Suite Of Programs Research Articles

Sustainable multi-disciplinary mathematics support

Sound mathematical knowledge is an essential ingredient for student success in many disciplines, and quality mathematics support is crucial to that success. How that support is delivered is often the key to student engagement, satisfaction and positive outcomes. Many students require sound mathematical knowledge to engage in their discipline activities. Since lack of mathematical skill is a barrier to student retention, progression and self-efficacy, the onus is on the university to provide quality support. This paper describes the expansion of a cross-disciplinary model of mathematics support that has grown to include a suite of programmes that accommodate diverse needs. A previous study evaluated the model’s delivery in 2010–2012 for Chemistry, Physics, Biology and Statistics. Since then, not only have these programmes continued to run and expand, new ones have been implemented for further disciplines. After 17 bi-annual iterations, it is timely to investigate the extension of the original model and evaluate whether it continues to address the original objectives. Our findings reveal a high proportion of students who engage in a Maths Skills programme report increased mathematics confidence and skill, and subject pass rates of those who engage are almost always higher than the pass rates of those who do not.

INPEX-led Ichthys Joint Venture – proudly partnering with Indigenous Groups in the Northern Territory

The INPEX-led Ichthys Joint Venture has established strong partnerships with the Northern Territory Government (NTG), cultural organisations and Traditional Owner groups in the Northern Territory to deliver social and environmental offset programs. The key governance model for delivery of the offset programs is the Ichthys Project Voluntary Offset Agreement (IPVOA), which commits $91 M AUD over a 40-year period through a suite of offset programs. This paper focuses on the journey to partner with the NTG-run Aboriginal Ranger Grants Program (ARGP). Through the IPVOA, INPEX and its Ichthys Joint Venture participants will contribute $24 M AUD over 22 years, to the ARGP, for Aboriginal Ranger programs addressing specific species and their associated habitat throughout the Top End. This is the first time where industry has contributed to the ARGP to deliver positive outcomes in the NT. This has been achieved by fostering collaborative, engaging and trustworthy relationships with the Commonwealth and NT governments; engaging with the Aboriginal Land Management Advisory Group; and meeting with Aboriginal Ranger groups. The key has been finding a common ground between the perspectives and the priorities of all stakeholders for how best to deliver conservation management on country in the NT. This common ground is likely to evolve over the next 22 years as the INPEX-led Ichthys Joint Venture and NTG deliver environmental outcomes, promote a connection to country and empower Aboriginal Ranger groups to better manage their country for future generations.

A Method to Estimate the Distribution of Proteins across Multiple Compartments Using Data from Quantitative Proteomics Subcellular Fractionation Experiments.

Knowledge of cellular location is key to understanding the biological function of proteins. One commonly used large-scale method to assign cellular locations is subcellular fractionation, followed by quantitative mass spectrometry to identify proteins and estimate their relative distribution among centrifugation fractions. In most of such subcellular proteomics studies, each protein is assigned to a single cellular location by comparing its distribution to those of a set of single-compartment reference proteins. However, in many cases, proteins reside in multiple compartments. To accurately determine the localization of such proteins, we previously introduced constrained proportional assignment (CPA), a method that assigns each protein a fractional residence over all reference compartments (Jadot Mol. Cell Proteomics 2017, 16(2), 194-212. 10.1074/mcp.M116.064527). In this Article, we describe the principles underlying CPA, as well as data transformations to improve accuracy of assignment of proteins and protein isoforms, and a suite of R-based programs to implement CPA and related procedures for analysis of subcellular proteomics data. We include a demonstration data set that used isobaric-labeling mass spectrometry to analyze rat liver fractions. In addition, we describe how these programs can be readily modified by users to accommodate a wide variety of experimental designs and methods for protein quantitation.

Parameterization and Application of the General Amber Force Field to Model Fluoro Substituted Furanose Moieties and Nucleosides.

Molecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments.

Lessons learnt applying a systemic functional model to teaching and learning in school contexts over the last thirty years

AbstractIn this paper we look back at our work over the last thirty years as education consultants in a range of educational contexts in which we sought to promote an explicit, language-based approach to teaching and learning. We trace our pathway from the earliest days of meeting systemic functional theory and its potential application in education to recent times where we now are able to offer a suite of professional development programmes designed to build the capacity of teachers and students to understand how language works to make meaning. We reflect on the many challenges of re-contextualising such an elaborate model of language in educational contexts: challenges that embrace the pedagogical, the political and the logistical among others. The intent is to highlight the affordances we have seen while working closely with teachers over the years in the hope that others will be inspired to continue the work.

Geo‐eco‐hydrology of the Upper Yellow River

AbstractA climate‐induced vegetation gradient induces marked variability in the character and behavior of anabranching reaches of the Upper Yellow River. Analysis of satellite imagery and field appraisal of biogeomorphic attributes shows that these reaches retain a good condition in geo‐eco‐hydrological terms. Degradational trends experienced in the late 20th century have been transformed into recovery pathways in recent decades. Changing land use practices, especially reduced stocking rates, and creation of various reserves have engendered environmental improvement. Recent climate change has supported improvements in geo‐eco‐hydrological conditions in the study reaches. A comprehensive suite of environmental protection programs of unprecedented scope and scale enhances the buffering capacity of landscapes and ecosystems in this region, supporting their ability to adapt to increasingly uncertain environmental futures.

Genome-wide association analysis for susceptibility to infection by Mycobacterium avium ssp. paratuberculosis in US Holsteins

Paratuberculosis, or Johne's disease, is a chronic, granulomatous, gastrointestinal tract disease of cattle and other ruminants caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Control of Johne's disease is based on programs of testing and culling animals positive for infection with MAP and concurrently modifying management to reduce the likelihood of infection. The current study was motivated by the hypothesis that genetic variation in host susceptibility to MAP infection can be dissected and quantifiable associations with genetic markers identified. Two separate GWAS analyses were conducted, the first using 897 genotyped Holstein artificial insemination sires with phenotypes derived from incidence of MAP infection among daughters based on milk ELISA testing records. The second GWAS analysis was a case-control design using US Holstein cows phenotyped for MAP infection by serum ELISA or fecal culture tests. Cases included cows positive for either serum ELISA, fecal culture, or both. Controls consisted of animals negative for all tests conducted. A total of 376 samples (70 cases and 306 controls) from a University of Minnesota Johne's management demonstration project and 184 samples (76 cases and 108 controls) from a Michigan State University study were used. Medium-density (sires) and high-density (cows) genotype data were imputed to full genome sequence for the analyses. Marker-trait associations were analyzed using the single-step (ss)GWAS procedure implemented in the BLUPF90 suite of programs. Evidence of significant genomic contributions for susceptibility to MAP infection were observed on multiple chromosomes. Results were combined across studies in a meta-analysis, and increased support for genomic regions on BTA7 and BTA21 were observed. Gene set enrichment analysis suggested pathways for antigen processing and presentation, antimicrobial peptides and natural killer cell-mediated cytotoxicity are relevant to variation in host susceptibility to MAP infection, among others. Genomic prediction was evaluated using a 5-fold cross-validation, and moderate correlations were observed between genomic breeding value predictions and daughter averages (∼0.43 to 0.53) for MAP infection in testing data sets. These results suggest that genomic selection against susceptibility to MAP infection is feasible in Holstein cattle.

Support, develop, empower: The co-development of a youth leadership framework

Engaging young people in organisational leadership offers opportunities for them to contribute and make a positive difference to their communities, benefitting both the young people and the organisations with which they are involved. However, best practices for engaging and supporting young leaders in cancer support organisations remain unclear. This article reports on the co-design and implementation of a Youth Leadership Framework within a national not-for-profit youth cancer organisation. Staff and young people worked together to develop a Framework which includes a model of youth leadership, defined roles and pathways, a resource toolkit and a suite of age-appropriate leadership development programs. This Framework better enables the organisation to fulfil its long-held goals of supporting, developing and empowering young leaders. This account of the Framework’s development and the insights gained in the implementation process serves as an exemplar to other community organisations and health services seeking to engage and support young leaders, expanding the evidence base on best practices in youth leadership in the cancer context.

Software update: The ORCA program system—Version 5.0

AbstractVersion 5.0 of the ORCA quantum chemistry program suite was released in July 2021. ORCA 5.0 represents a major improvement over all previous versions of ORCA and features (1) highly improved performance, (2) increased numerical robustness, (3) a host of new functionality, and (4) greatly improved user friendliness. The article describes the most salient features of the program.This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Data Science > Computer Algorithms and Programming Software > Quantum Chemistry

INVESTIGATION ON THE THERMOCHEMISTRY, MOLECULAR SPECTROSCOPY AND STRUCTURAL PARAMETERS OF PYRROLE AND ITS ISOMERS: A QUANTUM CHEMISTRY APPROACH

The isomers of C4H5N consisting of eleven members (2-vinyl-2H-azirene, Isocyanocyclopropane, Ally isocyanide, N-vinylethyleneimine, Cyanocyclopropane, 2H-pyrrole, 3H-pyrrole, Ally cyanide, 2-cyanopropene, 2-butenenitrile, Pyrrole) have been studied computationally using the Gaussian-4 (G4) compound model with the Gaussian 09 suite of programs. Quantum chemical parameters such as standard enthalpy of formation, vibrational frequencies, rotational constants, bond distance and angle, and dipole moment were obtained and compared with experimental values (where available). Pyrrole was predicted to be the most stable among the C4H5N isomers with the least standard enthalpy of formation of 24.1kcal/mol. The calculated bond distances and angles for pyrrole were observed to be in excellent agreement with the measured experimental values. Also, the calculated rotational constants (A= 9.1392127, B=9.0066121, C=4.5362140) and dipole moment (1.8628D) for pyrrole were accurately predicted when compared to the experimentally determined values. Thus, the high accuracy obtained from this quantum chemical calculation indicates that other isomers of C4H5N with no experimental values are well predicted with the Gaussian-4G4 compound model.

Making evaluation work for the practitioner evaluator: experience from the field of environmental education

Drawing on work from environmental education, evaluation, and practitioner research, this paper presents a discussion of programme evaluation practices from the practitioner’s perspective. This discussion is informed by a meta-evaluation conducted on ten-years (2008–2018) of data collected from a suite of place-based learning programmes delivered by a charity in Ireland. Analysis of the data available allowed for an evaluation of the programmes in question, and these were then further analysed to provide the meta-evaluation. Key findings and discussions from the analysis include the impact of time constraints on evaluation; evaluation as part of organisational culture; strengths/weaknesses of evaluations led by practitioner evaluators; and opportunities provided by meta-evaluation in directing organisational change. This paper serves as a valuable resource for researchers and practitioners as it provides a framework to support future evaluations led by practitioner evaluators.

Synergistic Experimental and Theoretical Studies of Luminescent-Magnetic Ln2Zn6 Clusters.

The present work is part of our ongoing quest for developing functional inorganic complexes using unorthodox pyridyl-pyrazolyl-based ligands. Accordingly, we report herein the synthesis, characterization, and luminescence and magnetic properties of four 3d-4f mixed-metal complexes with a general core of Ln2Zn6 (Ln = Dy, Gd, Tb, and Eu). In stark contrast to the popular wisdom of using a compartmental ligand with separate islands of hard and soft coordinating sites for selective coordination, we have vindicated our approach of using a ligand with overcrowded N-coordinating sites that show equal efficiency with both 4f and 3d metals toward multinuclear cage-cluster formation. The encouraging red and green photolumiscent features of noncytotoxic Eu2Zn6 and Tb2Zn6 complexes along with their existence in nanoscale dimension have been exploited with live-cell confocal microscopy imaging of human breast adenocarcinoma (MCF7) cells. The magnetic features of the Dy2Zn6 complex confirm the single-molecule-magnet behavior with befitting frequency- and temperature-dependent out-of-phase signals along with an Ueff value of ∼5 K and a relaxation time of 8.52 × 10-6 s. The Gd2Zn6 complex, on the other hand, shows cryogenic magnetic refrigeration with an entropy change of 11.25 J kg-1 K-1 at a magnetic field of 7 T and at 2 K. Another important aspect of this work reflects the excellent agreement between the experimental results and theoretical calculations. The theoretical studies carried out using the broken-symmetry density functional theory, ORCA suite of programs, and MOLCAS calculations using the complete-active-space self-consistent-field method show an excellent synergism with the experimentally measured magnetic and spectroscopic data.

Twist: sound reasoning for purity and entanglement in Quantum programs

Quantum programming languages enable developers to implement algorithms for quantum computers that promise computational breakthroughs in classically intractable tasks. Programming quantum computers requires awareness of entanglement , the phenomenon in which measurement outcomes of qubits are correlated. Entanglement can determine the correctness of algorithms and suitability of programming patterns. In this work, we formalize purity as a central tool for automating reasoning about entanglement in quantum programs. A pure expression is one whose evaluation is unaffected by the measurement outcomes of qubits that it does not own, implying freedom from entanglement with any other expression in the computation. We present Twist, the first language that features a type system for sound reasoning about purity. The type system enables the developer to identify pure expressions using type annotations. Twist also features purity assertion operators that state the absence of entanglement in the output of quantum gates. To soundly check these assertions, Twist uses a combination of static analysis and runtime verification. We evaluate Twist’s type system and analyses on a benchmark suite of quantum programs in simulation, demonstrating that Twist can express quantum algorithms, catch programming errors in them, and support programs that existing languages disallow, while incurring runtime verification overhead of less than 3.5%.

Molecular Modeling and Simulations of DNA and RNA: DNAzyme as a Model System.

Nowadays, the structural dynamics of DNA and RNA is accessible on an atomistic level on a micro- to millisecond time scale via molecular dynamics simulations. However, as DNA or RNA are highly charged molecules, performing such simulations is challenging as to the representation of intramolecular electrostatic interactions and those to solvent molecules and ions. This is particularly true for DNAzymes, where DNA and RNA backbones can come as close as 2.4Å with their charged phosphate groups during the catalytic cycle. Here, we present tools to simulate the structural dynamics of a DNAzyme, with a focus on detailed instructions for the Amber suite of programs. Furthermore, we will show how to analyze metal ion binding within the DNAzyme.

Investigation of induction motor operation from the soft starter in reverse mode with reduced speed

Ease of maintenance and high reliability of asynchronous electric drives actively popularize their using in manufacturing. At the same time, such drive has its drawbacks: high currents and significant torque during direct starting from contactor control systems. This problem can be solved using the so-called "service functions" of soft starters. This work at developing these functions and issuing recommendations for their use is aimed. The purpose of the investigation is to determine the possibility of using the "service functions" of soft starters for emergency and service modes of agricultural plants. The investigation of the operation of an induction motor with a soft starter using the provisions of the theory of electrical circuits of sinusoidal and non-sinusoidal currents and using computer analysis was carried out. Investigation on the mechanism of straw shredders using a soft starter was carried out. Performance increasing of such a mechanism is possible using the "reverse" function with a reduced speed, implemented, for example, in SSW900 soft starters. To configure the soft starter, the WEG programming Suite software was used, which, in addition to the function of writing parameters, also contains the function of reading parameters and visualizing them as trends. As a result of the investigation, it was found that the intelligent control of thyristors in soft starters allows to expand their functionality, namely, to reverse the induction motor without using an additional contactor. The implementation of the reverse speed function with appropriate restrictions in soft starters allows reducing the cost of the used electrical equipment for straw shredders. Too much JOG relative voltage to the soft starter can cause large fluctuations in motor speed and must be carefully adjusted.

OPALE: Operational assessment of landscape water eco-functionalities

The present article proposes a suite of programs aimed at (i) representing landscape organization in relation with the functioning of annual crops or breeding systems, (ii) evaluating water movements from biomass and hydrological exchanges, and (iii) analyzing the transfer dynamics of nutrients, suspended matter or fecal bacteria based on particle tracking methods. Simulations provided indications about the underlying processes that drive exchanges and sink-source effects operating at the landscape scale. OPALE was tested in three agricultural contexts and biophysical situations. Water flows and flows of associated matters were compared to data recorded at the catchment outlet, and showed the efficiency of the algorithms developed in the generic OPALE libraries. This article describes the underlying hypotheses and the full mathematical framework and procedures used to assess landscape eco-functionality. Several examples are given to illustrate the use of OPALE in landscape reconfiguration prospects (e.g. influence of landscape composition and structure on plant transpiration, stream flow, erosion, nutrient and organism fluxes in water) for the agroecological transition.

Types for Tables: A Language Design Benchmark

Context: Tables are ubiquitous formats for data. Therefore, techniques for writing correct programs over tables, and debugging incorrect ones, are vital. Our specific focus in this paper is on rich types that articulate the properties of tabular operations. We wish to study both their expressive power and _diagnostic quality_. Inquiry: There is no "standard library" of table operations. As a result, every paper (and project) is free to use its own (sub)set of operations. This makes artifacts very difficult to compare, and it can be hard to tell whether omitted operations were left out by oversight or because they cannot actually be expressed. Furthermore, virtually no papers discuss the quality of type error feedback. Approach: We combed through several existing languages and libraries to create a "standard library" of table operations. Each entry is accompanied by a detailed specification of its "type," expressed independent of (and hence not constrained by) any type language. We also studied and categorized a corpus of (student) program edits that resulted in table-related errors. We used this to generate a suite of erroneous programs. Finally, we adapted the concept of a datasheet to facilitate comparisons of different implementations. Knowledge: Our benchmark creates a common ground to frame work in this area. Language designers who claim to support typed programming over tables have a clear suite against which to demonstrate their system's expressive power. Our family of errors also gives them a chance to demonstrate the quality of feedback. Researchers who improve one aspect -- especially error reporting -- without changing the other can demonstrate their improvement, as can those who engage in trade-offs between the two. The net result should be much better science in both expressiveness and diagnostics. We also introduce a datasheet format for presenting this knowledge in a methodical way. Grounding: We have generated our benchmark from real languages, libraries, and programs, as well as personal experience conducting and teaching data science. We have drawn on experience in engineering and, more recently, in data science to generate the datasheet. Importance: Claims about type support for tabular programming are hard to evaluate. However, tabular programming is ubiquitous, and the expressive power of type systems keeps growing. Our benchmark and datasheet can help lead to more orderly science. It also benefits programmers trying to choose a language.

