Converse extensionality and apartness

In this paper we try to find a computational interpretation for a strong form of extensionality, which we call ``converse extensionality''. These converse extensionality principles, which arise as the Dialectica interpretation of the axiom of extensionality, were first studied by Howard. In order to give a computational interpretation to these principles, we reconsider Brouwer's apartness relation, a strong constructive form of inequality. Formally, we provide a categorical construction to endow every typed combinatory algebra with an apartness relation. We then exploit that functions reflect apartness, in addition to preserving equality, to prove that the resulting categories of assemblies model a converse extensionality principle.Comment: Fixed typos and added an appendix with a proof-theoretic treatment of our result

Competing interactions in semiconductor quantum dots

We introduce an integrability-based method enabling the study of semiconductor quantum dot models incorporating both the full hyperfine interaction as well as a mean-field treatment of dipole-dipole interactions in the nuclear spin bath. By performing free induction decay and spin echo simulations we characterize the combined effect of both types of interactions on the decoherence of the electron spin, for external fields ranging from low to high values. We show that for spin echo simulations the hyperfine interaction is the dominant source of decoherence at short times for low fields, and competes with the dipole-dipole interactions at longer times. On the contrary, at high fields the main source of decay is due to the dipole-dipole interactions. In the latter regime an asymmetry in the echo is observed. Furthermore, the non-decaying fraction previously observed for zero field free induction decay simulations in quantum dots with only hyperfine interactions, is destroyed for longer times by the mean-field treatment of the dipolar interactions.Comment: 10 pages, 5 figures [v2: subsection and references added

Laboratory-evolved Vanillyl-alcohol Oxidase Produces Natural Vanillin

The flavoenzyme vanillyl-alcohol oxidase was subjected to random mutagenesis to generate mutants with enhanced reactivity to creosol (2-methoxy-4-methylphenol). The vanillyl-alcohol oxidase-mediated conversion of creosol proceeds via a two-step process in which the initially formed vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) is oxidized to the widely used flavor compound vanillin (4-hydroxy-3-methoxybenzaldehyde). The first step of this reaction is extremely slow due to the formation of a covalent FAD N-5-creosol adduct. After a single round of error-prone PCR, seven mutants were generated with increased reactivity to creosol. The single-point mutants I238T, F454Y, E502G, and T505S showed an up to 40-fold increase in catalytic efficiency (k(cat)/K-m) with creosol compared with the wild-type enzyme. This enhanced reactivity was due to a lower stability of the covalent flavin-substrate adduct, thereby promoting vanillin formation. The catalytic efficiencies of the mutants were also enhanced for other ortho-substituted 4-methylphenols, but not for p-cresol (4-methylphenol). The replaced amino acid residues are not located within a distance of direct interaction with the substrate, and the determined three-dimensional structures of the mutant enzymes are highly similar to that of the wild-type enzyme. These results clearly show the importance of remote residues, not readily predicted by rational design, for the substrate specificity of enzymes

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and Related Family: Mechanistic Insights in Plant Disease Resistance

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and related NPR1-like proteins are a functionally similar, yet surprisingly diverse family of transcription co-factors. Initially, NPR1 in Arabidopsis was identified as a positive regulator of systemic acquired resistance (SAR), paralogs NPR3 and NPR4 were later shown to be negative SAR regulators. The mechanisms involved have been the subject of extensive research and debate over the years, during which time a lot has been uncovered. The known roles of this protein family have extended to include influences over a broad range of systems including circadian rhythm, endoplasmic reticulum (ER) resident proteins and the development of lateral organs. Recently, important advances have been made in understanding the regulatory relationship between members of the NPR1-like protein family, providing new insight regarding their interactions, both with each other and other defense-related proteins. Most importantly the influence of salicylic acid (SA) on these interactions has become clearer with NPR1, NPR3, and NPR4 being considered bone fide SA receptors. Additionally, post-translational modification of NPR1 has garnered attention during the past years, adding to the growing regulatory complexity of this protein. Furthermore, growing interest in NPR1 overexpressing crops has provided new insights regarding the role of NPR1 in both biotic and abiotic stresses in several plant species. Given the wealth of information, this review aims to highlight and consolidate the most relevant and influential research in the field to date. In so doing, we attempt to provide insight into the mechanisms and interactions which underly the roles of the NPR1-like proteins in plant disease responses

Risk Management Plan For the Hospital Environment

A risk management plan is placed in ISO 14971:2019 standard for mitigating different kinds of risk related to the use of medical electrical equipment including the electromagnetic interference (EMI) risk in the hospital environment. However, EMI accidents in the hospital are still happening indicating that further improvement in the risk management plan is required. Currently, the risk management plan in the standard does not factor in the hospital environment realistically, leading to incomplete risk analysis, evaluation, estimation, and control methods. Due to the dynamic environment of hospitals, the rule-based EMC approach is insufficient and the risk-based EMC approach should be utilized in improving risk management plans. In this paper, we utilized several risk-based EMC approach techniques and measurements such as the foot-printing technique, for properly examining the hospital environment, source-victim matrix tool, to categorize the severity of EMI issue, statistical tools like probability density function, cumulative density function, etc., to calculate probability and predict any future EMI risk. These techniques assist in the zoning of the hospital environment into low-risk, medium-risk, and high-risk for which risk control methods can be established. Overall, we hinted toward improving the risk management plan, in terms of flexibility, accuracy, and reliability, using risk-based EMC approach techniques

