An inverse oblique effect in human vision

AbstractIn the classic oblique effect contrast detection thresholds, orientation discrimination thresholds, and other psychophysical measures are found to be smallest for vertical or horizontal stimuli and significantly higher for stimuli near the ±45° obliques. Here we report a novel inverse oblique effect in which thresholds for detecting translational structure in random dot patterns [Glass, L. (1969). Moiré effect from random dots. Nature, 223, 578–580] are lowest for obliquely oriented structure and higher for either horizontal or vertical structure. Area summation experiments provide evidence that this results from larger pooling areas for oblique orientations in these patterns. The results can be explained quantitatively by a model for complex cells in which the final filtering stage in a filter–rectify–filter sequence is of significantly larger area for oblique orientations

Circle talks as situated experiential learning: Context, identity, and knowledgeability in \u27learning from reflection\u27

This article presents research that used ethnographic and sociolinguistic methods to study ways participants learn through reflection when carried out as a “circle talk.” The data indicate that participants in the event (a) invoked different contextual frames that (b) implicated them in various identity positions, which (c) affected how they could express their knowledge. These features worked together to generate socially shared meanings that enabled participants to jointly achieve conceptualization—the ideational role “reflection” is presumed to play in the experiential learning process. The analysis supports the claim that participants generate new knowledge in reflection, but challenges individualistic and cognitive assumptions regarding how this occurs. The article builds on situated views of experiential learning by showing how knowledge can be understood as socially shared and how learning and identity formation are mutually entailing processes

Agriculture Beyond Food: Experiences from Indonesia

The ABF programme addresses one of today’s major societal challenges, how to achieve a sustainable and inclusive biobased economy, with high-level scientific research on the thin lines between food and non-food, commodities and waste products, livelihood opportunities and risks, and local and global economy. This book provides insights into the main issues and key questions relating to the biobased economy, reflects on the objectives of the ABF programme, and offers policy recommendations. It summarises the projects conducted within the three major clusters at the heart of the programme: migration and forest transformation, breakthroughs in biofuel production technology, and the commoditisation of an alternative biofuel crop. The book ends with a number of lessons learned from the ABF programme on interdisciplinary programming

Evolution of a periodic eight-black-hole lattice in numerical relativity

The idea of black-hole lattices as models for the large-scale structure of the universe has been under scrutiny for several decades, and some of the properties of these systems have been elucidated recently in the context of the problem of cosmological backreaction. The complete, three-dimensional and fully relativistic evolution of these system has, however, never been tackled. We explicitly construct the first of these solutions by numerically integrating Einstein's equation in the case of an eight-black-hole lattice with the topology of S3.Comment: 21 pages, 13 figures. Corrected and clarified discussio

Formation of Giant Quasibound Cold Diatoms by Strong Atom-Cavity Coupling

We show that giant quasi-bound diatomic complexes, whose size is typically hundreds of nm, can be formed by intra-cavity cold diatom photoassociation or photodissociation in the strong atom-cavity coupling regime.Comment: 4 pages, 3 figure

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Background Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration. Conclusions Gene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Background Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration. Conclusions Gene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination

Common principles and best practices for engineering microbiomes

Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue hat structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries on the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyze microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy, and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture, and enabling the bioeconomy

Flash-lag chimeras: the role of perceived alignment in the composite face effect

Spatial alignment of different face halves results in a configuration that mars the recognition of the identity of either face half (). What would happen to the recognition performance for face halves that were aligned on the retina but were perceived as misaligned, or were misaligned on the retina but were perceived as aligned? We used the 'flash-lag' effect () to address these questions. We created chimeras consisting of a stationary top half-face initially aligned with a moving bottom half-face. Flash-lag chimeras were better recognized than their stationary counterparts. However when flashed face halves were presented physically ahead of moving halves thereby nulling the flash-lag effect, recognition was impaired. This counters the notion that relative movement between the two face halves per se is sufficient to explain better recognition of flash-lag chimeras. Thus, the perceived spatial alignment of face halves (despite retinal misalignment) impairs recognition, while perceived misalignment (despite retinal alignment) does not

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-offunction mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n¼40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC