solveME: fast and reliable solution of nonlinear ME models.

BackgroundGenome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints.ResultsHere, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints.ConclusionsJust as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields

Working Beyond 80: The Meaning of Work to An Octogenarian in The Workforce

There is an increasing share of people aged 50 years and over in the labor market structure and the rapid aging of the global workforce that supports the latter claim but with a little tank of information on qualitative research describing the experiences of a working octogenarian. An octogenarian is a person who is between 80 and 89 years old. This study aimed to investigate the experiences of a working octogenarian in her fieldwork through a qualitative case study analysis. From the interview, the following three themes were revealed: (a) Work as a legacy, (b) Work as an advocacy, and (c) Work as an opportunity. In the first theme, the participant described that she had a laden path and a mission. These had been sustained along with the desire to serve and make a difference. In work as advocacy, she presented the vision to make the lives of the elderly better by making the environment compatible with her aspiration extending beyond the confines of her organization. Considering every work that she took part in as an opportunity to explore and further her vision was the very core of the theme “work as an opportunity.” Working beyond 80 years old becomes possible when one dedicates the undertakings in the fulfillment of the individual’s vision and mission.   Abstrak Bekerja di Atas Usia 80: Sebuah Studi Kasus Kualitatif tentang Arti Bekerja bagi Seorang Tenaga Kerja Octogenarian. Terdapat peningkatan jumlah orang yang berusia 50 tahun ke atas dalam struktur pasar tenaga kerja dan penuaan dini dari tenaga kerja global yang mendukung klaim terakhir, namun masih sedikit informasi tentang penelitian kualitatif yang menggambarkan pengalaman seorang oktogenarian yang bekerja. Seorang octogenarian adalah orang yang berusia antara 80 dan 89 tahun. Penelitian ini bertujuan untuk menyelidiki pengalaman seorang oktogenarian yang bekerja pada lapangan kerjanya melalui analisis studi kasus kualitatif. Berdasarkan wawancara, tiga tema berikut terungkap: (a) Bekerja sebagai warisan, (b) Bekerja sebagai advokasi, dan (c) Bekerja sebagai peluang. Pada tema pertama, peserta menggambarkan bahwa dia memiliki jalan yang sarat dan misi. Hal ini telah dipertahankan dengan keinginan untuk melayani dan membuat perbedaan. Pada tema bekerja sebagai advokasi, ia mempresentasikan visi untuk membuat kehidupan lansia menjadi lebih baik dengan membuat lingkungan yang sesuai dengan aspirasinya melampaui batas organisasinya. Mempertimbangkan setiap pekerjaan yang ia ambil sebagai kesempatan untuk mengeksplorasi dan memajukan visinya adalah inti dari tema “bekerja sebagai sebuah peluang.” Bekerja lebih dari 80 tahun sangat mungkin ketika seseorang mendedikasikan upaya dalam pencapaian visi dan misi individu. Kata kunci: aging, gerontologi, octogenarian, pekerja, tenaga kerj

