Inter-node Level Research Articles

Ion-molecule collision cross-section calculations using trajectory parallelization in distributed systems

Ion Mobility coupled with Mass Spectrometry (IM-MS) stands as a strong analytical method for structurally characterizing complex molecules. In IM-MS, the sample under investigation is ionized and propelled by an electric field into a drift tube, which collides against a buffer gas. The separation of the ion gas phase is then measured through the differences in their rotationally averaged Collision Cross-Section (CCS) values. The effectiveness of the measured Collision Cross-Section (CCS) for structural characterization critically depends on the validation against theoretical calculations. This validation process relies on intensive molecular mechanics simulations, which can be computationally demanding, especially for large systems such as molecular assemblies and viruses. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS experimental data. This work presents the MassCCS software, which considerably increases the CCS simulation performance by implementing a linked-cell-based algorithm, incorporating High-Performance Computing (HPC) techniques. We performed extensive tests regarding the system size, shape, and number of CPU cores. Experimental results reveal speedups up to 3 orders of magnitude faster than Collision Simulator for Ion Mobility Spectrometry (CoSIMS) and High-Performance Collision Cross Section (HPCCS), optimized solutions for CCS simulations, for a single node execution. In addition, we extended MassCCS at the inter-node level by employing OpenMP Cluster (OMPC). OMPC is an innovative programming model designed for the development of HPC applications. It streamlines the development process and simplifies software maintenance using only OpenMP directives. Notably, OMPC delivers a performance level comparable to a pure MPI implementation. This enhancement enabled expensive CCS calculations using nitrogen buffer gas for large systems such as human adenovirus with ∼11 million atoms in just ∼4 min, making MassCCS the most performant software nowadays, to the best of our knowledge. MassCCS is available as free software for Academic use at https://github.com/cces-cepid/massccs.

Terminal drought effect on sugar partitioning and metabolism is modulated by leaf stay-green and panicle size in the stem of sweet sorghum (Sorghum bicolor L. Moench)

BackgroundThe benefits of leaf stay-green for maintaining grain filling in sorghum under drought was largely demonstrated. However, its role in the stability of a dual production (grain, stem sugar) in tall sweet sorghum remains to be elucidated. This study aimed to analyze the impact of a post-anthesis drought on sugar accumulation along stem internodes in sweet and tall West-African sorghum with variable leaf stay-green and grain yield abilities.MethodsFour accessions with similar phenology were studied in two consecutive years in the field at the National Agronomic Research Centre (CNRA) of Bambey (Senegal, West Africa) under two post-anthesis water treatments (irrigated, non-irrigated). Plant morphology, stem sugar related traits, grain production, and plant leaf area (PLA) variation were assessed. Carbohydrate contents (sucrose, hexoses, starch) were determined during grain filling in the whole stem juice and at three internode levels: bottom, median, top. Analysis of variance was performed to test post-anthesis water treatment, accession, organ, year effects and their interactions on the studied traits.ResultsPanicle dry weight (PDW) was not affected by drought, but strongly varied among years and accessions. The PDW/PLA ratio was negatively correlated with the variation of sucrose and hexoses at the three internodes levels. This carbohydrates reduction was mainly influenced by the PDW. The bigger the panicle the higher the carbohydrates remobilization from the stem to panicle for grain filling. This was mainly shown on accessions G3 and G11 which exhibited low stay green ability. However, G10 with low PDW/PLA ratio and showing higher stay green ability, exhibited a low reduction of total soluble sugars and sucrose and inversely higher increase of hexoses mainly at the median internode.ConclusionsThis ability to better maintain green leaf area and high hexoses in the stem under post-flowering drought could be an osmoregulation mechanism to adapt to drought. Therefore, stay-green is an important trait to consider for sweet sorghum breeding and particularly in the objective of developing dual purpose varieties in drought prone environments.

High throughput phenotyping of morpho-anatomical stem properties using X-ray computed tomography in sorghum

BackgroundIn bioenergy/forage sorghum, morpho-anatomical stem properties are major components affecting standability and juice yield. However, phenotyping these traits is low-throughput, and has been restricted by the lack of a high-throughput phenotyping platforms that can collect both morphological and anatomical stem properties. X-ray computed tomography (CT) offers a potential solution, but studies using this technology in plants have evaluated limited numbers of genotypes with limited throughput. Here we suggest that using a medical CT might overcome sample size limitations when higher resolution is not needed. Thus, the aim of this study was to develop a practical high-throughput phenotyping and image data processing pipeline that extracts stem morpho-anatomical traits faster, more efficiently and on a larger number of samples.ResultsA medical CT was used to image morpho-anatomical stem properties in sorghum. The platform and image analysis pipeline revealed extensive phenotypic variation for important morpho-anatomical traits in well-characterized sorghum genotypes at suitable repeatability rates. CT estimates were highly predictive of morphological traits and moderately predictive of anatomical traits. The image analysis pipeline also identified genotypes with superior morpho-anatomical traits that were consistent with ground-truth based classification in previous studies. In addition, stem cross section intensity measured by the CT was highly correlated with stem dry-weight density, and can potentially serve as a high-throughput approach to measure stem density in grass stems.ConclusionsThe use of CT on a diverse set of sorghum genotypes with a defined platform and image analysis pipeline was effective at predicting traits such as stem length, diameter, and pithiness ratio at the internode level. High-throughput phenotyping of stem traits using CT appears to be useful and feasible for use in an applied breeding program.

Influence of the radial stem composition on the thermal behaviour of miscanthus and sorghum genotypes

The hypothesis made is that thermal resistance of sorghum and miscanthus stem pieces taken at well-defined positions of the stem is simply related to their biochemical composition. For miscanthus, two different genotypes and two internode levels were selected. For each region, the stem was divided into three radial layers. For sorghum, two different genotypes were selected and the stem was divided into the same three radial layers. The results show that the thermal analysis is only sensitive to very large variations of compositions. But aside of such large composition differences, it is impossible to correlate thermal effects to biochemical composition even on very small size, well-identified pieces of plant materials. The interplay between sugar-based components, lignin and minerals is totally blurring the thermal response. Extreme care must be exercised when willing to explain why a given plant material has a thermal behaviour different of another plant material.

An adaptive and hierarchical task scheduling scheme for multi-core clusters

• An adaptive and hierarchical task scheduling scheme (AHS) is proposed. • Work-sharing is used in conjunction with work-stealing. • An initial partitioning is performed with respect to the pattern of task parallelism . • A practical implementation of AHS is described. • The theoretical, simulation and experimental studies of AHS are presented. Work-stealing and work-sharing are two basic paradigms for dynamic task scheduling. This paper introduces an adaptive and hierarchical task scheduling scheme (AHS) for multi-core clusters, in which work-stealing and work-sharing are adaptively used to achieve load balancing. Work-stealing has been widely used in task-based parallel programing languages and models, especially on shared memory systems. However, high inter-node communication costs hinder work-stealing from being directly performed on distributed memory systems. AHS addresses this issue with the following techniques: (1) initial partitioning, which reduces the inter-node task migrations; (2) hierarchical scheduling scheme, which performs work-stealing inside a node before going across the node boundary and adopts work-sharing to overlap computation and communication at the inter-node level; and (3) hierarchical and centralized control for inter-node task migration, which improves the efficiency of victim selection and termination detection. We evaluated AHS and existing work-stealing schemes on a 16-nodes multi-core cluster. Experimental results show that AHS outperforms existing schemes by 11–21.4%, for the benchmarks studied in this paper.

Distributed Agent-Based Computing in Material-Embedded Sensor Network Systems With the Agent-on-Chip Architecture

Distributed material-embedded systems like sensor networks integrated in sensorial materials require new data processing and communication architectures. Reliability and robustness of the entire heterogeneous environment in the presence of node, sensor, link, data processing, and communication failures must be offered, especially concerning limited service of material-embedded systems after manufacturing. In this paper, multiagent systems with state-based mobile agents are used for computing in unreliable mesh-like networks of nodes, usually consisting of a single microchip, introducing a novel design approach for reliable distributed and parallel data processing on embedded systems with static resources. An advanced high-level synthesis approach is used to map the agent behavior to multiagent systems implementable entirely on microchip-level supporting agent-on-chip (AoC) processing architectures. The agent behavior, interaction, and mobility are fully integrated on the microchip using a reconfigurable pipelined communicating process architecture implemented with finite-state machines and register-transfer logic. The agent processing architecture is related to Petri Net token processing. A reconfiguration mechanism of the agent processing system achieves some degree of agent adaptation and algorithmic selection. The agent behavior, interaction, and mobility features are modeled and specified with an activity-based agent behavior programming language. Agent interaction and communication is provided by a simple tuple-space database implemented on node level and signals providing remote inter-node level communication and interaction.

Location Feature Integration for Clustering-Based Speech Separation in Distributed Microphone Arrays

In distributed microphone arrays (DMAs) the source location information can be defined at the intra and inter-node levels. Indeed, while the first type of information results from the diversity of acoustic channels recorded by microphones embedded in the same node, the second is attributed to the differences between the acoustic channels observed by spatially distributed nodes. Both cues are very useful in DMA processing, and the aim of this paper is to utilize both of them to cluster and separate multiple competing speech signals. To capture the intra-node information, we employ the normalized recording vector, while at the inter-node level, we consider different features including the energy level differences with and without the phase differences between nodes. We model the intra-node information using the Watson mixture model (WMM), and propose using the Gamma mixture model (GaMM), Dirichlet mixture model (DMM), and WMM to model different inter-node location features. Furthermore, we propose several integrations of the intra-node and inter-node feature contributions to cluster speech recordings using the expectation maximization algorithm. Finally, simulation results are provided to demonstrate the performance of all ensuing methods.

Grain, sugar and biomass accumulation in photoperiod-sensitive sorghums. II. Biochemical processes at internode level and interaction with phenology

Sugar accumulation in sorghum (Sorghum bicolor (L.) Moench) stems is a complex trait that is particularly plastic in response to photoperiod. This study investigated sucrose accumulation in a sterile (no grain filling) and fertile near-isogenic line of the photoperiod-sensitive cultivar IS2848 in two greenhouse experiments. Variable phenology was induced by applying a short (12-h PP) and a long (13-h PP) photoperiod. Dynamics of plant growth, phenology, sugar accumulation and related enzyme activities in internodes were investigated. Under 13-h PP, plants flowered 28 days later and attained threefold higher sucrose concentration at anthesis compared with those under 12-h PP. Sucrose accumulation in individual internodes was driven by organ physiological age, not by plant phenology. Competition with grain filling was marginal but greater under 12-h PP (i.e. when sucrose accumulation in internodes occurred after flowering). Enzyme activities showed marked developmental patterns but contributed little to explaining differences between treatments and genotypes. The study demonstrates that sucrose storage physiology in sweet sorghum resembles that of sugarcane (Saccharum spp.) but is more complex due to photoperiod effects on phenology. It confirms the field results on 14 sorghum genotypes contrasting for phenology and photoperiod sensitivity presented in a companion paper. Perspectives for developing sorghum ideotype concepts for food and fuel crops are discussed.

Content of the pectic substances, calcium, magnesium and minerals in the nodes and internodes of winter wheat culms, lodging and non-lodging varieties in their flowering stage

Total amount of the pectdc substances and their fractions was estimated in wheat of several lodging and non-lodging varieties during the flowering stage. The node tissues contained three times as much total pectic substances as did internodes. Irrespective of the wheat variety, the nodes as compared to the internodes, contain three times as much soluble pectins, and two times as much protopectin fraction extractable at pH 4.5 as well as those extractable at pH 10.6. Non-lodging varieties ('Grana', 'Luna', 'Modzurowska') are characterized by high content of pectic substances both in nodes and internodes, high content of calcium and magnesium protopectin fractions are also characteristic of nodes and internodes of these varieties. The lowest content of calcium-magnesium protopectins is found in the in ternodes of tall, lodging wheat varieties. Nitrogen fertilization, up to 80 kg N/ha, does not influence the internode levels of calcium-magnesium protopectin fractions, ash substances, and the levels of calcium and magnesium in this tissue.

Monilethrix

A 12-year-old girl presented with a 2-year history of progressive hair loss involving the top of the scalp. She also complained of partial loss of eyebrows. Family history was unremarkable. Examination revealed mild widening of the central parting, suggesting a diagnosis of female pattern hair loss (Figure, A) and alopecia of the eyebrows and lower eyelashes (Figure, B). Dermoscopy of the scalp showed a few characteristic monilethrix hair shafts characterized by uniform elliptical nodes, separated by intermittent constrictions. Broken hair shafts at internode levels were also evident (Figure, C). Dermoscopy of the eyebrows was also diagnostic for monilethrix. The term monilethrix derives from both the Latin monile (necklace) and the Greek thrix (hair). The hair shaft has a beaded appearance due to the presence of elliptical nodes that have the diameter of normal hair and are medullated, regularly separated by internodes that are narrow, devoid of medulla and are the site of fracture.1Tosti A. Torres F. Dermoscopy in the diagnosis of hair and scalp disorders.Actas Dermosifliogr. 2009; 100: 114-119Crossref PubMed Scopus (35) Google Scholar, 2Rakowska A. Slowinska M. Kowalska-Oledzka E. Rudnicka L. Trichoscopy in genetic hair shaft abnormalities.J Dermatol Case Rep. 2008; 2: 14-20Crossref PubMed Google Scholar It is an autosomal dominant disorder, with variable expression, due to mutations of the human basic hair keratins hHb6 and hHb1. The hair is dull, fragile, and breaks easily, especially in the sites of friction such as the nape and occipital areas. Follicular keratosis of the affected scalp and keratosis pilaris are also typical. The severity of monilethrix considerably varies even among members of the same family and may range from an almost normal scalp, to total alopecia.3Gebhardt M. Fischer T. Claussen U. Wollina U. Elsner P. Monilethrix-improvement by hormonal influences?.Pediatr Dermatol. 1999; 16: 297-300Crossref PubMed Scopus (26) Google Scholar, 4Jain N. Khopkar U. Monilethrix in pattern distribution in siblings: diagnosis by trichoscopy.Int J Trichology. 2010; 2: 56-59Crossref PubMed Scopus (22) Google Scholar In this case, the disease was mild and went unnoticed until adolescence. The correct diagnosis was indicated by dermoscopy that easily evidenced the few hairs affected by the abnormality. The parents were advised to avoid trauma to scalp hair and informed that the condition may spontaneously improve with age, whereas no effective treatment is currently available.3Gebhardt M. Fischer T. Claussen U. Wollina U. Elsner P. Monilethrix-improvement by hormonal influences?.Pediatr Dermatol. 1999; 16: 297-300Crossref PubMed Scopus (26) Google Scholar, 5Finley E. Ertle J.O. Marschall S. Alopecia in a 19-month-old boy.Arch Dermatol. 1994; 130: 1055-1056Crossref PubMed Scopus (2) Google Scholar

Desenvolvimento e anatomia de plantas de carrapicho-beiço-de-boi (Desmodium canum (Gmel) Schinz et TheII) pré tratadas com trifluralin e fluchloralin

Sementes de carrapicho-beiço-de-boi (Desmodium canum) foram germinadas em placas de Petri, sobre papel de filtro, com diferentes concentrações de trifluralin e fluchloralin (0, 0,5, 2,5, 12,5 e 62,5 ppm). Após 28 dias nesse meio, as plântulas foram transferidas para vasos contendo solo sem herbicida, onde permaneceram até os 101 dias de desenvolvimento. O ensaio foi conduzido em condições de labora tório, com temperatura variando entre 25-28°C. Plantas com 101 dias de desenvolvimento, prétratadas com as concentrações mais baixas dos herbicidas, apresentaram-se atrofiadas e menos vigorosas quando comparadas com plantas testemunhas; nas mais elevadas, a maioria das plantas não sobreviveu aos tratamentos. A análise histológica do caule, ao nível do nó e entrenó, mostrou intensa desorganização dos tecidos, principalmente do tecido vascular.

Stem extension rate in light‐grown plants. Evidence for an endogenous circadian rhythm in Chenopodium rubrum

Stem extension in light‐grown plants of Chenopodium rubrum L. ecotype selection 184 (50°10′N; 150°35′W) was recorded continuously for periods up to one week at constant temperature. Stem extension rate measurements were made with linear voltage‐displacement transducer devices. At the beginning of experiments, the 3rd intenode above the cotyledons was about 5 mm long. Stem extension rate exhibited a rhythmic behaviour in continuous white light (20 W m−2), and in continuous darkness with a period of approximately 23 h. In continuous darkness, the amplitude of the rhythm damped out very quickly after 24 h and a second peak was just measurable. The mean value of the stem extension rate was dependent on the light fluence before the experiments. This overt rhythm, which could be observed at the individual plant or even internode level, exhibited the characteristics of an endogenous circadian rhythm. There was no correlation of the peak time to local time. The peak time was determined by the time of transfer from dark to light for dark periods equal to or longer than 8 h, and the phase was shifted by the time of transfer from light to dark at the proper phase of a pre‐existing rhythm.