Strategies for improving fermentation medium performance: a review

Many techniques are available in the fermentation medium designer’s toolbox (borrowing, component swapping, biological mimicry, one-at-a-time, statistical and mathematical techniques—experimental design and optimization, artificial neural networks, fuzzy logic, genetic algorithms, continuous fermentation, pulsed batch and stoichiometric analysis). Each technique has advantages and disadvantages, and situations where they are best applied. No one ‘magic bullet’ technique exists for all situations. However, considerable advantage can be gained by logical application of the techniques, combined with good experimental design. Received 24 December 1998/ Accepted in revised form 18 August 1999     

Unsupervised machine-learning method for improving the performance of ambulatory fall-detection systems

Background  

Falls can cause trauma, disability and death among older people. Ambulatory accelerometer devices are currently capable of detecting falls in a controlled environment. However, research suggests that most current approaches can tend to have insufficient sensitivity and specificity in non-laboratory environments, in part because impacts can be experienced as part of ordinary daily living activities.     

Simple method to isolate vacuoles and protoplasts for patch-clamp experiments

It was not possible to obtain protoplasts or vacuoles from the thallus of the liverwortConocephalum conicum by applying cell-wall-degrading enzymes. Therefore, a surgical method was developed to isolate protoplasts and vacuoles. A thallus was plasmolyzed and cut. The few protoplasts along the cutting edge that were not destroyed emerged from the edge under deplasmolysis and became thus accessible for a patch pipette. Whereas under slightly hypoosmolar conditions the emerging protoplast remained largely intact, more hypoosmolar conditions gave rise to isolated vacuoles. This method to isolate protoplasts and vacuoles could also be applied to other plant tissues like leaves ofArabidopsis thaliana. Patch-clamp measurements were performed with isolated vacuoles and excised tonoplast patches. A slowly activating vacuolar channel inC. conicum displayed the characteristic features of higher-plant slowly activating vacuolar channels.Abbreviations AP action potential - SV channel slowly activating vacuolar channel     

Hourglass SiO2 coating increases the performance of planar patch-clamp

Obtaining high-throughput electrophysiological recordings is an ongoing challenge in ion channel biophysics and drug discovery. One particular area of development is the replacement of glass pipettes with planar devices in order to increase throughput. However, successful patch-clamp recordings depend on a surface coating which ideally should promote and stabilize giga-seal formation. Here, we present data supporting the use of a structured SiO(2) coating to improve the ability of cells to form a "seal" with a planar patch-clamp substrate. The method is based on a correlation study taking into account structure and size of the pores, surface roughness and chip capacitance. The influence of these parameters on the quality of the seal was assessed. Plasma-enhanced chemical vapour deposition (PECVD) of SiO(2) led to an hourglass structure of the pore and a tighter seal than that offered by a flat, thermal SiO(2) surface. The performance of PECVD chips was validated by recording recombinant potassium channels, BK(Ca), expressed in stable HEK-293 cell lines and in inducible CHO cell lines and low conductance IRK1, and endogenous cationic currents from CHO cells. This multiparametric investigation led to the production of improved chips for planar patch-clamp applications which allow electrophysiological recordings from a wide range of cell lines.     

Modified reconstitution method used in patch-clamp studies of Escherichia coli ion channels.

We have modified the procedure of Criado and Keller (1987) to study ion channels of Escherichia coli reconstituted in liposomes. The modifications include (a) excluding the use of any detergent and (b) inducing blisters from liposomes with Mg2+. These blisters, which appear to be unilamellar, are stable for hours. They could be repeatedly sampled with different patch-clamp pipettes each achieving seal resistance greater than 10 GOhms. Activities of three types of ion channels are often observed by use of this method, including two voltage-sensitive cation channels of different conductances. Even the mechanosensitive channel, previously recorded from live E. coli cells (Martinac et al., 1987), was also detected in these blisters. Apparently the channel protein and any accessory structures, postulated to be needed for mechanotransduction, can be reconstituted together by this method.     

A patch-clamp study of Bacillus subtilis.

In patch-clamp experiments on giant protoplasts of the Gram-positive bacterium Bacillus subtilis, membrane stretch resulted in an initial transient collapse of the membrane resistance, after which stretch-activated, voltage modulated, high-conductance channels could be observed. The channel open probability increased exponentially with applied suction and positive voltage, as a result of variations of both the mean open and the mean closed times. The substate structure and other characteristics of the electrical activity suggested the presence of a family of pores exhibiting cooperative behavior. A role in osmotic protection is suggested. In the intact bacteria, the pores may be part of an unidentified envelope apparatus, having other functions as well.     

Strategies for improving a long-established terminal’s performance: a simulation study of a Turkish container terminal

Due to a long-lasting increase in global trade, only interrupted by the late-2000s economic crisis, container traffic has grown dramatically. As a result, new terminals have opened and existing terminals face much higher container handling than before. In order to meet these challenges, one of the biggest container terminals in Turkey has begun to reconsider its terminal operations and to achieve improvements of its overall logistics performance. Because the factors impacting the terminal’s performance are highly interrelated, a simulation model was developed to analyze the terminal operations, to identify potential bottleneck resources and to highlight directions for the future development of the configuration and the operational control system. For a long-established terminal like the one considered in this study the options for improving the overall performance are limited by the geographical dimensions and by the existing terminal equipment. By use of the simulation model the terminal operations are evaluated under different workload scenarios and alternative configurations are tested in order to support strategic decisions on the terminal’s development.     

A two-compartment model for the dependence of a postsynaptic potential on a postsynaptic current, measured by the patch-clamp method

As known, the dependence of a postsynaptic potential (PSP)1 on a postsynaptic current (PSC) is not satisfactorily approximated by simple Ohm's law due to a significant role of electrotonic propagation of currents along dendrites. The present work shows that a two-compartment model of a neuron, conjointly solving the two problems of voltage and current clamping, gives quite precisely the PSP-on-PSC dependence, in spite of inaccurate reconstruction of currents on dendritic terminals. The two-compartment model is compared with the neuron model consisting of a distributed cylindrical dendrite and a concentrated soma.     

MrHeter: improving MapReduce performance in heterogeneous environments

As GPUs, ARM CPUs and even FPGAs are widely used in modern computing, a data center gradually develops towards the heterogeneous clusters. However, many well-known programming models such as MapReduce are designed for homogeneous clusters and have poor performance in heterogeneous environments. In this paper, we reconsider the problem and make four contributions: (1) We analyse the causes of MapReduce poor performance in heterogeneous clusters, and the most important one is unreasonable task allocation between nodes with different computing ability. (2) Based on this, we propose MrHeter, which separates MapReduce process into map-shuffle stage and reduce stage, then constructs optimization model separately for them and gets different task allocation \(ml_{ij}, mr_{ij}, r_{ij}\) for heterogeneous nodes based on computing ability.(3) In order to make it suitable for dynamic execution, we propose D-MrHeter, which includes monitor and feedback mechanism. (4) Finally, we prove that MrHeter and D-MrHeter can greatly decrease total execution time of MapReduce from 30 to 70 % in heterogeneous cluster comparing with original Hadoop, having better performance especially in the condition of heavy-workload and large-difference between nodes computing ability.     

A collaborative brain-computer interface for improving human performance

Electroencephalogram (EEG) based brain-computer interfaces (BCI) have been studied since the 1970s. Currently, the main focus of BCI research lies on the clinical use, which aims to provide a new communication channel to patients with motor disabilities to improve their quality of life. However, the BCI technology can also be used to improve human performance for normal healthy users. Although this application has been proposed for a long time, little progress has been made in real-world practices due to technical limits of EEG. To overcome the bottleneck of low single-user BCI performance, this study proposes a collaborative paradigm to improve overall BCI performance by integrating information from multiple users. To test the feasibility of a collaborative BCI, this study quantitatively compares the classification accuracies of collaborative and single-user BCI applied to the EEG data collected from 20 subjects in a movement-planning experiment. This study also explores three different methods for fusing and analyzing EEG data from multiple subjects: (1) Event-related potentials (ERP) averaging, (2) Feature concatenating, and (3) Voting. In a demonstration system using the Voting method, the classification accuracy of predicting movement directions (reaching left vs. reaching right) was enhanced substantially from 66% to 80%, 88%, 93%, and 95% as the numbers of subjects increased from 1 to 5, 10, 15, and 20, respectively. Furthermore, the decision of reaching direction could be made around 100-250 ms earlier than the subject's actual motor response by decoding the ERP activities arising mainly from the posterior parietal cortex (PPC), which are related to the processing of visuomotor transmission. Taken together, these results suggest that a collaborative BCI can effectively fuse brain activities of a group of people to improve the overall performance of natural human behavior.     

Prospects for improving reproductive performance through genetic selection

Prospects for improving female fertility in dairy cattle using genetic selection are reviewed. Today's high producing cows have shorter estrous cycles, fewer standing events, shorter duration of estrus, and more frequent multiple ovulations. Although high milk production is often implicated as the cause of impaired fertility, the impact of inadequate body condition appears to be greater, as the latter has a significant impact on probability of conception, rate of embryonic loss, and proportion of anestrous animals. Genetic improvement of female fertility can be achieved by indirect selection for longevity or body condition score, or by direct selection for traits such as daughter pregnancy rate. Most leading dairy countries have implemented genetic evaluation systems for female fertility in the past decade, but refinement of these systems to account for hormonal synchronization, differences in the voluntary waiting period, exposure to natural service bulls, and other confounding factors is warranted. Recent work has focused on the development of data collection and genetic evaluation systems that will allow selection of bulls that have daughters that are resistant to common health disorders, including mastitis, lameness, ketosis, displaced abomasum, and metritis. Such systems will allow selection of animals that can remain healthy and fertile while producing large quantities of milk.     