Working Beyond 80: The Meaning of Work to An Octogenarian in The Workforce

There is an increasing share of people aged 50 years and over in the labor market structure and the rapid aging of the global workforce that supports the latter claim but with a little tank of information on qualitative research describing the experiences of a working octogenarian. An octogenarian is a person who is between 80 and 89 years old. This study aimed to investigate the experiences of a working octogenarian in her fieldwork through a qualitative case study analysis. From the interview, the following three themes were revealed: (a) Work as a legacy, (b) Work as an advocacy, and (c) Work as an opportunity. In the first theme, the participant described that she had a laden path and a mission. These had been sustained along with the desire to serve and make a difference. In work as advocacy, she presented the vision to make the lives of the elderly better by making the environment compatible with her aspiration extending beyond the confines of her organization. Considering every work that she took part in as an opportunity to explore and further her vision was the very core of the theme “work as an opportunity.” Working beyond 80 years old becomes possible when one dedicates the undertakings in the fulfillment of the individual’s vision and mission. Abstrak Bekerja di Atas Usia 80: Sebuah Studi Kasus Kualitatif tentang Arti Bekerja bagi Seorang Tenaga Kerja Octogenarian. Terdapat peningkatan jumlah orang yang berusia 50 tahun ke atas dalam struktur pasar tenaga kerja dan penuaan dini dari tenaga kerja global yang mendukung klaim terakhir, namun masih sedikit informasi tentang penelitian kualitatif yang menggambarkan pengalaman seorang oktogenarian yang bekerja. Seorang octogenarian adalah orang yang berusia antara 80 dan 89 tahun. Penelitian ini bertujuan untuk menyelidiki pengalaman seorang oktogenarian yang bekerja pada lapangan kerjanya melalui analisis studi kasus kualitatif. Berdasarkan wawancara, tiga tema berikut terungkap: (a) Bekerja sebagai warisan, (b) Bekerja sebagai advokasi, dan (c) Bekerja sebagai peluang. Pada tema pertama, peserta menggambarkan bahwa dia memiliki jalan yang sarat dan misi. Hal ini telah dipertahankan dengan keinginan untuk melayani dan membuat perbedaan. Pada tema bekerja sebagai advokasi, ia mempresentasikan visi untuk membuat kehidupan lansia menjadi lebih baik dengan membuat lingkungan yang sesuai dengan aspirasinya melampaui batas organisasinya. Mempertimbangkan setiap pekerjaan yang ia ambil sebagai kesempatan untuk mengeksplorasi dan memajukan visinya adalah inti dari tema “bekerja sebagai sebuah peluang.” Bekerja lebih dari 80 tahun sangat mungkin ketika seseorang mendedikasikan upaya dalam pencapaian visi dan misi individu. Kata Kunci: aging, gerontologi, octogenarian, pekerja, tenaga kerj

Use of probabilistic phrases in a coordination game: human versus GPT-4

English speakers use probabilistic phrases such as likely to communicate information about the probability or likelihood of events. Communication is successful to the extent that the listener grasps what the speaker means to convey and, if communication is successful, individuals can potentially coordinate their actions based on shared knowledge about uncertainty. We first assessed human ability to estimate the probability and the ambiguity (imprecision) of twenty-three probabilistic phrases in a coordination game in two different contexts, investment advice and medical advice. We then had GPT4 (OpenAI), a Large Language Model, complete the same tasks as the human participants. We found that the median human participant and GPT4 assigned probability estimates that were in good agreement (proportions of variance accounted for close to .90). GPT4's estimates of probability both in the investment and Medical contexts were as close or closer to that of the human participants as the human participants' estimates were to one another. Estimates of probability for both the human participants and GPT4 were little affected by context. In contrast, human and GPT4 estimates of ambiguity were not in such good agreement.Comment: Corrected typos, extended discussion, added reference

Plasmodium falciparum parasite population structure and gene flow associated to anti-malarial drugs resistance in Cambodia

Background: Western Cambodia is recognized as the epicentre of emergence of Plasmodium falciparum multi-drug resistance. The emergence of artemisinin resistance has been observed in this area since 2008–2009 and molecular signatures associated to artemisinin resistance have been characterized in k13 gene. At present, one of the major threats faced, is the possible spread of Asian artemisinin resistant parasites over the world threatening millions of people and jeopardizing malaria elimination programme efforts. To anticipate the diffusion of artemisinin resistance, the identification of the P. falciparum population structure and the gene flow among the parasite population in Cambodia are essential. Methods: To this end, a mid-throughput PCR-LDR-FMA approach based on LUMINEX technology was developed to screen for genetic barcode in 533 blood samples collected in 2010–2011 from 16 health centres in malaria endemics areas in Cambodia. Results: Based on successful typing of 282 samples, subpopulations were characterized along the borders of the country. Each 11-loci barcode provides evidence supporting allele distribution gradient related to subpopulations and gene flow. The 11-loci barcode successfully identifies recently emerging parasite subpopulations in western Cambodia that are associated with the C580Y dominant allele for artemisinin resistance in k13 gene. A subpopulation was identified in northern Cambodia that was associated to artemisinin (R539T resistant allele of k13 gene) and mefloquine resistance. Conclusions: The gene flow between these subpopulations might have driven the spread of artemisinin resistance over Cambodia

Wolbachia and DNA barcoding insects: patterns, potential and problems

Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region