Miracle-dz/UniFAR-FTUs huggingface dataset:
A lamin A/C variant causing striated muscle disease provides insights into filament organization

ABSTRACT The LMNA gene encodes the A-type lamins, which polymerize into ∼3.5-nm-thick filaments and, together with B-type lamins and associated proteins, form the nuclear lamina. Mutations in LMNA cause a wide variety of pathologies. In this study, we analyzed the nuclear lamina of embryonic fibroblasts from LmnaH222P/H222P mice, which develop cardiomyopathy and muscular dystrophy. Although the organization of the lamina appeared unaltered, there were changes in chromatin and B-type lamin expression. An increase in nuclear size and consequently a relative reduction in heterochromatin near the lamina allowed for a higher resolution structural analysis of lamin filaments using cryo-electron tomography. This was most apparent when visualizing lamin filaments in situ and using a nuclear extraction protocol. Averaging of individual segments of filaments in LmnaH222P/H222P mouse fibroblasts resolved two polymers that constitute the mature filaments. Our findings provide better views of the organization of lamin filaments and the effect of a striated muscle disease-causing mutation on nuclear structure. Highlighted Article: The lamin A/C H222P laminopathy mutation provides insights into lamin substructure organization.
A Critique for Ecology

1. Crisis in ecology 2. Criteria 3. Tautology 4. Operationalism of terms and concepts 5. Explanatory science-reduction 6. Cause and mechanism 7. Historical explanation and understanding 8. Weak predictions 9. Checklist of problems 10. Putting it together - competition 11. Predictive ecology.
Aging reduces EEG markers of recognition despite intact performance: Implications for forensic memory detection

ERP-based forensic memory detection is based on the logic that guilty suspects will hold incriminating knowledge about crimes they have committed, and therefore should show parietal ERP positivities related to recognition when presented with reminders of their crimes. We predicted that such forensic memory detection might however be inaccurate in older adults, because of changes to recognition-related brain activity that occurs with aging. We measured both ERPs and EEG oscillations associated with episodic old/new recognition and forensic memory detection in 30 younger (age < 30) and 30 older (age > 65) adults. EEG oscillations were included as a complementary measure which is less sensitive to temporal variability and component overlap than ERPs. In line with predictions, recognition-related parietal ERP positivities were significantly reduced in the older compared to younger group in both tasks, despite highly similar behavioural performance. We also observed ageing-related reductions in oscillatory markers of recognition in the forensic memory detection test, while the oscillatory effects associated with episodic recognition were similar across age groups. This pattern of results suggests that while both forensic memory detection and episodic recognition are accompanied by ageing-induced reductions in parietal ERP positivities, these reductions may be caused by non-overlapping mechanisms across the two tasks. Our findings suggest that EEG-based forensic memory detection tests are invalid in older populations, limiting their practical applications.
Asymmetries around the visual field: From retina to cortex to behavior

Visual performance varies around the visual field. It is best near the fovea compared to the periphery, and at iso-eccentric locations it is best on the horizontal, intermediate on the lower, and poorest on the upper meridian. The fovea-to-periphery performance decline is linked to the decreases in cone density, retinal ganglion cell (RGC) density, and V1 cortical magnification factor (CMF) as eccentricity increases. The origins of polar angle asymmetries are not well understood. Optical quality and cone density vary across the retina, but recent computational modeling has shown that these factors can only account for a small percentage of behavior. Here, we investigate how visual processing beyond the cone photon absorptions contributes to polar angle asymmetries in performance. First, we quantify the extent of asymmetries in cone density, midget RGC density, and V1 CMF. We find that both polar angle asymmetries and eccentricity gradients increase from cones to mRGCs, and from mRGCs to cortex. Second, we extend our previously published computational observer model to quantify the contribution of phototransduction by the cones and spatial filtering by mRGCs to behavioral asymmetries. Starting with photons emitted by a visual display, the model simulates the effect of human optics, cone isomerizations, phototransduction, and mRGC spatial filtering. The model performs a forced choice orientation discrimination task on mRGC responses using a linear support vector machine classifier. The model shows that asymmetries in a decision maker’s performance across polar angle are greater when assessing the photocurrents than when assessing isomerizations and are greater still when assessing mRGC signals. Nonetheless, the polar angle asymmetries of the mRGC outputs are still considerably smaller than those observed from human performance. We conclude that cone isomerizations, phototransduction, and the spatial filtering properties of mRGCs contribute to polar angle performance differences, but that a full account of these differences will entail additional contribution from cortical representations.
The Thermosynechococcus Genus: Wide Environmental Distribution, but a Highly Conserved Genomic Core

