Packing Of Units Research Articles

Dynamics of Nucleosome Assembly and Effects of DNA Methylation

The nucleosome is the fundamental packing unit of the eukaryotic genome, and CpG methylation is an epigenetic modification associated with gene repression and silencing. We investigated nucleosome assembly mediated by histone chaperone Nap1 and the effects of CpG methylation based on three-color single molecule FRET measurements, which enabled direct monitoring of histone binding in the context of DNA wrapping. According to our observation, (H3-H4)2 tetramer incorporation must precede H2A-H2B dimer binding, which is independent of DNA termini wrapping. Upon CpG methylation, (H3-H4)2 tetramer incorporation and DNA termini wrapping are facilitated, whereas proper incorporation of H2A-H2B dimers is inhibited. We suggest that these changes are due to rigidified DNA and increased random binding of histones to DNA. According to the results, CpG methylation expedites nucleosome assembly in the presence of abundant DNA and histones, which may help facilitate gene packaging in chromatin. The results also indicate that the slowest steps in nucleosome assembly are DNA termini wrapping and tetramer positioning, both of which are affected heavily by changes in the physical properties of DNA.

Reactive and Robust Planning of Moroccan Citrus Chain Based on Multi-agent System and Performance Indicators

As part of improving services done for various clients in all Moroccan areas, Moroccan exportation group of fruits and vegetables in collaboration with their packaging units and producers, tends to cooperate in order to face with international competitiveness. Indeed, the complexity of networks of partners has led policy-makers to implement new techniques and tools to help control different processes. For this reason, the implementation of a permanent monitoring of different operations ranging from production, packaging, and distribution of perishable products has become paramount. This article aims to propose a model of multi-agent citrus supply chain, based on indicators for monitoring and evaluation of performance of its logistics systems, in order to build a new independent, robust and responsive chain, and to optimize and control the flow of materials and information between the different actors and stakeholders of the chain. review summarizing existing models of modeling supply chains; second, a presentation of the principle of distributed modeling based on multi-agent approach and its impact on our case studied system; third, we project the model selected on Moroccan citrus supply chain; finally, we proposed a model of decision that is based on mixed architecture for reactive and robust chain compared to disturbances and uncertainties. 2. State of the Art

Application of internet of things in food packaging and transportation

Food safety is a scientific field which includes a number of routines and inspections at every stage of the food chain that should be adopted to avoid potentially dangerous health risks. Novel and efficient solutions across the supply chain are the consequence of constant upgrades of information and communication technologies. With the help of internet of things (IoT) connected testing equipment, food quality can be monitored at any point from farm to table, connecting at the same time food producers, transportation and hospitality/retail companies. Relying on the fact that food transporting and packaging units are the most critical points in food production, the survey of IoT applications in food packaging and transportation is given in this paper. To demonstrate the significance of IoT appliance and defined concepts, a proposal of low cost solution based on IoT for real-time food traceability and monitoring in food transportation process is presented.

Development of a Novel Coarse-Grained Model of the Nucleosome Core Particle for Long-Timescale Simulations

The Nucleosome Core Particle (NCP) is the fundamental unit of DNA packaging in eukaryotic cells. It consists of ∼147 base pairs of DNA that are wrapped around an octameric protein core. Despite extensive experimental and theoretical work, the detailed physical mechanisms of important processes such as nucleosome opening, NCP-NCP interactions, and chromatin folding are not fully understood. Atomistic molecular dynamics (MD) simulations can in theory be a useful method to study these processes, however the timescales accessible to MD simulations are too short to explore these mechanisms. Therefore, we have used all-atom MD simulation data to derive a new Coarse-Grained (CG) model of the NCP. In this model, NCP residues are modeled using spherical beads centered on the DNA phosphorus and protein α-carbon atoms. DNA is represented by two types of beads that distinguish between base pairs (i.e. A-T and C-G), whereas protein residues are divided into two types based on their structure (i.e. α-helices and coils/loops). Force field parameters were derived using a hybrid approach of the iterative Boltzmann inversion method for bonded parameters, and Force Matching for non-bonded parameters. Our CG model significantly speeds up NCP simulations, and is expected to be useful in examining nucleosome opening, NCP-NCP interactions, and chromatin folding. Moreover, it is capable of reproducing the structural properties of the underlying atomistic system.

Fluorescent in situ hybridization on comets: FISH comet.

The DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. The comet assay, a sensitive method for monitoring DNA damage and repair, involves electrophoresis of nucleoids comprising supercoiled DNA attached to the nuclear matrix. Breaks in the DNA relax the supercoiling and allow DNA loops to expand, and on electrophoresis to move towards the anode, giving the appearance of a comet tail. We use fluorescent in situ hybridization (FISH) to investigate the structure of the chromatin within comet preparations and to study specific DNA sequences within comets. In this chapter we describe our FISH comets protocols, deal with some technical questions and outline the theory. FISH with comets should be useful to researchers interested in the structural organization of DNA and chromatin, the localization of DNA damage, and the kinetics of repair of damage.

Effects of Histone Variants MacroH2A and H2A.Z on Nucleosome Dynamics

The Nucleosome Core Particle (NCP) forms the fundamental unit of DNA packaging in chromatin fibers. Historically, the NCP has been considered static and in a closed conformation. However, recent evidence suggests that it may have dynamical properties that play a key role in its structural stability and transcriptional accessibility. Modifications to the NCP via histone variant substitutions can alter the stability of the complex. For example, replacement of the canonical histone H2A by variants macroH2A or H2A.Z has been linked to transcriptional repression, the mechanisms of which are not well understood. Here, we have used all-atom molecular dynamics simulations to provide insight into the mechanism by which variants macroH2A and H2A.Z stabilize the NCP. Our results show that dynamics of variant nucleosomes deviate from the canonical NCP primarily at the local level on the hundreds of nanoseconds timescale. Inclusion of variants alters the dynamics of the entry and exit segments of the DNA in the form of tighter DNA winding. Simulations also suggest that the presence of variants results in tighter dimer compaction. Furthermore, mutations to the dimer interface elucidate allosteric pathways to key locations of the complex.

Biophysical Models of Nucleosome Positioning

A human body contains enough DNA to circle the Earth's Equator more than 2.5 million times. The basic units of DNA packaging are called nucleosomes. Their locations along the chromosomes play an essential role in gene regulation. We study nucleosome positioning in yeast, fly and mouse, and build biophysical models in order to explain the genome-wide nucleosome organization. We show that DNA sequence is not the major cause of the regular arrays of nucleosomes observed in vivo near the transcription start sites (TSS). We construct a minimal model in which nucleosomes are positioned by potential barriers located in the gene promoters, and which accurately reproduces the genome-wide nucleosome occupancy patterns observed over the transcribed regions in living cells. Our statistical mechanics model allows us to study nucleosome phasing against potential barriers and wells [1, 2], sequence-dependent nucleosome affinity [2], nucleosome unwrapping [3], competition between different DNA-binding proteins, and accessibility of transcription factors [4, 5] to target sites which are found in nucleosomal DNA, among others. We also discuss alternative nucleosome positioning mechanisms: nucleosome anchoring [6] and active nucleosome positioning by ATP-dependent remodelers [7].[1] RV Chereji, D Tolkunov, G Locke, AV Morozov, Phys. Rev. E 83, 050903 (2011)[2] RV Chereji and AV Morozov, J. Stat. Phys. 144, 379 (2011)[3] RV Chereji and AV Morozov, Proc. Natl. Acad. Sci. U.S.A. 111, 5236 (2014)[4] N Petrenko, RV Chereji, MN McClean, AV Morozov, JR Broach Mol. Biol. Cell 24, 2045 (2013)[5] N Elfving∗, RV Chereji∗, V Bharatula, S Bjorklund, AV Morozov, JR Broach, Nucleic Acids Res. 42, 5468 (2014) (∗ contributed equally)[6] RV Chereji, AV Morozov, YM Moshkin, in preparation[7] D Ganguli∗, RV Chereji∗, J Iben, HA Cole, DJ Clark, Genome Res. (2014) (∗ contributed equally)

Molecular Orbital-Based Verification of Conductivity of Tetramethylammonium Pentaiodide and Pentaiodide-Based Electrolytes in Dye-Sensitized Solar Cells

