Packaging Specificity Research Articles

Programme science methodologies and practices that address "FURRIE" challenges: examples from the field.

"Programme science" deploys scientific methods to address questions that are a priority to support the impact of public health programmes. As such, programme science responds to the challenges of making such studies: (1) feasible to undertake, (2) useful, (3) rigorous, (4) real-world-relevant, (5) informative, and undertaken by (6) equitable partnerships. The acronym "FURRIE" is proposed to describe this set of six challenges. This paper discusses selected HIV/STI (sexually transmitted infection) programme science case studies to illustrate how programme science rises to the FURRIE challenges. One way in which programme science is made more feasible is through the analysis and interpretation of data collected through service delivery. For some questions, these data can be augmented through methods that reach potential clients of services who have not accessed services or been lost to follow-up. Process evaluation can enhance the usefulness of programme science by studying implementation processes, programme-client interactions and contextual factors. Ensuring rigour by limiting bias and confounding in the real-world context of programme science studies requires methodological innovation. Striving for scientific rigour can also have the unintended consequence of creating a gap between what happens in a study, and what happens in the "real-world." Community-led monitoring is one approach to grounding data collection in the real-world experience of clients. Evaluating complex, context-specific strategies to strengthen health outcomes in a way that is informative for other settings requires clear specification of the intervention packages that are planned and delivered in practice. Programme science provides a model for equitable partnership through co-leadership between programmes, researchers and the communities they serve. Programme science addresses the FURRIE challenges, thereby improving programme impact and ultimately health outcomes and health equity. The adoption and adaptation of the types of novel programme science approaches showcased here should be promoted within and beyond the HIV/STI field.

Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability.

Multi-segmented viruses often multimerize their genomic segments to ensure efficient and stoichiometric packaging of the correct genetic cargo. In the bipartite Nodaviridae family, genome heterodimerization is also observed and conserved among different species. However, the nucleotide composition and biological function for this heterodimer remain unclear. Using Flock House virus as a model system, we developed a next-generation sequencing approach ("XL-ClickSeq") to probe heterodimer site sequences. We identified an intermolecular base-pairing site which contributed to heterodimerization in both wild-type and defective virus particles. Mutagenic disruption of this heterodimer site exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNAs. Furthermore, the disruption of this intermolecular interaction directly impacts the thermostability of the mature virions. These results demonstrate that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus have an important role on virus particle integrity and thus may impact its transmission to a new host.IMPORTANCEFlock House virus is a member of Nodaviridae family of viruses, which provides a well-studied model virus for non-enveloped RNA virus assembly, cell entry, and replication. The Flock House virus genome consists of two separate RNA molecules, which can form a heterodimer upon heating of virus particles. Although similar RNA dimerization is utilized by other viruses (such as retroviruses) as a packaging mechanism and is conserved among Nodaviruses, the role of heterodimerization in the Nodavirus replication cycle is unclear. In this research, we identified the RNA sequences contributing to Flock House virus genome heterodimerization and discovered that such RNA-RNA interaction plays an essential role in virus packaging efficiency and particle integrity. This provides significant insight into how the interaction of packaged viral RNA may have a broader impact on the structural and functional properties of virus particles.

Analyzing Marketing Issues in China's Juice Market Using Visualization Tools

China's juice market has been slow in recent years, and the market share is gradually decreasing. Based on the importance and research value of online reviews on e-commerce platforms today, this paper uses the python crawler tool to crawl the top three 100% juice product reviews on the JD platform, extract new words and keywords, and analyze positive and negative emotions, and then visualize them. According to the research results, it is suggested that fruit juice enterprises carry out taste innovation; Optimize packaging design, materials, and specifications; and make suggestions such as timely promotion activities on holidays. It aims to put forward targeted tips for recovering China's juice market.

