Miracle-dz/UniFAR-FTUs huggingface dataset:
Awareness and Use of Online Journals among Postgraduate Students in Select Nigerian Universities

Abstract Online journals are considered beneficial to researchers across the globe, however, research into awareness and use of online journals has been largely overshadowed by the whole gamut of electronic resources such as e-books, e-theses, and other electronic materials. Previous research in Nigeria has dwelt largely on the entirety of electronic resources, this study, specifically looked at online journals as a single component amongst other electronic resources. The objective of this study is to determine the awareness and use of online journals among postgraduate students in Nigeria. The survey revealed a mixed picture in terms of awareness and use of Open Access (OA) online journals and subscription based online journals. Among other findings, the study found that use is still a major challenge, which is rooted in a lack of awareness. This article contributes to the growing body of literature on the potentials of online journals (OA and subscription based), for the developing world in two ways: it provides information about online journals adoption in Nigeria, where little research has been done thus far, and it provides information about the practices of postgraduate students in public universities, a population area where little research has been done.
Radiation moms’ organizational survival for a decade: A shift from advocacy to non-advocacy activities

ABSTRACT This article examines changes in Japan’s social movement organizations (SMOs) after the Fukushima Daiichi nuclear disaster, focusing on mothers against radiation as key actors. After the Fukushima disaster, Japan’s SMOs enjoyed not only a resurgence of mass protests, but also an increase in advocacy activities and mothers’ participation in relation to radiation protection. Furthermore, some mothers’ SMOs against radiation survived for a decade. Such longevity is internationally unusual for an SMO. However, these SMOs have been virtually unstudied with regards to this longevity. How did mothers’ SMOs against radiation fight for survival for more than a decade? To answer this question, this project conducted long-term ethnographic research on a mothers’ SMO, the Kodomo-tachi o Hōshanō kara Mamoru Zenkoku Nettowāku (the National Network of Parents to Protect Children from Radiation; the “Kodomozenkoku”). Founded in 2011, Kodomozenkoku has been active for more than a decade. It recruited over 350 local SMOs as rank-and-file and shifted its focus from national advocacy activities to local non-advocacy activities. Based on this case study of Kodomozenkoku, this research argues that Kodomozenkoku’s flexibility in its transformation concerning goals, internal structure and interorganizational relations enabled this newcomer SMO to survive for over a decade.
Does the long-term contamination of lead (PbII) affect the bioremediation mechanisms of Microbacterium oxydans strain CM3 and CM7?

ABSTRACT Lead (Pb(II)) is a heavy metal with harmful effects on ecosystems and living organisms. Bacteria are used as part of the microorganisms involved in Pb(II) bioremediation. Herein, the effects of long-term (20 months) Pb(II) contamination (LTC) under a continuous sub-culturing system were evaluated on the growth rate, Pb-remediation potential, and Pb-remediation mechanisms of two strains, CM3 and CM7, of Microbacterium oxydans. LTC affected the optimal pH and temperature, and increased the growth rate of bacterial strains in the Pb(II) environment compared with native strains. Besides, the Pb-remediation potential of strains from LTC, CM3-b, and CM7-b, was significantly increased at pH 6.5. The biomass of strains was analyzed in terms of topographical and elemental percentage using SEM. LTC did not change the cell shape and dimensions of the studied strains. The Pb(II) percentage was significantly increased in sediments of the bacterial strains from LTC grown at pH 6.5, while the Pb(II) percentage was significantly reduced in the cell surface of strains grown under the LTC system. A correlation was found between P and Pb(II) percentage in the biomass of strains from LTC, indicating that these strains further precipitated Pb(II) in the form of lead phosphate. Furthermore, LTC reduced Pb(II) accumulation into the cell wall of strains.
Prior information enhances tactile representation in primary somatosensory cortex

Perception and adaptive decision making rely on the integration of incoming sensory input with prior knowledge or expectations. While tactile stimuli play a significant role in shaping our perception and decision making, if and how prior information modulates the representation of tactile stimuli in early somatosensory cortices is largely unknown. Here, we employed functional magnetic resonance imaging (fMRI) and a vibrotactile detection paradigm to study the effect of prior information on tactile perception and tactile stimulus representation in early somatosensory areas. The supra-voxel somatotopic organization of early somatosensory areas allowed us to assess the effect of prior information on finger-specific representations. We found that vibrotactile stimuli congruent with expectations are associated with improved vibrotactile detection performance and a decrease of the mean blood-oxygen-level-dependent (BOLD) signal in the contralateral primary somatosensory cortex (S1). Concurrently, finger-specific activity associated with anticipated vibrotactile stimulation revealed higher multivariate decoding accuracies and better alignment with S1’s somatotopic organization. In addition, we observed that prior information induced somatotopically organized activity in contralateral S1 even before tactile stimulation onset. The accuracy of the multivariate decoding of stimulus-specific expectations was therefore strongly associated with upcoming behavioral detection performance. Thus, our results reveal a role for S1 in the integration of upcoming tactile stimuli with prior information based on its somatotopic organization as well as the presence of behaviorally relevant activity in S1 before stimulation onset.
Causal models of human growth and their estimation using temporally-sparse data

Existing models of human growth provide little insight into the mechanisms responsible for inter-individual and inter-population variation in children’s growth trajectories. Building on general theories linking growth to metabolic rates, we develop causal parametric models of height and weight growth incorporating a novel representation of human body allometry and a phase-partitioned representation of ontogeny. These models permit separation of metabolic causes of growth variation, potentially influenced by diet and disease, from allometric factors, potentially under strong genetic control. We estimate model parameters using a Bayesian multilevel statistical design applied to temporally-dense height and weight measurements of U.S. children, and temporally-sparse measurements of Indigenous Amazonian children. This facilitates a comparison of the metabolic and allometric contributions to observed cross-cultural variation in the growth trajectories of the two populations. These theoretical growth models constitute an initial step toward a better understanding of the causes of growth variation in our species, while potentially guiding the development of appropriate, and desired, healthcare interventions in societies confronting growth-related health challenges. Short Summary New causal models of human growth facilitate cross-cultural comparisons of metabolism and allometry.
HDAC8-mediated inhibition of EP300 drives a neural crest-like transcriptional state that increases melanoma brain metastasis

Melanomas are heterogeneous and adopt multiple transcriptional states that can confer an invasive phenotype and resistance to therapy. Little is known about the epigenetic drivers of these cell states, limiting our ability to regulate melanoma heterogeneity and tumor progression. Here we identify stress-induced HDAC8 activity as the driver of a neural crest stem cell (NCSC)-like transcriptional state that increased the formation of melanoma brain metastases (MBM). Exposure of melanocytes and melanoma cells to multiple different stresses led to HDAC8 activation, a switch to a NCSC gene expression signature and the adoption of an amoeboid, invasive phenotype. This cell state enhanced the survival of melanoma cells under shear stress conditions and increased the formation of metastases in the brain. scRNA-seq analyses showed that HDAC8 expression was correlated with the NCSC cell state in clinical MBM specimens. ATAC-Seq and ChIP-Seq analysis showed HDAC8 to alter chromatin structure by increasing H3K27ac and accessibility at c-Jun binding sites without changing global histone acetylation. The increased accessibility of Jun binding sites was paralleled by decreased H3K27ac and accessibility at MITF binding sites and loss of melanoma-lineage gene expression. Mass spectrometry-based acetylomics demonstrated that HDAC8 deacetylated the histone acetyltransferase (HAT) EP300 leading to its enzymatic inactivation. This, in turn, led to an increased binding of EP300 to Jun-transcriptional sites and decreased binding to MITF-transcriptional sites. Increased expression of EP300 decreased invasion and increased the sensitivity of melanoma cells to multiple stresses while inhibition of EP300 function increased invasion and resistance to stress. We identified HDAC8 as a novel mediator of transcriptional co-factor inactivation and chromatin accessibility that increases MBM development.
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

We seek to transform how new and emergent variants of pandemic-causing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLMs) which can learn the evolutionary landscape of SARS-CoV-2 genomes. By pre-training on over 110 million prokaryotic gene sequences and fine-tuning a SARS-CoV-2-specific model on 1.5 million genomes, we show that GenSLMs can accurately and rapidly identify variants of concern. Thus, to our knowledge, GenSLMs represents one of the first whole-genome scale foundation models which can generalize to other prediction tasks. We demonstrate scaling of GenSLMs on GPU-based supercomputers and AI-hardware accelerators utilizing 1.63 Zettaflops in training runs with a sustained performance of 121 PFLOPS in mixed precision and peak of 850 PFLOPS. We present initial scientific insights from examining GenSLMs in tracking evolutionary dynamics of SARS-CoV-2, paving the path to realizing this on large biological data.
Ritualistic use of ayahuasca enhances a shared functional connectome identity with others

The knowledge that brain functional connectomes are both unique and reliable has enabled behaviourally relevant inferences at a subject level. However, it is unknown whether such “fingerprints” persist under altered states of consciousness. Ayahuasca is a potent serotonergic psychedelic which elicits a widespread dysregulation of functional connectivity. Used communally in religious ceremonies, its shared use may highlight relevant novel interactions between mental state and FC inherency. Using 7T fMRI, we assessed resting-state static and dynamic FCs for 21 Santo Daime members after collective ayahuasca intake in an acute, within-subject study. Here, connectome fingerprinting revealed a shared functional space, accompanied by a spatiotemporal reallocation of keypoint edges. Importantly, we show that interindividual differences in higher-order FCs motifs are relevant to experiential phenotypes, given that they can predict perceptual drug effects. Collectively, our findings offer an example as to how individualised connectivity markers can be used to trace a subject’s functional connectome across altered states of consciousness.
Cilium proteomics reveals Numb as a positive regulator of the Hedgehog signaling pathway

The transduction of Hedgehog (Hh) signaling relies on the primary cilium, a cell surface organelle acting as a signaling hub for the cell. Using proximity labeling and quantitative proteomics, we identified Numb as a new ciliary protein that positively regulates Hh signaling. Numb localizes to the ciliary pocket and acts as an endocytic adaptor to incorporate Ptch1 into clathrin-coated vesicles, thereby promoting Ptch1 exit from the cilium, a key step in Hh signaling activation. Numb loss impaired Sonic Hedgehog-induced Ptch1 departure from the cilium, resulting in severe attenuation of Hh signaling. Genetic ablation of Numb and its homolog Numblike in the developing cerebellum impaired the proliferation of granule cell precursors, a Hh-dependent process, resulting in reduced cerebellar size. This study demonstrates a key function of Numb in controlling protein levels in the cilium, and highlights Numb’s critical role in the regulation of Hh signaling.
Genetic analysis of a phenotypic loss in the mechanosensory entrainment of a circalunar clock

Genetic variants underlying traits that become either non-adaptive or selectively neutral are expected to have altered evolutionary trajectories. Uncovering genetic signatures associated with phenotypic loss presents the opportunity to discover the molecular basis for the phenotype in populations where it persists. Here we study circalunar clocks in populations of marine midge Clunio marinus. The circalunar clock synchronizes development to the lunar phase, and it is set by moonlight and tidal cycles of mechanical agitation. Two out of ten studied populations have lost their sensitivity to mechanical agitation while preserving sensitivity to moonlight. Intriguingly, the F1 offspring of the two insensitive populations regained the sensitivity to mechanical entrainment, implying a genetically independent loss of the phenotype. By combining quantitative trait locus mapping and genome-wide screens, we explored the genetics of this phenotypic loss. QTL analysis suggested an oligogenic origin with one prevalent additive locus in one of the strains. In addition, it confirmed a distinct genetic architecture in the two insensitive populations. Genomic screens further uncovered several candidate genes underlying QTL regions. The strongest signal under the most prominent QTL contains a duplicated STAT1 gene, which has a well-established role in development, and CG022363, an ortholog of the Drosophila melanogaster CG32100 gene, which plays a role in gravitaxis. Our results support the notion that adaptive phenotypes have a complex genetic basis with mutations occurring at several loci. By dissecting the most prevalent signals, we started to reveal the molecular machinery responsible for the entrainment of the circalunar clock.
Tidally-disrupted Molecular Clouds falling to the Galactic Center

Abstract We found a molecular cloud connecting from the outer region to the “Galactic Center Mini-spiral (GCMS)” which is a bundle of the ionized gas streams adjacent to Sgr A*. The molecular cloud has a filamentary appearance which is prominent in the CS J=2-1 emission line and is continuously connected with the GCMS. The velocity of the molecular cloud is also continuously connected with that of the ionized gas in the GCMS observed in the H42α recombination line. The morphological and kinematic relations suggest that the molecular cloud is falling from the outer region to the vicinity of Sgr A*, being disrupted by the tidal shear of Sgr A* and ionized by UV emission from the Central Cluster. We also found the SiO J=2-1 emission in the boundary area between the filamentary molecular cloud and the GCMS. There seems to exist shocked gas in the boundary area.
Recombinant Human Proteoglycan 4 (rhPRG4) Downregulates TNFα-Stimulated NFκB Activity and FAT10 Expression in Human Corneal Epithelial Cells