In order to verify the electrical conductivity of tetramethylammonium pentaiodide (TAPI, I5−(N(CH3)4+)) crystal, molecular orbital configurations and energy structures of the electron-carrying state TAPI packing unit (TAPI-6) are examined by density functional theory (DFT). The narrow energy gap of the electron-carrying state radical anion of [TAPI-6].− proves the semi-conductivity of TAPI together with the aligned configuration of singly occupied molecular orbital (SOMO) and the spin density distribution on SOMO. The molecular orbital analysis of the electron-accepted states of the vertical fragment unit of [TAPI-4].− and the coplanar fragment unit of [TAPI-3].− rationalize the anisotropic semiconducting property in TAPI. DFT-based molecular modeling for molecular integration of I5−N(CH3)4+ with I5− and with I5−N(CH3)4+ confirms the formation of I5− integrated complexes of respective I5−&I5−N(CH3)4+ and (I5−N(CH3)4+)2. The degenerate HOMO and LUMO in (I5−N(CH3)4+)2 suggest expanding integration of I5− net via van der Waals and coulomb interactions (vdW&Clb) in I5−-based electrolytes. The narrow energy gap (0.3 ∼ 0.35 eV) and the spin density on SOMO of the radical anions of [(I5−N(CH3)4+)2]− and [I5−&I5−N(CH3)4+]− explain that the I5−N((CH3)4+-derived self-integrated I5− cluster nets become semiconducting and the photo-formed electron is transported effectively through SOMOs on I5− units of the electron-carrying clusters of [I5−&I5−N(CH3)4+].− and [(I5−N(CH3)4+)2]−. The DFT-based molecular modeling verifies reasonably the semi-conductivity of I5−-based DSC electrolytes.

内服薬の調剤包装単位バーコードの読み取りに向けた検証

On most medical drugs, bar codes in the new format “GS1 data bar” are printed on the dispensing package. However, the printing patterns of GS1 data bars vary widely. It is unclear whether bar code scanners are able to scan all types of patterns and also whether all types of scanners are able to scan these patterns. In this study, we present the experimental results of scanning tests of GS1 data bar printed on PTP sheets.As a result, it was found that certain scanners were unable to scan GS1 data bars. Moreover, it was also verified that there were certain patterns of the GS1 data bar that could not be scanned. Factors adversely affecting the quality of scanning were identified such as “existence of a frame,” “repetitive printing,” “different background color,” and “[F] ISO quality grade.” Factors advantageously influencing the scanning quality were also identified such as “cost of product is 15,000 yen or more.”The printing environment required for GS1 data bars on PTP sheets differs from that for standard bar codes on paper. In this survey, it was found that certain GS1 data bars on PTP sheets could not be scanned. For printing scannable GS1 data bars on PTP sheets, a higher printing quality is required. As GS1 data bars printed on dispensing package units contribute towards pharmaceutical safety management, ensuring accurate scanning is important. For utilizing GS1 data bars effectively, significant effort needs to be made by both the pharmaceutical industry and scanner manufactures.

OPTIMIZATION OF UNIT LOAD FORMATION TAKING INTO ACCOUNT THE MASS OF PACKAGING UNITS

This article presents a mathematical formulation of the optimization problem of loading unit formation taking into account the mass of packaging units. Proposed model can be applied to optimize the arrangement of non-uniform cubical loading units in loading spaces. The model ensures possibility of defining various dimensions, masses, resistances of particular packaging units and their vertical axis rotation. Within the constraints of formulating optimization problem, taking into account masses and resistances ensures that all packaging units will rest on a pallet or on other packaging units, and the surface of contact between loading units guarantees stability of units arranged in subsequent layers. The mathematical model was verified. The paper provides an appropriate calculation example.

Using Latex Balls and Acrylic Resin Plates To Investigate the Stacking Arrangement and Packing Efficiency of Metal Crystals

A high-school third-year or undergraduate first-semester general chemistry laboratory experiment introducing simple-cubic, face-centered cubic, body-centered cubic, and hexagonal closest packing unit cells is presented. Latex balls and acrylic resin plates are employed to make each atomic arrangement. The volume of the vacant space in each cell is measured by weighing water poured into the unit cell model, and the packing efficiency of each unit is obtained from the volume of vacant space. The observed values are compared with the theoretical calculations. Students can easily understand experimentally and theoretically that the packing efficiency of the face-centered cubic is the same as that of the hexagonal closest packing and significantly greater than that of the body-centered cubic. Moreover, they can understand the number of the neighboring atoms for any atom (coordination number) in each cell.

Wrinkling crystallography on spherical surfaces

We present the results of an experimental investigation on the crystallography of the dimpled patterns obtained through wrinkling of a curved elastic system. Our macroscopic samples comprise a thin hemispherical shell bound to an equally curved compliant substrate. Under compression, a crystalline pattern of dimples self-organizes on the surface of the shell. Stresses are relaxed by both out-of-surface buckling and the emergence of defects in the quasi-hexagonal pattern. Three-dimensional scanning is used to digitize the topography. Regarding the dimples as point-like packing units produces spherical Voronoi tessellations with cells that are polydisperse and distorted, away from their regular shapes. We analyze the structure of crystalline defects, as a function of system size. Disclinations are observed and, above a threshold value, dislocations proliferate rapidly with system size. Our samples exhibit striking similarities with other curved crystals of charged particles and colloids. Differences are also found and attributed to the far-from-equilibrium nature of our patterns due to the random and initially frozen material imperfections which act as nucleation points, the presence of a physical boundary which represents an additional source of stress, and the inability of dimples to rearrange during crystallization. Even if we do not have access to the exact form of the interdimple interaction, our experiments suggest a broader generality of previous results of curved crystallography and their robustness on the details of the interaction potential. Furthermore, our findings open the door to future studies on curved crystals far from equilibrium.

