategy also exhibits additional advantages of simplicity, low cost and easy operation. To the best of our knowledge, the as-proposed strategy is the first example demonstrating the application of CdS QDs formed in situ for biphasic PEC detection of enzyme activity and inhibition. More significantly, it opens up a new horizon for the development of homogenous PEC sensing platforms, and has great potential in probing many other analytes. Copyright © 2015 Elsevier B.V. All rights reserved.

CKD Self-management: Phenotypes and Associations With Clinical Outcomes.

PubMed

Schrauben, Sarah J; Hsu, Jesse Y; Rosas, Sylvia E; Jaar, Bernard G; Zhang, Xiaoming; Deo, Rajat; Saab, Georges; Chen, Jing; Lederer, Swati; Kanthety, Radhika; Hamm, L Lee; Ricardo, Ana C; Lash, James P; Feldman, Harold I; Anderson, Amanda H

2018-03-24

To slow chronic kidney disease (CKD) progression and its complications, patients need to engage in self-management behaviors. The objective of this study was to classify CKD self-management behaviors into phenotypes and assess the association of these phenotypes with clinical outcomes. Prospective cohort study. Adults with mild to moderate CKD enrolled in the Chronic Renal Insufficiency Cohort (CRIC) Study. 3,939 participants in the CRIC Study recruited between 2003 and 2008 served as the derivation cohort and 1,560 participants recruited between 2013 and 2015 served as the validation cohort. CKD self-management behavior phenotypes. CKD progression, atherosclerotic events, heart failure events, death from any cause. Latent class analysis stratified by diabetes was used to identify CKD self-management phenotypes based on measures of body mass index, diet, physical activity, blood pressure, smoking status, and hemoglobin A 1c concentration (if diabetic); Cox proportional hazards models. 3 identified phenotypes varied according to the extent of implementation of recommended CKD self-management behaviors: phenotype I characterized study participants with the most recommended behaviors; phenotype II, participants with a mixture of recommended and not recommended behaviors; and phenotype III, participants with minimal recommended behaviors. In multivariable-adjusted models for those with and without diabetes, phenotype III was strongly associated with CKD progression (HRs of 1.82 and 1.49), death (HRs of 1.95 and 4.14), and atherosclerotic events (HRs of 2.54 and 1.90; each P < 0.05). Phenotype II was associated with atherosclerotic events and death among those with and without diabetes. No consensus definition of CKD self-management; limited to baseline behavior data. There are potentially 3 CKD self-management behavior phenotypes that distinguish risk for clinical outcomes. These phenotypes may inform the development of studies and guidelines regarding optimal self

Rare Variant Association Test with Multiple Phenotypes

PubMed Central

Lee, Selyeong; Won, Sungho; Kim, Young Jin; Kim, Yongkang; Kim, Bong-Jo; Park, Taesung

2016-01-01

Although genome-wide association studies (GWAS) have now discovered thousands of genetic variants associated with common traits, such variants cannot explain the large degree of “missing heritability,” likely due to rare variants. The advent of next generation sequencing technology has allowed rare variant detection and association with common traits, often by investigating specific genomic regions for rare variant effects on a trait. Although multiply correlated phenotypes are often concurrently observed in GWAS, most studies analyze only single phenotypes, which may lessen statistical power. To increase power, multivariate analyses, which consider correlations between multiple phenotypes, can be used. However, few existing multi-variant analyses can identify rare variants for assessing multiple phenotypes. Here, we propose Multivariate Association Analysis using Score Statistics (MAAUSS), to identify rare variants associated with multiple phenotypes, based on the widely used Sequence Kernel Association Test (SKAT) for a single phenotype. We applied MAAUSS to Whole Exome Sequencing (WES) data from a Korean population of 1,058 subjects, to discover genes associated with multiple traits of liver function. We then assessed validation of those genes by a replication study, using an independent dataset of 3,445 individuals. Notably, we detected the gene ZNF620 among five significant genes. We then performed a simulation study to compare MAAUSS's performance with existing methods. Overall, MAAUSS successfully conserved type 1 error rates and in many cases, had a higher power than the existing methods. This study illustrates a feasible and straightforward approach for identifying rare variants correlated with multiple phenotypes, with likely relevance to missing heritability. PMID:28039885

The evolution of phenotypic correlations and ‘developmental memory’

PubMed Central

Watson, Richard A.; Wagner, Günter P.; Pavlicev, Mihaela; Weinreich, Daniel M.; Mills, Rob

2014-01-01

Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent non-linear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can ‘store’ and ‘recall’ multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and ‘generalise’ (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviours follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well-understood in the context of neural networks. This helps to explain how development facilitates the evolution of high-fitness phenotypes and how this ability changes over evolutionary time. PMID:24351058

Macrophage Phenotypes Regulate Scar Formation and Chronic Wound Healing.

PubMed

Hesketh, Mark; Sahin, Katherine B; West, Zoe E; Murray, Rachael Z

2017-07-17

Macrophages and inflammation play a beneficial role during wound repair with macrophages regulating a wide range of processes, such as removal of dead cells, debris and pathogens, through to extracellular matrix deposition re-vascularisation and wound re-epithelialisation. To perform this range of functions, these cells develop distinct phenotypes over the course of wound healing. They can present with a pro-inflammatory M1 phenotype, more often found in the early stages of repair, through to anti-inflammatory M2 phenotypes that are pro-repair in the latter stages of wound healing. There is a continuum of phenotypes between these ranges with some cells sharing phenotypes of both M1 and M2 macrophages. One of the less pleasant consequences of quick closure, namely the replacement with scar tissue, is also regulated by macrophages, through their promotion of fibroblast proliferation, myofibroblast differentiation and collagen deposition. Alterations in macrophage number and phenotype disrupt this process and can dictate the level of scar formation. It is also clear that dysregulated inflammation and altered macrophage phenotypes are responsible for hindering closure of chronic wounds. The review will discuss our current knowledge of macrophage phenotype on the repair process and how alterations in the phenotypes might alter wound closure and the final repair quality.

REGULATION OF GEOGRAPHIC VARIABILITY IN HAPLOID:DIPLOD RATIOS OF BIPHASIC SEAWEED LIFE CYCLES(1).

PubMed

da Silva Vieira, Vasco Manuel Nobre de Carvalho; Santos, Rui Orlando Pimenta

2012-08-01

The relative abundance of haploid and diploid individuals (H:D) in isomorphic marine algal biphasic cycles varies spatially, but only if vital rates of haploid and diploid phases vary differently with environmental conditions (i.e. conditional differentiation between phases). Vital rates of isomorphic phases in particular environments may be determined by subtle morphological or physiological differences. Herein, we test numerically how geographic variability in H:D is regulated by conditional differentiation between isomorphic life phases and the type of life strategy of populations (i.e. life cycles dominated by reproduction, survival or growth). Simulation conditions were selected using available data on H:D spatial variability in seaweeds. Conditional differentiation between ploidy phases had a small effect on the H:D variability for species with life strategies that invest either in fertility or in growth. Conversely, species with life strategies that invest mainly in survival, exhibited high variability in H:D through a conditional differentiation in stasis (the probability of staying in the same size class), breakage (the probability of changing to a smaller size class) or growth (the probability of changing to a bigger size class). These results were consistent with observed geographic variability in H:D of natural marine algae populations. © 2012 Phycological Society of America.

[Development of biphasic drug-loading lipid emulsion of Salvia miltiorrhiza and its quality evaluation].

PubMed

Wang, Yin-Yan; Li, Xi; Lai, Xiu-Jun; Li, Wei; Yang, Ya-Jing; Chu, Ting; Mao, Sheng-Jun

2014-10-01

The feasibility of simultaneously loading both liposoluble and water-soluble components of Salvia miltiorrhiza in emulsion was discussed, in order to provide new ideas in comprehensive application of effective components in S. miltiorrhiza in terms of technology of pharmaceutics. With tanshinone II (A) and salvianolic acid B as raw materials, soybean phospholipid and poloxamer 188 as emulsifiers, and glycerin as isoosmotic regulator, the central composite design-response surface method was employed to optimize the prescription. The coarse emulsion was prepared with the high-speed shearing method and then homogenized in the high pressure homogenizer. The biphasic drug-loading intravenous emulsion was prepared to investigate its pharmaceutical properties and stability. The prepared emulsion is orange-yellow, with the average diameter of 241 nm and Zeta potential of -35.3 mV. Specifically, the drug loading capacity of tanshinone II (A) and salvianolic acid B were 0.5 g x L(-1) and 1 g x L(-1), respectively, with a good stability among long-term retention samples. According to the results, the prepared emulsion could load liposoluble tanshinone II (A) and water-soluble salvianolic acid B simultaneously, which lays a pharmaceutical foundation for giving full play to the efficacy of S. miltiorrhiza.

Trypsin induces biphasic muscle contraction and relaxation via transient receptor potential vanilloid 1 and neurokinin receptors 1/2 in porcine esophageal body.

PubMed

Xiaopeng, Bai; Tanaka, Yoshimasa; Ihara, Eikichi; Hirano, Katsuya; Nakano, Kayoko; Hirano, Mayumi; Oda, Yoshinao; Nakamura, Kazuhiko

2017-02-15

Duodenal reflux of fluids containing trypsin relates to refractory gastroesophageal reflux disease (GERD). Esophageal peristalsis and clearance are important factors in GERD pathogenesis. However, the function of trypsin in esophageal body contractility is not fully understood. In this study, effects of trypsin on circular smooth muscle (CSM) and longitudinal smooth muscle (LSM) of the porcine esophageal body were examined. Trypsin elicited a concentration dependent biphasic response, a major contraction and a subsequent relaxation only in CSM. In CSM, contraction occurred at trypsin concentrations of 100nM and relaxation at 1μM. A proteinase-activated receptor (PAR)2 activating peptide, SLIGKV-NH 2 (1mM), induced a monophasic contraction. Those responses were unaffected by tetrodotoxin though abolished by the gap junction uncouplers carbenoxolone and octanol. They were also partially inhibited by a transient receptor potential vanilloid type 1 (TRPV1) antagonist and abolished by combination of neurokinin receptor 1 (NK 1 ) and NK 2 antagonists, but not by an NK 3 antagonist, suggesting a PAR2-TRPV1-substance P pathway in sensory neurons. Substance P (100nM), an agonist for various NK receptors (NK 1 , NK 2 and NK 3 ) with differing affinities, induced significant contraction in CSM, but not in LSM. The contraction was also blocked by the combination of NK 1 and NK 2 antagonists, but not by the NK 3 antagonist. Moreover, substance P-induced contractions were unaffected by the TRPV1 antagonist, but inhibited by a gap junction uncoupler. In conclusion, trypsin induced a biphasic response only in CSM and this was mediated by PAR2, TRPV1 and NK 1/2 . Gap junctions were indispensable in this tachykinin-induced response. Copyright © 2017 Elsevier B.V. All rights reserved.

Ion Pair Formation between Tertiary Aliphatic Amines and Perchlorate in the Biphasic Water/Dichloromethane System.

PubMed

Badocco, Denis; Di Marco, Valerio; Venzo, Alfonso; Frasconi, Marco; Frezzato, Diego; Pastore, Paolo

2017-10-12

The ability of aliphatic amines (AAs), namely, tripropylamine (TPrA), trisobutylamine (TisoBuA), and tributylamine (TBuA), to form ion pairs with perchlorate anion (ClO 4 - ) in biphasic aqueous/dichloromethane (CH 2 Cl 2 ) mixtures containing ClO 4 - 0.1 M has been demonstrated by GC with flame ionization (FID) and mass detectors (MS) and by NMR measurements. The extraction efficiency of the AAs to the organic phase was modeled by equations that were used to fit the experimental GC data, allowing us to determine values for K P (partition constant of the free AA), K IP (formation constant of the ion pair), and K P IP (partition constant of the ion pair) for TPrA, TisoBuA, and TBuA at 25 °C. Ion pairs were shown to form in CH 2 Cl 2 also when ClO 4 - is replaced by other inorganic anions, like NO 3 - , ClO 3 - , Cl - , H 2 PO 4 - , and IO 3 - . No ion pairs formed when CH 2 Cl 2 was replaced by n-hexane, suggesting that aliphatic amine ion pairs can form in polar organic solvents but not in nonpolar ones.

Mono- and biphasic plasma concentration-time curves of mesalazine from a 500 mg suppository in healthy male volunteers controlled by the time of defecation before dosing.

PubMed

Vree, T B; Dammers, E; Exler, P S; Maes, R A

2000-06-01

This study was based on data from a bioequivalence study (n=24) of two different formulations of suppositories containing 500 mg mesalazine (formulation I and II), with a similar dissolution profile in phosphate buffer pH 6.8. There was a large intra- and intersubject variability in the plasma concentration-time curves of mesalazine from both suppositories. The aim of the investigation was to identify the parameters that caused the observed large variations in release and absorption of mesalazine in the rectum. Plasma mesalazine and acetylmesalazine, and urine acetylmesalazine concentrations were determined according to validated methods involving HPLC analysis with coulometric detection. Lower limit of quantitation values were respectively 10.4 and 19.4 ng mL(-1) in plasma and 0.96 microg mL(-1) in urine. The time of defecation before and after insertion was recorded. There was a clear distinction between subjects who showed monophasic mesalazine release/absorption and those who showed biphasic and more extended release/absorption. With formulation I there was a correlation between time of defecation before dosing and the type of absorption, monophasic and biphasic absorbers showed a significant difference in the time of defecation, e.g. 9.7+/-5.6 h vs 18.8+/-11.9 h (P = 0.0218). The impact of time of defecation before dosing was non-significant with formulation II, 16.7+/-7.2 h vs 15.1+/-4.2 h (P = 0.67). The impact of the time elapsed between administration and time of defecation after the insertion of the suppository was not significant for the type of release/absorption. The plasma concentration-time curves of the metabolite ran parallel to that of the parent drug, the more parent drug was released/absorbed, the more was acetylated (P = 0.0013) and excreted into the urine (P = 0.0004). After absorption the compound was metabolized into acetylmesalazine, and renally excreted (12-13% of the dose). Monophasic release/ absorption resulted in 7.1% metabolite with I

Study of the sensitising potential of various textile dyes using a biphasic murine local lymph node assay.

