Raising the efficiency of a plasma opening switch by applying an external magnetic field

The influence of an external magnetic field on the performance of a high-impedance plasma opening switch is studied experimentally. A 1.5-fold increase in the output voltage of a plasma opening switch operating in the erosion mode is achieved by applying an external magnetic field. The magnetic field strength and the parameters of the plasma opening switch at which the maximum output voltage is attained are determined. It is shown experimentally that the predicted dependence of the maximum output voltage on the Marx generator voltage, U _POS [MV]=3.6 (U _MG [MV])^4/7, is confirmed experimentally.     

Regulation of Sex Determination in Mice by a Non-coding Genomic Region

To identify novel genomic regions that regulate sex determination, we utilized the powerful C57BL/6J-Y^POS (B6-Y^POS) model of XY sex reversal where mice with autosomes from the B6 strain and a Y chromosome from a wild-derived strain, Mus domesticus poschiavinus (Y^POS), show complete sex reversal. In B6-Y^POS, the presence of a 55-Mb congenic region on chromosome 11 protects from sex reversal in a dose-dependent manner. Using mouse genetic backcross designs and high-density SNP arrays, we narrowed the congenic region to a 1.62-Mb genomic region on chromosome 11 that confers 80% protection from B6-Y^POS sex reversal when one copy is present and complete protection when two copies are present. It was previously believed that the protective congenic region originated from the 129S1/SviMJ (129) strain. However, genomic analysis revealed that this region is not derived from 129 and most likely is derived from the semi-inbred strain POSA. We show that the small 1.62-Mb congenic region that protects against B6-Y^POS sex reversal is located within the Sox9 promoter and promotes the expression of Sox9, thereby driving testis development within the B6-Y^POS background. Through 30 years of backcrossing, this congenic region was maintained, as it promoted male sex determination and fertility despite the female-promoting B6-Y^POS genetic background. Our findings demonstrate that long-range enhancer regions are critical to developmental processes and can be used to identify the complex interplay between genome variants, epigenetics, and developmental gene regulation.     

Comparative analysis of the ileal bacterial composition of post-weaned pigs fed different high-quality protein sources

To further understand the contribution of feedstuff ingredients to gut health in swine, gut histology and intestinal bacterial profiles associated with the use of two high-quality protein sources, microbially enhanced soybean meal (MSBM) and Menhaden fishmeal (FM) were assessed. Weaned pigs were fed one of three experimental diets: (1) basic diet containing corn and soybean meal (Negative Control (NEG)), (2) basic diet + fishmeal (FM; Positive Control (POS)) and (3) basic diet + MSBM (MSBM). Phase I POS and MSBM diets (d 0 to d 7 post-wean) included FM or MSBM at 7.5%, while Phase II POS and MSBM diets (d 8 to d 21) included FM or MSBM at 5.0%. Gastrointestinal tissue and ileal digesta were collected from euthanised pigs at d 21 (eight pigs/diet) to assess gut histology and intestinal bacterial profiles, respectively. Data were analysed using Proc Mixed in SAS, with pig as the experimental unit and pig (treatment) as the random effect. Histological and immunohistochemical analyses of stomach and small intestinal tissue using haematoxylin–eosin, Periodic Acid Schiff/Alcian blue and inflammatory cell staining did not reveal detectable differences in host response to dietary treatment. Ileal bacterial composition profiles were obtained from next-generation sequencing of PCR generated amplicons targeting the V1 to V3 regions of the 16S rRNA gene. Lactobacillus-affiliated sequences were found to be the most highly represented across treatments, with an average relative abundance of 64.0%, 59.9% and 41.80% in samples from pigs fed the NEG, POS and MSBM diets, respectively. Accordingly, the three most abundant Operational Taxonomic Units (OTUs) were affiliated to Lactobacillus, showing a distinct abundance pattern relative to dietary treatment. One OTU (SD_Ssd_00001), most closely related to Lactobacillus amylovorus, was found to be more abundant in NEG and POS samples compared to MSBM (23.5% and 35.0% v. 9.2%). Another OTU (SD_Ssd_00002), closely related to Lactobacillus johnsonii, was more highly represented in POS and MSBM samples compared to NEG (14.0% and 15.8% v. 0.1%). Finally, OTU Sd_Ssd-00011, highest sequence identity to Lactobacillus delbrueckii, was found in highest abundance in ileal samples from MSBM-fed pigs (1.9% and 3.3% v. 11.3, in POS, NEG and MSBM, respectively). There was no effect of protein source on bacterial taxa to the genus level or diversity based on principal component analysis. Dietary protein source may provide opportunity to enhance presence of specific members of Lactobacillus genus that are associated with immune-modulating properties without altering overall intestinal bacterial diversity.     

Association between simple sequence repeat-rich chromosome regions and intergenomic translocation breakpoints in natural populations of allopolyploid wild wheats

Background and Aims

Repetitive DNA sequences are thought to be involved in the formation of chromosomal rearrangements. The aim of this study was to analyse the distribution of microsatellite clusters in Aegilops biuncialis and Aegilops geniculata, and its relationship with the intergenomic translocations in these allotetraploid species, wild genetic resources for wheat improvement.

Methods

The chromosomal localization of (ACG)_n and (GAA)_n microsatellite sequences in Ae. biuncialis and Ae. geniculata and in their diploid progenitors Aegilops comosa and Aegilops umbellulata was investigated by sequential in situ hybridization with simple sequence repeat (SSR) probes and repeated DNA probes (pSc119·2, Afa family and pTa71) and by dual-colour genomic in situ hybridization (GISH). Thirty-two Ae. biuncialis and 19 Ae. geniculata accessions were screened by GISH for intergenomic translocations, which were further characterized by fluorescence in situ hybridization and GISH.

Key Results

Single pericentromeric (ACG)_n signals were localized on most U and on some M genome chromosomes, whereas strong pericentromeric and several intercalary and telomeric (GAA)_n sites were observed on the Aegilops chromosomes. Three Ae. biuncialis accessions carried 7U^b–7M^b reciprocal translocations and one had a 7U^b–1M^b rearrangement, while two Ae. geniculata accessions carried 7U^g–1M^g or 5U^g–5M^g translocations. Conspicuous (ACG)_n and/or (GAA)_n clusters were located near the translocation breakpoints in eight of the ten translocated chromosomes analysed, SSR bands and breakpoints being statistically located at the same chromosomal site in six of them.

Conclusions

Intergenomic translocation breakpoints are frequently mapped to SSR-rich chromosomal regions in the allopolyploid species examined, suggesting that microsatellite repeated DNA sequences might facilitate the formation of those chromosomal rearrangements. The (ACG)_n and (GAA)_n SSR motifs serve as additional chromosome markers for the karyotypic analysis of UM genome Aegilops species.     

Practical Considerations for Determination of Glass Transition Temperature of a Maximally Freeze Concentrated Solution

Glass transition temperature is a unique thermal characteristic of amorphous systems and is associated with changes in physical properties such as heat capacity, viscosity, electrical resistance, and molecular mobility. Glass transition temperature for amorphous solids is referred as (T _g), whereas for maximally freeze concentrated solution, the notation is (T _g′). This article is focused on the factors affecting determination of T _g′ for application to lyophilization process design and frozen storage stability. Also, this review provides a perspective on use of various types of solutes in protein formulation and their effect on T _g′. Although various analytical techniques are used for determination of T _g′ based on the changes in physical properties associated with glass transition, the differential scanning calorimetry (DSC) is the most commonly used technique. In this article, an overview of DSC technique is provided along with brief discussion on the alternate analytical techniques for T _g′ determination. Additionally, challenges associated with T _g′ determination, using DSC for protein formulations, are discussed. The purpose of this review is to provide a practical industry perspective on determination of T _g′ for protein formulations as it relates to design and development of lyophilization process and/or for frozen storage; however, a comprehensive review of glass transition temperature (T _g, T _g′), in general, is outside the scope of this work.     