The light-sensitive conductance of hyperpolarizing invertebrate photoreceptors: a patch-clamp study

Tight-seal recording was employed to investigate membrane currents in hyperpolarizing ciliary photoreceptors enzymatically isolated from the eyes of the file clam (Lima scabra) and the bay scallop (Pecten irradians). These two organisms are unusual in that their double retinas also possess a layer of depolarizing rhabdomeric cells. Ciliary photoreceptors from Lima have a rounded soma, 15-20 microns diam, and display a prominent bundle of fine processes up to 30 microns long. The cell body of scallop cells is similar in size, but the ciliary appendages are modified, forming small spherical structures that protrude from the cell. In both species light stimulation at a voltage near the resting potential gives rise to a graded outward current several hundred pA in amplitude, accompanied by an increase in membrane conductance. The reversal potential of the photocurrent is approximately -80 mV, and shifts in the positive direction by approximately 39 mV when the concentration of extracellular K is increased from 10 to 50 mM, consistent with the notion that light activates K-selective channels. The light-activated conductance increases with depolarization in the physiological range of membrane voltages (-30 to -70 mV). Such outward rectification is greatly reduced after removal of divalent cations from the superfusate. In Pecten, cell- attached recordings were also obtained; in some patches outwardly directed single-channel currents could be activated by light but not by voltage. The unitary conductance of these channels was approximately 26 pS. Solitary ciliary cells also gave evidence of the post stimulus rebound, which is presumably responsible for initiating the "off" discharge of action potentials at the termination of a light stimulus: in patches containing only voltage-dependent channels, light stimulation suppressed depolarization-induced activity, and was followed by a strong burst of openings, directly related to the intensity of the preceding photostimulation.     

A spectrofluorometer to measure difference in fluorescence spectra: a simple method for improving sensitivity

To accurately measure small changes in fluorescence spectra a difference spectrofluorometer was designed and constructed. The instrument simultaneously measures fluorescence from two samples. Routinely, two identical samples are used; one serving as the reference while the other is subjected to experimentation. This procedure minimizes variations in fluorescence arising from instabilities in either the sensitivity of the instrument or from the sample with time.     

Real-time interactive isosurfacing: a new method for improving marching isosurfacing algorithm output and efficiency

Efficient rendering of a changing volumetric data-set is central to the development of effective medical simulations that incorporate haptic feedback. A new method referred to as real-time interactive isosurfacing (RTII) is described in this paper. RTII is an algorithm that can be applied to output from Marching Cubes-like algorithms to improve performance for real-time applications. The approach minimises processing by re-evaluating the isosurface around changing sub-volumes resulting from user interactions. It includes innovations that significantly reduce mesh complexity and improve mesh quality as triangles are created from the Marching Tetrahedra isosurfacing algorithm. Rendering efficiency is further improved over other marching isosurfacing algorithm outputs by maintaining an indexed triangle representation of the mesh. The effectiveness of RTII is discussed within the context of an endoscopic sinus surgery simulation currently being developed by the authors.     

一种适合膜片钳单通道记录的大鼠DRG神经元急性分离方法

目的：建立一种适合膜片钳单通道记录的脊髓背根神经节神经元急性分离方法。方法：用酶消化和机械分离相结合的方法急性分离大鼠DRG神经元。结果：用本方法分离的DRG细胞容易形成较高的封接电阻（〉5GΩ）,降低了噪音干扰,可记录到pA级的单通道电流。结论：本方法急性分离的DRG神经元适合单通道膜片钳实验研究。     

Giant liposomes: a model system in which to obtain patch-clamp recordings of ionic channels.

Cell-size, giant liposomes have been formed by submitting a mixture of asolectin lipid vesicles and native membranes from Torpedo, highly enriched in acetylcholine receptor (AcChR), to a partial dehydration/rehydration cycle [Criado, M., & Keller, B. U. (1987) FEBS Lett. 224, 172-176]. Giant liposomes can be prepared in bulk quantities, in the absence of potentially damaging detergents or organic solvents, and their formation is mediated by membrane fusion phenomena. In fact, fluorescence microscopy and freeze-fracture data indicate that protein and lipid components of the initial membranes and lipid vesicles are homogenously distributed in the resulting liposomes. Giant liposomes containing AcChR have been used as a model to evaluate whether this system can be used to monitor the activity of ionic channels by using high-resolution, patch-clamp techniques. Excised liposome patches in an "inside-out" configuration have been used in this work. We find that the most frequent pattern of electrical activity in response to the presence of acetylcholine in the patch pipet corresponds to a cation-specific channel exhibiting a dominant conductance level and a sublevel of approximately 78 and 25 pS, respectively. Such channel activity exhibits the pharmacological specificity, ion channel activation, ion selectivity, and desensitization properties expected from native Torpedo AcChR. Thus, it appears that the giant liposome technique offers a distinct advantage over other reconstitution procedures in that it provides a unique opportunity to undertake simultaneous biochemical, morphological, and electrophysiological studies of the incorporated ionic channel proteins.     

