Miracle-dz/UniFAR-FTUs huggingface dataset:
“Tarred with the Same Brush”: Racist and Anti-racist Constructions of Muslim Asylum Seekers in Australia

Abstract Despite Australia's longstanding reputation as a multicultural nation, xenophobic and integrationist ideas remain embedded within political, media and public discourse surrounding migration, especially within discussions of Muslims and asylum seekers. Existing literature indicates that within arguments that oppose refugee resettlement in Australia, Islam is routinely constructed as incompatible with Australian society. Some research, however, has highlighted resistance to these ideas, yet few studies have explored how these narratives of resistance are constructed. This paper, presents a Critical Discourse Analysis of semi-structured interviews with 24 Western Australians who discussed their perspectives concerning asylum seekers. Participants who supported restrictive asylum policies reproduced integrationist attitudes toward Muslims, however those who expressed welcoming asylum views routinely challenged these ideas. I discuss the discursive and rhetorical features of these opposing takes on Australia's asylum debate, outlining some important implications for democracy and political communication, as well as for critical race analysis and sociological scholarship.
Phospholipid-Cytochrome c Interaction EVIDENCE FOR THE EXTENDED LIPID ANCHORAGE*

Binding of cytochrome c (cyt c ) to fatty acids and acidic phospholipid membranes produces pronounced and essentially identical changes in the spectral properties of cyt c , revealing conformational changes in the protein. The exact mechanism of the interaction of fatty acids and acidic phospholipids with cyt c is unknown. Binding of cyt c to liposomes with high contents (mole fraction X > 0.7) of acidic phospholipids spectral changes identical to those due to binding of oleic acid. Interactions of fatty acids and phospho- lipids with [Zn 2 (cid:1) -heme] cyt c were assessed by fluorescence spectroscopy. These measurements were conducted with a PerkinElmer Life Sciences LS50B spectrofluorometer using 5- and 10-nm band passes for excitation at 412 nm and emission at 588 nm, respectively. Two milli- liters of 0.7 (cid:1) M [Zn 2 (cid:1) -heme] cyt c in 20 m M Hepes, 0.1 m M EDTA, 7.0, into magnetically four-window quartz cuvette in a holder thermostatted with a circulating water bath at 25 °C. Subsequently, the indicated lipids (fatty acid or liposomes) were added to yield the desired final concentrations and the fluorescence of the Zn 2 (cid:1) -heme moiety was observed. Fatty acids were added in 1- to 5- (cid:1) l aliquots in ethanol solution. Control experiments indicated no detectable changes in fluorescence intensities by this solvent (data not shown). Because of the low concentrations of both lipids and cyt c used minimal interference by the inner filter effect is expected.
Adjacent crop type impacts potential pollinator communities and their pollination services in remnants of natural vegetation

Pollination plays a crucial role in the conservation of many plant species persisting in fragmented, human‐dominated landscapes. Pollinators are known to be instrumental in maintaining genetic diversity and metapopulation dynamics for many plant species and are important for providing ecological services that are essential in agricultural landscapes where populations of native plants are highly isolated. Numerous studies have explored the value of remnant native vegetation for supporting pollination services to crop species, yet the effect of mass‐flowering crops on the pollinator communities and the pollination services they provide to native plant communities persisting in fragmented landscapes are less well understood. Here, we assess the influence of the presence and phenology of a mass‐flowering crop to pollinator community structure, abundance, and pollen load composition in remnant vegetation in complex agricultural landscapes.
Dynamin2 stabilizes plasma membrane-connected caveolae by restraining fission

