Heat and water transport in soils and across the soil-atmosphere interface: 2. Numerical analysis

In an accompanying paper, we presented an overview of a wide variety of modeling concepts, varying in complexity, used to describe evaporation from soil. Using theoretical analyses, we explained the simplifications and parameterizations in the different approaches. In this paper, we numerically evaluate the consequences of these simplifications and parameterizations. Two sets of simulations were performed. The first set investigates lateral variations in vertical fluxes, which emerge from both homogeneous and heterogeneous porous media, and their importance to capturing evaporation behavior. When evaporation decreases from parts of the heterogeneous soil surface, lateral flow and transport processes in the free flow and in the porous medium generate feedbacks that enhance evaporation from wet surface areas. In the second set of simulations, we assume that the vertical fluxes do not vary considerably in the simulation domain and represent the system using one-dimensional models which also consider dynamic forcing of the evaporation process, for example, due to diurnal variations in net radiation. Simulated evaporation fluxes subjected to dynamic forcing differed considerably between model concepts depending on how vapor transport in the air phase and the interaction at the interface between the free flow and porous medium were represented or parameterized. However, simulated cumulative evaporation losses from initially wet soil profiles were very similar between model concepts and mainly controlled by the desorptivity, Sevap, of the porous medium, which depends mainly on the liquid flow properties of the porous medium

Developing Global Sociotechnical Competency Through Humanitarian Engineering: A Comparison of In-Person and Virtual International Project Experiences

In response to the COVID-19 pandemic, a group of engineering educators in the United States and Colombia designed and led a two-week virtual “field session” for engineering undergraduate students that aimed at achieving the same educational outcomes as those from the previous in-country field session. Our NSF PIRE funded Responsible Mining, Resilient Communities (RMRC) project uses multi-country, interinstitutional, and interdisciplinary collaboration to train U.S. engineering students to co-design socially responsible and sustainable artisanal and small-scale gold mining (ASGM) systems with mining communities and engineers in Latin America. Drawing from pre- and post-field session student interviews, essays, and survey responses, this article analyzes how the virtual 2020 field session and the in-person 2019 session influenced students’ global sociotechnical competency. We offer a conceptualization of global sociotechnical competency that synthesizes notions of global engineering competency with theories of socially responsible engineering that emphasize problem definition and solution with underserved communities. Our research suggests that whereas many educators raised concerns about the efficacy of virtual formats for student learning and professional development, the 2020 session was effective for enhancing students’ abilities to identify stakeholders and methods to engage them, as well as for using sociotechnical coordination while engaging in problem definition. While the small number of student participants cautions against making broad generalizations, the virtual (2020) and in-person (2019) students experienced similar increases in self-reported empathizing practices with the intended users of their designs; a desire and ability to integrate social concerns into their design; a desire and ability to work with people from different backgrounds; and self-efficacy in engineering. The virtual students were less likely, however, than their in-person counterparts to desire a humanitarian engineering career. While the small number of students raises questions for extrapolating the results of our findings, our research does signal fruitful areas of future research for making humanitarian engineering projects more equitable and effective, even in virtual settings

Dendritic cell vaccination as postremission treatment to prevent or delay relapse in acute myeloid leukemia

Relapse is a major problem in acute myeloid leukemia (AML) and adversely impacts survival. In this phase II study, we investigated the effect of vaccination with dendritic cells (DCs) electroporated with Wilms’ tumor 1 (WT1) mRNA as post-remission treatment in 30 AML patients at very high risk of relapse. There was a demonstrable anti-leukemic response in 13 patients. Nine patients achieved molecular remission as demonstrated by normalization of WT1 transcript levels, 5 of which are sustained after a median follow-up of 109.4 months. Disease stabilization was achieved in 4 other patients. Five-year overall survival (OS) was higher in responders than in non-responders (53.8% vs. 25.0%; P=0.01). In patients receiving DCs in first complete remission (CR1), there was a vaccine-induced relapse reduction rate of 25% and the 5-year relapse-free survival was higher in responders than in non-responders (50% vs. 7.7%; P65 years who received DCs in CR1, 5-year OS was 69.2% and 30.8% respectively, as compared to 51.7% and 18% in the Swedish Acute Leukemia Registry (SALR). Long-term clinical response was correlated with increased circulating frequencies of poly-epitope WT1-specific CD8+ T-cells. Long-term OS was correlated with interferon-γ+ and tumor necrosis factor-α+ WT1-specific responses in delayed type hypersensitivity-infiltrating CD8+ T-lymphocytes. In conclusion, vaccination of AML patients with WT1 mRNA-electroporated DCs can be an effective strategy to prevent or delay relapse after standard chemotherapy, translating into improved OS rates, which are correlated with the induction of WT1-specific CD8+ T-cell response. This trial was registered at www.clinicaltrials.gov as #NCT00965224

A de novo paradigm for male infertility

De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF < 0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes (p -value = 1.00 × 10 −5) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes (p -value = 5.01 × 10 −4) in contrast to predicted benign de novo mutations. One gene we identify, RBM5, is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men (p -value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility. Germline de novo mutations can impact individual fitness, but their role in human male infertility is understudied. Trio-based exome sequencing identifies many new candidate genes affecting male fertility, including an essential regulator of male germ cell pre-mRNA splicing

Similar Gene Estimates from Circular and Linear Standards in Quantitative PCR Analyses Using the Prokaryotic 16S rRNA Gene as a Model

Conceived and designed the experiments: ALO KED. Performed the experiments: ALO. Analyzed the data: ALO. Contributed reagents/materials/analysis tools: KED. Wrote the paper: ALO KED. Revised and approved final version of paper: ALO KED.Quantitative PCR (qPCR) is one of the most widely used tools for quantifying absolute numbers of microbial gene copies in test samples. A recent publication showed that circular plasmid DNA standards grossly overestimated numbers of a target gene by as much as 8-fold in a eukaryotic system using quantitative PCR (qPCR) analysis. Overestimation of microbial numbers is a serious concern in industrial settings where qPCR estimates form the basis for quality control or mitigation decisions. Unlike eukaryotes, bacteria and archaea most commonly have circular genomes and plasmids and therefore may not be subject to the same levels of overestimation. Therefore, the feasibility of using circular DNA plasmids as standards for 16S rRNA gene estimates was assayed using these two prokaryotic systems, with the practical advantage being rapid standard preparation for ongoing qPCR analyses. Full-length 16S rRNA gene sequences from Thermovirga lienii and Archaeoglobus fulgidus were cloned and used to generate standards for bacterial and archaeal qPCR reactions, respectively. Estimates of 16S rRNA gene copies were made based on circular and linearized DNA conformations using two genomes from each domain: Desulfovibrio vulgaris, Pseudomonas aeruginosa, Archaeoglobus fulgidus, and Methanocaldocococcus jannaschii. The ratio of estimated to predicted 16S rRNA gene copies ranged from 0.5 to 2.2-fold in bacterial systems and 0.5 to 1.0-fold in archaeal systems, demonstrating that circular plasmid standards did not lead to the gross over-estimates previously reported for eukaryotic systems.Yeshttp://www.plosone.org/static/editorial#pee