Life cycle assessment as a tool for improving process performance: A case study on boron products

This paper explores the use of LCA as a tool for process environmental management, thereby moving the focus from product to process oriented analysis. The emphasis is on Improvement Assessment in which the “hot spots” in the system are targeted for maximum environmental improvements. In this context, it is useful to use multiobjective optimisation which renders Valuation unnecessary. The approach is illustrated by the case study of the system processing boron ores to make five different products. The results of Inventory Analysis and Impact Assessment are presented and discussed. In Improvement Assessment, a number of improvement options are identified and evaluated, using system optimisation. It is shown that the site environmental performance can be improved over current operation by an average of 20% over the whole life cycle. Thus the study demonstrates that the optimisation approach to environmental process management may assist in identifying optimal ways to operate a process or plant from “cradle to grave”. This may help the process industries not only to comply with legislation but also provide a framework for taking a more proactive approach to environmental management leading to more sustainable industrial operations and practices.     

Reconstruction of axial tomographic high resolution data from confocal fluorescence microscopy: a method for improving 3D FISH images.

Fluorescent confocal laser scanning microscopy allows an improved imaging of microscopic objects in three dimensions. However, the resolution along the axial direction is three times worse than the resolution in lateral directions. A method to overcome this axial limitation is tilting the object under the microscope, in a way that the direction of the optical axis points into different directions relative to the sample. A new technique for a simultaneous reconstruction from a number of such axial tomographic confocal data sets was developed and used for high resolution reconstruction of 3D-data both from experimental and virtual microscopic data sets. The reconstructed images have a highly improved 3D resolution, which is comparable to the lateral resolution of a single deconvolved data set. Axial tomographic imaging in combination with simultaneous data reconstruction also opens the possibility for a more precise quantification of 3D data. The color images of this publication can be accessed from http://www.esacp.org/acp/2000/20-1/heintzmann.++ +htm. At this web address an interactive 3D viewer is additionally provided for browsing the 3D data. This java applet displays three orthogonal slices of the data set which are dynamically updated by user mouse clicks or keystrokes.     

A miniaturized planar patch-clamp system for transportable use

In the last decade, planar patch-clamp (PPC) has emerged as an innovative technology allowing parallel recordings of cellular electrophysiological activity on planar substrates. If PPC is widely adopted by the pharmaceutical sector, it remains poorly extended to other areas (i.e. environment and safety organizations) probably because of the large, expensive and non-easily transportable format of those commercial equipments. The present work describes for the first time a new compact and transportable planar patch-clamp system (named Toxint'patch or TIP, for Toxin detection with integrated patch-clamp) focusing on environmental matters and meant to be used in coastal laboratories, for direct on-site monitoring of the seawater and shellfish quality. The TIP system incorporates silicon chips tailored to monitor cellular ionic currents from cultured cells stably expressing a phycotoxin molecular target. The functionality of this novel briefcase-sized PPC system is described in terms of fluidic control, electronic performances with amplifying and filtering boards and of user interface for data acquisition and control implemented on a computer.     

Series resistance compensation for whole-cell patch-clamp studies using a membrane state estimator

Whole-cell patch-clamp techniques are widely used to measure membrane currents from isolated cells. While suitable for a broad range of ionic currents, the series resistance (R(s)) of the recording pipette limits the bandwidth of the whole-cell configuration, making it difficult to measure rapid ionic currents. To increase bandwidth, it is necessary to compensate for R(s). Most methods of R(s) compensation become unstable at high bandwidth, making them hard to use. We describe a novel method of R(s) compensation that overcomes the stability limitations of standard designs. This method uses a state estimator, implemented with analog computation, to compute the membrane potential, V(m), which is then used in a feedback loop to implement a voltage clamp; we refer to this as state estimator R(s) compensation. To demonstrate the utility of this approach, we built an amplifier incorporating state estimator R(s) compensation. In benchtop tests, our amplifier showed significantly higher bandwidths and improved stability when compared with a commercially available amplifier. We demonstrated that state estimator R(s) compensation works well in practice by recording voltage-gated Na(+) currents under voltage-clamp conditions from dissociated neonatal rat sympathetic neurons. We conclude that state estimator R(s) compensation should make it easier to measure large rapid ionic currents with whole-cell patch-clamp techniques.