Modelling the impacts of climate change on the sustainability of rainfed and irrigated maize in Pakistan

Maize is a globally significant food crop but its future sustainability under rainfed conditions is at risk due to climate change and increased climate uncertainty. In Pakistan most maize is rainfed but there is increasing interest in the role of supplemental irrigation to reduce the vulnerability of crop yields to future drought and climate risks. Using a crop model (DSSAT CERES-Maize) with downscaled data from a weather generator (LARS-WG) and for five selected GCMs, two RCPs (4.5 and 8.5) and two time slices (2050s and 2080s), this study assessed the impacts of climate change and climate variability on rainfed maize grown in the Pothwar region of Pakistan, and the extent to which irrigation could offset future yield reductions. Model simulations were calibrated and validated using experimental data from 2021 and 2022. The outputs showed that on average the yield of maize could be increased by 55% with a single irrigation of 60 mm during the reproductive stage. For the baseline (1991–2020) the average rainfed yield was 3370 kg/ha. The climate change scenarios for the 2050s indicated a −13.5% and −5.8% decline in rainfed yield under RCP4.5 and RCP8.5, respectively. Irrigation applications (between 162 mm and 180 mm) increased grain yields by 5615 kg/ha and 5732 kg/ha, respectively. For the 2080s scenarios there was a projected decrease in yield by -9.3% and -39.7% under RCP4.5 and RCP8.5, respectively. Modelling also confirmed significant reductions in maize biomass production which would negatively impact on feedstocks for both livestock and renewable energy generation.Commonwealth Scholarship Commission in the U

An image-processing methodology for extracting bloodstain pattern features

There is a growing trend in forensic science to develop methods to make forensic pattern comparison tasks more objective. This has generally involved the application of suitable image-processing methods to provide numerical data for identification or comparison. This paper outlines a unique image-processing methodology that can be utilised by analysts to generate reliable pattern data that will assist them in forming objective conclusions about a pattern. A range of features were defined and extracted from a laboratory-generated impact spatter pattern. These features were based in part on bloodstain properties commonly used in the analysis of spatter bloodstain patterns. The values of these features were consistent with properties reported qualitatively for such patterns. The image-processing method developed shows considerable promise as a way to establish measurable discriminating pattern criteria that are lacking in current bloodstain pattern taxonomies

Massively parallel sequencing of short tandem repeats—Population data and mixture analysis results for the PowerSeq™ system

AbstractCurrent forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts

The DNAxs software suite: A three-year retrospective study on the development, architecture, testing and implementation in forensic casework

In forensic DNA casework software tools aid in the data management and efficient, with low risk for error, interpretation and comparison of DNA profiling data. The need for such software has grown with increased numbers of genetic markers, more sensitive analysis methods and growing numbers of crime scene samples send for DNA analysis. To that end, the DNA eXpert System, DNAxs, was developed. This study describes how the expert system was realized and how it evolved during the first three years after the initial implementation. Insight is given in the software architecture, its modular design enabling to communicate with various software systems and how this system was implemented in a casework setting. The importance of quality aspects are highlighted, such as (automated) software testing at various levels. The code coverage is presented as well as the numbers of software bugs that were discovered. These bugs were more severe in earlier software versions than in the more recent versions and did not affect the interpretation of DNA results. The usefulness of the overall software suite and automated steps in DNA profile interpretation were evaluated based on its usage in forensic DNA casework during the first three years after its implementation at the developing laboratory. Because of automated profile comparisons, cases with larger numbers of profiles can be handled, are less prone to error and are extremely less time consuming. The implementation of an integrated quantitative probabilistic genotyping module into DNAxs enabled a more efficient workflow as no longer data files have to be exported and imported into different software. Extensive automated software tests and an audit trail serve as quality aspects for the usage of DNAxs. In times of the pandemic this software was found even more valuable than ever thought as it enabled working from home and it proved robust when used with many simultaneous users. The DNAxs software is regarded future proof and many new features and applications are envisioned

Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations

We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium. FST between both populations was 0.0178 for autosomal SNPs, 0.0146 for autosomal STRs, 0.0101 for X-STRs and 0.1866 for Y-STRs. Combined a priori statistics showed quite large; for instance, pooling all the autosomal loci, the a priori probabilities of discriminating a suspect become 1 − (2.3 × 10−70) and 1 − (5.9 × 10−73), for Roma and Catalans respectively, and the chances of excluding a false father in a trio are 1 − (2.6 × 10−20) and 1 − (2.0 × 10−21).Funding was provided by the Spanish Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), and by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866

Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations

We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium. FST between both populations was 0.0178 for autosomal SNPs, 0.0146 for autosomal STRs, 0.0101 for X-STRs and 0.1866 for Y-STRs. Combined a priori statistics showed quite large; for instance, pooling all the autosomal loci, the a priori probabilities of discriminating a suspect become 1 − (2.3 × 10−70) and 1 − (5.9 × 10−73), for Roma and Catalans respectively, and the chances of excluding a false father in a trio are 1 − (2.6 × 10−20) and 1 − (2.0 × 10−21).Funding was provided by the Spanish Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), and by Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014 SGR 866

Multi-laboratory validation of DNAxs including the statistical library DNAStatistX

This study describes a multi-laboratory validation of DNAxs, a DNA eXpert System for the data management and probabilistic interpretation of DNA profiles D. and its statistical library DNAStatistX to which, besides the organising laboratory, four laboratories participated. The software was modified to read multiple data formats and the study was performed prior to the release of the software to the forensic community. The first exercise explored all main functionalities of DNAxs with feedback on user-friendliness, installation and general performance. Next, every laboratory performed likelihood ratio (LR) calculations using their own dataset and a dataset provided by the organising laboratory. The organising laboratory performed LR calculations using all datasets. The datasets were generated with different STR typing kits or analysis systems and consisted of samples varying in DNA amounts, mixture ratios, number of contributors and drop-out level. Hypothesis sets had the correct, under- and over-assigned number of contributors and true and false donors as person of interest. When comparing the results between laboratories, the LRs were foremost within one unit on log10 scale. The few LR results that deviated more had differences for the parameters estimated by the optimizer within DNAStatistX. Some of these were indicated by failed iteration results, others by a failed model validation, since unrealistic hypotheses were included. When these results that do not meet the quality criteria were excluded, as is in accordance with interpretation guidelines, none of the analyses in the different laboratories yielded a different statement in the casework report. Nonetheless, changes in software parameters were sought that minimized differences in outcomes, which made the DNAStatistX module more robust. Overall, the software was found intuitive, user-friendly and valid for use in multiple laboratories

Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on short tandem repeat sequence nomenclature

Funding Information: The authors are grateful to Peter de Knijff and Sascha Willuweit for their early contributions to this DNA Commission. Additionally, Peter M. Schneider served on this DNA Commission until his passing in 2022, and we honor his contribution with posthumous authorship. NIST: This DNA Commission of the ISFG has sole responsibility for the contents of this report and the questions, findings, and recommendations within. The views expressed in this report do not necessarily represent the views of the U.S. Department of Commerce or the National Institute of Standards and Technology. Certain commercial entities are identified in order to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that any of the entities identified are necessarily the best available for the purpose. FBI: This DNA Commission of the ISFG has sole responsibility for the contents of this report and the questions, findings, and recommendations within. Names of commercial manufacturers are provided for identification purposes only, and inclusion does not imply endorsement of the manufacturer, or its products or services by the FBI. The views expressed are those of the author(s) and do not necessarily reflect the official policy or position of the FBI or the U.S. Government. Publisher Copyright: © 2023The DNA Commission of the International Society for Forensic Genetics (ISFG) has developed a set of nomenclature recommendations for short tandem repeat (STR) sequences. These recommendations follow the 2016 considerations of the DNA Commission of the ISFG, incorporating the knowledge gained through research and population studies in the intervening years. While maintaining a focus on backward compatibility with the CE data that currently populate national DNA databases, this report also looks to the future with the establishment of recommended minimum sequence reporting ranges to facilitate interlaboratory comparisons, automated solutions for sequence-based allele designations, a suite of resources to support bioinformatic development, guidance for characterizing new STR loci, and considerations for incorporating STR sequences and other new markers into investigative databases.Peer reviewe

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise

Molecular Technology and Informatics for Personalised Medicine and Healt