Converse extensionality and apartness

In this paper we try to find a computational interpretation for a strong form of extensionality, which we call "converse extensionality". Converse extensionality principles, which arise as the Dialectica interpretation of the axiom of extensionality, were first studied by Howard. In order to give a computational interpretation to these principles, we reconsider Brouwer's apartness relation, a strong constructive form of inequality. Formally, we provide a categorical construction to endow every typed combinatory algebra with an apartness relation. We then exploit that functions reflect apartness, in addition to preserving equality, to prove that the resulting categories of assemblies model a converse extensionality principle

C4:The future of solid organ transplantation from the perspective of young transplant professionals

With great interest, we read the first C4 Article titled "Current opinions in organ allocation", the result of pioneering work by the editorial board of the American Journal of Transplantation. The effort of the editorial board to realize their four C's goal, establishing a crowdsourced collaboration on current and controversial subjects, has resulted in a state-of-the-art review. Over a hundred transplant professionals contributed to this project, making it a one-of-a-kind, interdisciplinary and cross border collaboration. This article is protected by copyright. All rights reserved

Nano-inclusion in one step: spontaneous ice-templating of porous hierarchical nanocomposites for selective hydrogen release

3-Dimensional porous scaffold materials can be fabricated by ice templating sheets of graphene oxide (GO) or partially reduced graphene oxide (rGO). Aqueous suspensions of GO (or rGO) can be cast into monoliths or formed as beads on cooling and the solid matrices then fashioned with either laminar or radial porosity as result. Further, ammonia borane (AB) can be integrated into the hierarchical structures in situ in a one-step process without the requirement of melt infiltration or solution impregnation techniques. Compared to AB itself, the ensuing self-assembled beads release hydrogen at a reduced onset temperature and without volume expansion on heating, suppressing the release of diborane, borazine and ammonia. Pre-reduction of the GO matrix material (to rGO) eliminates CO/CO2 release from the composites

The expression of the NPR1-dependent defense response pathway genes in Persea americana (Mill.) following infection with Phytophthora cinnamomi

AVAILABILITY OF DATA AND MATERIALS : The raw datasets supporting the conclusions of this article are available in the Sequence Read Archive of NCBI Genbank repository, PRJNA675400 (https:// www. ncbi. nlm. nih. gov/ biopr oject/ PRJNA 675400/). In addition, the processed datasets supporting the conclusions of this article are included within the article (and its additional file(s)).SUPPLEMENTARY INFORMATION : TABLE S1. Plant proteomes obtained as input for orthologue identification using OrthoFinder v2.5.4. TABLE S2. Candidate NPR1 pathway-associated genes in Persea americana. Putative functional descriptions are the result of a combined annotation approach by using original functional annotations (Avocado Genome Consortium) and eggNOG-mapper, InterProScan and BLASTp descriptions. Candidates with no expression data, determined using baseMean following DeSeq2 analyses, were not assigned descriptors. TABLE S3. Protein-protein BLAST of identified Persea americana NPR1-dependent defense response pathway proteins. The NCBI non-redundant protein sequences database was used and limited by entrez entry Viridiplantae with an Expected (E) value cutoff 0.05, word size 3, BLOSUM 62, Gap cost (existence 11, extension 1), max hits per sequence 5. TABLE S4. Differentially expressed Persea americana NPR1- pathway-associated genes (log2(fold change; log2FC) > 0.58 | 0.58 | < -0.58, adjusted p-value (FDR; p-adj) < 0.05) comparing the expression of uninoculated (Control) sample libraries or various Phytophthora cinnamomi inoculated libraries, of the partially resistant rootstock Dusa ® with the respective libraries in the susceptible rootstock R0.12. lfcSE - standard error of log2FC.A plant’s defense against pathogens involves an extensive set of phytohormone regulated defense signaling pathways. The salicylic acid (SA)-signaling pathway is one of the most well-studied in plant defense. The bulk of SA-related defense gene expression and the subsequent establishment of systemic acquired resistance (SAR) is dependent on the nonexpressor of pathogenesis-related genes 1 (NPR1). Therefore, understanding the NPR1 pathway and all its associations has the potential to provide valuable insights into defense against pathogens. The causal agent of Phytophthora root rot (PRR), Phytophthora cinnamomi, is of particular importance to the avocado (Persea americana) industry, which encounters considerable economic losses on account of this pathogen each year. Furthermore, P. cinnamomi is a hemibiotrophic pathogen, suggesting that the SA-signaling pathway plays an essential role in the initial defense response. Therefore, the NPR1 pathway which regulates downstream SA-induced gene expression would be instrumental in defense against P. cinnamomi. Thus, we identified 92 NPR1 pathway-associated orthologs from the P. americana West Indian pure accession genome and interrogated their expression following P. cinnamomi inoculation, using RNA-sequencing data. In total, 64 and 51 NPR1 pathway-associated genes were temporally regulated in the partially resistant (Dusa®) and susceptible (R0.12) P. americana rootstocks, respectively. Furthermore, 42 NPR1 pathway-associated genes were differentially regulated when comparing Dusa® to R0.12. Although this study suggests that SAR was established successfully in both rootstocks, the evidence presented indicated that Dusa® suppressed SA-signaling more effectively following the induction of SAR. Additionally, contrary to Dusa®, data from R0.12 suggested a substantial lack of SA- and NPR1-related defense gene expression during some of the earliest time-points following P. cinnamomi inoculation. This study represents the most comprehensive investigation of the SA-induced, NPR1-dependent pathway in P. americana to date. Lastly, this work provides novel insights into the likely mechanisms governing P. cinnamomi resistance in P. americana.The Hans Merensky Foundation.https://bmcplantbiol.biomedcentral.comam2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan