Multiple Buffers Research Articles

Mathematical Models for Network Card Packet Buffering Simulation

Objectives: Current network card buffer optimizations are focusing on optimal configuration of transmission's sender with singular buffer. However, there exists receiver-oriented network card module with multiple buffers. In our research, we mirrored PF_RING, which alters the traditional packet processing that requires copying the packets to application space. Methods/Statistical Analysis: PF_RING provides buffers for higher layer applications to access packets directly. Findings: Each buffer's capacity, transmission size, packet size, number of packets, and number of applications give raise to the question on the number of buffers required, because it affects the duration of packets read by the applications. Optimal number of buffers is therefore needed to generate minimum packet reading duration of the applications. Application/Improvements: We propose mathematical models to represent the simulation of packet buffering in a multibuffer receiver's network card. Our simulation models are used to determine the optimal number of buffers for specific network transmission with distinct properties, which include transmission size, packet size, and number of packets.

Unusual Salt and pH Induced Changes in Polyethylenimine Solutions.

Linear PEI is a cationic polymer commonly used for complexing DNA into nanoparticles for cell-transfection and gene-therapy applications. The polymer has closely-spaced amines with weak-base protonation capacity, and a hydrophobic backbone that is kept unaggregated by intra-chain repulsion. As a result, in solution PEI exhibits multiple buffering mechanisms, and polyelectrolyte states that shift between aggregated and free forms. We studied the interplay between the aggregation and protonation behavior of 2.5 kDa linear PEI by pH probing, vapor pressure osmometry, dynamic light scattering, and ninhydrin assay. Our results indicate that:At neutral pH, the PEI chains are associated and the addition of NaCl initially reduces and then increases the extent of association.The aggregate form is uncollapsed and co-exists with the free chains.PEI buffering occurs due to continuous or discontinuous charging between stalled states.Ninhydrin assay tracks the number of unprotonated amines in PEI.The size of PEI-DNA complexes is not significantly affected by the free vs. aggregated state of the PEI polymer.Despite its simple chemical structure, linear PEI displays intricate solution dynamics, which can be harnessed for environment-sensitive biomaterials and for overcoming current challenges with DNA delivery.

CE-C4D method development and validation for the assay of ciprofloxacin

A capillary electrophoresis method with capacitively coupled contactless conductivity detection (CE-C4D) has been developed, optimized and validated for the determination of ciprofloxacin.Ciprofloxacin is a member of the fluoroquinolone antibiotics with a broad spectrum bactericidal activity and recommended for complicated respiratory infections, sexually transmitted diseases, tuberculosis, bacterial diarrhea etc.Method development was conducted with major focus on the quality by design (QbD) approach. During method development, multiple buffers were tried at different ionic strength. However, the optimized method finally involved a very simple background electrolyte, monosodium citrate at a concentration of 10mM without pH adjustment.The optimized CE-C4D method involved an uncoated fused silica capillary (59/39cm, 50μm i.d.) and hydrodynamic sample injection at a pressure of 0.5 p.s.i. for 5s. The actual separation was conducted for 10min at normal polarity with a voltage of 20kV corresponding to 5.9μA current. LiCl (1mg/mL) was used as an internal standard.The optimized method is robust and accurate (recovery >98%) which rendered the ciprofloxacin peak within five minutes with good linearity (R2>0.999) in the concentration range of 0.0126–0.8mg/mL. The repeatability is expressed by percentage relative standard deviation (%RSD) of the relative peak areas (RPA) and it showed good repeatability both intra-day (<3%) and inter-day (3.1%). This method, proven to be free of matrix interference, showed that the estimated percent content of ciprofloxacin (102%) was within the official requirements.Moreover, due to its ease of use and robustness, the method should also be applicable in less well controlled laboratory environments.

Compositional diversity of rehabilitated tropical lands supports multiple ecosystem services and buffers uncertainties.

High landscape diversity is assumed to increase the number and level of ecosystem services. However, the interactions between ecosystem service provision, disturbance and landscape composition are poorly understood. Here we present a novel approach to include uncertainty in the optimization of land allocation for improving the provision of multiple ecosystem services. We refer to the rehabilitation of abandoned agricultural lands in Ecuador including two types of both afforestation and pasture rehabilitation, together with a succession option. Our results show that high compositional landscape diversity supports multiple ecosystem services (multifunction effect). This implicitly provides a buffer against uncertainty. Our work shows that active integration of uncertainty is only important when optimizing single or highly correlated ecosystem services and that the multifunction effect on landscape diversity is stronger than the uncertainty effect. This is an important insight to support a land-use planning based on ecosystem services.

"Process and perish" or multiple buffers with push-down stacks?

This commentary raises two issues: (1) Language processing is hastened not only by internal pressures but also externally by turn-taking in language use; (2) the theory requires nested levels of processing, but linguistic levels do not fully nest; further, it would seem to require multiple memory buffers, otherwise there's no obvious treatment for discontinuous structures, or for verbatim recall.

Associations between neighborhood alcohol availability and young adolescent alcohol use.

We investigated the association between alcohol outlet density and adolescent alcohol use, including whether this association differed by sociodemographic characteristics. We geocoded and mapped active license data from the year 2011 to calculate the number of outlets within multiple circular buffers of varying sizes (density), centered at households of adolescents ages 10-16 (n = 2,724). We examined 2 indicators of alcohol use: any lifetime use, but not in past month, and any past month heavy use. Cross-sectional hierarchal multivariate regression analyses were used to examine associations between alcohol outlet density and alcohol use, including the potential moderating effect of age, gender, race/ethnicity, and socioeconomic status. Analyses controlled for neighborhood-level socioeconomic status and accounted for census tract-level clustering. A higher number of on- and off-premise outlets within 0.10, 0.25, and 0.50 miles around the respondents' homes was associated with higher odds of being a heavy drinker. In addition, the number of on-premise outlets within the 0.25-mile radius was associated with greater odds of lifetime drinking. For on-premise outlets where minors were not allowed (clubs/bars), we observed a positive and significant association between clubs/bars within the 0.25-mile buffer zone and higher odds of both lifetime and heavy drinking. Findings suggest that youth who are exposed to higher densities of on-premise alcohol outlets are at risk for both lifetime use and recent heavy use. It is critical to advocate for stricter laws limiting the number of alcohol outlets in neighborhoods, including clubs/bars where minors are restricted, and putting into place more stringent enforcement of age identification requirements to limit distribution of alcohol to minors.

Bacterial Thymidylate Synthase Binds Two Molecules of Substrate and Cofactor without Cooperativity.

Thymidylate synthase (TSase) is a clinically important enzyme because it catalyzes synthesis of the sole de novo source of deoxy-thymidylate. Without this enzyme, cells die a "thymineless death" since they are starved of a crucial DNA synthesis precursor. As a drug target, TSase is well studied in terms of its structure and reaction mechanism. An interesting mechanistic feature of dimeric TSase is that it is "half-the-sites reactive", which is a form of negative cooperativity. Yet, the basis for this is not well-understood. Some experiments point to cooperativity at the binding steps of the reaction cycle as being responsible for the phenomenon, but the literature contains conflicting reports. Here we use ITC and NMR to resolve these inconsistencies. This first detailed thermodynamic dissection of multisite binding of dUMP to E. coli TSase shows the nucleotide binds to the free and singly bound forms of the enzyme with nearly equal affinity over a broad range of temperatures and in multiple buffers. While small but significant differences in ΔC°P for the two binding events show that the active sites are not formally equivalent, there is little-to-no allostery at the level of ΔG°bind. In addition NMR titration data reveal that there is minor intersubunit cooperativity in formation of a ternary complex with the mechanism based inhibitor, 5F-dUMP, and cofactor. Taken together, the data show that functional communication between subunits is minimal for both binding steps of the reaction coordinate.

Zeolites in Sustainable Chemistry: Synthesis, Characterization and Catalytic Applications (Green Chemistry and Sustainable Technology Series)

A capillary electrophoresis method with capacitively coupled contactless conductivity detection (CE-C4D) has been developed, optimized and validated for the determination of ciprofloxacin.Ciprofloxacin is a member of the fluoroquinolone antibiotics with a broad spectrum bactericidal activity and recommended for complicated respiratory infections, sexually transmitted diseases, tuberculosis, bacterial diarrhea etc.Method development was conducted with major focus on the quality by design (QbD) approach. During method development, multiple buffers were tried at different ionic strength. However, the optimized method finally involved a very simple background electrolyte, monosodium citrate at a concentration of 10 mM without pH adjustment.The optimized CE-C4D method involved an uncoated fused silica capillary (59/39 cm, 50 μm i.d.) and hydrodynamic sample injection at a pressure of 0.5 p.s.i. for 5 s. The actual separation was conducted for 10 min at normal polarity with a voltage of 20 kV corresponding to 5.9 μA current. LiCl (1 mg/mL) was used as an internal standard.The optimized method is robust and accurate (recovery >98%) which rendered the ciprofloxacin peak within five minutes with good linearity (R2 > 0.999) in the concentration range of 0.0126–0.8 mg/mL. The repeatability is expressed by percentage relative standard deviation (%RSD) of the relative peak areas (RPA) and it showed good repeatability both intra-day (<3%) and inter-day (3.1%). This method, proven to be free of matrix interference, showed that the estimated percent content of ciprofloxacin (102%) was within the official requirements.Moreover, due to its ease of use and robustness, the method should also be applicable in less well controlled laboratory environments.

BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators.

The computational demand of exact-search procedures has pressed the exploitation of parallel processing accelerators to reduce the execution time of many applications. However, this often imposes strict restrictions in terms of the problem size and implementation efforts, mainly due to their possibly distinct architectures. To circumvent this limitation, a new exact-search alignment tool (BowMapCL) based on the Burrows-Wheeler Transform and FM-Index is presented. Contrasting to other alternatives, BowMapCL is based on a unified implementation using OpenCL, allowing the exploitation of multiple and possibly different devices (e.g., NVIDIA, AMD/ATI, and Intel GPUs/APUs). Furthermore, to efficiently exploit such heterogeneous architectures, BowMapCL incorporates several techniques to promote its performance and scalability, including multiple buffering, work-queue task-distribution, and dynamic load-balancing, together with index partitioning, bit-encoding, and sampling. When compared with state-of-the-art tools, the attained results showed that BowMapCL (using a single GPU) is 2 × to 7.5 × faster than mainstream multi-threaded CPU BWT-based aligners, like Bowtie, BWA, and SOAP2; and up to 4 × faster than the best performing state-of-the-art GPU implementations (namely, SOAP3 and HPG-BWT). When multiple and completely distinct devices are considered, BowMapCL efficiently scales the offered throughput, ensuring a convenient load-balance of the involved processing in the several distinct devices.

English

The emergence of 528 new Census Towns (CTs) in 2011 and their contribution to the growth of urban population brought significant changes in the nature of urbanization in West Bengal, a state in India. This present treatise made an effort to see the locational distribution of these new CTs with respect to Class I towns/cities in each district of West Bengal in quest of the contesting views of concentrated and dispersed urbanization using multiple ring buffers with varying radial distances and a robustness check. Number of new CTs and their population fall within and outside the buffers has counted to assess the intra-state nature of concentrated and dispersed urbanization. The study further examines Centrality Value, using eight nodal services to make a four-tier hierarchical order of new CTs so as to find out the places of eminence in terms of available institutional services. Results show that in highly urbanized districts, non-urban places close to Class I towns have transformed rapidly into urban and symbolized concentrated urbanization. Whereas in low urbanized districts, this kind of transformation can be observed for places located away from Class I towns which can be explained by their functional importance as rural service centres in general. This brought dispersed urbanization in the state, particularly in low urbanized districts. Although, higher order new CTs could be a viable option to develop subsidiary urban centres for the future, particularly in low urbanized districts of the state. Key words: Census towns (CTs), Class I towns, concentrated and dispersed urbanization, Centrality Value, Hierarchical Order, Rural Service Centre.