Analyse et modélisation de la chaîne agrumicole marocaine basée sur le système multi-agents et indicateurs de performance : planification réactive et robuste

As part of the improvement of the services addressed to the various customers in all the Moroccan production zones, the Moroccan fruit and vegetable export groups in collaboration with their packaging units and their producers tend to cooperate with each other in order to face international competitiveness. Indeed, the growing complexity of partner networks has prompted decision-makers to put in place techniques and tools contributing to the control of the various processes. For this, the establishment of a permanent monitoring of the various operations ranging from production, packaging, to the distribution of perishable products has become essential. This article aims to propose a multi-agent modeling of the citrus supply chain based on indicators for monitoring and evaluating the performance of its logistics systems. This with the aim of building a new autonomous, robust and responsive chain, thus making it possible to optimize and control the flow of materials and information between the various actors and stakeholders in the chain. The article is presented along four major axes: first, a literature review summarizing the different existing models for the modeling of supply chains. Then, a presentation of the principle of distributed modeling based on the multi-agent system and its application on our case study. On the third axis, we have projected the principle of the model chosen on the Moroccan citrus chain. Finally, we proposed a decision-making model based on a mixed architecture allowing a reactive and robust chain with regard to disturbances and uncertainties.

Cytomegalovirus.

To consider new treatment options for cytomegalovirus (CMV) infection, review recent trials, and anticipate their use in clinical practice, focussing on bone marrow transplantation, congenital infection, and intervention during pregnancy. Three double-blind randomized placebo-controlled phase 2 proof-of-concept studies have each identified a novel antiviral drug with activity against CMV infection in bone marrow transplant patients. One of these (brincidofovir) inhibits the DNA polymerase that is the target of the currently licensed drug ganciclovir. Another new drug (maribavir) inhibits a protein kinase which, coincidentally, is the enzyme responsible for activating ganciclovir through phosphorylation. The third drug (letermovir) inhibits the terminase enzyme complex responsible for packaging unit length DNA into assembling virions.In addition, in a double-blind randomized placebo-controlled trial in neonates with symptomatic congenital CMV infection, a 6-month course of valganciclovir was superior to the standard 6-week course of the same drug. In pregnant women with primary CMV infection, administration of hyperimmune immunoglobulin did not significantly reduce transmission of CMV across the placenta. The ability to diagnose CMV infections reliably in different clinical settings through application of molecular laboratory methods has ushered in new ways of evaluating potential new treatments for CMV. Several of these may help control the diseases caused by this important human pathogen.

Homogenization of precipitation time series with ACMANT

New method for the time series homogenization of observed precipitation (PP) totals is presented; this method is a unit of the ACMANT software package. ACMANT is a relative homogenization method; minimum four time series with adequate spatial correlations are necessary for its use. The detection of inhomogeneities (IHs) is performed with fitting optimal step function, while the calculation of adjustment terms is based on the minimization of the residual variance in homogenized datasets. Together with the presentation of PP homogenization with ACMANT, some peculiarities of PP homogenization as, for instance, the frequency and seasonal variation of IHs in observed PP data and their relation to the performance of homogenization methods are discussed. In climatic regions of snowy winters, ACMANT distinguishes two seasons, namely, rainy season and snowy season, and the seasonal IHs are searched with bivariate detection. ACMANT is a fully automatic method, is freely downloadable from internet and treats either daily or monthly input. Series of observed data in the input dataset may cover different periods, and the occurrence of data gaps is allowed. False zero values instead of missing data code or physical outliers should be corrected before running ACMANT. Efficiency tests indicate that ACMANT belongs to the best performing methods, although further comparative tests of automatic homogenization methods are needed to confirm or reject this finding.

Analysis of medicine consumption in peacekeeping level II hospitals.