Building Software for Hierarchical Events in Biodiversity Informatics

In 2019, the Atlas of Living Australia (ALA) ran a national consultation, clarifying a long-held suspicion that while simple occurrence records provide invaluable discoverability and analysis for biodiversity data, the lack of contextual information on data collection methodology and protocols limits its usefulness for species abundance estimation and time-series analysis. The consultation recognised that the ALA has strong leadership in biodiversity standards and development, and that our 12-year history and investment in projects and engagement demonstrates a clear capacity to transition to a repository capable of capturing and aggregating the monitoring and survey data required for conservation efforts (Daly 2019). Around the same time, the larger data landscape was undergoing change in a similar direction, both internationally through the Global Biodiversity Information Facility’s (GBIF) Unified Model engagements, and nationally through the development of the Australian Biodiversity Information Standard (ABIS), an ontology for describing environmental data (Anonymous 2021). We embarked on a project to examine existing data standards and practices, extend our own occurrence model, and build software that could ingest event-based datasets and make them discoverable and interoperable. Initially we focused on well-structured surveys, both marine and terrestrial, to develop the system and user interface (UI). During the project, we restructured and modeled other exemplar datasets, collaborating with GBIF to develop event terms, vocabularies, and user interface components. Seeking interoperability with existing standards, we integrated concepts from both ABIS and the Ocean Biodiversity Information System’s (OBIS) ENV-DATA model (De Pooter et al. 2017) into a standardised yet flexible implementation of Event Core, navigable via a friendly user interface. The initial software release is comprised of an ingestion pipeline for events in parallel to occurrences, an index capable of handling nested data structures, and a user interface. The UI guides the user to explore and filter datasets; includes visualisations for data structures, taxonomic scope, repeat location surveys, extended measurements or facts; and links out to child occurrence records. Users can download filtered original and interpreted datasets with Digital Object Identifiers (DOI), in compressed files that comply simultaneously with Darwin Core Archive and Frictionless Data Package specifications. On release, we will present a range of datasets covering different event-based scenarios. The model has serendipitously provided the flexibility to encapsulate complex seed bank data. During the project, we developed a draft extension, which we used to service a new data portal for the Australian Seed Bank Partnership, a testament to the model’s serviceability for novel use cases. The ALA has taken innovative steps beyond simple collection of complex data types and worked with our local biodiversity informatics community to provide a navigable interface to this data. We intend to continue working with our own data providers and the international community, to realise the benefits of a more complex data model.

The curious case of genome packaging and assembly in RNA viruses infecting plants.

Genome packaging is the crucial step for maturation of plant viruses containing an RNA genome. Viruses exhibit a remarkable degree of packaging specificity, despite the probability of co-packaging cellular RNAs. Three different types of viral genome packaging systems are reported so far. The recently upgraded type I genome packaging system involves nucleation and encapsidation of RNA genomes in an energy-dependent manner, which have been observed in most of the plant RNA viruses with a smaller genome size, while type II and III packaging systems, majorly discovered in bacteriophages and large eukaryotic DNA viruses, involve genome translocation and packaging inside the prohead in an energy-dependent manner, i.e., utilizing ATP. Although ATP is essential for all three packaging systems, each machinery system employs a unique mode of ATP hydrolysis and genome packaging mechanism. Plant RNA viruses are serious threats to agricultural and horticultural crops and account for huge economic losses. Developing control strategies against plant RNA viruses requires a deep understanding of their genome assembly and packaging mechanism. On the basis of our previous studies and meticulously planned experiments, we have revealed their molecular mechanisms and proposed a hypothetical model for the type I packaging system with an emphasis on smaller plant RNA viruses. Here, in this review, we apprise researchers the technical breakthroughs that have facilitated the dissection of genome packaging and virion assembly processes in plant RNA viruses.

Improving local rice consumption in Sub-Saharan Africa through social marketing: evidence from Ghana

The efforts and strategies of governments and other stakeholders to achieve self-rice sufficiency on the African continent have failed to achieve the intended results. Although scholars have primarily attributed this problem to poor attitudes and behaviour toward the consumption of locally produced rice, limited attention has been paid to behavioural change approaches. Thus, from the perspective of the theory of planned behaviour, the study sought to understand the factors that influence consumers’ intention to consume locally produced rice and to suggest solutions from a social marketing perspective to elicit voluntary changes in behaviour toward the consumption of local rice. Quantitative and qualitative data were collected from 375 to 40 participants, respectively. Qualitative data were analysed thematically, while quantitative data were analysed using partial least squares structural equation modelling. The results showed a strong positive and significant relationship between attitude, subjective norms, perceived behavioural control, and intention to consume locally produced rice. The results showed a weak significant negative relationship between intention and actual consumption of local rice, suggesting a high intention-behaviour gap. However, the qualitative results identified six critical factors that prevented people from consuming local rice though having the intention. These factors include cooking difficulty, suitability for few local dishes, lack of taste and aroma, foreign materials, poor packaging and standard specification, and unavailability. Thus, interventions addressing these barriers will significantly increase the consumption of local rice in Ghana. The study contributes to literature by using the mixed method approach and the theory of planned behaviour to predict factors that could improve local rice consumption in a developing country context. We also addressed how the 4Ps of social marketing could be used to address the identified barriers.

A Review on Force Degradation Studies for Drug Substances

The objective of the review article is to give detailed description and guidance of the forced degradation studies as per regulatory guidelines. Forced degradation or alternatively referred as stress testing and it demonstrates specificity when developing stability indicating methods, especially when little is known about potential degradation products. Forced degradation study provides information about the degradation pathways and degradation products of the drug substance that could form during storage, transportation. Force degradation study also helps in the elucidation of the structure of the degradation products. Forced degradation study provide the chemical behaviour and chemical nature of the molecule which ultimately helps in the development of formulation during manufacturing and packaging specification, thus this review article provides knowledge of the current trends in performance of forced degradation study and establishing the analytical methods that helpful for development of stability indicating method.

Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase.

The phage-inducible chromosomal islands (PICIs) of Gram-negative bacteria are analogous to defective prophages that have lost the ability to propagate without the aid of a helper phage. PICIs have acquired genes that alter the genetic repertoire of the bacterial host, including supplying virulence factors. Recent work by the Penadés laboratory elucidates how a helper phage infection or prophage induction induces the island to excise from the bacterial chromosome, replicate, and become packaged into functional virions. PICIs lack a complete set of morphogenetic genes needed to construct mature virus particles. Rather, PICIs hijack virion assembly functions from an induced prophage acting as a helper phage. The hijacking strategy includes preventing the helper phage from packaging its own DNA while enabling PICI DNA packaging. In the case of recently described Gram-negative PICIs, the PICI changes the specificity of DNA packaging. This is achieved by an island-encoded protein (Rpp) that binds to the phage protein (TerS), which normally selects phage DNA for packaging from a DNA pool that includes the helper phage and host DNAs. The Rpp–TerS interaction prevents phage DNA packaging while sponsoring PICI DNA packaging. Our communication reviews published data about the hijacking mechanism and its implications for phage DNA packaging. We propose that the Rpp–TerS complex binds to a site in the island DNA that is positioned analogous to that of the phage DNA but has a completely different sequence. The critical role of TerS in the Rpp–TerS complex is to escort TerL to the PICI cosN, ensuring appropriate DNA cutting and packaging.

The design of an intelligent packaging based on immunochromatography to detect ciprofloxacin residues in different types of poultry meat

AbstractIn this study, an intelligent packaging based on immunochromatography was designed for detection of ciprofloxacin residues in different types of poultry meat, including chicken, quail, turkey, ostrich and partridge. This study showed that the sensitivity, specificity, accuracy and precision of this intelligent packaging were 96%, 100%, 100% and 96%, respectively. Also, the minimum diagnostic concentration was 18 μg/kg, and the minimum diagnostic time was 1 min. By the intelligent packaging, anyone can easily detect the presence or absence of antibiotics at packaging stage.

Bayesian Approach for Multigamma Radionuclide Quantification Applied on Weakly Attenuating Nuclear Waste Drums

Gamma spectrometry is a passive nondestructive assay method used to quantify radionuclides present in nuclear objects. Basic methods using empirical calibration with a standard to quantify the activity of nuclear materials by determining the calibration coefficient are ineffective on nonreproducible nuclear objects such as waste packages. Package specifications such as composition or geometry change from one package to another and exhibit large variability of objects. The current standard quantification process uses numerical modeling of the measured scene with few available data such as geometry or composition, in particular density, material, screen, geometric shape, matrix composition, matrix, and source distribution. Some of them are strongly dependent on package data knowledge and operator backgrounds. The French Atomic Energy Commission (CEA) is developing a methodology to quantify nuclear materials in waste packages and waste drums without operator adjustment and internal package configuration knowledge. This method suggests combining a stochastic approach which uses, among others, surrogate models available to simulate the gamma attenuation behavior, a Bayesian approach considering conditional probability densities and prior information of problem inputs, and Markov Chain Monte Carlo (MCMC) algorithms which solve inverse problems, with gamma ray emission radionuclide spectra, and the outside dimensions of the objects of interest. The methodology has been tested to quantify actinide activity with a low bulk density matrix, weakly attenuating compositions, without information on the distribution of the source in terms of actinide masses and materials composing the drums. Activity uncertainties are taken into account.

Zero touch provisioning compliant with authentications of IEEE PON packages A and B for SDN-enabled broadband access

Passive optical networks (PONs) are widely deployed worldwide as access networks, and various standards have been created to serve the demands of different markets. In recent years, software-defined-network-enabled broadband access (SEBA) has been studied for the realization of flexible and cost-effective PONs, while the zero touch provisioning (ZTP) function of optical line terminals (OLTs) and optical network units (ONUs) is being studied for automatic management. However, although ZTP for ITU-T standards has already been implemented, ZTP for IEEE standards has not been achieved, since the workflow is significantly different for each access standard due to differences in the authentication method. The subdivided package specifications and medium access control (MAC) dress authentication are barriers that hinder achieving ZTP for the IEEE standards. This paper proposes a workflow driver based on a model that implements authentication compliant with IEEE PON packages A and B according to events produced by SEBA components and specification information obtained from OLT profiles. The feature of our proposal is to fabricate an IEEE-compliant driver package that automatically switches the authentication method by acquiring the technology profile of the orchestrator, and as soon as IEEE802.1X authentication or MAC address authentication is completed, the subscriber setting is registered to the SDN controller in order to enable data plane service. We demonstrate the proposed workflow driver on a system consisting of SEBA-focused commercially available OLT/ONU hardware and open source software. The results show that the orchestrator can automatically provision ONUs and that managing various access devices on a common access platform is feasible.

A smart meat packaging to show ciprofloxacin residues based on immunochromatography

The aim of this study was to design a novel smart packaging based on immunochromatography to show ciprofloxacin residues in beef meat. Sensitivity, specificity, accuracy, and precision of this smart packaging were 97%, 100%, 100%, and 97%, respectively. The minimum diagnostic concentration and the minimum diagnostic time were 25 μg/kg and 1 min, respectively. Also, intra- and inter-assays showed all assays were all identical. This means that the smart packaging was a stable and reproducible tool for ciprofloxacin analysis. It is recommended that this type of smart packaging be designed, analyzed, and used to show the residues of common antibiotics in the livestock industry. It is hoped that by obtaining the necessary permits and relevant approvals, this type of packaging can be used for the export and import of various types of meat.

Predicting Silicon Die Breaking Force in Semiconductor Package Assembly through Mechanical Simulation

Die crack is a common problem in the semiconductor industry and being able to predict the breaking force at a given loading condition could help prevent such crack problem. This paper presents the use of mechanical simulation in predicting the force at which the silicon die breaks in semiconductor package assembly process. A computer simulation with finite element analysis (FEA) technique was used. The applied force or displacement in a die bending simulation with 3 mm, 4 mm and 15 mm support span was varied until the resulting maximum principal stress of the die becomes equal to its fracture strength. Results revealed that the breaking force for the 70 µm die with 6 mm width is around 5 N for the 3 mm support span and only around 1 N for the 15 mm support span. With the good agreement between modeling and actual results, the study showed that mechanical simulation is an effective approach in predicting die breaking force and can be used to simulate different mechanical loads in the package assembly where possible die crack could happen and be avoided. This is a fast and cost-effective way of assessing risk of die crack and obtaining package assembly process parameters and specifications that are safe to the silicon die.

Using Genericity and Reflection to Create a Declarative Elaboration Logger for Large Scale Real-time Embedded Ada Systems

Large complex Ada real-time embedded software systems typically contain critical order-dependent unit elaboration sequences executed during system startup. However, software enhancements and maintenance activities can inadvertently alter unit dependencies and produce grammatically legal yet semantically illegal elaboration sequence orders. Location of failure during system boot-up is traditionally difficult to diagnose, as large legacy systems typically do not contain trace logging capabilities in unit elaboration regions. Additionally, the Ada language does not provide constructs for executing non-declarative expressions in package specifications, making unit specification elaboration trace logging impossible. Typical system boot failure diagnosis is a combination of educated guesswork, ad-hoc insertions of trace logging code at suspicious locations, and/or the creation of large quantities of temporary trace logging code, resulting in time-consuming iterations of altered builds, system execution, and subsequent analysis. This paper describes a Generic Reflective Declarative Elaboration Logger (GRDEL) which can be used in non-traditional source code locations anywhere declarations are grammatically legal. The tool provides previously unavailable Ada package Specification elaboration trace logging, formal run-time discovery of arbitrarily deeply nested unit name usage locations, implicit generation of trace information during separate logging instance creations, and facilitation of electronic code augmentation via identically formed logging usage expressions, which can automate a repeatable and deterministic instrumentation of extremely large and complex systems with or without permanent source code modifications.

Automation of Longitudinal Time Series Data Visualization using Plot Specifications obtained from XL file

Longitudinal Time Series data visualization plays important role in all sector of business decision making [9]. With enormous amount of complex data [11] from cloud and business requirement, number of graphs needed for decision making increased many folds. Generating enormous number of plots manually with more human input is tedious, time consuming and error prone. To avoid these issues, suitable visualization techniques with solid design principles become very important. We conceptualized and designed a novel method for automation of these processes. R-GGPLOT2[7] package and XL specifications file were primarily used to achieve this goal. We here show as how we can create multiple plots from time series data, plots specifications-XL file and R package GGPLOT2[7] in a single run. Since all required information are entered in XL sheet, R function can be run with no modification. Multiple plots can be generated by using enormous data available in production and service sectors such as finance, healthcare, transportation and food industries etc.