Cyanobacteria thrive in very diverse environments. In Earth history however, delayed oxygenation has raised questions of growth limitation in ancient environmental conditions. As a single genus, the Thermosynechococcus are known to be cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain and only 18 protein clusters appearing in all Thermosynechococcus but not in any other cyanobacteria in our analysis. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of protein coding genes has implications for understanding the basis of thermophily within this clade, and also suggests that ferrous iron in ancient oceans may not have inhibited the proliferation of Cyanobacteria on Earth. The conserved core genome may be indicative of an allopatric lifestyle – or reduced genetic complexity of hot spring habitats relative to other environments.
A Genetic Pathway Composed of EDT1/HDG11, ERECTA, and E2Fa Loci Regulates Water Use Efficiency by Modulating Stomatal Density

Improvement of crop drought resistance and water use efficiency (WUE) has been a major endeavor in agriculture. ERECTA is the first identified major effector of water use efficiency. However, the underlying molecular mechanism is not well understood. Here, we report a genetic pathway, composed of EDT1/HDG11, ERECTA, and E2Fa loci, which regulates water use efficiency by modulating stomatal density. The HD-START transcription factor EDT1/HDG11 transcriptionally activates ERECTA expression by binding to an HD cis-element in the ERECTA promoter. ERECTA in turn relies on E2Fa to control the expression of cell-cycle related genes and the transition from mitosis to endocycle, which leads to increased nuclear DNA content in leaf cells, and therefore increased cell size and decreased stomatal density. The decreased stomatal density improves plant WUE. Our study demonstrates the EDT1/HDG11-ERECTA-E2Fa genetic pathway that reduces stomatal density by increasing cell size, providing a new avenue to improve WUE of crops.
Auditory cortex is susceptible to lexical influence as revealed by informational vs. energetic masking of speech categorization

Speech perception requires the grouping of acoustic information into meaningful phonetic units via the process of categorical perception (CP). Environmental masking influences speech perception and CP. However, it remains unclear at which stage of processing (encoding, decision, or both) masking affects listeners’ categorization of speech signals. The purpose of this study was to determine whether linguistic interference influences the early acoustic-phonetic conversion process inherent to CP. To this end, we measured source level, event related brain potentials (ERPs) from auditory cortex (AC) and inferior frontal gyrus (IFG) as listeners rapidly categorized speech sounds along a /da/ to /ga/ continuum presented in three listening conditions: quiet, and in the presence of forward (informational masker) and time-reversed (energetic masker) 2-talker babble noise. Maskers were matched in overall SNR and spectral content and thus varied only in their degree of linguistic interference (i.e., informational masking). We hypothesized a differential effect of informational versus energetic masking on behavioral and neural categorization responses, where we predicted increased activation of frontal regions when disambiguating speech from noise, especially during lexical-informational maskers. We found (1) informational masking weakens behavioral speech phoneme identification above and beyond energetic masking; (2) low-level AC activity not only codes speech categories but is susceptible to higher-order lexical interference; (3) identifying speech amidst noise recruits a cross hemispheric circuit (ACleft → IFGright) whose engagement varies according to task difficulty. These findings provide corroborating evidence for top-down influences on the early acoustic-phonetic analysis of speech through a coordinated interplay between frontotemporal brain areas.
Hippocampal replay of experience at real-world speeds

Representations related to past experiences play a critical role in memory and decision-making processes. The rat hippocampus expresses these types of representations during sharp-wave ripple (SWR) events, and previous work identified a minority of SWRs that contain “replay” of spatial trajectories at ~20x the movement speed of the animal. Efforts to understand replay typically make multiple assumptions about which events to examine and what sorts of representations constitute replay. We therefore lack a clear understanding of both the prevalence and the range of representational dynamics associated with replay. Here we develop a state space model that uses a combination of movement dynamics of different speeds to capture the spatial content and time evolution of replay during SWRs. Using this model, we find that the large majority of replay events contain spatially coherent, interpretable content. Furthermore, many events progress at real-world, rather than accelerated, movement speeds, consistent with actual experiences.
The decolonial bandwagon and the dangers of intellectual decolonisation

ABSTRACT In recent years, ‘intellectual decolonisation’ has become so popular in the Global North that we can now speak of there being a ‘decolonial bandwagon’. This article identifies some of the common limitations that can be found in this growing field of intellectual decolonisation. First and foremost, it is suggested that intellectual decolonisation in the Global North may be characterised by Northerncentrism due to the way in which decolonial scholarship may ignore decolonial scholars from the Global South. In order to address this ‘decolonisation without decolonising’, this article offers an alternative genealogy of intellectual decolonisation by discussing some of the most important yet neglected decolonial theory from the Global South. Thereafter, five other common limitations which may appear in discussions about intellectual decolonisation are identified, which are: reducing intellectual decolonisation to a simple task; essentialising and appropriating the Global South; overlooking the multifaceted nature of marginalisation in academia; nativism; and tokenism. The objective of this article is to highlight common limitations which may be present in discussions about intellectual decolonisation so as to provide a warning that some manifestations of intellectual decolonisation may not only be inadequate but may even reinscribe coloniality.
Social origins of support for democracy: a study of intergenerational mobility

ABSTRACT Recent evidence suggests that popular disaffection with liberal-democratic norms and institutions has been growing in different regions of the world, but studying the social origins of democratic versus authoritarian political preferences are especially relevant in countries with immature democratic practices. The main concern of this article is the association between intergenerational social mobility and support for democracy in post-socialist societies. I present a theoretical framework in which individuals’ political attitudes are affected by their intergenerational social mobility experiences. I model this theoretical argument using two complementary data-sets and various multivariable and multilevel statistical techniques. The results indicate that intergenerational social mobility, particularly its subjective perception, has statistically significant links with attitudes towards democracy and that this association is moderated by the attained level of democracy in the country where an individual resides. This may suggest that studying social origins of support for democracy by means of intergenerational social mobility can be an important tool to understand the conundrum of democratisation and democratic backsliding in post-socialist societies.
Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Here we analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We show that South Asia played a central role in the dispersion of these two lineages to neighboring regions. Moreover, we found that L1 exhibits signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.
TOX defines the degree of CD8+ T cell dysfunction in distinct phases of chronic HBV infection

Objective Chronic hepatitis B virus (HBV) infection is characterised by HBV-specific CD8+ T cell dysfunction that has been linked to Tcell exhaustion, a distinct differentiation programme associated with persisting antigen recognition. Recently, Thymocyte Selection-Associated High Mobility Group Box (TOX) was identified as master regulator of CD8+ T cell exhaustion. Here, we addressed the role of TOX in HBV-specific CD8+ T cell dysfunction associated with different clinical phases of infection. Design We investigated TOX expression in HBV-specific CD8+ T cells from 53 HLA-A*01:01, HLA-A*11:01 and HLA-A*02:01 positive patients from different HBV infection phases and compared it to hepatitis C virus (HCV)-specific, cytomegalovirus (CMV)-specific, Epstein-Barr virus (EBV)-specific and influenza virus (FLU)-specific CD8+ T cells. Phenotypic and functional analyses of virus-specific CD8+ T cells were performed after peptide-loaded tetramer-enrichment and peptide-specific expansion. Results Our results show that TOX expression in HBV-specific CD8+ T cells is linked to chronic antigen stimulation, correlates with viral load and is associated with phenotypic and functional characteristics of T-cell exhaustion. In contrast, similar TOX expression in EBV-specific and CMV-specific CD8+ T cells is not linked to T-cell dysfunction suggesting different underlying programmes. TOX expression in HBV-specific CD8+ T cells is also affected by targeted antigens, for example, core versus polymerase. In HBV-specific CD8+ T cells, TOX expression is maintained after spontaneous or therapy-mediated viral control in chronic but not self-limiting acute HBV infection indicating a permanent molecular imprint after chronic but not temporary stimulation. Conclusion Our data highlight TOX as biomarker specific for dysfunctional virus-specific CD8+ T cells in the context of an actively persisting infection.
Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

Comparative analysis of 162 (nearly) complete genomes of Asgard archaea, including 75 not reported previously, substantially expands the phylogenetic and metabolic diversity of the Asgard superphylum, with six additional phyla proposed. Phylogenetic analysis does not strongly support origin of eukaryotes from within Asgard, leaning instead towards a three-domain topology, with eukaryotes branching outside archaea. Comprehensive protein domain analysis in the 162 Asgard genomes results in a major expansion of the set of eukaryote signature proteins (ESPs). The Asgard ESPs show variable phyletic distributions and domain architectures, suggestive of dynamic evolution via horizontal gene transfer (HGT), gene loss, gene duplication and domain shuffling. The results appear best compatible with the origin of the conserved core of eukaryote genes from an unknown ancestral lineage deep within or outside the extant archaeal diversity. Such hypothetical ancestors would accumulate components of the mobile archaeal ‘eukaryome’ via extensive HGT, eventually, giving rise to eukaryote-like cells.
A meta-analysis of mesophyll conductance to CO2 in relation to major abiotic stresses in poplar species