PubMed

Ahuja, V; Platzek, T; Fink, H; Sonnenburg, A; Stahlmann, R

2010-09-01

Disperse dyes, which are suitable for dyeing synthetic fibres, are responsible for the great majority of allergic contact dermatitis (ACD) cases to textile dyes. The aim of the present study was to investigate the sensitising potential of various disperse dyes using a biphasic protocol of the local lymph node assay (LLNA). Briefly, mice were shaved over a surface of approximately 2 cm(2) on their backs and treated using a "sensitisation-challenge protocol". The shaved surface was treated once daily on days 1-3 with 50 microl of the test solution. Animals remained untreated on days 4-14. On days 15-17, mice were treated with 25 microl of the test solution on the dorsum of both ears. Mice were killed on day 19 with deep CO(2) anaesthesia, the lymph nodes prepared and various end points, such as ear thickness, ear punch weight, lymph node weight, lymph node cell count and the proportion of various lymphocyte subpopulations, were determined by flow cytometry. The results were compared to control group treated with the vehicle alone. Our results showed that almost all of the tested textile dyes caused a significant increase in lymph node cell count and lymph node weight. We also observed an increase in ear thickness and ear punch weight in most of the concentrations tested for various textile dyes. We observed a decrease in CD4+ and CD8+ cells and an increase in CD19+, CD45+ and CD45+/1A+ cells in most of the cases, which is characteristic for allergens. The CD4+/CD69+ cells increased in only few experiments mainly with Disperse Blue 124 and Disperse Blue 106. Based on our results, the disperse dyes could be arranged in four groups on the basis of their sensitising potency in the following decreasing order (in parenthesis: lowest concentration causing a significant increase in lymph node cell number): group 1, strong: Disperse Blue 124 and Disperse Blue 106 (0.003%); group 2, moderate: Disperse Red 1 and Disperse Blue 1 (3%); group 3, weak: Disperse Orange 37 and

Phenotypic plasticity in a population of odonates.

PubMed

Bowman, Randi M; Schmidt, Sharol; Weeks, Chelsea; Clark, Hunter; Brown, Christopher; Latta, Leigh C; Edgehouse, Michael

2018-05-31

The maintenance of phenotypic plasticity within a species ensures survival through environmental flux. Plastic strategies are increasingly important given the number and magnitude of modern anthropogenic threats to the environment. We tested for phenotypic plasticity in the odonate Argia vivida in response to resource limitation. By limiting food availability, effectively inducing hunger, we were able to quantify shifts in agonistic behavior during intraspecific interactions. Scoring behavior in one-on-one combat trials after 1 and 4 days without food revealed phenotypic plasticity. Three classes of genotypes were identified, genotypes exhibiting either increased aggression, decreased aggression, or no phenotypic plasticity, in response to resource limitation. The variable plastic strategies in this population of odonates likely aids in maintaining fitness in fluctuating environments.

Low-cost industrially available molybdenum boride and carbide as "platinum-like" catalysts for the hydrogen evolution reaction in biphasic liquid systems.

PubMed

Scanlon, Micheál D; Bian, Xiaojun; Vrubel, Heron; Amstutz, Véronique; Schenk, Kurt; Hu, Xile; Liu, BaoHong; Girault, Hubert H

2013-02-28

Rarely reported low-cost molybdenum boride and carbide microparticles, both of which are available in abundant quantities due to their widespread use in industry, adsorb at aqueous acid-1,2-dichloroethane interfaces and efficiently catalyse the hydrogen evolution reaction in the presence of the organic electron donor - decamethylferrocene. Kinetic studies monitoring biphasic reactions by UV/vis spectroscopy, and further evidence provided by gas chromatography, highlight (a) their superior rates of catalysis relative to other industrially significant transition metal carbides and silicides, as well as a main group refractory compound, and (b) their highly comparable rates of catalysis to Pt microparticles of similar dimensions. Insight into the catalytic processes occurring for each adsorbed microparticle was obtained by voltammetry at the liquid-liquid interface.

Behavioural phenotypes predict disease susceptibility and infectiousness.

PubMed

Araujo, Alessandra; Kirschman, Lucas; Warne, Robin W

2016-08-01

Behavioural phenotypes may provide a means for identifying individuals that disproportionally contribute to disease spread and epizootic outbreaks. For example, bolder phenotypes may experience greater exposure and susceptibility to pathogenic infection because of distinct interactions with conspecifics and their environment. We tested the value of behavioural phenotypes in larval amphibians for predicting ranavirus transmission in experimental trials. We found that behavioural phenotypes characterized by latency-to-food and swimming profiles were predictive of disease susceptibility and infectiousness defined as the capacity of an infected host to transmit an infection by contacts. While viral shedding rates were positively associated with transmission, we also found an inverse relationship between contacts and infections. Together these results suggest intrinsic traits that influence behaviour and the quantity of pathogens shed during conspecific interactions may be an important contributor to ranavirus transmission. These results suggest that behavioural phenotypes provide a means to identify individuals more likely to spread disease and thus give insights into disease outbreaks that threaten wildlife and humans. © 2016 The Author(s).

Biphasic thermoelectric materials derived from the half-Heusler/full-Heusler system Ti-Ni-Sn

NASA Astrophysics Data System (ADS)

Douglas, Jason Everett

Among the possible avenues for increasing the efficiency of global energy usage, thermoelectrics are an exciting, solid-state option. Thermoelectric materials, which convert an internal temperature gradient into a voltage and vice versa, have found applications in refrigeration as well as power generation from waste heat. TiNiSn, a semiconductor of the half-Heusler (hH) crystal structure, is of particular interest due to its very favorable electronic transport properties, conductivity (sigma) and Seebeck coefficient ( S), at relevant temperature regimes (between 600 K and 900 K). Unfortunately, its overall efficiency is hampered by a comparatively high thermal conductivity (kappa). In the design of thermoelectric materials, a number of approaches have been taken to increase the thermoelectric figure of merit, ZT = ( S2sigma/kappa)T, where T is temperature. In this work we examine how microstructure can be used to alter these thermoelectric propertiesin a biphasic Ti-Ni-Sn materials containing full-Heusler (fH) TiNi2Sn embedded within hH thermoelectric TiNiSn. We explored a wide range of Ni compositions in TiNi1+xSn--from stoichiometric TiNiSn to high Heusler volume fraction, TiNi1.25Sn--materials prepared by levitation induction melting followed by annealing. Phase distributions and microstructure were characterized using synchrotron x-ray diffraction and optical and electron microscopy. In a sample of the nominal composition TiNi1.15Sn, a significant decrease in thermal conductivity (about 30%) is observed for the biphasic material despite the metallic second-phase particles existing at the micrometer scale; a 50% increase in the electrical conductivity is also measured. These result in a maximum figure of merit, ZT, of 0.44 at 800 K, which is 25% greater than is observed for the x = 0 sample. Density functional theory calculations using hybrid functionals were performed to determine band alignments between the half- and full-Heusler compounds, as well as

Phenotype detection in morphological mutant mice using deformation features.

PubMed

Roy, Sharmili; Liang, Xi; Kitamoto, Asanobu; Tamura, Masaru; Shiroishi, Toshihiko; Brown, Michael S

2013-01-01

Large-scale global efforts are underway to knockout each of the approximately 25,000 mouse genes and interpret their roles in shaping the mammalian embryo. Given the tremendous amount of data generated by imaging mutated prenatal mice, high-throughput image analysis systems are inevitable to characterize mammalian development and diseases. Current state-of-the-art computational systems offer only differential volumetric analysis of pre-defined anatomical structures between various gene-knockout mice strains. For subtle anatomical phenotypes, embryo phenotyping still relies on the laborious histological techniques that are clearly unsuitable in such big data environment. This paper presents a system that automatically detects known phenotypes and assists in discovering novel phenotypes in muCT images of mutant mice. Deformation features obtained from non-linear registration of mutant embryo to a normal consensus average image are extracted and analyzed to compute phenotypic and candidate phenotypic areas. The presented system is evaluated using C57BL/10 embryo images. All cases of ventricular septum defect and polydactyly, well-known to be present in this strain, are successfully detected. The system predicts potential phenotypic areas in the liver that are under active histological evaluation for possible phenotype of this mouse line.

Auditory Phenotype of Smith-Magenis Syndrome

ERIC Educational Resources Information Center

Brendal, Megan A.; King, Kelly A.; Zalewski, Christopher K.; Finucane, Brenda M.; Introne, Wendy; Brewer, Carmen C.; Smith, Ann C. M.

2017-01-01

Purpose: The purpose of this study was to describe the auditory phenotype of a large cohort with Smith-Magenis syndrome (SMS), a rare disorder including physical anomalies, cognitive deficits, sleep disturbances, and a distinct behavioral phenotype. Method: Hearing-related data were collected for 133 individuals with SMS aged 1-49 years. Audiogram…

Parental effects and the evolution of phenotypic memory.

PubMed

Kuijper, B; Johnstone, R A

2016-02-01

Despite growing evidence for nongenetic inheritance, the ecological conditions that favour the evolution of heritable parental or grandparental effects remain poorly understood. Here, we systematically explore the evolution of parental effects in a patch-structured population with locally changing environments. When selection favours the production of a mix of offspring types, this mix differs according to the parental phenotype, implying that parental effects are favoured over selection for bet-hedging in which the mixture of offspring phenotypes produced does not depend on the parental phenotype. Positive parental effects (generating a positive correlation between parental and offspring phenotype) are favoured in relatively stable habitats and when different types of local environment are roughly equally abundant, and can give rise to long-term parental inheritance of phenotypes. By contrast, unstable habitats can favour negative parental effects (generating a negative correlation between parental and offspring phenotype), and under these circumstances, even slight asymmetries in the abundance of local environmental states select for marked asymmetries in transmission fidelity. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Relational machine learning for electronic health record-driven phenotyping.

PubMed

Peissig, Peggy L; Santos Costa, Vitor; Caldwell, Michael D; Rottscheit, Carla; Berg, Richard L; Mendonca, Eneida A; Page, David

2014-12-01

Electronic health records (EHR) offer medical and pharmacogenomics research unprecedented opportunities to identify and classify patients at risk. EHRs are collections of highly inter-dependent records that include biological, anatomical, physiological, and behavioral observations. They comprise a patient's clinical phenome, where each patient has thousands of date-stamped records distributed across many relational tables. Development of EHR computer-based phenotyping algorithms require time and medical insight from clinical experts, who most often can only review a small patient subset representative of the total EHR records, to identify phenotype features. In this research we evaluate whether relational machine learning (ML) using inductive logic programming (ILP) can contribute to addressing these issues as a viable approach for EHR-based phenotyping. Two relational learning ILP approaches and three well-known WEKA (Waikato Environment for Knowledge Analysis) implementations of non-relational approaches (PART, J48, and JRIP) were used to develop models for nine phenotypes. International Classification of Diseases, Ninth Revision (ICD-9) coded EHR data were used to select training cohorts for the development of each phenotypic model. Accuracy, precision, recall, F-Measure, and Area Under the Receiver Operating Characteristic (AUROC) curve statistics were measured for each phenotypic model based on independent manually verified test cohorts. A two-sided binomial distribution test (sign test) compared the five ML approaches across phenotypes for statistical significance. We developed an approach to automatically label training examples using ICD-9 diagnosis codes for the ML approaches being evaluated. Nine phenotypic models for each ML approach were evaluated, resulting in better overall model performance in AUROC using ILP when compared to PART (p=0.039), J48 (p=0.003) and JRIP (p=0.003). ILP has the potential to improve phenotyping by independently delivering

Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits.

PubMed

Chitwood, Daniel H; Topp, Christopher N

2015-04-01

The plant phenotype is infinite. Plants vary morphologically and molecularly over developmental time, in response to the environment, and genetically. Exhaustive phenotyping remains not only out of reach, but is also the limiting factor to interpreting the wealth of genetic information currently available. Although phenotyping methods are always improving, an impasse remains: even if we could measure the entirety of phenotype, how would we interpret it? We propose the concept of cryptotype to describe latent, multivariate phenotypes that maximize the separation of a priori classes. Whether the infinite points comprising a leaf outline or shape descriptors defining root architecture, statistical methods to discern the quantitative essence of an organism will be required as we approach measuring the totality of phenotype. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthesis of furfural from xylose, xylan, and biomass using AlCl3·6H2O in biphasic media via xylose isomerization to xylulose.

PubMed

Yang, Yu; Hu, Chang-Wei; Abu-Omar, Mahdi M

2012-02-13

Furfural was prepared in high yields (75 %) from the reaction of xylose in a water-tetrahydrofuran biphasic medium containing AlCl(3)·6H2O and NaCl under microwave heating at 140 °C. The reaction profile revealed the formation of xylulose as an intermediate en route to the dehydration product (furfural). The reaction under these conditions reached completion in 45 min. The aqueous phase containing AlCl(3)·6H(2)O and NaCl could be recycled multiple times (>5) without any loss of activity or selectivity for furfural. Extension of this biphasic reaction system to include xylan as the starting material afforded furfural in 64 % yield. The use of corn stover, pinewood, switchgrass, and poplar gave furfural in 55, 38, 56, and 64 % yield, respectively, at 160 °C. Even though AlCl(3)·6H(2)O did not affect the conversion of crystalline cellulose, moderate yields of the by-product 5-hydroxymethylfurfural (HMF) were noted. The highest HMF yield of 42 % was obtained from pinewood. The coproduction of HMF and furfural from biomass was attributed to the weakening of the cellulose network in the biomass, as a result of hemicellulose hydrolysis. The multifunctional capacity of AlCl(3)·6H(2)O (hemicellulose hydrolysis, xylose isomerization, and xylulose dehydration) in combination with its ease of recyclability make it an attractive candidate/catalyst for the selective synthesis of furfural from various biomass feedstocks. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Neuroanatomy of the Autistic Phenotype

ERIC Educational Resources Information Center

Fahim, Cherine; Meguid, Nagwa A.; Nashaat, Neveen H.; Yoon, Uicheul; Mancini-Marie, Adham; Evans, Alan C.

2012-01-01

The autism phenotype is associated with an excess of brain volume due in part to decreased pruning during development. Here we aimed at assessing brain volume early in development to further elucidate previous findings in autism and determine whether this pattern is restricted to idiopathic autism or shared within the autistic phenotype (fragile X…

Daddy issues: paternal effects on phenotype

PubMed Central

Rando, Oliver J.

2012-01-01

The once-popular, then heretical, idea that ancestral environment can affect the phenotype of future generations is coming back into vogue, due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the phenotype of progeny is now a tractable question, and researchers are exploring potential mechanisms underlying such effects. PMID:23141533

New phenotypes for new breeding goals in pigs.

PubMed

Merks, J W M; Mathur, P K; Knol, E F

2012-04-01

Pig breeders in the past have adopted their breeding goals according to the needs of the producers, processors and consumers and have made remarkable genetic improvements in the traits of interest. However, it is becoming more and more challenging to meet the market needs and expectations of consumers and in general of the citizens. In view of the current and future trends, the breeding goals have to include several additional traits and new phenotypes. These phenotypes include (a) vitality from birth to slaughter, (b) uniformity at different levels of production, (c) robustness, (d) welfare and health and (e) phenotypes to reduce carbon footprint. Advancements in management, genomics, statistical models and other technologies provide opportunities for recording these phenotypes. These new developments also provide opportunities for making effective use of the new phenotypes for faster genetic improvement to meet the newly adapted breeding goals.

[Biocompatibility of HA/TCP biphasic ceramics with co-cultured human osteoblasts in vitro].

PubMed

Lu, X; Li, S; Zhang, J; Zhang, Z; Lu, B; Bu, H; Li, Y; Cheng, J

2001-12-01

The biocompatibility of HA/TCP ceramic was evaluated by investigation of attachment and growth of osteoblasts on biomaterial, as well as monitoring the effects of biomaterial on expression of functional phenotypes of co-cultured osteoblasts in vitro. When co-cultured with HA/TCP ceramics, osteoblasts firstly attached to the surface of HA/TCP disk, then attached to notches and grew into the micropores of biomaterial during further culture period. At last, the ceramics were almost packed with osteoblasts. Additionally, osteoblasts co-cultured with HA/TCP were similar to osteoblasts cultured under normal condition in osteoblastic phenotypes; the secreted lots of collagen type I, possess strong activity of Alkaline Phosphatase and mineralized extracellular matrix. The fact that osteoblasts could grow well on HA/TCP ceramics and the biomaterial did not affect their physiological function suggest that HA/TCP ceramic is biocompatible with human osteoblasts.

Probing the limit of magnesium uptake by β-tricalcium phosphate in biphasic mixtures formed from calcium deficient apatites

NASA Astrophysics Data System (ADS)

Kumar, P. Nandha; Mishra, Sandeep K.; Kannan, S.

2015-11-01

A series of magnesium doped non-stoichiometric calcium deficient apatites were synthesized through an aqueous precipitation route. The resultant structural changes during heat treatment were investigated by X-ray diffraction, Raman and FT-IR spectroscopy and Rietveld refinement. The results confirmed the formation of biphasic mixtures comprising Ca10(PO4)6(OH)2 and β-Ca3(PO4)2 after heat treatment at 1000 °C with the preferential occupancy of Mg2+ at the crystal lattice of β-Ca3(PO4)2. The concentration of Mg2+ uptake in β-Ca3(PO4)2 is limited till reaching the stoichiometric ratio of (Ca+Mg)/P=1.67 and beyond this stoichiometric value [(Ca+Mg)/P>1.67], Mg2+ precipitates as Mg(OH)2 and thereafter gets converted to MgO during heat treatment. Any kind of Mg2+ uptake in the crystal lattice of Ca10(PO4)6(OH)2 is discarded from the investigation.

Improving the extraction of l-phenylalanine by the use of ionic liquids as adjuvants in aqueous biphasic systems.

PubMed

Yang, Hongpeng; Chen, Li; Zhou, Cunshan; Yu, Xiaojie; Yagoub, Abu ElGasim A; Ma, Haile

2018-04-15

Polyethylene glycol (PEG) is widely used in the polymer-salt systems. However, the low polarity of the PEG-rich phase limits the application of aqueous biphasic systems (ABS). To overcome this disadvantage, a small quantity of ionic liquid (IL) was used as an adjuvant in ABS to enlarge the polarity range. Therefore, an innovative study involving addition of 4wt% imidazolium-based ILs to the PEG 600/NaH 2 PO 4 ABS, aiming at controlling the phase behavior and extraction ability, was carried out. The phase diagrams, the tie-lines and the partitioning behavior of l-phenylalanine and ILs were studied in these systems. The results reveal that l-phenylalanine preferentially partitions for the PEG-rich phase. The addition of 4wt% IL to ABS controls the partitioning behavior of l-phenylalanine, which depends on the type of IL employed. Moreover, it is verified that increasing temperature lead to a decrease in the partition coefficient of l-phenylalanine. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution of cooperation in a multidimensional phenotype space.

PubMed

Kroumi, Dhaker; Lessard, Sabin

2015-06-01

The emergence of cooperation in populations of selfish individuals is a fascinating topic that has inspired much theoretical work. An important model to study cooperation is the phenotypic model, where individuals are characterized by phenotypic properties that are visible to others. The phenotype of an individual can be represented for instance by a vector x = (x1,…,xn), where x1,…,xn are integers. The population can be well mixed in the sense that everyone is equally likely to interact with everyone else, but the behavioral strategies of the individuals can depend on their distance in the phenotype space. A cooperator can choose to help other individuals exhibiting the same phenotype and defects otherwise. Cooperation is said to be favored by selection if it is more abundant than defection in the stationary state. This means that the average frequency of cooperators in the stationary state strictly exceeds 1/2. Antal et al. (2009c) found conditions that ensure that cooperation is more abundant than defection in a one-dimensional (i.e. n = 1) and an infinite-dimensional (i.e. n = ∞) phenotype space in the case of the Prisoner's Dilemma under weak selection. However, reality lies between these two limit cases. In this paper, we derive the corresponding condition in the case of a phenotype space of any finite dimension. This is done by applying a perturbation method to study a mutation-selection equilibrium under weak selection. This condition is obtained in the limit of a large population size by using the ancestral process. The best scenario for cooperation to be more likely to evolve is found to be a high population-scaled phenotype mutation rate, a low population-scaled strategy mutation rate and a high phenotype space dimension. The biological intuition is that a high population-scaled phenotype mutation rate reduces the quantity of interactions between cooperators and defectors, while a high population-scaled strategy mutation rate introduces newly

Phenotypic Evolution With and Beyond Genome Evolution.

PubMed

Félix, M-A

2016-01-01

DNA does not make phenotypes on its own. In this volume entitled "Genes and Phenotypic Evolution," the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis. © 2016 Elsevier Inc. All rights reserved.

EMPReSS: European mouse phenotyping resource for standardized screens.

PubMed

Green, Eain C J; Gkoutos, Georgios V; Lad, Heena V; Blake, Andrew; Weekes, Joseph; Hancock, John M

2005-06-15

Standardized phenotyping protocols are essential for the characterization of phenotypes so that results are comparable between different laboratories and phenotypic data can be related to ontological descriptions in an automated manner. We describe a web-based resource for the visualization, searching and downloading of standard operating procedures and other documents, the European Mouse Phenotyping Resource for Standardized Screens-EMPReSS. Direct access: http://www.empress.har.mrc.ac.uk e.green@har.mrc.ac.uk.

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution

PubMed Central

Cottinet, Denis; Condamine, Florence; Bremond, Nicolas; Griffiths, Andrew D.; Rainey, Paul B.; de Visser, J. Arjan G. M.; Baudry, Jean; Bibette, Jérôme

2016-01-01

Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes–via growth–over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology. PMID:27077662

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution.

PubMed

Cottinet, Denis; Condamine, Florence; Bremond, Nicolas; Griffiths, Andrew D; Rainey, Paul B; de Visser, J Arjan G M; Baudry, Jean; Bibette, Jérôme

2016-01-01

Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes-via growth-over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology.

A Review of Imaging Techniques for Plant Phenotyping

PubMed Central

Li, Lei; Zhang, Qin; Huang, Danfeng

2014-01-01

Given the rapid development of plant genomic technologies, a lack of access to plant phenotyping capabilities limits our ability to dissect the genetics of quantitative traits. Effective, high-throughput phenotyping platforms have recently been developed to solve this problem. In high-throughput phenotyping platforms, a variety of imaging methodologies are being used to collect data for quantitative studies of complex traits related to the growth, yield and adaptation to biotic or abiotic stress (disease, insects, drought and salinity). These imaging techniques include visible imaging (machine vision), imaging spectroscopy (multispectral and hyperspectral remote sensing), thermal infrared imaging, fluorescence imaging, 3D imaging and tomographic imaging (MRT, PET and CT). This paper presents a brief review on these imaging techniques and their applications in plant phenotyping. The features used to apply these imaging techniques to plant phenotyping are described and discussed in this review. PMID:25347588

Biphasic reduction model for predicting the impacts of dye-bath constituents on the reduction of tris-azo dye Direct Green-1 by zero valent iron (Fe0).

PubMed

Kumar, Raja; Sinha, Alok

2017-02-01

Influence of common dye-bath additives, namely sodium chloride, ammonium sulphate, urea, acetic acid and citric acid, on the reductive decolouration of Direct Green 1 dye in the presence of Fe 0 was investigated. Organic acids improved dye reduction by augmenting Fe 0 corrosion, with acetic acid performing better than citric acid. NaCl enhanced the reduction rate by its 'salting out' effect on the bulk solution and by Cl - anion-mediated pitting corrosion of iron surface. (NH 4 ) 2 SO 4 induced 'salting out' effect accompanied by enhanced iron corrosion by SO 4 2- anion and buffering effect of NH 4 + improved the reduction rates. However, at 2g/L (NH 4 ) 2 SO 4 concentration, complexating of SO 4 2- with iron oxides decreased Fe 0 reactivity. Urea severely compromised the reduction reaction, onus to its chaotropic and 'salting in' effect in solution, and due to it masking the Fe 0 surface. Decolouration obeyed biphasic reduction kinetics (R 2 >0.993 in all the cases) exhibiting an initial rapid phase, when more than 95% dye reduction was observed, preceding a tedious phase. Maximum rapid phase reduction rate of 0.955/min was observed at pH2 in the co-presence of all dye-bath constituents. The developed biphasic model reckoned the influence of each dye-bath additive on decolouration and simulated well with the experimental data obtained at pH2. Copyright © 2016. Published by Elsevier B.V.

The division of labor: genotypic versus phenotypic specialization.

PubMed

Wahl, L M

2002-07-01

A model of the division of labor in simple evolving systems is explored to compare two strategies evident in natural populations: phenotypic specialization (such as differentiation by regulated gene expression) and genotypic specialization (such as co-infection by complementary covirus populations). While genotypic specialization is vulnerable to the chance extinction of an essential specialist type and to parasitism, phenotypic specialization is able to overcome these hurdles. When simple spatial effects are included, phenotypic specialization has further benefits, protecting against destructive dynamic patterns. Many of the advantages of phenotypic specialization, however, can only be realized when a high degree of relatedness within groups is ensured.

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

PubMed Central

Bell, Rayna C.; Mason, Nicholas A.

2016-01-01

Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes. PMID:27432983

Holistic and component plant phenotyping using temporal image sequence.

PubMed

Das Choudhury, Sruti; Bashyam, Srinidhi; Qiu, Yumou; Samal, Ashok; Awada, Tala

2018-01-01

Image-based plant phenotyping facilitates the extraction of traits noninvasively by analyzing large number of plants in a relatively short period of time. It has the potential to compute advanced phenotypes by considering the whole plant as a single object (holistic phenotypes) or as individual components, i.e., leaves and the stem (component phenotypes), to investigate the biophysical characteristics of the plants. The emergence timing, total number of leaves present at any point of time and the growth of individual leaves during vegetative stage life cycle of the maize plants are significant phenotypic expressions that best contribute to assess the plant vigor. However, image-based automated solution to this novel problem is yet to be explored. A set of new holistic and component phenotypes are introduced in this paper. To compute the component phenotypes, it is essential to detect the individual leaves and the stem. Thus, the paper introduces a novel method to reliably detect the leaves and the stem of the maize plants by analyzing 2-dimensional visible light image sequences captured from the side using a graph based approach. The total number of leaves are counted and the length of each leaf is measured for all images in the sequence to monitor leaf growth. To evaluate the performance of the proposed algorithm, we introduce University of Nebraska-Lincoln Component Plant Phenotyping Dataset (UNL-CPPD) and provide ground truth to facilitate new algorithm development and uniform comparison. The temporal variation of the component phenotypes regulated by genotypes and environment (i.e., greenhouse) are experimentally demonstrated for the maize plants on UNL-CPPD. Statistical models are applied to analyze the greenhouse environment impact and demonstrate the genetic regulation of the temporal variation of the holistic phenotypes on the public dataset called Panicoid Phenomap-1. The central contribution of the paper is a novel computer vision based algorithm for

HLA phenotypes and cadmium blood level.

PubMed

Gualde, N; Delage, C

1979-10-01

The distribution of HLA phenotypes was studied and the amount of cadmium blood level was determined in a group of 100 healthy subjects. The HLA-A3 phenotype seems associated with high cadmium levels in the blood. The lymphocytes transformation test with PHA and different concentrations of cadmium indicates that A3 cells are more sensitive than others to inhibition by cadmium.

Daddy issues: paternal effects on phenotype.

PubMed

Rando, Oliver J

2012-11-09

The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the phenotype of progeny is now a tractable question, and researchers are exploring potential mechanisms underlying such effects. Copyright © 2012 Elsevier Inc. All rights reserved.

Micropore-induced Capillarity Enhances Bone Distribution in vivo in Biphasic Calcium Phosphate Scaffolds

PubMed Central

Rustom, Laurence E.; Boudou, Thomas; Lou, Siyu; Pignot-Paintrand, Isabelle; Nemke, Brett W.; Lu, Yan; Markel, Mark D.; Picart, Catherine; Wagoner Johnson, Amy J.

2016-01-01

The increasing demand for bone repair solutions calls for the development of efficacious bone scaffolds. Biphasic calcium phosphate (BCP) scaffolds with both macropores and micropores (MP) have improved healing compared to those with macropores and no micropores (NMP), but the role of micropores is unclear. Here, we evaluate capillarity induced by micropores as a mechanism that can affect bone growth in vivo. Three groups of cylindrical scaffolds were implanted in pig mandibles for three weeks: MP were implanted either dry (MP-Dry), or after submersion in phosphate buffered saline, which fills pores with fluid and therefore suppresses micropore-induced capillarity (MP-Wet); NMP were implanted dry. The amount and distribution of bone in the scaffolds were quantified using micro-computed tomography. MP-Dry had a more homogeneous bone distribution than MP-Wet, although the average bone volume fraction, BVF¯, was not significantly different for these two groups (0.45±0.03 and 0.37±0.03, respectively). There was no significant difference in the radial bone distribution of NMP and MP-Wet, but the BVF¯ of NMP was significantly lower among the three groups (0.25±0.02). These results suggest that micropore-induced capillarity enhances bone regeneration by improving the homogeneity of bone distribution in BCP scaffolds. The explicit design and use of capillarity in bone scaffolds may lead to more effective treatments of large and complex bone defects. PMID:27544807

Multidimensionality of behavioural phenotypes in Atlantic cod, Gadus morhua.

