JURNAL AGROTEKNOLOGI
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Hatemoji: A test suite and adversarially-generated dataset for benchmarking and detecting emoji-based hate
No full textDetecting online hate is a complex task, and low-performing detection models have harmful consequences when used for sensitive applications such as content moderation. Emoji-based hate is a key emerging challenge for online hate detection. We present HatemojiCheck, a test suite of 3,930 short-form statements that allows us to evaluate how detection models perform on hateful language expressed with emoji. Using the test suite, we expose weaknesses in existing hate detection models. To address these weaknesses, we create the HatemojiTrain dataset using an innovative human-and-model-in-the-loop approach. Models trained on these 5,912 adversarial examples perform substantially better at detecting emoji-based hate, while retaining strong performance on text-only hate. Both HatemojiCheck and HatemojiTrain are made publicly available
When the genome bluffs: a tandem duplication event during generation of a novel Agmo knockout mouse model fools routine genotyping
No full textBackground
Genome editing in mice using either classical approaches like homologous recombination or CRISPR/Cas9 has been reported to harbor off target effects (insertion/deletion, frame shifts or gene segment duplications) that lead to mutations not only in close proximity to the target site but also outside. Only the genomes of few engineered mouse strains have been sequenced. Since the role of the ether-lipid cleaving enzyme alkylglycerol monooxygenase (AGMO) in physiology and pathophysiology remains enigmatic, we created a knockout mouse model for AGMO using EUCOMM stem cells but unforeseen genotyping issues that did not agree with Mendelian distribution and enzyme activity data prompted an in-depth genomic validation of the mouse model.
Results
We report a gene segment tandem duplication event that occurred during the generation of an Agmo knockout-first allele by homologous recombination. Only low homology was seen between the breakpoints. While a single copy of the recombinant 18 kb cassette was integrated correctly around exon 2 of the Agmo gene, whole genome nanopore sequencing revealed a 94 kb duplication in the Agmo locus that contains Agmo wild-type exons 1–3. The duplication fooled genotyping by routine PCR, but could be resolved using qPCR-based genotyping, targeted locus amplification sequencing and nanopore sequencing. Despite this event, this Agmo knockout mouse model lacks AGMO enzyme activity and can therefore be used to study its physiological role.
Conclusions
A duplication event occurred at the exact locus of the homologous recombination and was not detected by conventional quality control filters such as FISH or long-range PCR over the recombination sites. Nanopore sequencing provides a cost convenient method to detect such underrated off-target effects, suggesting its use for additional quality assessment of gene editing in mice and also other model organisms
Complex interactions between commercial and noncommercial drivers of illegal trade for a threatened felid
No full textIllegal trade and human-wildlife conflict are two key drivers of biodiversity loss and are recognized as leading threats to large carnivores. Although human-wildlife conflict involving jaguars (Panthera onca) has received significant attention in the past, less is known about traditional use or commercial trade in jaguar body parts, including their potential links with retaliatory killing. Understanding the drivers of jaguar killing, trade and consumption is necessary to develop appropriate jaguar conservation strategies, particularly as demand for jaguar products appears to be rising due to Chinese demand. We interviewed 1107 rural households in north-western Bolivia, an area with an active history of human–jaguar conflict, which has also been at the epicentre of recent jaguar trade cases. We collected information on participants' experiences with jaguars, their jaguar killing, trading and consuming behaviours and potential drivers of these behaviours. We found that the relationships between local people and jaguars are complex and are driven largely by traditional practices, opportunism, human–jaguar conflict and market incentives from foreign and domestic demand, in the absence of law awareness and enforcement. Addressing jaguar trade and building human–jaguar coexistence will require a multifaceted approach that considers the multiple drivers of jaguar killing, trade and consumption, from foreign and local demand to human–jaguar conflict
Host genotype and genetic diversity shape the evolution of a novel bacterial infection
No full textPathogens continue to emerge from increased contact with novel host species. Whilst these hosts can represent distinct environments for pathogens, the impacts of host genetic background on how a pathogen evolves post-emergence are unclear. In a novel interaction, we experimentally evolved a pathogen (Staphylococcus aureus) in populations of wild nematodes (Caenorhabditis elegans) to test whether host genotype and genetic diversity affect pathogen evolution. After ten rounds of selection, we found that pathogen virulence evolved to vary across host genotypes, with differences in host metal ion acquisition detected as a possible driver of increased host exploitation. Diverse host populations selected for the highest levels of pathogen virulence, but infectivity was constrained, unlike in host monocultures. We hypothesise that population heterogeneity might pool together individuals that contribute disproportionately to the spread of infection or to enhanced virulence. The genomes of evolved populations were sequenced, and it was revealed that pathogens selected in distantly-related host genotypes diverged more than those in closely-related host genotypes. S. aureus nevertheless maintained a broad host range. Our study provides unique empirical insight into the evolutionary dynamics that could occur in other novel infections of wildlife and humans
Subthalamic deep brain stimulation induces finely-tuned gamma oscillations in the absence of levodopa
No full textFinely-tuned gamma (FTG) oscillations can be recorded from cortex or the subthalamic nucleus (STN) in patients with Parkinson's disease (PD) on dopaminergic medication, and have been associated with dyskinesias. When recorded during deep brain stimulation (DBS) on medication the FTG is entrained to half the stimulation frequency. We investigated whether these characteristics are shared off medication by recording local field potentials (LFP) from the STN from externalised DBS leads in 14 PD patients after overnight withdrawal of medication. FTG was induced de-novo by DBS in the absence of dyskinesias in a third of our cohort. The FTG could outlast stimulation or arise only after DBS ceased. FTG frequencies decreased during and across consecutive DBS blocks, but did not shift with changing stimulation frequency off medication. Together with the sustained after-effects this argues against simple entrainment by DBS in the off medication state. We also found significant coherence between STN-LFP and electroencephalogram (EEG) signals at FTG frequencies. We conclude that FTG is a network phenomenon that behaves differently in the off medication state, when it is neither associated with dyskinesias nor susceptible to entrainment