Influence of a Nitrogen Admixture on the Anomalous Memory Effect in the Breakdown of Low-Pressure Argon in a Long Discharge Tube

The memory effect (the dependence of the dynamic breakdown voltage U _b on the time interval τ between voltage pulses) in pulse-periodic discharges in pure argon and the Ar + 1%N₂ mixture was studied experimentally. The discharge was ignited in a 2.8-cm-diameter tube with an interelectrode distance of 75 cm. The measurements were performed at gas pressures of P = 1, 2, and 5 Torr and discharge currents in a steady stage of the discharge of I = 20 and 56 mA. Breakdown was produced by applying positive-polarity voltage pulses, the time interval between pulses being in the range of τ = 0.5–40 ms. In this range of τ values, a local maximum (the anomalous memory effect) was observed in the dependence U _b (τ). It is shown that addition of nitrogen to argon substantially narrows the range of τ values at which this effect takes place. To analyze the measurement results, the plasma parameters in a steady-state discharge (in both pure argon and the Ar + 1%N₂ mixture) and its afterglow were calculated for the given experimental conditions. Analysis of the experimental data shows that the influence of the nitrogen admixture on the shape of the dependence U _b (τ) is, to a large extent, caused by the change in the decay rate of the argon afterglow plasma in the presence of a nitrogen admixture.     

Body Fineness Ratio as a Predictor of Maximum Prolonged-Swimming Speed in Coral Reef Fishes

The ability to sustain high swimming speeds is believed to be an important factor affecting resource acquisition in fishes. While we have gained insights into how fin morphology and motion influences swimming performance in coral reef fishes, the role of other traits, such as body shape, remains poorly understood. We explore the ability of two mechanistic models of the causal relationship between body fineness ratio and endurance swimming-performance to predict maximum prolonged-swimming speed (U_max) among 84 fish species from the Great Barrier Reef, Australia. A drag model, based on semi-empirical data on the drag of rigid, submerged bodies of revolution, was applied to species that employ pectoral-fin propulsion with a rigid body at U _max. An alternative model, based on the results of computer simulations of optimal shape in self-propelled undulating bodies, was applied to the species that swim by body-caudal-fin propulsion at U_max. For pectoral-fin swimmers, U_max increased with fineness, and the rate of increase decreased with fineness, as predicted by the drag model. While the mechanistic and statistical models of the relationship between fineness and U_max were very similar, the mechanistic (and statistical) model explained only a small fraction of the variance in U_max. For body-caudal-fin swimmers, we found a non-linear relationship between fineness and U_max, which was largely negative over most of the range of fineness. This pattern fails to support either predictions from the computational models or standard functional interpretations of body shape variation in fishes. Our results suggest that the widespread hypothesis that a more optimal fineness increases endurance-swimming performance via reduced drag should be limited to fishes that swim with rigid bodies.     

Proof of concept: nitrogen use efficiency of contrasting spring wheat varieties grown in greenhouse and field

Aims

Major aims were to test and evaluate a new concept for assessment of nitrogen use efficiency (NUE) of crops by growing six spring wheat varieties in greenhouse and field environments. NUE was calculated with a plant based concept integrating the entire crop life history and separating plant characteristics from environmental factors affecting NUE. Specific hypotheses were tested related to the varieties’ drought and nutrient fertilisation responses for NUE components, and coherence of those responses in field and greenhouse.

Methods

The wheat (Triticum aestivum L.) cultivated varieties ‘Diskett’, ‘Granary’, ‘Quarna’, ‘Stilett’, ‘Vinjett’, and a Swedish landrace (‘Dala’) were grown in field and greenhouse environments in Central Sweden. Two fertilisation treatments were included in a field and greenhouse experiment, and in the greenhouse also drought. The NUE components N uptake efficiency (U_N), grain-specific N efficiency (E_N,g) and grain N concentration (C_N,g) were assessed.

Results

Drought reduced yield and NUE through E_N,g, and more so when drought occurred prior to anthesis than after anthesis. Effect of fertilisation treatment on NUE components was similar in the two set-ups, but there were fewer variety × fertilisation interactions in the field. U_N was higher in the field and E_N,g was higher in the greenhouse, while C_N,g and overall NUE were similar in the two environments. Ranking of varieties regarding NUE and U_N was similar in the greenhouse and field, but different regarding E_N,g and C_N,g.

Conclusions

The NUE concept is a useful tool to describe and integrate important NUE components for crops grown in different treatments (nutrient fertilisation, drought) and experimental set-ups, i.e. greenhouse and field. Similar variety ranking in overall NUE across experimental set-ups indicates stable results in different environments.     

Pseudomonas fluorescens lipase immobilization on polysiloxane–polyvinyl alcohol composite chemically modified with epichlorohydrin

The technique based on sol–gel approach was used to generate silica matrices derivatives by hydrolysis of silane compounds. The present work evaluates a hybrid matrix obtained with tetraethoxysilane (TEOS) and polyvinyl alcohol (PVA) on the immobilization yield of lipase from Pseudomonas fluorescens. The resulting polysiloxane–polyvinyl alcohol (POS–PVA) matrix combines the property of PVA as a suitable polymer to retain proteins with an excellent optical, thermal and chemical stability of the host silicon oxide matrix. Aiming to render adequate functional groups to the covalent binding with the enzyme the POS–PVA matrix was chemically modified using epichlorohydrin. The results were compared with immobilized derivative on POS–PVA activated with glutaraldehyde. Immobilization yield based on the recovered lipase activity depended on the activating agent and the highest efficiency (32%) was attained when lipase was immobilized on POS–PVA activated with epichlorohydrin, which, probably, provided more linkage points for the covalent bind of the enzyme on the support. This was confirmed by determining the morphological properties using different techniques as X-ray diffraction and scanning electron microscopy (SEM). Comparative studies were carried out to attain optimal activities for free lipase and immobilized systems. For this purpose, a central composite experimental design with different combinations of pH and temperature was performed. Enzymatic hydrolysis with the immobilized enzyme in the framework of the Michaelis–Menten mechanism was also reported. Under optimum conditions, the immobilized derivative on POS–PVA activated with epichlorohydrin showed to have more affinity for the substrate in the hydrolysis of olive oil, with a Michaelis–Menten constant value (K_m) of 293 mM, compared to the value of 401 mM obtained for the immobilized lipase on support activated with glutaraldehyde. Data generated by DSC showed that both immobilized derivatives have similar thermal stabilities.     

Large-Scale Purification of Porcine or Bovine Photoreceptor Outer Segments for Phagocytosis Assays on Retinal Pigment Epithelial Cells

Analysis of one of the vital functions of retinal pigment epithelial (RPE) cells, the phagocytosis of spent aged distal fragments of photoreceptor outer segments (POS) can be performed in vitro. Photoreceptor outer segments with stacks of membranous discs containing the phototransduction machinery are continuously renewed in the retina. Spent POS are eliminated daily by RPE cells. Rodent, porcine/bovine and human RPE cells recognize POS from various species in a similar manner. To facilitate performing large series of experiments with little variability, a large stock of POS can be isolated from porcine eyes and stored frozen in aliquots. This protocol takes advantage of the characteristic of photopigments that display an orange color when kept in the dark. Under dim red light, retinae are collected in a buffer from opened eyecups cut in halves. The retinal cell suspension is homogenized, filtered and loaded onto a continuous sucrose gradient. After centrifugation, POS are located in a discrete band in the upper part of the gradient that has a characteristic orange color. POS are then collected, spun, resuspended sequentially in wash buffers, counted and aliquoted. POS obtained this way can be used for phagocytosis assays and analysis of protein activation, localization or interaction at various times after POS challenge. Alternatively, POS can be labeled with fluorophores, e.g., FITC, before aliquoting for subsequent fluorescence quantification of POS binding or engulfment. Other possible applications include the use of modified POS or POS challenge combined with stress conditions to study the effect of oxidative stress or aging on RPE cells.     

Production of C 2 * radicals in a transverse volume discharge

Conditions for producing stable transverse volume discharges in freon-containing media (CCl₄/air mixtures at a pressure of P=0.1?2 kPa) are studied. It is shown that a transverse discharge produced in the CCl₄/air=(1–2)/0.03 kPa mixture at a moderate discharge voltage (U _ch=8–15 kV) and an interelectrode distance of d=2.2 cm is a selective source of C₂(d ³Π_g-a ³Π_u) 468.0-and 516.5-nm radiation and C(2p-3s) 247.9-nm radiation. The brightness of the C₂(d-a) band is comparable with that of the N₂(C-B) 337.1-and 357-nm bands. The transverse discharge in CCl₄ is of interest for generating pulsed emission via the d-a transitions of C₂ molecules in the blue-green region of the visible spectrum.     

Effect of aneurysm on biomechanical properties of “radially-oriented” collagen fibers in human ascending thoracic aortic media

We recently reported a mechanistic model to link micro-architectural information to the delamination strength (S_d) of human ascending thoracic aorta (ATA). That analysis demonstrated that the number density (N) and failure energy (U_f) of the radially-oriented collagen fibers contribute to the S_d of both aneurysmal (ATAA) and non-aneurysmal (CTRL-ATA) aortic tissue. Among the set of ATAA samples, we studied specimens from patients displaying bicuspid (BAV) and tricuspid aortic valve (TAV) morphologic phenotypes. Results from our prior work were based on the assumption that the U_f was independent of dissection direction. In the current study, we excluded that assumption and hypothesized that U_f correlates with the S_d of ATAA. To test the hypothesis, we used previously-reported experimentally-determined S_d measurements and N of radially-oriented collagen fibers as input in our validated mechanistic model to calculate U_f for BAV-ATAA, TAV-ATAA and CTRL-ATA tissue specimens. The results of our analysis revealed that U_f is significantly lower for both BAV-ATAA and TAV-ATAA compared to CTRL-ATA cases, and does not differ between BAV-ATAA and TAV-ATAA. Furthermore, we found that U_f is consistent between circumferential-radial and longitudinal-radial planes in either of BAV-ATAA, TAV-ATAA or CTRL-ATA specimens. These findings employ a novel mechanistic model to increase our understanding of the putative interrelationship between biomechanical properties, extracellular matrix biology, and failure energy of aortic dissection.     

The effect of isokinetic dynamometer deceleration phase on maximum ankle joint range of motion and plantar flexor mechanical properties tested at different angular velocities

During range of motion (max-ROM) tests performed on an isokinetic dynamometer, the mechanical delay between the button press (by the participant to signal their max-ROM) and the stopping of joint rotation resulting from system inertia induces errors in both max-ROM and maximum passive joint moment. The present study aimed to quantify these errors by comparing data when max-ROM was obtained from the joint position data, as usual (max-ROM_POS), to data where max-ROM was defined as the first point of dynamometer arm deceleration (max-ROM_ACC). Fifteen participants performed isokinetic ankle joint max-ROM tests at 5, 30 and 60° s⁻¹. Max-ROM, peak passive joint moment, end-range musculo-articular (MAC) stiffness and area under the joint moment-position curve were calculated. Greater max-ROM was observed in max-ROM_POS than max-ROM_ACC (P < 0.01) at 5 (0.2 ± 0.15%), 30 (1.8 ± 1.0%) and 60° s⁻¹ (5.9 ± 2.3%), with the greatest error at the fastest velocity. Peak passive moment was greater and end-range MAC stiffness lower in max-ROM_POS than in max-ROM_ACC only at 60° s⁻¹ (P < 0.01), whilst greater elastic energy storage was found at all velocities. Max-ROM and peak passive moment are affected by the delay between button press and eventual stopping of joint rotation in an angular velocity-dependent manner. This affects other variables calculated from the data. When high data accuracy is required, especially at fast joint rotation velocities (≥30° s⁻¹), max-ROM (and associated measures calculated from joint moment data) should be taken at the point of first change in acceleration rather than at the dynamometer’s ultimate joint position.     

Mechanism and Function of Mixed-Mode Oscillations in Vibrissa Motoneurons

Vibrissa motoneurons in the facial nucleus innervate the intrinsic and extrinsic muscles that move the whiskers. Their intrinsic properties affect the way they process fast synaptic input from the vIRT and Bötzinger nuclei together with serotonergic neuromodulation. In response to constant current (I _app) injection, vibrissa motoneurons may respond with mixed mode oscillations (MMOs), in which sub-threshold oscillations (STOs) are intermittently mixed with spikes. This study investigates the mechanisms involved in generating MMOs in vibrissa motoneurons and their function in motor control. It presents a conductance-based model that includes the M-type K⁺ conductance, g _M, the persistent Na⁺ conductance, g _NaP, and the cationic h conductance, g _h. For g _h = 0 and moderate values of g _M and g _NaP, the model neuron generates STOs, but not MMOs, in response to I _app injection. STOs transform abruptly to tonic spiking as the current increases. In addition to STOs, MMOs are generated for g _h>0 for larger values of I _app; the I _app range in which MMOs appear increases linearly with g _h. In the MMOs regime, the firing rate increases with I _app like a Devil''s staircase. Stochastic noise disrupts the temporal structure of the MMOs, but for a moderate noise level, the coefficient of variation (CV) is much less than one and varies non-monotonically with I _app. Furthermore, the estimated time period between voltage peaks, based on Bernoulli process statistics, is much higher in the MMOs regime than in the tonic regime. These two phenomena do not appear when moderate noise generates MMOs without an intrinsic MMO mechanism. Therefore, and since STOs do not appear in spinal motoneurons, the analysis can be used to differentiate different MMOs mechanisms. MMO firing activity in vibrissa motoneurons suggests a scenario in which moderate periodic inputs from the vIRT and Bötzinger nuclei control whisking frequency, whereas serotonergic neuromodulation controls whisking amplitude.     

Relationship of respiration to body weight in the tilapia Oreochromis niloticus under resting and normoxic conditions

• 1.1. The relationships of oxygen consumption (V_o2, ml/min/fish), ventilation volume (V_g, ml/min/fish), stroke volume (V_s, ml/stroke/fish), respiration frequency (RF, stroke/min) and oxygen utilization (U, %) to body weight (W, g) in the tilapia under resting and normoxic conditions were V_o2 = 0.002835W^0.754193, V_g = 0.688965W^0.722786, V_s = 0.002790W^1.017188, RF = 248.58210W^−0.296139, U = 0.000935W + 87.394288, respectively.

     

Emission from a transverse volume discharge in neon with small admixtures of water vapor and air

Emission from the plasma of a pulsed discharge in neon with small admixtures of water vapor and air in the wavelength range 210–620 nm is investigated. A transverse volume discharge with spark UV preionization is ignited in neon at a pressure of 100–200 kPa and charging voltage of U _ch≤20 kV. It is shown that the discharge acts as a source of pulsed UV radiation on OH(A-X) (λ=308–314 nm) and NO(B-X) (247.8 nm) transitions, which is of interest for the use in an ecologically safe lamp based on the mixtures of neon with water vapor and air. In the visible spectral region, plasma emission consists of the NeI (3s, 3s′-3p, 3p′) band and H_β 486.1-nm spectral line. On the short-wavelength side of the spectrum, a broadband emission (the third continuum of neon) is observed, whose intensity increases with increasing neon pressure and decreasing emission wavelength.     

Experimental study of a low-pressure glow discharge in air in large-diameter discharge tubes: I. conditions for the normal regime of a glow discharge

The initiation and characteristics of a low-pressure glow discharge in air in large-diameter discharge tubes are studied. A deviation from the Paschen law is observed: the breakdown curves U _dc(pL) shift toward the higher values of U _dc and pL as the interelectrode distance L increases. It is shown that the normal regime of a glow discharge is accompanied by gas ionization in the anode sheath. This takes place only for pL values lying to the right of the inflection point in the breakdown curve. The cathode-sheath characteristics in the normal and abnormal regimes of an air discharge for a duralumin cathode are determined. The axial profiles of the ion density, electron temperature, and plasma potential, as well as the anode voltage drop, are measured at various air pressures.     

Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages

Background

Cancer immunotherapy has recently entered a remarkable renaissance phase with the approval of several agents for treatment. Cancer treatment platforms have demonstrated profound tumor regressions including complete cure in patients with metastatic cancer. Moreover, technological advances in next-generation sequencing (NGS) as well as the development of devices for scanning whole-slide bioimages from tissue sections and image analysis software for quantitation of tumor-infiltrating lymphocytes (TILs) allow, for the first time, the development of personalized cancer immunotherapies that target patient specific mutations. However, there is currently no bioinformatics solution that supports the integration of these heterogeneous datasets.

Results

We have developed a bioinformatics platform – Personalized Oncology Suite (POS) – that integrates clinical data, NGS data and whole-slide bioimages from tissue sections. POS is a web-based platform that is scalable, flexible and expandable. The underlying database is based on a data warehouse schema, which is used to integrate information from different sources. POS stores clinical data, genomic data (SNPs and INDELs identified from NGS analysis), and scanned whole-slide images. It features a genome browser as well as access to several instances of the bioimage management application Bisque. POS provides different visualization techniques and offers sophisticated upload and download possibilities. The modular architecture of POS allows the community to easily modify and extend the application.

Conclusions

The web-based integration of clinical, NGS, and imaging data represents a valuable resource for clinical researchers and future application in medical oncology. POS can be used not only in the context of cancer immunology but also in other studies in which NGS data and images of tissue sections are generated. The application is open-source and can be downloaded at http://www.icbi.at/POS.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-306) contains supplementary material, which is available to authorized users.     

Frequency preference in two-dimensional neural models: a linear analysis of the interaction between resonant and amplifying currents

Many neuron types exhibit preferred frequency responses in their voltage amplitude (resonance) or phase shift to subthreshold oscillatory currents, but the effect of biophysical parameters on these properties is not well understood. We propose a general framework to analyze the role of different ionic currents and their interactions in shaping the properties of impedance amplitude and phase in linearized biophysical models and demonstrate this approach in a two-dimensional linear model with two effective conductances g _L and g ₁. We compute the key attributes of impedance and phase (resonance frequency and amplitude, zero-phase frequency, selectivity, etc.) in the g _L ???g ₁ parameter space. Using these attribute diagrams we identify two basic mechanisms for the generation of resonance: an increase in the resonance amplitude as g ₁ increases while the overall impedance is decreased, and an increase in the maximal impedance, without any change in the input resistance, as the ionic current time constant increases. We use the attribute diagrams to analyze resonance and phase of the linearization of two biophysical models that include resonant (I _h or slow potassium) and amplifying currents (persistent sodium). In the absence of amplifying currents, the two models behave similarly as the conductances of the resonant currents is increased whereas, with the amplifying current present, the two models have qualitatively opposite responses. This work provides a general method for decoding the effect of biophysical parameters on linear membrane resonance and phase by tracking trajectories, parametrized by the relevant biophysical parameter, in pre-constructed attribute diagrams.     

A low-cost integrator for preparative ultracentrifuges

An integrator is described for the measurement of the time integral ∫₀^t rpm²dt in preparative ultracentrifuge where linearity exists either (a) between tachometer generator ac voltage amplitude and rpm (e.g., Sorvall RC2-B) or dc voltage and rpm, or (b) between the square-wave frequency from the tachometer generator and rpm (e.g., Beckman L2-65B). The construction and the precision levels of an integrator for Sorvall RC2-B preparative ultracentrifuge in the range 0–10,000 rpm and for Beckman L2-65B preparative ultracentrifuge in the range 0–40,000 rpm are described.