The peacekeeping military units of contributing countries are unfamiliar with the conditions prevailing in foreign mission areas and therefore have difficulties with medical supplies storage. The aim of this study is to provide reasonable and practical guidance on the maintenance of medical supplies in the peacekeeping military units of contributing countries. A total of 1,972 prescriptions were received by the pharmacy in the peacekeeping level II hospital in the Republic of Sudan from February to July of 2009 including a total of 186 drug categories and 17,713 minimum packing units. Pairwise comparison was performed using the c2 test. When the total number of samples was smaller than 40, the Fisher's exact test was adopted for pairwise comparison. The majority of the consumed medicines mainly belonged to 6 categories, including specialty drugs, anti-microbial drugs, Chinese patent medicines, gastrointestinal drugs, central nervous system drugs, and drugs regulating fluids, electrolytes, and acid-base balance. Altogether, the drugs in the 6 categories accounted for 74% of all consumed medicines that were divided into a total of 20 categories. Medicine consumption in peacekeeping level II hospitals is unique, therefore the drugs used in military medical facilities should be prepared according to their actual needs in the area of peacekeeping operations.

Development and evaluation of a system to assess antimicrobial drug use in farm animals: results of an Austrian study

The objective of this study was to develop and evaluate a feasible system for the collection of antimicrobial consumption data in farm animals in Austria. An electronic registry of all...

Thermo-economic optimization of condenser coil configuration for HVAC performance enhancement

The purpose of this study is to develop an optimization methodology for the detailed energy and cost effective design of a finned-tube condenser coil in order to enhance the system performance. Using this method, the frontal area of the condenser coil is maintained as constant, while other geometrical parameters of the thermal and economic performance of the system are varied and investigated. An existing air-cooled direct expansion (DX) rooftop package unit of a real-world commercial building is used for experimental data collection. First, the theoretical–empirical model for the system components is developed. Based on mathematical models and using collected data, a numerical algorithm is developed and embedded in a transient simulation tool. The integrated simulation tool is then validated by using the wide range of operating data obtained experimentally from the cooling plant during summer time. Furthermore, a mixed heuristic–deterministic optimization algorithm was implemented to determine the synthesis and design variables that influence the cost and energy efficiency of each configuration. Different new designs for condenser coil were then constructed to evaluate the potential of design improvements. Afterwards, the computer model was used to predict how changes in condenser coil geometry would affect the cost and energy consumption of the system.

Grocery retail operations and automotive logistics: a functional cross-industry comparison

Purpose – The purpose of this paper is to identify and describe similarities between logistics structures and mid-term planning problems in the grocery retail and automotive industries in a specific internal section of their respective supply chains. Design/methodology/approach – The benchmarking approach is used as a framework for this paper. It is based on insights resulting from several joint projects with grocery retailers and automobile producers. A particular focus of the research was participating in an exchange of ideas and experience between logistics managers in both industry sectors. Findings – The authors have identified parallels when comparing the internal retail supply chain of the grocery retail industry, which consists of distribution centres, transportation and in-store logistics, with the internal logistics network in the automotive industry, which consists of logistics supermarkets, transportation and work zone operations at the assembly line. Strong similarities have been found for three planning problems related to tactical planning tasks: assigning products and parts to delivery modes, selecting packaging units and loading carriers, and determining delivery cycles. In comparison to retailing, there is a clearer trend in the automotive industry to plan line-back and align processes with the operator's requirements at the assembly line. Practical implications – For logisticians in grocery retailing and the automotive industry, this paper provides relevant input for functional benchmarking initiatives and offers an inspirational view beyond the horizon. Originality/value – This paper is the first to focus on similarities in logistics network structures and planning tasks between the two industries from the viewpoint of grocery retailing.

AFM analysis of changes in nucleosome wrapping induced by DNA epigenetic modification.

The wrapping and unwrapping of the nucleosome, which is a fundamental packing unit of chromatin, are tied to the regulation of gene expression. The accessibility of DNA within nucleosomes is controlled not only by chromatin-remodeling molecules, but also by chemical modifications of histones and DNA. Understanding the structural changes of a nucleosome during epigenetic modifications is a key to unravel the mechanisms of gene regulation. Here, we reconstituted nucleosomes using methylcytosine- or hydroxymethylcytosine-substituted DNA, and analyzed their morphological features by atomic force microscopy (AFM). Our results indicate that cytosine methylation induces overwrapping of the DNA around the histone octamer, whereas cytosine hydroxymethylation has a lesser effect on the overwrapping of the DNA. These results suggest that two types of DNA modification yield different wrapping states of nucleosomes, which may contribute to the compaction and relaxation of the chromatin structure.