PubMed

Meager, Justin J; Fernö, Anders; Skjæraasen, Jon Egil; Järvi, Torbjörn; Rodewald, Petra; Sverdrup, Gisle; Winberg, Svante; Mayer, Ian

2012-06-25

Much of the inter-individual variation observed in animal behaviour is now attributed to the existence of behavioural phenotypes or animal personalities. Such phenotypes may be fundamental to fisheries and aquaculture, yet there have been few detailed studies of this phenomenon in exploited marine animals. We investigated the behavioural and neuroendocrine responses of Atlantic cod (Gadus morhua L.), to situations reflecting critical ecological challenges: predator attacks and territorial challenges. Both hatchery-reared and wild fish were tested and behavioural profiles were compared with baseline conditions. We then used an objective, multivariate approach, rather than assigning individuals along one-dimensional behavioural axes, to examine whether distinct behavioural phenotypes were present. Our results indicate that two distinct behavioural phenotypes were evident in fish from each background. In hatchery-reared fish, phenotypes displayed divergent locomotor activity, sheltering, brain monoamine concentrations and responses to competitive challenges. In wild fish, phenotypes were distinguished primarily by locomotor activity, sheltering and responsiveness to predator stimuli. Hatcheries presumably represent a more stressful social environment, and social behaviour and neuroendocrine responses were important in discerning behavioural phenotypes in hatchery fish, whereas antipredator responses were important in discerning phenotypes in wild fish that have previously encountered predators. In both fish types, behavioural and physiological traits that classified individuals into phenotypes were not the same as those that were correlated across situations. These results highlight the multidimensionality of animal personalities, and that the processes that regulate one suite of behavioural traits may be very different to the processes that regulate other behaviours. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparative study on in vivo response of porous calcium carbonate composite ceramic and biphasic calcium phosphate ceramic.

PubMed

He, Fupo; Ren, Weiwei; Tian, Xiumei; Liu, Wei; Wu, Shanghua; Chen, Xiaoming

2016-07-01

In a previous study, robust calcium carbonate composite ceramics (CC/PG) were prepared by using phosphate-based glass (PG) as an additive, which showed good cell response. In the present study the in vivo response of porous CC/PG was compared to that of porous biphasic calcium phosphate ceramics (BCP), using a rabbit femoral critical-size grafting model. The materials degradation and bone formation processes were evaluated by general observation, X-ray radiography, micro-computed tomography, and histological examination. The results demonstrated excellent biocompatibility and osteoconductivity, and progressive degradation of CC/PG and BCP. Although the in vitro degradation rate of CC/PG was distinctly faster than that of BCP, at 4week post-implantation, the bone generation and material degradation of CC/PG were less than those of BCP. Nevertheless, at postoperative week 8, the increment of bone formation and material degradation of CC/PG was pronouncedly larger than that of BCP. These results show that CC/PG is a potential resorbable bone graft aside from the traditional synthetic ones. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of filler content on mechanical and dynamic mechanical properties of particulate biphasic calcium phosphate--polylactide composites.

PubMed

Bleach, N C; Nazhat, S N; Tanner, K E; Kellomäki, M; Törmälä, P

2002-04-01

A bioabsorbable self-reinforced polylactide/biphasic calcium phosphate (BCP) composite is being developed for fracture fixation plates. One manufacturing route is to produce preimpregnated sheets by pulling polylactide (PLA) fibres through a suspension of BCP filler in a PLA solution and compression moulding the prepreg to the desired shape. To aid understanding of the process, interactions between the matrix and filler were investigated. Composite films containing 0-0.25 volume fraction filler, produced by solvent casting, were analysed using SEM, tensile testing and dynamic mechanical analysis (DMA). Homogeneous films could be made, although some particle agglomeration was seen at higher filler volume fractions. As the filler content increased, the failure strain decreased due to a reduction in the amount of ductile polymer present and the ultimate tensile strength (UTS) decreased because of agglomeration and void formation at higher filler content. The matrix glass transition temperature increased due to polymer chain adsorption and immobilization onto the BCP particles. Complex damping mechanisms, such as particle-particle agglomeration, may exist at the higher BCP volume fractions.

EuroPhenome and EMPReSS: online mouse phenotyping resource

PubMed Central

Mallon, Ann-Marie; Hancock, John M.

2008-01-01

EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC). PMID:17905814

EuroPhenome and EMPReSS: online mouse phenotyping resource.

PubMed

Mallon, Ann-Marie; Blake, Andrew; Hancock, John M

2008-01-01

EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC).

Social Cognition, Social Skill, and the Broad Autism Phenotype

ERIC Educational Resources Information Center

Sasson, Noah J.; Nowlin, Rachel B.; Pinkham, Amy E.

2013-01-01

Social-cognitive deficits differentiate parents with the "broad autism phenotype" from non-broad autism phenotype parents more robustly than other neuropsychological features of autism, suggesting that this domain may be particularly informative for identifying genetic and brain processes associated with the phenotype. The current study…

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

PubMed Central

Chong, Jessica X.; Buckingham, Kati J.; Jhangiani, Shalini N.; Boehm, Corinne; Sobreira, Nara; Smith, Joshua D.; Harrell, Tanya M.; McMillin, Margaret J.; Wiszniewski, Wojciech; Gambin, Tomasz; Coban Akdemir, Zeynep H.; Doheny, Kimberly; Scott, Alan F.; Avramopoulos, Dimitri; Chakravarti, Aravinda; Hoover-Fong, Julie; Mathews, Debra; Witmer, P. Dane; Ling, Hua; Hetrick, Kurt; Watkins, Lee; Patterson, Karynne E.; Reinier, Frederic; Blue, Elizabeth; Muzny, Donna; Kircher, Martin; Bilguvar, Kaya; López-Giráldez, Francesc; Sutton, V. Reid; Tabor, Holly K.; Leal, Suzanne M.; Gunel, Murat; Mane, Shrikant; Gibbs, Richard A.; Boerwinkle, Eric; Hamosh, Ada; Shendure, Jay; Lupski, James R.; Lifton, Richard P.; Valle, David; Nickerson, Deborah A.; Bamshad, Michael J.

2015-01-01

Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families. PMID:26166479

Clinical experience with insulin detemir, biphasic insulin aspart and insulin aspart in people with type 2 diabetes: Results from the Northern Tunisia cohort of the A1chieve study

PubMed Central

Blouza, Samira; Jamoussi, Henda

2013-01-01

Background: The A1chieve, a multicentric (28 countries), 24-week, non-interventional study evaluated the safety and effectiveness of insulin detemir, biphasic insulin aspart and insulin aspart in people with T2DM (n = 66,726) in routine clinical care across four continents. Materials and Methods: Data was collected at baseline, at 12 weeks and at 24 weeks. This short communication presents the results for patients enrolled from Northern Tunisia. Results: A total of 443 patients were enrolled in the study. Four different insulin analogue regimens were used in the study. Study patients had started on or were switched to biphasic insulin aspart (n = 137), insulin detemir (n = 243), insulin aspart (n = 11), basal insulin plus insulin aspart (n = 39) and other insulin combinations (n = 13). At baseline glycaemic control was poor for both insulin naïve (mean HbA1c: 10.2%) and insulin user (mean HbA1c: 9.8%) groups. After 24 weeks of treatment, both the study groups showed improvement in HbA1c (insulin naïve: −2.1%, insulin users: −0.9%). SADRs including major hypoglycaemic events or episodes did not occur in any of the study patients. Conclusion: Starting or switching to insulin analogues was associated with improvement in glycaemic control with a low rate of hypoglycaemia. PMID:24404473

Distribution of phenotypes among Bacillus thuringiensis strains

USDA-ARS?s Scientific Manuscript database

An extensive collection of Bacillus thuringiensis isolates from around the world were phenotypically profiled using standard biochemical tests. Six phenotypic traits occurred in 20-86% of the isolates and were useful in distinguishing isolates: production of urease (U; 20.5% of isolates), hydrolysis...

PCAN: phenotype consensus analysis to support disease-gene association.

PubMed

Godard, Patrice; Page, Matthew

2016-12-07

Bridging genotype and phenotype is a fundamental biomedical challenge that underlies more effective target discovery and patient-tailored therapy. Approaches that can flexibly and intuitively, integrate known gene-phenotype associations in the context of molecular signaling networks are vital to effectively prioritize and biologically interpret genes underlying disease traits of interest. We describe Phenotype Consensus Analysis (PCAN); a method to assess the consensus semantic similarity of phenotypes in a candidate gene's signaling neighborhood. We demonstrate that significant phenotype consensus (p < 0.05) is observable for ~67% of 4,549 OMIM disease-gene associations, using a combination of high quality String interactions + Metabase pathways and use Joubert Syndrome to demonstrate the ease with which a significant result can be interrogated to highlight discriminatory traits linked to mechanistically related genes. We advocate phenotype consensus as an intuitive and versatile method to aid disease-gene association, which naturally lends itself to the mechanistic deconvolution of diverse phenotypes. We provide PCAN to the community as an R package ( http://bioconductor.org/packages/PCAN/ ) to allow flexible configuration, extension and standalone use or integration to supplement existing gene prioritization workflows.

GenomeRNAi: a database for cell-based RNAi phenotypes.

PubMed

Horn, Thomas; Arziman, Zeynep; Berger, Juerg; Boutros, Michael

2007-01-01

RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible at http://rnai.dkfz.de.

GenomeRNAi: a database for cell-based RNAi phenotypes

PubMed Central

Horn, Thomas; Arziman, Zeynep; Berger, Juerg; Boutros, Michael

2007-01-01

RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible at PMID:17135194

Furfural Production from d-Xylose and Xylan by Using Stable Nafion NR50 and NaCl in a Microwave-Assisted Biphasic Reaction.

PubMed

Le Guenic, Sarah; Gergela, David; Ceballos, Claire; Delbecq, Frederic; Len, Christophe

2016-08-22

Pentose dehydration and direct transformation of xylan into furfural were performed in a water-cyclopentyl methyl ether (CPME) biphasic system under microwave irradiation. Heated up between 170 and 190 °C in the presence of Nafion NR50 and NaCl, d-xylose, l-arabinose and xylan gave furfural with maximum yields of 80%, 42% and 55%, respectively. The influence of temperature and reaction time on the reaction kinetics was discussed. This study was also completed by the survey of different reactant ratios, such as organic layer-water or catalyst-inorganic salt ratios. The exchange between proton and cation induced by an excess of NaCl was monitored, and a synergetic effect between the remaining protons and the released HCl was also discovered.

Bethlem myopathy: An autosomal dominant myopathy with flexion contractures, keloids, and follicular hyperkeratosis.

PubMed

Saroja, Aralikatte Onkarappa; Naik, Karkal Ravishankar; Nalini, Atcharayam; Gayathri, Narayanappa

2013-10-01

Bethlem myopathy and Ullrich congenital muscular dystrophy form a spectrum of collagenopathies caused by genetic mutations encoding for any of the three subunits of collagen VI. Bethlem phenotype is relatively benign and is characterized by proximal dominant myopathy, keloids, contractures, distal hyperextensibility, and follicular hyperkeratosis. Three patients from a single family were diagnosed to have Bethlem myopathy based on European Neuromuscular Centre Bethlem Consortium criteria. Affected father and his both sons had slowly progressive proximal dominant weakness and recurrent falls from the first decade. Both children aged 18 and 20 years were ambulant at presentation. All had flexion contractures, keloids, and follicular hyperkeratosis without muscle hypertrophy. Creatinine kinase was mildly elevated and electromyography revealed myopathic features. Muscle imaging revealed severe involvement of glutei and vasti with "central shadow" in rectus femoris. Muscle biopsy in the father showed dystrophic changes with normal immmunostaining for collagen VI, sarcoglycans, and dysferlin.

Novel SNP array analysis and exome sequencing detect a homozygous exon 7 deletion of MEGF10 causing early onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD)

PubMed Central

Pierson, Tyler Mark; Markello, Thomas; Accardi, John; Wolfe, Lynne; Adams, David; Sincan, Murat; Tarazi, Noor M.; Fajardo, Karin Fuentes; Cherukuri, Praveen F.; Bajraktari, Ilda; Meilleur, Katy G.; Donkervoort, Sandra; Jain, Mina; Hu, Ying; Lehky, Tanya J.; Cruz, Pedro; Mullikin, James C.; Bonnemann, Carsten; Gahl, William A.; Boerkoel, Cornelius F.; Tifft, Cynthia J.

2013-01-01

Early-onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD) is a myopathic disorder associated with mutations in MEGF10. By novel analysis of SNP array hybridization and exome sequence coverage, we diagnosed a 10-year old girl with EMARDD following identification of a novel homozygous deletion of exon 7 in MEGF10. In contrast to previously reported EMARDD patients, her weakness was more prominent proximally than distally, and involved her legs more than her arms. MRI of her pelvis and thighs showed muscle atrophy and fatty replacement. Ultrasound of several muscle groups revealed dense homogenous increases in echogenicity. Cloning and sequencing of the deletion breakpoint identified features suggesting the mutation arose by fork stalling and template switching. These findings constitute the first genomic deletion causing EMARDD, expand the clinical phenotype, and provide new insight into the pattern and histology of its muscular pathology. PMID:23453856

WWOX-related encephalopathies: delineation of the phenotypical spectrum and emerging genotype-phenotype correlation.