Caveolae are small membrane invaginations that generally are stably attached to the plasma membrane. Their release is believed to depend on the GTPase dynamin 2 (Dyn2), in analogy with its role in fission of clathrin-coated vesicles. The mechanistic understanding of caveola fission, and in particular the role of Dyn2, is however sparse. Here, we used microscopy-based tracking of individual caveolae in living cells to determine the role of Dyn2 in caveola dynamics. We report that Dyn2 stably associated with a subset of caveolae, but was not required for formation or fission of caveolae. The Dyn2-positive subset of caveolae displayed longer plasma membrane duration times, whereas depletion of Dyn2 resulted in shorter duration times and increased caveola fission. The stabilizing role of Dyn2 was independent of its GTPase activity and the caveola stabilizing protein EHD2. Thus, we propose that, in contrast to the current view, Dyn2 restrains caveolae at the plasma membrane and prevents fission.
Loss-of-function mutation in human Oxidation Resistance gene 1 disrupts the spatial-temporal regulation of histone arginine methylation in early brain development

We report a loss-of-function mutation in the TLDc domain of human Oxidation Resistance 1 (OXR1) gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generated patient derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identified that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1 dependent mechanisms regulating gene expression during neurodevelopment. We modeled the function of OXR1 in early human brain development using patient derived brain organoids revealing that OXR1 contributes to the spatial-temporal regulation of histone arginine methylation in specific brain regions. Our work provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency, highlighting the therapeutic potential of OXR1 in numerous neurodegenerative and neurodevelopmental disorders.
Midfrontal theta is associated with errors, but no evidence for a link with error-related memory

Midfrontal theta is widely observed in situations with increased demand for cognitive control, such as monitoring response errors. It also plays an important role in the cognitive control involved in memory, supporting processes like the binding of single items into a memory representation or encoding contextual information. In the current study, we explored the link between midfrontal theta and error-related memory. To this end, we recorded EEG from 31 participants while they performed a modified Flanker task. Their memory for the errors made during the task was assessed after each experimental block, and its relationship with error-related midfrontal theta effects was investigated. We have replicated the error-related increase in midfrontal theta power, reported in previous literature. However, this error-related theta effect could not predict subsequent memory of the committed errors. Our findings add to a growing literature on the prefrontal cortex-guided control process in error monitoring and episodic memory.
Phosphoproteomic mapping reveals distinct signaling actions and activation of protein synthesis and muscle hypertrophy by Isthmin-1

The secreted protein Isthmin-1 (Ism1) mitigates diabetes by increasing adipocyte and skeletal muscle glucose uptake by activating the PI3K-Akt pathway. However, while both Ism1 and insulin converge on these common targets, Ism1 has distinct cellular actions suggesting divergence in downstream intracellular signaling pathways. To understand the biological complexity of Ism1 signaling, we performed phosphoproteomic analysis after acute exposure, revealing overlapping and distinct pathways of Ism1 and insulin. We identify a 53 % overlap between Ism1 and insulin signaling and Ism1-mediated phosphoproteome-wide alterations in ∼ 450 proteins that are not shared with insulin. Interestingly, we find several unknown phosphorylation sites on proteins related to protein translation, mTOR pathway and, unexpectedly, muscle function in the Ism1 signaling network. Physiologically, Ism1 ablation in mice results in altered proteostasis, including lower muscle protein levels under fed and fasted conditions, reduced amino acid incorporation into proteins, and reduced phosphorylation of the key protein synthesis effectors Akt and downstream mTORC1 targets. As metabolic disorders such as diabetes are associated with accelerated loss of skeletal muscle protein content, these studies define a non-canonical mechanism by which this anti-diabetic circulating protein controls muscle biology.
Machine learning enables accurate prediction of breast cancer five-year survival using somatic genomic variants

Breast cancer is one of the most common cancers, accounting for about 30% of female cancers and a mortality rate of 15%. The 5-year survival rate is most commonly used to assess cancer progression and guide clinical practice. We used the CatBoost model to systematically construct a five-year mortality risk prediction model based on two independent data sets (BRCA_METABRIC, BRCA_TCGA). The model input data are the somatic genomic variants (copy number variation, SNP locus, cumulative mutation number of genes) and phenotype data of cancer samples. The optimal model combined all the above characteristics, and the AUC reached 0.70 in an independent external data set. At the same time, we also conducted a biological analysis of the characteristics of the model and found some potential biomarkers (TP53, DNAH11, MAP3K1, PHF20L1, etc.). The results of model risk stratification can be used as a guide for the prognosis of breast cancer.
Efficient querying of genomic reference databases with gget

Motivation A recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. Currently, there is no tool implementing automated, easy programmatic access to curated reference information stored in a diverse collection of large, public genomic databases. Results gget is a free and open-source command-line tool and Python package that enables efficient querying of genomic reference databases, such as Ensembl. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying required for genomic data analysis in a single line of code. Availability The manual and source code are available at https://github.com/pachterlab/gget. Contact lpachter@caltech.edu
Impact of bioactive molecule inclusion in lyophilized silk scaffolds varies between in vivo and in vitro assessments

Biomaterials can influence the coordinated efforts required to achieve tissue rehabilitation. Sponge-like silk fibroin scaffolds that include bioactive molecules have been shown to influence tissue repair. However, the mechanisms by which scaffold formulations elicit desired in vivo responses is unclear. Here, acellular silk scaffolds consisting of type I collagen, heparin, and/or vascular endothelial growth factor (VEGF) were used to investigate material fabrication and composition parameters that drive scaffold degradation, cell infiltration, and adipose tissue deposition in vivo. In subcutaneous implants, scaffold degradation was assessed, and results show that the percentage of cells infiltrating the scaffold increased when scaffold formulations contained bioactive molecules. To gain further insight, calculated in vitro enzymatic degradation rates increased with higher enzyme concentrations and theoretical cleavage sites. However, the addition of type I collagen and heparin to the scaffold at relevant concentrations did not change degradation rates, compared to silk alone. These in vitro results are contrary to observations in vivo, where bioactive molecules influence local protein deposition, immune cell infiltration rates, and vascularization. Thus, quantitative in vitro and in vivo evaluations aid in determining the mechanisms by which biomaterials influence tissue repair and support intentional biomaterial design for clinical applications. Graphical Abstract This work examines the role of scaffold fabrication and bioactive molecule inclusion on the enzymatic degradation of silk fibroin-based lyophilized sponges. Specifically, the roles of collagen I, heparin, and vascular endothelial growth factor are analyzed to determine the impact of formulation on rate of degradation. In addition, scaffolds are either pre-fabricated, where these bioactive molecules are included in the polymer solution prior to casting the scaffold or the bioactive molecules are introduced following scaffold formation through passive adsorption to the silk fibroin scaffold surface. Scaffolds are enzymatically degraded in vitro, and kinetic rate constants are calculated for the different formulations. In vivo, cellularity, adipose tissue accumulation, and scaffold area are assessed over time. Additionally, immunohistochemistry is used to visualize VEGF Receptor 2, CD 68, and α-smooth muscle actin over time.
Microenvironmental Ammonia Enhances T cell Exhaustion in Colorectal Cancer

Effective therapies are lacking for patients with advanced colorectal cancer (CRC). The CRC tumor microenvironment has elevated metabolic waste products due to altered metabolism and proximity to the microbiota. The role of metabolite waste in tumor development, progression, and treatment resistance is unclear. We generated an autochthonous metastatic mouse model of CRC and unbiased multi-omic analyses in this model reveals a robust accumulation of tumoral ammonia. The high ammonia levels induce T cell metabolic reprogramming, increase exhaustion and decrease proliferation. CRC patients have increased serum ammonia, and our ammonia-related gene signature correlates with altered T cell response, adverse patient outcomes, and lack of response to immune checkpoint blockade. We demonstrate that enhancing ammonia clearance reactivates T cells, decreases tumor growth, and extends survival. Moreover, decreasing tumor-associated ammonia enhances anti-PD-L1 efficacy. Our findings indicate that ammonia detoxification can reactivate T cells, highlighting a new approach to enhance the efficacy of immunotherapies. Statement of Significance We demonstrate that ammonia accumulates in the microenvironment of colorectal cancer. Ammonia alters T-cells redox singling leading to a decrease in T cell proliferation and an increase in T cell exhaustion. Enhancing ammonia clearance reduces tumor size, increases survival, and increases the efficacy to immunotherapies.
An individualized fMRI protocol to assess semantic congruency effects on episodic memory in an ageing multilingual population

The cognitive stimulation induced by multilingualism may slow down age-related memory impairment. However, a suitable neuroscientific framework to assess the influence of multilingualism on age-related memory processes is missing. We propose an experimental paradigm that assesses the effects of semantic congruency on episodic memory using functional magnetic resonance imaging (fMRI). To this end, we modified the picture-word interference (PWI) task to be suitable for multilingual subjects undergoing functional magnetic resonance imaging (fMRI). In particular, stimulus material was prepared in multiple languages and closely matched in semantic properties, thus enabling participants to perform the experiment in a language of their choice. This paradigm was validated in a group (n = 62) of healthy older (>64 years) multilingual subjects, all practicing three or more languages. Consistent with the engagement of semantic congruency processes, we found that the encoding and recognition of semantically related vs. unrelated picture-word pairs evoked robust differences in behavior and the neural activity of parietal-temporal networks. These effects were not modulated by the language in which the task was performed. Based on this validation in a multilingual population, we conclude that the proposed paradigm will allow future studies to evaluate whether multilingualism aptitude engages neural systems in a manner that protects long-term memory from aging-related decline.
Effect of biomaterial stiffness on cardiac mechanics in a biventricular infarcted rat heart model with microstructural representation of in situ intramyocardial injectate

Intramyocardial delivery of biomaterials is a promising concept for treating myocardial infarction. The delivered biomaterial provides mechanical support and attenuates wall thinning and elevated wall stress in the infarct region. This study aimed at developing a biventricular finite element model of an infarcted rat heart with a microstructural representation of an in situ biomaterial injectate, and a parametric investigation of the effect of the injectate stiffness on the cardiac mechanics. A three-dimensional subject-specific biventricular finite element model of a rat heart with left ventricular infarct and microstructurally dispersed biomaterial delivered one week after infarct induction was developed from ex vivo microcomputed tomography data. The volumetric mesh density varied between 303 mm-3 in the myocardium and 3,852 mm-3 in the injectate region due to the microstructural intramyocardial dispersion. Parametric simulations were conducted with the injectate’s elastic modulus varying from 4.1 to 405,900 kPa, and myocardial and injectate strains were recorded. With increasing injectate stiffness, the end-diastolic median myocardial fibre and cross-fibre strain decreased in magnitude from 3.6% to 1.1% and from −6.0% to −2.9%, respectively. At end-systole, the myocardial fibre and cross-fibre strain decreased in magnitude from −20.4% to −11.8% and from 6.5% to 4.6%, respectively. In the injectate, the maximum and minimum principal strains decreased in magnitude from 5.4% to 0.001% and from −5.4% to −0.001%, respectively, at end-diastole and from 38.5% to 0.06% and from −39.0% to −0.06%, respectively, at end-systole. With the microstructural injectate geometry, the developed subject-specific cardiac finite element model offers potential for extension to cellular injectates and in silico studies of mechanotransduction and therapeutic signalling in the infarcted heart with an infarct animal model extensively used in preclinical research.
The Effects of Propofol Anaesthesia on Molecular-enriched Networks During Resting-state and Naturalistic Stimulation

Placing a patient in a state of anaesthesia is crucial for modern surgical practice. However, the mechanisms by which anaesthetic drugs, such as propofol, impart their effects on consciousness remain poorly understood. Propofol potentiates GABAergic transmission, which purportedly has direct actions on cortex as well as indirect actions via ascending neuromodulatory systems. Functional imaging studies to date have been limited in their ability to unravel how these effects on neurotransmission impact system-level dynamics of the brain. Here, we leveraged advances in multi-modal imaging, Receptor-Enriched Analysis of functional Connectivity by Targets (REACT), to investigate how different levels of propofol-induced sedation alters neurotransmission-related functional connectivity (FC), both at rest and when individuals are exposed to naturalistic auditory stimulation. Propofol increased GABA-A- and noradrenaline transporter-enriched FC within occipital and somatosensory regions respectively. Additionally, during auditory stimulation, the network related to the vesicular acetylcholine transporter showed reduced FC within the right superior temporal gyrus, regardless of level of anaesthesia, and a spatial configuration correlating with a broad range of meta-analytic measures of audition- and emotion-related cognition. In bringing together these micro- and macro-scale systems, we provide support for both direct GABAergic and indirect noradrenergic-related network changes under anaesthesia and describe a cognition-related reconfiguration of the cholinergic network, highlighting the utility of REACT to explore the molecular substrates consciousness and cognition.
Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics

Sweet basil (Ocimum basilicum L.) production is threatened by the oomycete pathogen Peronospora belbahrii causing basil downy mildew (BDM); BDM resistant cultivar ‘Mrihani’ (MRI) was identified in a germplasm screen, and fertile progeny were produced through a breeding program with BDM- susceptible ‘Newton’ (SB22), but the molecular mechanisms conferring resistance in MRI and progeny remained unknown Comparative transcriptomics was performed to identify candidate resistance genes and potential mechanisms for BDM resistance; RNA samples from BDM- infected MRI and SB22 plants were harvested at 4 time points during the first 3 days of infection to differentiate interactions in resistant and susceptible plants. Three categories of genes uniquely induced in resistant MRI upon pathogen challenge were identified: nucleotide-binding leucine rich repeat proteins (NLRs), multi-functional receptor-like kinases (RLKs), and secondary metabolic enzymes; validation of the top resistance candidate NLR gene confirmed its unique presence in MRI as well as in two of four resistant MRIxSB22 F2 progeny. In MRI, pathogen challenge also upregulated transcripts in the salicylic acid synthesis pathway, suggesting its role in BDM resistance, and demonstrating the application of using comparative transcriptomics to identify resistance genes and mechanisms in non-model crops for marker-assisted breeding approaches.
Chemical effects on ecological interactions within a model-experiment loop

We propose in this paper a method to assess the effects of a contaminant on a micro-ecosystem, integrating the population dynamics and the interactions between species. For that, we developed a dynamic model to describe the functioning of a microcosm exposed to a contaminant and to discriminate direct and indirect effects. Then, we get back from modelling to experimentation in order to identify which of the collected data have really been necessary and sufficient to estimate model parameters in order to propose a more efficient experimental design for further investigations. We illustrated our approach using a 2-L laboratory microcosm involving three species (the duckweed Lemna minor, the microalgae Pseudokirchneriella subcapitata and the daphnids Daphnia magna) exposed to cadmium contamination. We modelled the dynamics of the three species and their interactions using a mechanistic model based on coupled ordinary differential equations. The main processes occurring in this three-species microcosm were thus formalized, including growth and settling of algae, growth of duckweeds, interspecific competition between algae and duckweeds, growth, survival and grazing of daphnids, as well as cadmium effects. We estimated model parameters by Bayesian inference, using simultaneously all the data issued from multiple laboratory experiments specifically conducted for this study. Cadmium concentrations ranged between 0 and 50 μg. L-1 . For all parameters of our model, we obtained biologically realistic values and reasonable uncertainties. The cascade of cadmium effects, both direct and indirect, was identified. Critical effect concentrations were provided for the life history traits of each species. An example of experimental design adapted to this kind a microcosm was also proposed. This approach appears promising when studying contaminant effects on ecosystem functioning.