Thermodynamics of substrate binding to the metal site in homoprotocatechuate 2,3-dioxygenase: Using ITC under anaerobic conditions to study enzyme–substrate interactions

BackgroundExtradiol dioxygenases are a family of nonheme iron (and sometimes manganese) enzymes that catalyze an O2-dependent ring-opening reaction in a biodegradation pathway of aromatic compounds. Here we characterize the thermodynamics of two substrates binding in homoprotocatechuate 2,3-dioxygenase (HPCD) prior to the O2 activation step. MethodsThis study uses microcalorimetry under an inert atmosphere to measure thermodynamic parameters associated with catechol binding to nonheme metal centers in HPCD. Several stopped-flow rapid mixing experiments were used to support the calorimetry experiments. ResultsThe equilibria constant for 4-nitrocatechol and homoprotocatechuate binding to the iron(II) and manganese(II) forms of HPCD range from 2×104 to 1×106, suggesting there are distinctive differences in how the enzyme–substrate complexes are stabilized. Further experiments in multiple buffers allowed us to correct the experimental ΔH for substrate ionization and to fully derive the pH and buffer independent thermodynamic parameters for substrate binding to HPCD. Fewer protons are released from the iron(II) dependent processes than their manganese(II) counterparts. ConclusionsCondition independent thermodynamic parameters for 4-nitrocatechol and homoprotocatechuate binding to HPCD are highly consistent with each other, suggesting these enzyme–substrate complexes are more similar than once thought, and the ionization state of metal coordinated waters may be playing a role in tuning redox potential and in governing reactivity. General significanceSubstrate binding to HPCD is a complex set of equilibria that includes ionization of substrate and water release, yet it is also the key step in O2 activation. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.

Using Multi-Core to Debug Interactive Applications

Instrumentation technology has been widely used in debugging interactive applications, such as interactive games and virtual reality. Debug codes are instrumented into a target program in order to collect run-time information. Although instrumentation provides detail information of the target program behavior, it can significantly prolong execution time, change program behavior and lead to incorrect debugging results, especially for time dependent and real-time applications. This paper aims to design a scalable parallel debugging mechanism to reduce instrumentation overhead while collecting detail run-time information. We design a new synchronization mechanism of instrumentation, named MDM, which uses multiple buffers to process debug messages. Also, a binding mechanism is used to specify the relationship between the target program, helper threads and cores. We conduct a case study of augmented reality interactive games on an Intel Core i7-2600 processor with Linux 2.6.38. Compared to existing methods, MDM can reduce instrumentation overhead by up to 19%.

Universal buffers for use in biochemistry and biophysical experiments.

The use of buffers that mimic biological solutions is a foundation of biochemical and biophysical studies. However, buffering agents have both specific and nonspecific interactions with proteins. Buffer molecules can induce changes in conformational equilibria, dynamic behavior, and catalytic properties merely by their presence in solution. This effect is of concern because many of the standard experiments used to investigate protein structure and function involve changing solution conditions such as pH and/or temperature. In experiments in which pH is varied, it is common practice to switch buffering agents so that the pH is within the working range of the weak acid and conjugate base. If multiple buffers are used, it is not always possible to decouple buffer induced change from pH or temperature induced change. We have developed a series of mixed biological buffers for protein analysis that can be used across a broad pH range, are compatible with biologically relevant metal ions, and avoid complications that may arise from changing the small molecule composition of buffers when pH is used as an experimental variable.

Biomass measurement by flow cytometry during solid-state fermentation of basidiomycetes.