PubMed

Mignot, Cyril; Lambert, Laetitia; Pasquier, Laurent; Bienvenu, Thierry; Delahaye-Duriez, Andrée; Keren, Boris; Lefranc, Jérémie; Saunier, Aline; Allou, Lila; Roth, Virginie; Valduga, Mylène; Moustaïne, Aissa; Auvin, Stéphane; Barrey, Catherine; Chantot-Bastaraud, Sandra; Lebrun, Nicolas; Moutard, Marie-Laure; Nougues, Marie-Christine; Vermersch, Anne-Isabelle; Héron, Bénédicte; Pipiras, Eva; Héron, Delphine; Olivier-Faivre, Laurence; Guéant, Jean-Louis; Jonveaux, Philippe; Philippe, Christophe

2015-01-01

Homozygous mutations in WWOX were reported in eight individuals of two families with autosomal recessive spinocerebellar ataxia type 12 and in two siblings with infantile epileptic encephalopathy (IEE), including one who deceased prior to DNA sampling. By combining array comparative genomic hybridisation, targeted Sanger sequencing and next generation sequencing, we identified five further patients from four families with IEE due to biallelic alterations of WWOX. We identified eight deleterious WWOX alleles consisting in four deletions, a four base-pair frameshifting deletion, one missense and two nonsense mutations. Genotype-phenotype correlation emerges from the seven reported families. The phenotype in four patients carrying two predicted null alleles was characterised by (1) little if any psychomotor acquisitions, poor spontaneous motility and absent eye contact from birth, (2) pharmacoresistant epilepsy starting in the 1st weeks of life, (3) possible retinal degeneration, acquired microcephaly and premature death. This contrasted with the less severe autosomal recessive spinocerebellar ataxia type 12 phenotype due to hypomorphic alleles. In line with this correlation, the phenotype in two siblings carrying a null allele and a missense mutation was intermediate. Our results obtained by a combination of different molecular techniques undoubtedly incriminate WWOX as a gene for recessive IEE and illustrate the usefulness of high throughput data mining for the identification of genes for rare autosomal recessive disorders. The structure of the WWOX locus encompassing the FRA16D fragile site might explain why constitutive deletions are recurrently reported in genetic databases, suggesting that WWOX-related encephalopathies, although likely rare, may not be exceptional. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Development of modified-release tablets of zolpidem tartrate by biphasic quick/slow delivery system.

PubMed

Mahapatra, Anjan Kumar; Sameeraja, N H; Murthy, P N

2015-06-01

Zolpidem tartrate is a non-benzodiazepine analogue of imidazopyridine of sedative and hypnotic category. It has a short half-life with usual dosage regimen being 5 mg, two times a day, or 10 mg, once daily. The duration of action is considered too short in certain circumstances. Thus, it is desirable to lengthen the duration of action. The formulation design was implemented by preparing extended-release tablets of zolpidem tartrate using the biphasic delivery system technology, where sodium starch glycolate acts as a superdisintegrant in immediate-release part and hydroxypropyl methyl cellulose as a release retarding agent in extended-release core. Tablets were prepared by direct compression. Both the core and the coat contained the drug. The pre-compression blends were evaluated for angle of repose, bulk density, and compressibility index. The tablets were evaluated for thickness, hardness, weight variation test, friability, and in vitro release studies. No interaction was observed between zolpidem tartrate and excipients from the Fourier transform infrared spectroscopy and differential scanning calorimetry analysis. The results of all the formulations prepared were compared with reference product Stilnoct®. Optimized formulations showed release patterns that match the United States Pharmacopeia (USP) guidelines for zolpidem tartrate extended-release tablets. The mechanism of drug release was studied using different mathematical models, and the optimized formulation has shown Fickian diffusion. Accelerated stability studies were performed on the optimized formulation.

Unsupervised automated high throughput phenotyping of RNAi time-lapse movies.

PubMed

Failmezger, Henrik; Fröhlich, Holger; Tresch, Achim

2013-10-04

Gene perturbation experiments in combination with fluorescence time-lapse cell imaging are a powerful tool in reverse genetics. High content applications require tools for the automated processing of the large amounts of data. These tools include in general several image processing steps, the extraction of morphological descriptors, and the grouping of cells into phenotype classes according to their descriptors. This phenotyping can be applied in a supervised or an unsupervised manner. Unsupervised methods are suitable for the discovery of formerly unknown phenotypes, which are expected to occur in high-throughput RNAi time-lapse screens. We developed an unsupervised phenotyping approach based on Hidden Markov Models (HMMs) with multivariate Gaussian emissions for the detection of knockdown-specific phenotypes in RNAi time-lapse movies. The automated detection of abnormal cell morphologies allows us to assign a phenotypic fingerprint to each gene knockdown. By applying our method to the Mitocheck database, we show that a phenotypic fingerprint is indicative of a gene's function. Our fully unsupervised HMM-based phenotyping is able to automatically identify cell morphologies that are specific for a certain knockdown. Beyond the identification of genes whose knockdown affects cell morphology, phenotypic fingerprints can be used to find modules of functionally related genes.

Phenotypic Plasticity of Cuticular Hydrocarbon Profiles in Insects.

PubMed

Otte, Tobias; Hilker, Monika; Geiselhardt, Sven

2018-03-01

The insect integument is covered by cuticular hydrocarbons (CHCs) which provide protection against environmental stresses, but are also used for communication. Here we review current knowledge on environmental and insect-internal factors which shape phenotypic plasticity of solitary living insects, especially herbivorous ones. We address the dynamics of changes which may occur within minutes, but may also last weeks, depending on the species and conditions. Two different modes of changes are suggested, i.e. stepwise and gradual. A switch between two distinct environments (e.g. host plant switch by phytophagous insects) results in stepwise formation of two distinct adaptive phenotypes, while a gradual environmental change (e.g. temperature gradients) induces a gradual change of numerous adaptive CHC phenotypes. We further discuss the ecological and evolutionary consequences of phenotypic plasticity of insect CHC profiles by addressing the question at which conditions is CHC phenotypic plasticity beneficial. The high plasticity of CHC profiles might be a trade-off for insects using CHCs for communication. We discuss how insects cope with the challenge to produce and "understand" a highly plastic, environmentally dependent CHC pattern that conveys reliable and comprehensible information. Finally, we outline how phenotypic plasticity of CHC profiles may promote speciation in insects that rely on CHCs for mate recognition.

Informatics and machine learning to define the phenotype.

PubMed

Basile, Anna Okula; Ritchie, Marylyn DeRiggi

2018-03-01

For the past decade, the focus of complex disease research has been the genotype. From technological advancements to the development of analysis methods, great progress has been made. However, advances in our definition of the phenotype have remained stagnant. Phenotype characterization has recently emerged as an exciting area of informatics and machine learning. The copious amounts of diverse biomedical data that have been collected may be leveraged with data-driven approaches to elucidate trait-related features and patterns. Areas covered: In this review, the authors discuss the phenotype in traditional genetic associations and the challenges this has imposed.Approaches for phenotype refinement that can aid in more accurate characterization of traits are also discussed. Further, the authors highlight promising machine learning approaches for establishing a phenotype and the challenges of electronic health record (EHR)-derived data. Expert commentary: The authors hypothesize that through unsupervised machine learning, data-driven approaches can be used to define phenotypes rather than relying on expert clinician knowledge. Through the use of machine learning and an unbiased set of features extracted from clinical repositories, researchers will have the potential to further understand complex traits and identify patient subgroups. This knowledge may lead to more preventative and precise clinical care.

Influence of strontium on the synthesis and surface properties of biphasic calcium phosphate (BCP) bioceramics.

PubMed

Kanchana, Ponnusamy; Sekar, Chinnathambi

2010-01-01

Biphasic calcium phosphate (BCP) ceramics are suitable for synthetic bone applications. The strontium substituted calcium phosphate ceramics have potential for use in orthopedic surgeries. Aim of the present work is to introduce strontium into BCP (composed of hydroxyapatite and tricalcium phosphate) ceramics and to study their bioactivity and mechanical properties. BCP ceramics have been synthesized at room temperature under the physiological pH of 7.4 by gel method in the presence of strontium (5, 10 M %). The appropriate choice of anhydrous CaCl₂ as precursor solution has promoted the formation of BCP instead of pure HA for CaCl₂.2H₂O. Powder X-ray diffraction analysis confirmed the formation of BCP with different HA and ß -TCP ratios depending upon the Sr content. The presence of Sr has reduced the nucleation and growth rate of BCP when compared to pure system. The SEM micrographs showed that the microstructural morphology of BCP changes from fibrous to platelet. Nanoindentation studies indicate a significant decrease in the hardness and elastic modulus values of BCP ceramics due to Sr doping. In vitro bioactivity study has revealed the formation of apatite layer on the Sr doped BCP samples and the doping enhanced its bioactivity.

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

PubMed Central

Jolly, Mohit Kumar; Boareto, Marcelo; Huang, Bin; Jia, Dongya; Lu, Mingyang; Ben-Jacob, Eshel; Onuchic, José N.; Levine, Herbert

2015-01-01

Transitions between epithelial and mesenchymal phenotypes – the epithelial to ­mesenchymal transition (EMT) and its reverse the mesenchymal to epithelial transition (MET) – are hallmarks of cancer metastasis. While transitioning between the epithelial and mesenchymal phenotypes, cells can also attain a hybrid epithelial/mesenchymal (E/M) (i.e., partial or intermediate EMT) phenotype. Cells in this phenotype have mixed epithelial (e.g., adhesion) and mesenchymal (e.g., migration) properties, thereby allowing them to move collectively as clusters. If these clusters reach the bloodstream intact, they can give rise to clusters of circulating tumor cells (CTCs), as have often been seen experimentally. Here, we review the operating principles of the core regulatory network for EMT/MET that acts as a “three-way” switch giving rise to three distinct phenotypes – E, M and hybrid E/M – and present a theoretical framework that can elucidate the role of many other players in regulating epithelial plasticity. Furthermore, we highlight recent studies on partial EMT and its association with drug resistance and tumor-initiating potential; and discuss how cell–cell communication between cells in a partial EMT phenotype can enable the formation of clusters of CTCs. These clusters can be more apoptosis-resistant and have more tumor-initiating potential than singly moving CTCs with a wholly mesenchymal (complete EMT) phenotype. Also, more such clusters can be formed under inflammatory conditions that are often generated by various therapies. Finally, we discuss the multiple advantages that the partial EMT or hybrid E/M phenotype have as compared to a complete EMT phenotype and argue that these collectively migrating cells are the primary “bad actors” of metastasis. PMID:26258068

Breeding to adapt agriculture to climate change: affordable phenotyping solutions.

PubMed

Araus, José L; Kefauver, Shawn C

2018-05-28

Breeding is one of the central pillars of adaptation of crops to climate change. However, phenotyping is a key bottleneck that is limiting breeding efficiency. The awareness of phenotyping as a breeding limitation is not only sustained by the lack of adequate approaches, but also by the perception that phenotyping is an expensive activity. Phenotyping is not just dependent on the choice of appropriate traits and tools (e.g. sensors) but relies on how these tools are deployed on their carrying platforms, the speed and volume of data extraction and analysis (throughput), the handling of spatial variability and characterization of environmental conditions, and finally how all the information is integrated and processed. Affordable high throughput phenotyping aims to achieve reasonably priced solutions for all the components comprising the phenotyping pipeline. This mini-review will cover current and imminent solutions for all these components, from the increasing use of conventional digital RGB cameras, within the category of sensors, to open-access cloud-structured data processing and the use of smartphones. Emphasis will be placed on field phenotyping, which is really the main application for day-to-day phenotyping. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hormone signaling and phenotypic plasticity in nematode development and evolution.

PubMed

Sommer, Ralf J; Ogawa, Akira

2011-09-27

Phenotypic plasticity refers to the ability of an organism to adopt different phenotypes depending on environmental conditions. In animals and plants, the progression of juvenile development and the formation of dormant stages are often associated with phenotypic plasticity, indicating the importance of phenotypic plasticity for life-history theory. Phenotypic plasticity has long been emphasized as a crucial principle in ecology and as facilitator of phenotypic evolution. In nematodes, several examples of phenotypic plasticity have been studied at the genetic and developmental level. In addition, the influence of different environmental factors has been investigated under laboratory conditions. These studies have provided detailed insight into the molecular basis of phenotypic plasticity and its ecological and evolutionary implications. Here, we review recent studies on the formation of dauer larvae in Caenorhabditis elegans, the evolution of nematode parasitism and the generation of a novel feeding trait in Pristionchus pacificus. These examples reveal a conserved and co-opted role of an endocrine signaling module involving the steroid hormone dafachronic acid. We will discuss how hormone signaling might facilitate life-history and morphological evolution. Copyright © 2011 Elsevier Ltd. All rights reserved.

Haptoglobin Phenotype Among Arab Patients With Mental Disorders.

PubMed

Armaly, Zaher; Farhat, Kamal; Kinaneh, Safa; Farah, Joseph

2018-03-01

Depression, schizophrenia and panic disorder are common mental disorders in the community and hospitalized patients. These mental disorders negatively affect life quality and even expectancy of life. Haptoglobin (Hp) phenotype (Hp 1-1, 1-2, or 2-2) is associated with risk for cardiovascular diseases, but its association with psychiatric disorders, a growing concern in the modern society, has not been studied thoroughly. The aim of the study was to examine whether Hp phenotype is associated with common mental disorders such as depression, schizophrenia, and panic disorder. The study included 92 Arab patients with mental disorders, and among them 44 suffered from schizophrenia (mean age 39 ± 1.5 years), 17 from depression (mean age 44.5 ± 3.1 years), 31 from panic disorder (mean age of 44.9 ± 2.7 years), and 206 healthy Arab control subjects with a mean age of 42.6 ± 0.9 years. Beck's depression inventory assessment and Hamilton depression scale were administered for depression and panic disorder diagnosis. Schizophrenia was evaluated with positive and negative affect schedule (Panas) test. All mental disorders were evaluated by clinical review. Blood analysis for Hp phenotype was performed. Diagnosis was made using the Diagnostic and Statistical Manual of Mental Disorders axis to correlate depression with Hp phenotype. In mentally healthy controls, 10.7% were Hp 1-1, 38.8% Hp 2-1, and 50.5% Hp 2-2. In patients with the studied psychiatric disorders, Hp phenotype was comparable to healthy subjects; 8.7% were Hp 1-1, 50% Hp 2-1, and 41.3% Hp 2-2. When Hp phenotyping was analyzed in the psychiatric subgroups, Hp 2-1 was more common among depressed and schizophrenic patients, as compared with healthy subjects (58.8% and 52.3% vs. 38.8%). In patients who suffer from panic disorder, Hp phenotype distribution was 6.5% Hp 1-1, 41.9% Hp 2-1, and 51.6% Hp 2-2, suggesting a lower prevalence among Hp 1-1 phenotype. Arab patients who carry Hp 2-1 phenotype may be at risk to

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.

PubMed

Hoehndorf, Robert; Alshahrani, Mona; Gkoutos, Georgios V; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; de Oliveira, Sylvia Mota; Schmidt, Marco; Sierra, Soraya; Smets, Erik; Vos, Rutger A; Weiland, Claus

2016-11-14

The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather

Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes

PubMed Central

Scharfe, Curt; Lu, Henry Horng-Shing; Neuenburg, Jutta K.; Allen, Edward A.; Li, Guan-Cheng; Klopstock, Thomas; Cowan, Tina M.; Enns, Gregory M.; Davis, Ronald W.

2009-01-01

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the

Early constraints in sexual dimorphism: survival benefits of feminized phenotypes.