Mesophyll conductance (gm) determines the diffusion of CO2 from the substomatal cavities to the site of carboxylation in the chloroplasts and represents a critical limiting factor to photosynthesis. In this study, we evaluated the average effect sizes of different environmental constraints on gm in Populus spp. , a forest tree model. We collected raw data of 815 A-Ci response curves from 26 datasets to estimate gm, using a single curve-fitting method to alleviate method-related bias. We performed a meta-analysis to assess the effects of different abiotic stresses on gm. We found a significant increase in gm from the bottom to the top of the canopy that was concomitant with the increase of maximum rate of carboxylation and light-saturated photosynthetic rate (Amax). gm was positively associated with increases in soil moisture and nutrient availability, but insensitive to increasing soil copper concentration, and did not vary with atmospheric CO2 concentration. Our results showed that gm was strongly related to Amax and to a lesser extent to stomatal conductance (gs). Also, a negative linear relation was obtained between gm and specific leaf area, which may be used to scale-up gm within the canopy.
Parental CG and CHG methylation variation is associated with allelic-specific expression in elite hybrid rice

Heterosis refers to the superior performance of the hybrid over the inbred parental lines. Besides genetic variation, epigenetic difference between the parental lines has been suggested to be involved in heterosis. However, precise nature and extent of parental epigenome difference and reprograming in hybrids governing heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, of which the high-quality reference genomic sequences are available. We show that the parental varieties display important variation in genic methylation at CG and CHG (H=A, C, or T) sequences. Compared with the parents the hybrids display dynamic methylation variation during development. However, many parental differentially methylated regions (DMR) at CG and CHG sites are maintained in the hybrid. Only a small fraction of the DMRs display non-additive DNA methylation variation which, however, shows no overall correlation with gene expression variation. By contrast, most of the allelic-specific expression (ASE) genes in the hybrid are associated with DNA methylation and the ASE negatively correlates with allelic-specific methylation (ASM) at CHG but positively at CG sites. The results reveal a specific DNA methylation reprogramming pattern in the hybrid rice and point to a role of parental CG and CHG methylation divergence in allelic specific expression that has been associated with phenotype variation and hybrid vigor in several plant species. One sentence summary Parental CG and CHG methylation divergence is maintained in hybrid and is related to allelic specific expression associated with phenotype variation and hybrid vigor.
GDF15 knockdown suppresses cervical cancer cell migration in vitro through the TGF‐β/Smad2/3/Snail1 pathway

Growth differentiation factor 15 (GDF15), a member of the transforming growth factor β (TGF‐β) superfamily, is a prognostic biomarker of cervical cancer. In addition, GDF15 has been reported to enhance the migration of colorectal cancer cells and liver cancer stem‐like cells. However, the mechanism by which GDF15 promotes cervical cancer cell migration is not completely understood. Here, we report that GDF15 expression is enhanced in cervical cancer tissues, as well as in cultured cervical cancer cells. ShGDF15 transfection markedly inhibited expression of Vimentin, N‐cadherin and Snail1, and resulted in up‐regulation of E‐cadherin expression in HT‐3 and HeLa cells. Moreover, knockdown of GDF15 suppressed wound healing rate and reduced the number of invasive cells. Furthermore, knockdown of GDF15 significantly suppressed the expression of phosphorylated Smad2 and Smad3. The addition of TGF‐β1 partially abolished the inhibitory effects of GDF15 knockdown on the migration and invasion of cervical cancer cells. In summary, we report here that GDF15 knockdown inhibits migration and invasion of cervical cancer cells in vitro through the TGF‐β/Smad2/3/Snail1 pathway.
An Unusual Source of Sinonasal Disease in an Immunocompromised Patient: A Case Report of the Clinical Presentation, Diagnosis, and Treatment of Acanthamoeba Rhinosinusitis

Chronic nasal crusting is a commonly encountered entity in an otolaryngology office. Progressive, extensive nasal crusting with erosion is relatively unusual, however. We present the case a 58-year-old renal transplant patient with a history of vasculitis and immunosuppression who presents with subjective headache and facial pain, nasal crusting, and isolated left ethmoid sinusitis. She developed extensive intranasal necrosis and underwent multiple endoscopic sinus surgeries with intraoperative biopsies, which played a critical role in her workup and eventual diagnosis of Acanthamoeba rhinosinusitis. Although she endured a difficult course, proper diagnosis and treatment allowed for her recovery over time. The differential diagnosis for intranasal necrosis is often broad. This case highlights the wide range of etiologies to be considered in a patient with extensive nasal crusting and erosion/necrosis, and the importance of thorough diagnostic evaluation in these patients, especially those in an immunocompromised state.