Solid-state fermentation (SSF) is a robust process that is well suited to the on-site cultivation of basidiomycetes that produce enzymes for the treatment of lignocellulosics. Reliable methods for biomass quantification are essential for the analysis of fungal growth kinetics. However, direct biomass determination is not possible during SSF because the fungi grow into the substrate and use it as a nutrient source. This necessitates the use of indirect methods that are either very laborious and time consuming or can only provide biomass measurements during certain growth periods. Here, we describe the development and optimization of a new rapid method for fungal biomass determination during SSF that is based on counting fungal nuclei by flow cytometry. Fungal biomass was grown on an organic substrate and its concentration was measured by isolating the nuclei from the fungal hyphae after cell disruption, staining them with SYTOX(®) Green, and then counting them using a flow cytometer. A calibration curve relating the dry biomass of the samples to their concentrations of nuclei was established. Multiple buffers and disruption methods were tested. The results obtained were compared with values determined using the method of ergosterol determination, a classical technique for fungal biomass measurement during SSF. Our new approach can be used to measure fungal biomass on a range of different scales, from 15 mL cultures to a laboratory reactor with a working volume of 10 L (developed by the Research Center for Medical Technology and Biotechnology (fzmb GmbH)). © 2014 International Society for Advancement of Cytometry.

Untargeted soil metabolomics methods for analysis of extractable organic matter

The cycling of soil organic matter (SOM) by microorganisms is a critical component of the global carbon cycle but remains poorly understood. There is an emerging view that much of SOM, and especially the dissolved fraction (DOM), is composed of small molecules of plant and microbial origin resulting from lysed cells and released metabolites. Unfortunately, little is known about the small molecule composition of soils and how these molecules are cycled (by microbes or plants or by adsorption to mineral surfaces). The water-extractable organic matter (WEOM) fraction is of particular interest given that this is presumably the most biologically-accessible component of SOM. Here we describe the development of a simple soil metabolomics workflow and a novel spike recovery approach using 13C bacterial lysates to assess the types of metabolites remaining in the WEOM fraction. Soil samples were extracted with multiple mass spectrometry-compatible extraction buffers (water, 10 mM K2SO4 or NH4HCO3, 10–100% methanol or isopropanol/methanol/water [3:3:2 v/v/v]) with and without prior chloroform vapor fumigation. Profiling of derivatized extracts was performed using gas chromatography/mass spectrometry (GC/MS) with 55 metabolites identified by comparing fragmentation patterns and retention times with authentic standards. As expected, fumigation, which is thought to lyse microbial cells, significantly increased the range and abundance of metabolites relative to unfumigated samples. To assess the types of microbial metabolites from lysed bacterial cells that remain in the WEOM fraction, an extract was prepared from the soil bacterium Pseudomonas stutzerii RCH2 grown on 13C acetate. This approach produced highly labeled metabolites that were easily discriminated from the endogenous soil metabolites. Comparing the composition of the fresh bacterial extract with what was recovered following a 15 min incubation with soil revealed that only 27% of the metabolites showed >50% recovery in the WEOM. Many, especially cations (polyamines) and anions, showed <10% recovery. These represent metabolites that may be inaccessible to microbes in this environment and would be most likely to accumulate as SOM presumably due to binding with minerals and negatively-charged clay particles. This study presents a simple untargeted metabolomics workflow for extractable organic matter and an approach to estimate microbial metabolite availability in soils. These methods can be used to further our understanding of SOM and DOM composition and examine the link between metabolic pathways and microbial communities to terrestrial carbon cycling.

Fine control of plastic and elastic relaxation in Ge/Si vertical heterostructures

We present a theoretical investigation of plasticity onset and strain relaxation in Ge on Si pillar-like, vertical heterostructures (VHEs). By means of linear elasticity theory solved by Finite Element Methods, we determine the critical thickness hc for the insertion of a 60° dislocation in Si1–xGex/Si VHEs as a function of their lateral extension. Then, we quantify the effect of inserting one or more buffer layers in further delaying plasticity when growing a Ge-pure layer on top of the VHEs. The presence of intermediate layers of suitable Ge content allows for the formation of fully coherent structures up to the micron scale. The optimal thickness of one or multiple buffers to avoid dislocations is also discussed.

Inventory control for peak electricity demand reduction of manufacturing systems considering the tradeoff between production loss and energy savings

Abstract The effective reduction of the electricity consumption during peak periods plays a critical role in reducing the cost and improving the reliability of the operation of power grid. The unbalanced situation between the supply and the demand of the electricity during peak periods can be relieved. The need for installing and running some peaking power plants and associated power delivery infrastructure can be partially avoided. This paper proposes an analytical model focusing on the electricity load management aiming at reducing the electricity consumption during peak periods by buffer inventory control for the typical manufacturing systems with multiple machines and buffers. Compared with the previous research that is strictly under the constraint of the throughput of manufacturing systems, this research is advanced by considering the tradeoff between the penalty due to production loss and the benefit resulted from energy savings, and thus more load management options are available. The optimal load management actions and corresponding buffer inventory control policies for the whole system are identified by minimizing the summation of the buffer inventory holding cost, electricity consumption cost, and potential production loss penalty throughout the production horizon. A numerical case study based on an automotive assembly line is used to illustrate the effectiveness of the proposed method.

Time-of-use based electricity cost of manufacturing systems: Modeling and monotonicity analysis

Traditionally, manufacturing enterprises pay flat rates for each kiloWatt-hour (kWh) of electricity consumed. Newly available electric tariffs that charge both energy consumption (in kWh) and peak demand (in kiloWatts, i.e., kW) with varying time-of-use (TOU) rates have started to gain popularity. In this paper, the per-product electricity cost as a function of manufacturing system parameters and the TOU rates is modeled. The contributions of both electricity energy consumption and peak demand are combined to formulate the electricity cost of manufacturing systems with multiple machines and buffers. New knowledge of the effects of various modeling parameters on the electricity cost is acquired through monotonicity analysis. The formulated model is utilized to answer the following two questions facing manufacturers: With the availability of TOU rates in mind, is switching from the flat rates to the TOU rates economically sound? What changes can be made on electric use routines to take advantage of the TOU rates? The findings based on case studies show that with appropriate adjustment of production routines, a significant saving of up to 24.8% of the per-product electricity cost can be achieved by adopting the TOU rates.

Parallel Implementation of Real-Time Communication and IP Communication by using Multiple Ring Buffers

Recent Linux[7] kernel introduced an interrupt mitigation method called NAPI to reduce the overhead of interrupt handling procedures caused by frame arrival and transmission. However, NAPI caused serious delay and jitter in such procedures. On the other hand, many conventional real-time communication mechanisms were implemented independently to the existing network stack, and most of such mechanisms disabled the stack. There-fore, it is difficult to utilize both of real-time communication and IP communication in parallel. This paper proposed a parallel implementation method to realize both of real-time communication and IP communication simultaneously in a single computer unit. This method implement real-time network stack and IP network stack in parallel by using multiple queue functionality in a NIC (network interface card). Also, this method applied the interrupt mitigation method only to the IP stack. Therefore, this method achieved to reduce the overhead of the wide bandwidth of IP traffic, also to keep delay and jitter of real-time traffic enough small. Some experiments were conducted to measure the performance of the proposed method. The RTT (round trip time) delay of realtime communication was kept lower than 100μs even in high traffic load of 800 Mbit/s with small jitter; while the RTT of IP communication varied between 100μs to 20 ms. This paper introduced the design, implementation, and evaluation of the proposed method.

Undo/Redo Operations in Complex Environments

During the past thirty years, several types of non-linear undo models have been presented, but almost none of them solves undoing and redoing actions in environments, where multiple history buffers are involved and when there are causal dependencies among separate actions.This paper describes a new model which allows a user to select any action from any history buffer. The key part of the model is a smart command design and an undo manager, which searches for dependencies and offers possible solutions to the user. The results are presented in the context of evolution-management framework called DaemonX.