THEREDA – Thermodynamic Reference Database

Abstract. Part of the process to ensure the safety of radioactive waste disposal is the predictive modeling of the solubility of all relevant toxic components in a complex aqueous solution. To ensure the reliability of thermodynamic equilibrium modeling as well as to facilitate the comparison of such calculations done by different institutions, it is necessary to create a mutually accepted thermodynamic reference database. To meet this demand several institutions in Germany joined efforts and created THEREDA (Moog et al., 2015). THEREDA is a suite of programs at the base of which resides a relational databank. Special emphasis is put on thermodynamic data along with suitable Pitzer coefficients, which enable the calculation of solubilities in high-saline solutions. Registered users may either download single thermodynamic data or ready-to-use parameter files for the geochemical speciation codes PHREEQC, Geochemist's Workbench, CHEMAPP, or TOUGHREACT. Data can also be downloaded in a generic JSON format to enable the import into other codes. The database can be accessed via the world wide web: http://www.thereda.de (last access: 1 November 2021). Prior to release, the released part of the database is subjected to many tests. Results are compared to results from earlier releases and among the different codes. This is to ensure that by additions of new and modification of existing data no adverse side effects on calculations are caused. Furthermore, our website offers an increasing number of examples for applications, including graphical representation, which can be filtered by components of the calculated system.

Automated high confidence compound identification of electron ionization mass spectra for nontargeted analysis

Nontargeted analysis based on mass spectrometry is a rising practice in environmental monitoring for identifying contaminants of emerging concern. Nontargeted analysis performed using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC/TOF-MS) generates large numbers of possible analytes. Moreover, the default spectral library similarity score-based search algorithm used by LECO® ChromaTOF® does not ensure that high similarity scores result in correct library matches. Therefore, an additional manual screening is necessary, but leads to human errors especially when dealing with large amounts of data. To improve the speed and accuracy of the chemical identification, we developed CINeMA.py (Classification Is Never Manual Again). This programming suite automates GC×GC/TOF-MS data interpretation by determining the confidence of a match between the observed analyte mass spectrum and the LECO® ChromaTOF® software generated library hit from the NIST Electron Ionization Mass Spectral (NIST EI-MS) library. Our script allows the user to evaluate the confidence of the match using an algorithmic method that mimics the manual curation process and two different machine learning approaches (neural networks and random forest). The script allows the user to adjust various parameters (e.g., similarity threshold) and study their effects on prediction accuracy. To test CINeMA.py, we used data from two different environmental contaminant studies: an EPA study on household dust and a study on stormwater runoff. Using a reference set based on the analysis performed by highly trained users of the ChromaTOF and GC×GC/TOF-MS systems, the random forest model had the highest prediction accuracies of 86% and 83% on the EPA and Stormwater data sets, respectively. The algorithmic approach had the second-best prediction accuracy (82% and 79%), while the neural network accuracy had the lowest (63% and 67%). All the approaches required less than 1 min to classify 986 observed analytes, whereas manual data analysis required hours or days to complete. Our methods were also able to detect high confidence matches missed during the manual review. Overall, CINeMA.py provides users with a powerful suite of tools that should significantly speed-up data analysis while reducing the possibilities of manual errors and discrepancies among users, and can be applicable to other GC/EI-MS instrument based nontargeted analysis.

SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications.

We present the SSIPTools suite of programs. SSIPTools is a collection of software modules enabling the use of the Surface Site Interaction Point (SSIP) molecular descriptors, used for the modeling of noncovalent interactions in neutral organic molecules. It contains an implementation of the workflow for the generation of the SSIP descriptors, as well as the Functional Group Interaction Profiles (FGIPs) and Solvent Similarity Indexes (SSIs) applications, based on the SSIMPLE (Surface Site Interaction model for the Properties of Liquids at Equilibria) approach.