The high energy Universe at ultra-high resolution: the power and promise of X-ray interferometry
No full textWe propose the development of X-ray interferometry (XRI), to reveal the Universe at high energies with ultra-high spatial resolution. With baselines which can be accommodated on a single spacecraft, XRI can reach 100 μ as resolution at 10 Å (1.2 keV) and 20 μ as at 2 Å (6 keV), enabling imaging and imaging-spectroscopy of (for example) X-ray coronae of nearby accreting supermassive black holes (SMBH) and the SMBH ‘shadow’; SMBH accretion flows and outflows; X-ray binary winds and orbits; stellar coronae within ∼ 100 pc and many exoplanets which transit across them. For sufficiently luminous sources XRI will resolve sub-pc scales across the entire observable Universe, revealing accreting binary SMBHs and enabling trigonometric measurements of the Hubble constant with X-ray light echoes from quasars or explosive transients. A multi-spacecraft ‘constellation’ interferometer would resolve well below 1 μ as, enabling SMBH event horizons to be resolved in many active galaxies and the detailed study of the effects of strong field gravity on the dynamics and emission from accreting gas close to the black hole
Truth and Christian ethics: a narratival perspective
No full textIn this paper, I am going to consider some of the forms that truthfulness can take in the Christian
life. At the core of this account will be the idea of storied identity, and in the course of the
discussion, I hope to throw some light on the following questions. In general terms, what does it
take to live truthfully with respect to some narrative? More exactly, how might that truthfulness be
realised in bodily terms? And, finally, how might living truthfully with respect to a narrative
contribute to the further elaboration of the narrative? Of course, in our present context, my aim is
to address these questions with reference to the concerns of Christian ethics in particular – and I
shall take as my focus, therefore, the kind of storied truthfulness that is embodied in the practice of
neighbour love, and the question of how that truthfulness might be extended through participation
in the eucharist
An explicit formulation of the macroscopic strength criterion for porous media with pressure and Lode angle dependent matrix under axisymmetric loading
No full textThis paper aims to propose an explicit formulation of the macroscopic strength criterion for porous media with spherical voids. The matrix is assumed rigid and perfectly plastic with yield surface described by the three-parameter strength criterion, which is Lode angle and pressure dependent and capable of accounting for distinct values of the uniaxial tensile strength, uniaxial compressive strength (UCS) and equal biaxial compressive strength (eBCS). An exact upper bound of the macroscopic strength is derived for porous media subjected to purely hydrostatic loading. Besides, an estimate of the macroscopic strength profile of porous media under axisymmetric loading is obtained in parametric form. Moreover, a heuristic strength criterion in explicit form is further developed by examining limit cases of the parametric strength criterion. The developed strength criteria are assessed by finite-element based numerical solutions. Compared with the parametric strength criterion which involves cumbersome functions, the heuristic one is convenient for practical applications. For specific values of the matrix's strength surface, the proposed heuristic strength criterion can recover the well-known Gurson criterion. The present work also addresses the effect of the ratio of matrix's eBCS to UCS on the macroscopic strength of porous media. For matrix with distinct values of eBCS and UCS, neglecting the difference between eBCS and UCS would result in an underestimation of the macroscopic strength, especially when the pressure is large
Airway care interventions for invasively ventilated critically ill adults: A Dutch national survey
No full textAirway care interventions may prevent accumulation of airway secretions and promote their evacuation, but evidence is scarce. Interventions include heated humidification, nebulization of mucolytics and/or bronchodilators, manual hyperinflation and use of mechanical insufflation-exsufflation (MI-E). Our aim is to identify current airway care practices for invasively ventilated patients in intensive care units (ICU) in the Netherlands. A self–administered web-based survey was sent to a single pre–appointed representative of all ICUs in the Netherlands. Response rate was 85% (72 ICUs). We found substantial heterogeneity in the intensity and combinations of airway care interventions used. Most (81%) ICUs reported using heated humidification as a routine prophylactic intervention. All (100%) responding ICUs used nebulized mucolytics and/or bronchodilators; however, only 43% ICUs reported nebulization as a routine prophylactic intervention. Most (81%) ICUs used manual hyperinflation, although only initiated with a clinical indication like difficult oxygenation. Few (22%) ICUs used MI-E for invasively ventilated patients. Use was always based on the indication of insufficient cough strength or as a continuation of home use. In the Netherlands, use of routine prophylactic airway care interventions is common despite evidence of no benefit. There is an urgent need for evidence of the benefit of these interventions to inform evidence-based guidelines
Phase transitions for nonlinear nonlocal aggregation-diffusion equations
No full textWe are interested in studying the stationary solutions and phase transitions
of aggregation equations with degenerate diffusion of porous medium-type, with
exponent . We first prove the existence of possibly infinitely
many bifurcations from the spatially homogeneous steady state. We then focus
our attention on the associated free energy proving existence of minimisers and
even uniqueness for sufficiently weak interactions. In the absence of
uniqueness, we show that the system exhibits phase transitions: we classify
values of and interaction potentials for which these phase transitions
are continuous or discontinuous. Finally, we comment on the limit and the influence that the presence of a phase transition has on this
limit