PubMed

López-Rull, I; Vergara, P; Martínez-Padilla, J; Fargallo, J A

2016-02-01

Sexual dimorphism (SD) has evolved in response to selection pressures that differ between sexes. Since such pressures change across an individual's life, SD may vary within age classes. Yet, little is known about how selection on early phenotypes may drive the final SD observed in adults. In many dimorphic species, juveniles resemble adult females rather than adult males, meaning that out of the selective pressures established by sexual selection feminized phenotypes may be adaptive. If true, fitness benefits of early female-like phenotypes may constrain the expression of male phenotypes in adulthood. Using the common kestrel Falco tinnunculus as a study model, we evaluated the fitness advantages of expressing more feminized phenotypes at youth. Although more similar to adult females than to adult males, common kestrel fledglings are still sexually dimorphic in size and coloration. Integrating morphological and chromatic variables, we analysed the phenotypic divergence between sexes as a measure of how much each individual looks like the sex to which it belongs (phenotypic sexual resemblance, PSR). We then tested the fitness benefits associated with PSR by means of the probability of recruitment in the population. We found a significant interaction between PSR and sex, showing that in both sexes more feminized phenotypes recruited more into the population than less feminized phenotypes. Moreover, males showed lower PSR than females and a higher proportion of incorrect sex classifications. These findings suggest that the mechanisms in males devoted to resembling female phenotypes in youth, due to a trend to increase fitness through more feminized phenotypes, may provide a mechanism to constrain the SD in adulthood. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Microbial genotype-phenotype mapping by class association rule mining.

PubMed

Tamura, Makio; D'haeseleer, Patrik

2008-07-01

Microbial phenotypes are typically due to the concerted action of multiple gene functions, yet the presence of each gene may have only a weak correlation with the observed phenotype. Hence, it may be more appropriate to examine co-occurrence between sets of genes and a phenotype (multiple-to-one) instead of pairwise relations between a single gene and the phenotype. Here, we propose an efficient class association rule mining algorithm, netCAR, in order to extract sets of COGs (clusters of orthologous groups of proteins) associated with a phenotype from COG phylogenetic profiles and a phenotype profile. netCAR takes into account the phylogenetic co-occurrence graph between COGs to restrict hypothesis space, and uses mutual information to evaluate the biconditional relation. We examined the mining capability of pairwise and multiple-to-one association by using netCAR to extract COGs relevant to six microbial phenotypes (aerobic, anaerobic, facultative, endospore, motility and Gram negative) from 11,969 unique COG profiles across 155 prokaryotic organisms. With the same level of false discovery rate, multiple-to-one association can extract about 10 times more relevant COGs than one-to-one association. We also reveal various topologies of association networks among COGs (modules) from extracted multiple-to-one correlation rules relevant with the six phenotypes; including a well-connected network for motility, a star-shaped network for aerobic and intermediate topologies for the other phenotypes. netCAR outperforms a standard CAR mining algorithm, CARapriori, while requiring several orders of magnitude less computational time for extracting 3-COG sets. Source code of the Java implementation is available as Supplementary Material at the Bioinformatics online website, or upon request to the author. Supplementary data are available at Bioinformatics online.

Collective Motion in Bacterial Populations with Mixed Phenotypic Behaviors

NASA Astrophysics Data System (ADS)

Hoeger, Kentaro; Strickland, Ben; Shoup, Daniel; Ursell, Tristan

The motion of large, densely packed groups of organisms is often qualitatively distinct from the motion of individuals, yet hinges on individual properties and behaviors. Collective motion of bacteria depends strongly on the phenotypic behaviors of individual cells, the physical interactions between cells, and the geometry of their environment, often with multiple phenotypes coexisting in a population. Thus, to characterize how these selectively important interactions affect group traits, such as cell dispersal, spatial segregation of phenotypes, and material transport in groups, we use a library of Bacillus subtilis mutants that modulate chemotaxis, motility, and biofilm formation. By mixing phenotypes and observing bacterial behaviors and motion at single cell resolution, we probe collective motion as a function of phenotypic mixture and environmental geometry. Our work demonstrates that collective microbial motion exhibits a transition, from `turbulence' to semiballistic burrowing, as phenotypic composition varies. This work illuminates the role that individual cell behaviors play in the emergence of collective motion, and may signal qualitatively distinct regimes of material transport in bacterial populations. University of Oregon.

Interferon-γ biphasically regulates angiotensinogen expression via a JAK-STAT pathway and suppressor of cytokine signaling 1 (SOCS1) in renal proximal tubular cells

PubMed Central

Satou, Ryousuke; Miyata, Kayoko; Gonzalez-Villalobos, Romer A.; Ingelfinger, Julie R.; Navar, L. Gabriel; Kobori, Hiroyuki

2012-01-01

Renal inflammation modulates angiotensinogen (AGT) production in renal proximal tubular cells (RPTCs) via inflammatory cytokines, including interleukin-6, tumor necrosis factor α, and interferon-γ (IFN-γ). Among these, the effects of IFN-γ on AGT regulation in RPTCs are incompletely delineated. This study aimed to elucidate mechanisms by which IFN-γ regulates AGT expression in RPTCs. RPTCs were incubated with or without IFN-γ up to 48 h. AGT expression, STAT1 and STAT3 activities, and SOCS1 expression were evaluated. RNA interference studies against STAT1, SOCS1, and STAT3 were performed to elucidate a signaling cascade. IFN-γ decreased AGT expression at 6 h (0.61±0.05, ratio to control) and 12 h (0.47±0.03). In contrast, longer exposure for 24 and 48 h increased AGT expression (1.76±0.18, EC50=3.4 ng/ml, and 1.45±0.08, respectively). IFN-γ treatment for 6 h strongly induced STAT1 phosphorylation and SOCS1 augmentation, and decreased STAT3 activity. However, STAT1 phosphorylation and SOCS1 augmentation waned at 24 h, while STAT3 activity increased. RNA interference studies revealed that activation of STAT1-SOCS1 axis decreased STAT3 activity. Thus, IFN-γ biphasically regulates AGT expression in RPTCs via STAT3 activity modulated by STAT1-SOCS1 axis, suggesting the STAT1-SOCS1 axis is important in IFN-γ-induced activation of the intrarenal renin-angiotensin system.—Satou, R., Miyata, K., Gonzalez-Villalobos, R. A., Ingelfinger, J. R., Navar, L. G., Kobori, H. Interferon-γ biphasically regulates angiotensinogen expression via a JAK-STAT pathway and suppressor of cytokine signaling 1 (SOCS1) in renal proximal tubular cells. PMID:22302831

Wine Expertise Predicts Taste Phenotype.

PubMed

Hayes, John E; Pickering, Gary J

2012-03-01

Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance - with appropriate caveats about populations tested, outcomes measured and psychophysical methods used - an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli.

Uniparental disomy and prenatal phenotype

PubMed Central

Li, Xiaofei; Liu, Yan; Yue, Song; Wang, Li; Zhang, Tiejuan; Guo, Cuixia; Hu, Wenjie; Kagan, Karl-Oliver; Wu, Qingqing

2017-01-01

Abstract Rationale: Uniparental disomy (UPD) gives a description of the inheritance of both homologues of a chromosome pair from the same parent. The consequences of UPD depend on the specific chromosome/segment involved and its parental origin. Patient concerns: We report prenatal phenotypes of 2 rare cases of UPD. Diagnoses: The prenatal phenotype of case 1 included sonographic markers such as enlarged nuchal translucency (NT), absent nasal bone, short femur and humerus length, and several structural malformations involving Dandy–Walker malformation and congenital heart defects. The prenatal phenotype of Case 2 are sonographic markers, including enlarged NT, thickened nuchal fold, ascites, and polyhydramnios without apparent structural malformations. Interventions: Conventional G-band karyotype appears normal in case 1, while it shows normal chromosomes with a small supernumerary marker chromosome (sSMC) in case 2. Genetic etiology was left unknown until single-nucleotide polymorphism-based array (SNP-array) was performed, and segmental paternal UPD 22 was identified in case 1 and segmental paternal UPD 14 was found in case 2. Outcomes: The parents of case 1 chose termination of pregnancy. The neonate of case 2 was born prematurely with a bellshaped small thorax and died within a day. Lessons: UPD cases are rare and the phenotypes are different, which depend on the origin and affected chromosomal part. If a fetus shows multiple anomalies that cannot be attributed to a common aneuploidy or a genetic syndrome, or manifests some features possibly related to an UPD syndrome, such as detection of sSMC, SNP-array should be considered. PMID:29137034

Arabidopsis phenotyping through Geometric Morphometrics.

PubMed

Manacorda, Carlos A; Asurmendi, Sebastian

2018-06-18

Recently, much technical progress was achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it now possible to extract shape and size parameters for genetic, physiological and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of platform and segmentation software used are still lacking and shape descriptions still rely on ad hoc or even sometimes contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations amongst groups and measure them in shape distance units. Here, a particular scheme of landmarks placement on Arabidopsis rosette images is proposed to study shape variation in the case of viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown and reproducibility issues are assessed. Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.

Radiofrequency treatment alters cancer cell phenotype

NASA Astrophysics Data System (ADS)

Ware, Matthew J.; Tinger, Sophia; Colbert, Kevin L.; Corr, Stuart J.; Rees, Paul; Koshkina, Nadezhda; Curley, Steven; Summers, H. D.; Godin, Biana

2015-07-01

The importance of evaluating physical cues in cancer research is gradually being realized. Assessment of cancer cell physical appearance, or phenotype, may provide information on changes in cellular behavior, including migratory or communicative changes. These characteristics are intrinsically different between malignant and non-malignant cells and change in response to therapy or in the progression of the disease. Here, we report that pancreatic cancer cell phenotype was altered in response to a physical method for cancer therapy, a non-invasive radiofrequency (RF) treatment, which is currently being developed for human trials. We provide a battery of tests to explore these phenotype characteristics. Our data show that cell topography, morphology, motility, adhesion and division change as a result of the treatment. These may have consequences for tissue architecture, for diffusion of anti-cancer therapeutics and cancer cell susceptibility within the tumor. Clear phenotypical differences were observed between cancerous and normal cells in both their untreated states and in their response to RF therapy. We also report, for the first time, a transfer of microsized particles through tunneling nanotubes, which were produced by cancer cells in response to RF therapy. Additionally, we provide evidence that various sub-populations of cancer cells heterogeneously respond to RF treatment.

Phenotype-Driven Therapeutics in Severe Asthma.

PubMed

Opina, Maria Theresa D; Moore, Wendy C

2017-02-01

Inhaled corticosteroids are the mainstay of asthma treatment using a step-up approach with incremental dosing and additional controller medications in order to achieve symptom control and prevent exacerbations. While most patients respond well to this treatment approach, some patients remain refractory despite high doses of inhaled corticosteroids and a long-acting β-agonist. The problem lies in the heterogeneity of severe asthma, which is further supported by the emergence of severe asthma phenotypes. This heterogeneity contributes to the variability in treatment response. Randomized controlled trials involving add-on therapies in poorly controlled asthma have challenged the idea of a "one size fits all" approach targeting specific phenotypes in their subject selection. This review discusses severe asthma phenotypes from unbiased clustering approaches and the most recent scientific evidence on novel treatments to provide a guide in personalizing severe asthma treatment.

Nasal lavage, blood or sputum: Which is best for phenotyping asthma?

PubMed

de Farias, Camyla F; Amorim, Maria M F; Dracoulakis, Michel; Caetano, Lilian B; Santoro, Ilka L; Fernandes, Ana L G

2017-05-01

Determination of asthma phenotypes, particularly inflammatory phenotypes, helps guide treatment and management of this heterogeneous disease. Induced sputum cytology has been the gold standard for determination of inflammatory phenotypes, but sputum induction is fairly invasive and technically challenging. Blood and nasal lavage cytology have been suggested as substitutes, but have not been fully verified. The aim of this study is to determine the accuracy of blood and nasal lavage cytometry as indicators of inflammatory phenotypes in asthma. Clinical evaluation, Asthma Control Questionnaire (ACQ) and spirometry were performed for 121 adult asthma patients, and blood, nasal lavage and induced sputum samples were taken. Eosinophils and neutrophils were counted in three samples from each subject. Inflammatory phenotypes (eosinophilic, neutrophilic, mixed and paucicellular) and cells counts were analysed using Venn diagram and receiver operating characteristic (ROC) curve, respectively. ACQ score, spirometry and bronchodilator response did not differ among subjects with different inflammatory phenotypes. Inflammatory phenotypes defined by nasal lavage cytometry were in better concordance than those defined by blood cell counts with phenotypes determined by sputum cytology, and were significantly correlated with sputum phenotypes. For eosinophilia, nasal lavage cytology showed better accuracy than blood cytology (area under the curve (AUC): 0.89 vs 0.65). For all phenotypes, sensitivity and positive and negative predictive power were higher for nasal lavage cytometry than for blood. Blood cell counts gave a high level of false positives for all inflammatory phenotypes. We recommend nasal lavage cytology over blood cell count as a substitute for sputum cytology to identify inflammatory phenotypes in asthma. © 2016 Asian Pacific Society of Respirology.

Endocrine regulation of predator-induced phenotypic plasticity.

PubMed

Dennis, Stuart R; LeBlanc, Gerald A; Beckerman, Andrew P

2014-11-01

Elucidating the developmental and genetic control of phenotypic plasticity remains a central agenda in evolutionary ecology. Here, we investigate the physiological regulation of phenotypic plasticity induced by another organism, specifically predator-induced phenotypic plasticity in the model ecological and evolutionary organism Daphnia pulex. Our research centres on using molecular tools to test among alternative mechanisms of developmental control tied to hormone titres, receptors and their timing in the life cycle. First, we synthesize detail about predator-induced defenses and the physiological regulation of arthropod somatic growth and morphology, leading to a clear prediction that morphological defences are regulated by juvenile hormone and life-history plasticity by ecdysone and juvenile hormone. We then show how a small network of genes can differentiate phenotype expression between the two primary developmental control pathways in arthropods: juvenoid and ecdysteroid hormone signalling. Then, by applying an experimental gradient of predation risk, we show dose-dependent gene expression linking predator-induced plasticity to the juvenoid hormone pathway. Our data support three conclusions: (1) the juvenoid signalling pathway regulates predator-induced phenotypic plasticity; (2) the hormone titre (ligand), rather than receptor, regulates predator-induced developmental plasticity; (3) evolution has favoured the harnessing of a major, highly conserved endocrine pathway in arthropod development to regulate the response to cues about changing environments (risk) from another organism (predator).

Overeating phenotypes in overweight and obese children.

PubMed

Boutelle, Kerri N; Peterson, Carol B; Crosby, Ross D; Rydell, Sarah A; Zucker, Nancy; Harnack, Lisa

2014-05-01

The purpose of this study was to identify overeating phenotypes and their correlates in overweight and obese children. One hundred and seventeen treatment-seeking overweight and obese 8-12year-old children and their parents completed the study. Children completed an eating in the absence of hunger (EAH) paradigm, the Eating Disorder Examination interview, and measurements of height and weight. Parents and children completed questionnaires that evaluated satiety responsiveness, food responsiveness, negative affect eating, external eating and eating in the absence of hunger. Latent profile analysis was used to identify heterogeneity in overeating phenotypes in the child participants. Latent classes were then compared on measures of demographics, obesity status and nutritional intake. Three latent classes of overweight and obese children were identified: High Satiety Responsive, High Food Responsive, and Moderate Satiety and Food Responsive. Results indicated that the High Food Responsive group had higher BMI and BMI-Z scores compared to the High Satiety Responsive group. No differences were found among classes in demographics or nutritional intake. This study identified three overeating phenotypes, supporting the heterogeneity of eating patterns associated with overweight and obesity in treatment-seeking children. These finding suggest that these phenotypes can potentially be used to identify high risk groups, inform prevention and intervention targets, and develop specific treatments for these behavioral phenotypes. Copyright © 2014. Published by Elsevier Ltd.

Social-Cognition and the Broad Autism Phenotype: Identifying Genetically Meaningful Phenotypes

ERIC Educational Resources Information Center

Losh, Molly; Piven, Joseph

2007-01-01

Background: Strong evidence from twin and family studies suggests that the genetic liability to autism may be expressed through personality and language characteristics qualitatively similar, but more subtly expressed than those defining the full syndrome. This study examined behavioral features of this "broad autism phenotype" (BAP) in relation…

On the value of the phenotypes in the genomic era.

PubMed

Gonzalez-Recio, O; Coffey, M P; Pryce, J E

2014-12-01

Genetic improvement programs around the world rely on the collection of accurate phenotypic data. These phenotypes have an inherent value that can be estimated as the contribution of an additional record to genetic gain. Here, the contribution of phenotypes to genetic gain was calculated using traditional progeny testing (PT) and 2 genomic selection (GS) strategies that, for simplicity, included either males or females in the reference population. A procedure to estimate the theoretical economic contribution of a phenotype to a breeding program is described for both GS and PT breeding programs through the increment in genetic gain per unit of increase in estimated breeding value reliability obtained when an additional phenotypic record is added. The main factors affecting the value of a phenotype were the economic value of the trait, the number of phenotypic records already available for the trait, and its heritability. Furthermore, the value of a phenotype was affected by several other factors, including the cost of establishing the breeding program and the cost of phenotyping and genotyping. The cost of achieving a reliability of 0.60 was assessed for different reference populations for GS. Genomic reference populations of more sires with small progeny group sizes (e.g., 20 equivalent daughters) had a lower cost than those reference populations with either large progeny group sizes for fewer genotyped sires, or female reference populations, unless the heritability was large and the cost of phenotyping exceeded a few hundred dollars; then, female reference populations were preferable from an economic perspective. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Text-mined phenotype annotation and vector-based similarity to improve identification of similar phenotypes and causative genes in monogenic disease patients.

PubMed

Saklatvala, Jake R; Dand, Nick; Simpson, Michael A

2018-05-01

The genetic diagnosis of rare monogenic diseases using exome/genome sequencing requires the true causal variant(s) to be identified from tens of thousands of observed variants. Typically a virtual gene panel approach is taken whereby only variants in genes known to cause phenotypes resembling the patient under investigation are considered. With the number of known monogenic gene-disease pairs exceeding 5,000, manual curation of personalized virtual panels using exhaustive knowledge of the genetic basis of the human monogenic phenotypic spectrum is challenging. We present improved probabilistic methods for estimating phenotypic similarity based on Human Phenotype Ontology annotation. A limitation of existing methods for evaluating a disease's similarity to a reference set is that reference diseases are typically represented as a series of binary (present/absent) observations of phenotypic terms. We evaluate a quantified disease reference set, using term frequency in phenotypic text descriptions to approximate term relevance. We demonstrate an improved ability to identify related diseases through the use of a quantified reference set, and that vector space similarity measures perform better than established information content-based measures. These improvements enable the generation of bespoke virtual gene panels, facilitating more accurate and efficient interpretation of genomic variant profiles from individuals with rare Mendelian disorders. These methods are available online at https://atlas.genetics.kcl.ac.uk/~jake/cgi-bin/patient_sim.py. © 2018 Wiley Periodicals, Inc.

Phenotypic screening in cancer drug discovery - past, present and future.

PubMed

Moffat, John G; Rudolph, Joachim; Bailey, David

2014-08-01

There has been a resurgence of interest in the use of phenotypic screens in drug discovery as an alternative to target-focused approaches. Given that oncology is currently the most active therapeutic area, and also one in which target-focused approaches have been particularly prominent in the past two decades, we investigated the contribution of phenotypic assays to oncology drug discovery by analysing the origins of all new small-molecule cancer drugs approved by the US Food and Drug Administration (FDA) over the past 15 years and those currently in clinical development. Although the majority of these drugs originated from target-based discovery, we identified a significant number whose discovery depended on phenotypic screening approaches. We postulate that the contribution of phenotypic screening to cancer drug discovery has been hampered by a reliance on 'classical' nonspecific drug effects such as cytotoxicity and mitotic arrest, exacerbated by a paucity of mechanistically defined cellular models for therapeutically translatable cancer phenotypes. However, technical and biological advances that enable such mechanistically informed phenotypic models have the potential to empower phenotypic drug discovery in oncology.

Network motifs that stabilize the hybrid epithelial/mesenchymal phenotype

NASA Astrophysics Data System (ADS)

Jolly, Mohit Kumar; Jia, Dongya; Tripathi, Satyendra; Hanash, Samir; Mani, Sendurai; Ben-Jacob, Eshel; Levine, Herbert

Epithelial to Mesenchymal Transition (EMT) and its reverse - MET - are hallmarks of cancer metastasis. While transitioning between E and M phenotypes, cells can also attain a hybrid epithelial/mesenchymal (E/M) phenotype that enables collective cell migration as a cluster of Circulating Tumor Cells (CTCs). These clusters can form 50-times more tumors than individually migrating CTCs, underlining their importance in metastasis. However, this hybrid E/M phenotype has been hypothesized to be only a transient one that is attained en route EMT. Here, via mathematically modeling, we identify certain `phenotypic stability factors' that couple with the core three-way decision-making circuit (miR-200/ZEB) and can maintain or stabilize the hybrid E/M phenotype. Further, we show experimentally that this phenotype can be maintained stably at a single-cell level, and knockdown of these factors impairs collective cell migration. We also show that these factors enable the association of hybrid E/M with high stemness or tumor-initiating potential. Finally, based on these factors, we deduce specific network motifs that can maintain the E/M phenotype. Our framework can be used to elucidate the effect of other players in regulating cellular plasticity during metastasis. This work was supported by NSF PHY-1427654 (Center for Theoretical Biological Physics) and the CPRIT Scholar in Cancer Research of the State of Texas at Rice University.

Tag-mediated cooperation with non-deterministic genotype-phenotype mapping

NASA Astrophysics Data System (ADS)

Zhang, Hong; Chen, Shu

2016-01-01

Tag-mediated cooperation provides a helpful framework for resolving evolutionary social dilemmas. However, most of the previous studies have not taken into account genotype-phenotype distinction in tags, which may play an important role in the process of evolution. To take this into consideration, we introduce non-deterministic genotype-phenotype mapping into a tag-based model with spatial prisoner's dilemma. By our definition, the similarity between genotypic tags does not directly imply the similarity between phenotypic tags. We find that the non-deterministic mapping from genotypic tag to phenotypic tag has non-trivial effects on tag-mediated cooperation. Although we observe that high levels of cooperation can be established under a wide variety of conditions especially when the decisiveness is moderate, the uncertainty in the determination of phenotypic tags may have a detrimental effect on the tag mechanism by disturbing the homophilic interaction structure which can explain the promotion of cooperation in tag systems. Furthermore, the non-deterministic mapping may undermine the robustness of the tag mechanism with respect to various factors such as the structure of the tag space and the tag flexibility. This observation warns us about the danger of applying the classical tag-based models to the analysis of empirical phenomena if genotype-phenotype distinction is significant in real world. Non-deterministic genotype-phenotype mapping thus provides a new perspective to the understanding of tag-mediated cooperation.

Integrating Multiple Correlated Phenotypes for Genetic Association Analysis by Maximizing Heritability

PubMed Central

Zhou, Jin J.; Cho, Michael H.; Lange, Christoph; Lutz, Sharon; Silverman, Edwin K.; Laird, Nan M.

2015-01-01

Many correlated disease variables are analyzed jointly in genetic studies in the hope of increasing power to detect causal genetic variants. One approach involves assessing the relationship between each phenotype and each single nucleotide polymorphism (SNP) individually and using a Bonferroni correction for the effective number of tests conducted. Alternatively, one can apply a multivariate regression or a dimension reduction technique, such as principal component analysis (PCA), and test for the association with the principal components (PC) of the phenotypes rather than the individual phenotypes. Inspired by the previous approaches of combining phenotypes to maximize heritability at individual SNPs, in this paper, we propose to construct a maximally heritable phenotype (MaxH) by taking advantage of the estimated total heritability and co-heritability. The heritability and co-heritability only need to be estimated once, therefore our method is applicable to genome-wide scans. MaxH phenotype is a linear combination of the individual phenotypes with increased heritability and power over the phenotypes being combined. Simulations show that the heritability and power achieved agree well with the theory for large samples and two phenotypes. We compare our approach with commonly used methods and assess both the heritability and the power of the MaxH phenotype. Moreover we provide suggestions for how to choose the phenotypes for combination. An application of our approach to a COPD genome-wide association study shows the practical relevance. PMID:26111731

To Genotype or Phenotype for Personalized Medicine? CYP450 Drug Metabolizing Enzyme Genotype-Phenotype Concordance and Discordance in the Ecuadorian Population.

PubMed

De Andrés, Fernando; Terán, Santiago; Hernández, Francisco; Terán, Enrique; LLerena, Adrián

2016-12-01

Genetic variations within the cytochrome P450 (CYP450) superfamily of drug metabolizing enzymes confer substantial person-to-person and between-population differences in pharmacokinetics, and by extension, highly variable clinical effects of medicines. In this context, "personalized medicine," "precision medicine," and "stratified medicine" are related concepts attributed to what is essentially targeted therapeutics and companion diagnostics, aimed at improving safety and effectiveness of health interventions. We report here, to the best of our knowledge, the first comparative clinical pharmacogenomics study, in an Ecuadorian population sample, of five key CYP450s involved in drug metabolism: CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4. In 139 unrelated, medication-free, and healthy Ecuadorian subjects, we measured the phenotypic activity of these drug metabolism pathways using the CEIBA multiplexed phenotyping cocktail. The subjects were genotyped for each CYP450 enzyme gene as well. Notably, based on the CYP450 metabolic phenotypes estimated by the genotype data, 0.75% and 3.10% of the subjects were genotypic poor metabolizers (gPMs) for CYP2C19 and CYP2D6, respectively. Additionally, on the other extreme, genotype-estimated ultrarapid metabolizer (gUMs) phenotype was represented by 15.79% of CYP2C19, and 5.43% of CYP2D6. There was, however, considerable discordance between directly measured phenotypes (mPMs and mUMs) and the above genotype-estimated enzyme phenotypes. For example, among individuals genotypically carrying enhanced activity alleles (gUMs), many showed a lower actual drug metabolism capacity than expected by their genotypes, even lower than individuals with reduced or no activity alleles. In conclusion, for personalized medicine in the Ecuadorian population, we recommend CYP450 multiplexed phenotyping, or genotyping and phenotyping in tandem, rather than CYP450 genotypic tests alone. Additionally, we recommend, in consideration of equity, ethical

Relationship between endophenotype and phenotype in ADHD

PubMed Central

Rommelse, Nanda NJ; Altink, Marieke E; Martin, Neilson C; Buschgens, Cathelijne JM; Faraone, Stephen V; Buitelaar, Jan K; Sergeant, Joseph A; Oosterlaan, Jaap

2008-01-01

Background It has been hypothesized that genetic and environmental factors relate to psychiatric disorders through the effect of intermediating, vulnerability traits called endophenotypes. The study had a threefold aim: to examine the predictive validity of an endophenotypic construct for the ADHD diagnosis, to test whether the magnitude of group differences at the endophenotypic and phenotypic level is comparable, and to investigate whether four factors (gender, age, IQ, rater bias) have an effect (moderation or mediation) on the relation between endophenotype and phenotype. Methods Ten neurocognitive tasks were administered to 143 children with ADHD, 68 non-affected siblings, and 120 control children (first-borns) and 132 children with ADHD, 78 non-affected siblings, and 113 controls (second-borns) (5 – 19 years). The task measures have been investigated previously for their endophenotypic viability and were combined to one component which was labeled 'the endophenotypic construct': one measure representative of endophenotypic functioning across several domains of functioning. Results The endophenotypic construct classified children with moderate accuracy (about 50% for each of the three groups). Non-affected children differed as much from controls at the endophenotypic as at the phenotypic level, but affected children displayed a more severe phenotype than endophenotype. Although a potentially moderating effect (age) and several mediating effects (gender, age, IQ) were found affecting the relation between endophenotypic construct and phenotype, none of the effects studied could account for the finding that affected children had a more severe phenotype than endophenotype. Conclusion Endophenotypic functioning is moderately predictive of the ADHD diagnosis, though findings suggest substantial overlap exists between endophenotypic functioning in the groups of affected children, non-affected siblings, and controls. Results suggest other factors may be crucial and

Phenotypic approaches to drought in cassava: review

PubMed Central

Okogbenin, Emmanuel; Setter, Tim L.; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

2012-01-01

Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12–18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding. PMID

Programmed Death 1 Regulates Memory Phenotype CD4 T Cell Accumulation, Inhibits Expansion of the Effector Memory Phenotype Subset and Modulates Production of Effector Cytokines

PubMed Central

Charlton, Joanna J.; Tsoukatou, Debbie; Mamalaki, Clio; Chatzidakis, Ioannis

2015-01-01

Memory phenotype CD4 T cells are found in normal mice and arise through response to environmental antigens or homeostatic mechanisms. The factors that regulate the homeostasis of memory phenotype CD4 cells are not clear. In the present study we demonstrate that there is a marked accumulation of memory phenotype CD4 cells, specifically of the effector memory (TEM) phenotype, in lymphoid organs and tissues of mice deficient for the negative co-stimulatory receptor programmed death 1 (PD-1). This can be correlated with decreased apoptosis but not with enhanced homeostatic turnover potential of these cells. PD-1 ablation increased the frequency of memory phenotype CD4 IFN-γ producers but decreased the respective frequency of IL-17A-producing cells. In particular, IFN-γ producers were more abundant but IL-17A producing cells were more scarce among PD-1 KO TEM-phenotype cells relative to WT. Transfer of peripheral naïve CD4 T cells suggested that accumulated PD-1 KO TEM-phenotype cells are of peripheral and not of thymic origin. This accumulation effect was mediated by CD4 cell-intrinsic mechanisms as shown by mixed bone marrow chimera experiments. Naïve PD-1 KO CD4 T cells gave rise to higher numbers of TEM-phenotype lymphopenia-induced proliferation memory cells. In conclusion, we provide evidence that PD-1 has an important role in determining the composition and functional aspects of memory phenotype CD4 T cell pool. PMID:25803808

Application of phenotypic microarrays to environmental microbiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borglin, sharon; Joyner, Dominique; DeAngelis, Kristen

2012-01-01

Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. This review describes applications of phenotype arrays to anaerobic and thermophilic microorganisms, use of the plates in stress response studies, in development of culture media for newly discovered strains, and for assessment of phenotype of environmental communities. Also discussed are considerationsmore » and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting.« less

The Nutritional Phenotype in the Age of Metabolomics

PubMed Central

Zeisel, S. H.; Freake, H. C.; Bauman, D. E.; Bier, D. M.; Burrin, D. G.; German, J. B.; Klein, S.; Marquis, G. S.; Milner, J. A.; Pelto, G. H.; Rasmussen, K. M.

2008-01-01

The concept of the nutritional phenotype is proposed as a defined and integrated set of genetic, proteomic, metabolomic, functional, and behavioral factors that, when measured, form the basis for assessment of human nutritional status. The nutritional phenotype integrates the effects of diet on disease/wellness and is the quantitative indication of the paths by which genes and environment exert their effects on health. Advances in technology and in fundamental biological knowledge make it possible to define and measure the nutritional phenotype accurately in a cross section of individuals with various states of health and disease. This growing base of data and knowledge could serve as a resource for all scientific disciplines involved in human health. Nutritional sciences should be a prime mover in making key decisions that include: what environmental inputs (in addition to diet) are needed; what genes/proteins/metabolites should be measured; what end-point phenotypes should be included; and what informatics tools are available to ask nutritionally relevant questions. Nutrition should be the major discipline establishing how the elements of the nutritional phenotype vary as a function of diet. Nutritional sciences should also be instrumental in linking the elements that are responsive to diet with the functional outcomes in organisms that derive from them. As the first step in this initiative, a prioritized list of genomic, proteomic, and metabolomic as well as functional and behavioral measures that defines a practically useful subset of the nutritional phenotype for use in clinical and epidemiological investigations must be developed. From this list, analytic platforms must then be identified that are capable of delivering highly quantitative data on these endpoints. This conceptualization of a nutritional phenotype provides a concrete form and substance to the recognized future of nutritional sciences as a field addressing diet, integrated metabolism, and health

Design of synthetic bacterial communities for predictable plant phenotypes

PubMed Central

Herrera Paredes, Sur; Gao, Tianxiang; Law, Theresa F.; Finkel, Omri M.; Mucyn, Tatiana; Teixeira, Paulo José Pereira Lima; Salas González, Isaí; Feltcher, Meghan E.; Powers, Matthew J.; Shank, Elizabeth A.; Jones, Corbin D.; Jojic, Vladimir; Dangl, Jeffery L.; Castrillo, Gabriel

2018-01-01

Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities. PMID:29462153

Cluster Analysis Identifies 3 Phenotypes within Allergic Asthma.

PubMed

Sendín-Hernández, María Paz; Ávila-Zarza, Carmelo; Sanz, Catalina; García-Sánchez, Asunción; Marcos-Vadillo, Elena; Muñoz-Bellido, Francisco J; Laffond, Elena; Domingo, Christian; Isidoro-García, María; Dávila, Ignacio

Asthma is a heterogeneous chronic disease with different clinical expressions and responses to treatment. In recent years, several unbiased approaches based on clinical, physiological, and molecular features have described several phenotypes of asthma. Some phenotypes are allergic, but little is known about whether these phenotypes can be further subdivided. We aimed to phenotype patients with allergic asthma using an unbiased approach based on multivariate classification techniques (unsupervised hierarchical cluster analysis). From a total of 54 variables of 225 patients with well-characterized allergic asthma diagnosed following American Thoracic Society (ATS) recommendation, positive skin prick test to aeroallergens, and concordant symptoms, we finally selected 19 variables by multiple correspondence analyses. Then a cluster analysis was performed. Three groups were identified. Cluster 1 was constituted by patients with intermittent or mild persistent asthma, without family antecedents of atopy, asthma, or rhinitis. This group showed the lowest total IgE levels. Cluster 2 was constituted by patients with mild asthma with a family history of atopy, asthma, or rhinitis. Total IgE levels were intermediate. Cluster 3 included patients with moderate or severe persistent asthma that needed treatment with corticosteroids and long-acting β-agonists. This group showed the highest total IgE levels. We identified 3 phenotypes of allergic asthma in our population. Furthermore, we described 2 phenotypes of mild atopic asthma mainly differentiated by a family history of allergy. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Percolation on fitness landscapes: effects of correlation, phenotype, and incompatibilities

PubMed Central

Gravner, Janko; Pitman, Damien; Gavrilets, Sergey

2009-01-01

We study how correlations in the random fitness assignment may affect the structure of fitness landscapes, in three classes of fitness models. The first is a phenotype space in which individuals are characterized by a large number n of continuously varying traits. In a simple model of random fitness assignment, viable phenotypes are likely to form a giant connected cluster percolating throughout the phenotype space provided the viability probability is larger than 1/2n. The second model explicitly describes genotype-to-phenotype and phenotype-to-fitness maps, allows for neutrality at both phenotype and fitness levels, and results in a fitness landscape with tunable correlation length. Here, phenotypic neutrality and correlation between fitnesses can reduce the percolation threshold, and correlations at the point of phase transition between local and global are most conducive to the formation of the giant cluster. In the third class of models, particular combinations of alleles or values of phenotypic characters are “incompatible” in the sense that the resulting genotypes or phenotypes have zero fitness. This setting can be viewed as a generalization of the canonical Bateson-Dobzhansky-Muller model of speciation and is related to K- SAT problems, prominent in computer science. We analyze the conditions for the existence of viable genotypes, their number, as well as the structure and the number of connected clusters of viable genotypes. We show that analysis based on expected values can easily lead to wrong conclusions, especially when fitness correlations are strong. We focus on pairwise incompatibilities between diallelic loci, but we also address multiple alleles, complex incompatibilities, and continuous phenotype spaces. In the case of diallelic loci, the number of clusters is stochastically bounded and each cluster contains a very large sub-cube. Finally, we demonstrate that the discrete NK model shares some signature properties of models with high

Wine Expertise Predicts Taste Phenotype

PubMed Central

Hayes, John E; Pickering, Gary J

2011-01-01

Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance – with appropriate caveats about populations tested, outcomes measured and psychophysical methods used – an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli. PMID:22888174

Phenotypes Associated with SHOX Deficiency.

PubMed

Ross, J L; Scott, C; Marttila, P; Kowal, K; Nass, A; Papenhausen, P; Abboudi, J; Osterman, L; Kushner, H; Carter, P; Ezaki, M; Elder, F; Wei, F; Chen, H; Zinn, A R

2001-12-01

Leri-Weill dyschondrosteosis (LWD) (MIM 127300) is a dominantly inherited skeletal dysplasia characterized phenotypically by Madelung wrist deformity, mesomelia, and short stature. LWD can now be defined genetically by haploinsufficiency of the SHOX (short stature homeobox-containing) gene. We have studied 21 LWD families (43 affected LWD subjects, including 32 females and 11 males, ages 3-56 yr) with confirmed SHOX abnormalities. We investigated the relationship between SHOX mutations, height deficit, and Madelung deformity to determine the contribution of SHOX haploinsufficiency to the LWD and Turner syndrome (TS) phenotypes. Also, we examined the effects of age, gender, and female puberty (estrogen) on the LWD phenotype. SHOX deletions were present in affected individuals from 17 families (81%), and point mutations were detected in 4 families (19%). In the LWD subjects, height deficits ranged from -4.6 to +0.6 SD (mean +/- SD = -2.2 +/- 1.0). There were no statistically significant effects of age, gender, pubertal status, or parental origin of SHOX mutations on height z-score. The height deficit in LWD is approximately two thirds that of TS. Madelung deformity was present in 74% of LWD children and adults and was more frequent and severe in females than males. The prevalence of the Madelung deformity was higher in the LWD vs. a TS population. The prevalence of increased carrying angle, high arched palate, and scoliosis was similar in the two populations. In conclusion, SHOX deletions or mutations accounted for all of our LWD cases. SHOX haploinsufficiency accounts for most, but not all, of the TS height deficit. The LWD phenotype shows some gender- and age-related differences.

Phenotype adjustment promotes adaptive evolution in a game without conflict.

PubMed

Yamaguchi, Sachi; Iwasa, Yoh

2015-06-01

Organisms may adjust their phenotypes in response to social and physical environments. Such phenotypic plasticity is known to help or retard adaptive evolution. Here, we study the evolutionary outcomes of adaptive phenotypic plasticity in an evolutionary game involving two players who have no conflicts of interest. A possible example is the growth and sex allocation of a lifelong pair of shrimps entrapped in the body of a sponge. We consider random pair formation, the limitation of total resources for growth, and the needs of male investment to fertilize eggs laid by the partner. We compare the following three different evolutionary dynamics: (1) No adjustment: each individual develops a phenotype specified by its own genotype; (2) One-player adjustment: the phenotype of the first player is specified by its own genotype, and the second player chooses the phenotype that maximizes its own fitness; (3) Two-player adjustment: the first player exhibits an initial phenotype specified by its own genotype, the second player chooses a phenotype given that of the first player, and finally, the first player readjusts its phenotype given that of the second player. We demonstrate that both one-player and two-player adjustments evolve to achieve maximum fitness. In contrast, the dynamics without adjustment fails in some cases to evolve outcomes with the highest fitness. For an intermediate range of male cost, the evolution of no adjustment realizes two hermaphrodites with equal size, whereas the one-player and two-player adjustments realize a small male and a large female. Copyright © 2015 Elsevier Inc. All rights reserved.

Muscle biopsy

MedlinePlus

... muscle ( myopathic changes ) Tissue death of the muscle (necrosis) Disorders that involve inflammation of the blood vessels and affect muscles ( necrotizing vasculitis ) Traumatic muscle damage ...

EuroPhenome: a repository for high-throughput mouse phenotyping data

PubMed Central

Morgan, Hugh; Beck, Tim; Blake, Andrew; Gates, Hilary; Adams, Niels; Debouzy, Guillaume; Leblanc, Sophie; Lengger, Christoph; Maier, Holger; Melvin, David; Meziane, Hamid; Richardson, Dave; Wells, Sara; White, Jacqui; Wood, Joe; de Angelis, Martin Hrabé; Brown, Steve D. M.; Hancock, John M.; Mallon, Ann-Marie

2010-01-01

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies. PMID:19933761

Mesenchymal stem cell-based repair of articular cartilage with polyglycolic acid-hydroxyapatite biphasic scaffold.

PubMed

Zhou, X Z; Leung, V Y; Dong, Q R; Cheung, K M; Chan, D; Lu, W W

2008-06-01

This study investigates the capacity of a composite scaffold composed of polyglycolic acid-hydroxyapatite (PGA-HA) and autologous mesenchymal stem cells (MSCs) to promote repair of osteochondral defects. MSCs from culture-expanded rabbits were seeded onto a PGA and HA scaffold. After a 72-hour co-culture period, the cell-adhered PGA and HA were joined together, forming an MSCs-PGA-HA composite. Full-thickness cartilage defects in the intercondylar fossa of the femur were then implanted with the MSC-PGA-HA composite, the PGA-HA scaffold only, or they were left empty (n=20). Animals were sacrificed 16 or 32 weeks after surgery and the gross appearance of the defects was evaluated. The specimens were examined histologically for morphologic features, and stained immunohistochemically for type 2 collagen. Specimens of the MSCs-PGA-HA composite implantation group demonstrated hyaline cartilage and a complete subchondral bone formation. At 16 weeks post-implantation, significant integration of the newly formed tissue with surrounding normal cartilage and subchondral bone was observed when compared to the two control groups. At 32 weeks, no sign of progressive degeneration of the newly formed tissue was found. A significant difference in histological grading score was found compared with the control groups. The novel MSCs-seeded, PGA-HA biphasic graft facilitated both articular cartilage and subchondral bone regeneration in an animal model and might serve as a new approach for clinical applications.

Molecular mechanisms of phenotypic plasticity in social insects

USDA-ARS?s Scientific Manuscript database

Polyphenism in insects, whereby a single genome expresses different phenotypes in response to environmental cues, is a fascinating biological phenomenon. Social insects are especially intriguing examples of phenotypic plasticity because division of labor results in the development of extreme morphol...

Analyzing the effects of instillation volume on intravesical delivery using biphasic solute transport in a deformable geometry.

PubMed

Smith, Sean G; Griffith, Boyce E; Zaharoff, David A

2018-04-05

Ailments of the bladder are often treated via intravesical delivery-direct application of therapeutic into the bladder through a catheter. This technique is employed hundreds of thousands of times every year, but protocol development has largely been limited to empirical determination. Furthermore, the numerical analyses of intravesical delivery performed to date have been restricted to static geometries and have not accounted for bladder deformation. This study uses a finite element analysis approach with biphasic solute transport to investigate several parameters pertinent to intravesical delivery including solute concentration, solute transport properties and instillation volume. The volume of instillation was found to have a substantial impact on the exposure of solute to the deeper muscle layers of the bladder, which are typically more difficult to reach. Indeed, increasing the instillation volume from 50-100 ml raised the muscle solute exposure as a percentage of overall bladder exposure from 60-70% with higher levels achieved for larger instillation volumes. Similar increases were not seen for changes in solute concentration or solute transport properties. These results indicate the role that instillation volume may play in targeting particular layers of the bladder during an intravesical delivery.