The Catalogue of Life Data Package - A new format for exchanging nomenclatural and taxonomic information

The Catalogue of Life Data Package (COLDP) format was developed to overcome limitations existing in currently used formats for sharing taxonomic information, namely Darwin Core Archives (DwC-A) and the Catalogue of Life (CoL) submission format also known as the Annual Checklist Exchange Format (ACEF). The tabular text based format, strongly influenced by DwC-A and ACEF, was designed to work with the Frictionless Data Package specification, but includes support for other well established formats like BibTeX and CSL-JSON for literature citations. It is the recommended exchange format for data published to, and downloaded from, the CoL Clearinghouse.

A Multipollutant Smoke Emissions Sensing and Sampling Instrument Package for Unmanned Aircraft Systems: Development and Testing

Poor air quality arising from prescribed and wildfire smoke emissions poses threats to human health and therefore must be taken into account for the planning and implementation of prescribed burns for reducing contemporary fuel loading and other management goals. To better understand how smoke properties vary as a function of fuel beds and environmental conditions, we developed and tested a compact portable instrument package that integrates direct air sampling with air quality and meteorology sensing, suitable for in situ data collection within burn units and as a payload on multi-rotor small unmanned aircraft systems (sUASs). Co-located sensors collect carbon dioxide, carbon monoxide, and particulate matter data at a sampling rate of ~0.5 Hz with a microcontroller-based system that includes independent data logging, power systems, radio telemetry, and global positioning system data. Sensor data facilitates precise remote canister collection of air samples suitable for laboratory analysis of volatile organic compounds (VOCs) and other major and trace gases. Instrument package specifications are compatible with common protocols for ground-based and airborne measurements. We present and discuss design specifications for the system and preliminary data collected in controlled burns at Tall Timbers Research Station, FL, USA and Sycan Marsh Preserve, OR, USA.

RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy.

Viruses, entities composed of nucleic acids, proteins, and in some cases lipids lack the ability to replicate outside their target cells. Their components self-assemble at the nanoscale with exquisite precision-a key to their biological success in infection. Recent advances in structure determination and the development of biophysical tools such as single-molecule spectroscopy and noncovalent mass spectrometry allow unprecedented access to the detailed assembly mechanisms of simple virions. Coupling these techniques with mathematical modeling and bioinformatics has uncovered a previously unsuspected role for genomic RNA in regulating formation of viral capsids, revealing multiple, dispersed RNA sequence/structure motifs [packaging signals (PSs)] that bind cognate coat proteins cooperatively. The PS ensemble controls assembly efficiency and accounts for the packaging specificity seen in vivo. The precise modes of action of the PSs vary between viral families, but this common principle applies across many viral families, including major human pathogens. These insights open up the opportunity to block or repurpose PS function in assembly for both novel antiviral therapy and gene/drug/vaccine applications.

Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story.

The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle.

Encapsidation of viral RNA in Picornavirales: studies on cowpea mosaic virus demonstrate dependence on viral replication

To elucidate linkage between replication and encapsidation in Picornavirales, we have taken advantage of the bipartite nature of the plant-infecting member of the order, cowpea mosaic virus (CPMV), to decouple the two processes. RNA-free virus-like particles (eVLPs) can be generated by transiently co-expressing the RNA-2-encoded coat protein precursor (VP60) with the RNA-1-encoded 24K protease, in the absence of the replication machinery (Saunders et al., 2009). We have made use of the ability to produce assembled capsids of CPMV in the absence of replication to examine the putative linkage between RNA replication and packaging in the Picornavirales. We show here that the remarkable specificity of packaging observed in CPMV is due to a functional linking between the two processes of viral replication and encapsidation. We have created a series of mutant RNA-1 and RNA-2 molecules and have assessed the effect of the mutations on both the replication and packaging of the viral RNAs. We demonstrate that mutations that affect replication have a concomitant impact on encapsidation, and that RNA-1-mediated replication is required for encapsidation of both RNA-1 and RNA-2. This close coupling between replication and encapsidation provides a means for the specific packaging of viral RNAs. Moreover, we demonstrate that this feature of CPMV can be used to specifically encapsidate custom RNA by placing a sequence of choice between the RNA-2 sequences required for replication, which opens the door to novel research and therapeutic applications in the field of custom RNA packaging and delivery technologies.