Dry Eye Disease (DED) is a complex pathology affecting millions of people with significant impact on quality of life. Corneal inflammation, including via the NFκB pathway, plays a key etiological role in DED. Recombinant human proteoglycan 4 (rhPRG4) has been shown to be a clinically effective treatment for DED that has anti-inflammatory effects in corneal epithelial cells, but the underlying mechanism is still not understood. Our goal was to understand if rhPRG4 affects TNFα-stimulated inflammatory activity in corneal epithelial cells. We treated hTERT-immortalized corneal epithelial (hTCEpi) cells ±TNFα ±rhPRG4 and performed Western blotting on cell lysate and RNA sequencing. Bioinformatics analysis revealed that rhPRG4 had a significant effect on TNFα-mediated inflammation with potential effects on matricellular homeostasis. rhPRG4 reduced activation of key inflammatory pathways and decreased expression of transcripts for key inflammatory cytokines, interferons, interleu-kins, and transcription factors. TNFα treatment significantly increased phosphorylation and nuclear translocation of p65, and rhPRG4 significantly reduced both these effects. RNA sequencing identified FAT10, which has not been studied in the context of DED, as a key pro-inflammatory transcript increased by TNFα and decreased by rhPRG4. These results were confirmed at the protein level. In summary, rhPRG4 is able to downregulate NFκB activity in hTCEpi cells, suggesting a potential biological mechanism by which it may act as a therapeutic for DED.
A path to DOT: formalizing fully path-dependent types

The Dependent Object Types (DOT) calculus aims to formalize the Scala programming language with a focus on path-dependent types — types such as x.a1… an.T that depend on the runtime value of a path x.a1… an to an object. Unfortunately, existing formulations of DOT can model only types of the form x.A which depend on variables rather than general paths. This restriction makes it impossible to model nested module dependencies. Nesting small components inside larger ones is a necessary ingredient of a modular, scalable language. DOT’s variable restriction thus undermines its ability to fully formalize a variety of programming-language features including Scala’s module system, family polymorphism, and covariant specialization. This paper presents the pDOT calculus, which generalizes DOT to support types that depend on paths of arbitrary length, as well as singleton types to track path equality. We show that naive approaches to add paths to DOT make it inherently unsound, and present necessary conditions for such a calculus to be sound. We discuss the key changes necessary to adapt the techniques of the DOT soundness proofs so that they can be applied to pDOT. Our paper comes with a Coq-mechanized type-safety proof of pDOT. With support for paths of arbitrary length, pDOT can realize DOT’s full potential for formalizing Scala-like calculi.
Evidence for a Spoken Word Lexicon in the Auditory Ventral Stream

The existence of a neural representation for whole words (i.e., a lexicon) is a common feature of many models of speech processing. Prior studies have provided evidence for a visual lexicon containing representations of whole written words in an area of the ventral visual stream known as the “Visual Word Form Area” (VWFA). Similar experimental support for an auditory lexicon containing representations of spoken words has yet to be shown. Using fMRI rapid adaptation techniques, we provide evidence for an auditory lexicon in the “Auditory Word Form Area” (AWFA) in the human left anterior superior temporal gyrus that contains representations highly selective for individual spoken words. Furthermore, we show that familiarization with novel auditory words sharpens the selectivity of their representations in the AWFA. These findings reveal strong parallels in how the brain represents written and spoken words, showing convergent processing strategies across modalities in the visual and auditory ventral streams. Highlights Individual auditory word form areas (AWFA) were defined via an auditory localizer The AWFA shows tuning for individual real words but not untrained pseudowords The AWFA develops tuning for individual pseudowords after training
Proteomics of resilience to Alzheimer’s disease identifies brain regional soluble Aβ levels, actin filament processes, and response to injury

Resilience to Alzheimer’s disease (RAD) is an uncommon combination of high disease burden without dementia that may provide critical insights into limiting the clinical impact of this incurable disease. In this study, we used mass spectrometry-based proteomics to quantify regional protein differences that characterize RAD. Starting with over 700 brain donations, we identified 43 extensively annotated research participants who met stringent inclusion exclusion criteria and analyzed matched isocortical regions, hippocampus, and caudate nucleus. Differential expression analysis of 7,115 soluble proteins identified lower isocortical and hippocampal soluble Aβ peptide levels as a significant feature of RAD. Protein co-expression analysis revealed a group of 181 densely-interacting proteins significantly associated with RAD that were enriched for actin filament-based process, cellular detoxification, and wound healing in isocortex and hippocampus. We further support our findings using data from 689 human isocortical samples from four independent external cohorts that were the closest approximations of our clinico-pathologic groups. The molecular basis of RAD, a widely replicated state in older adults for which there is no experimental model, likely holds important insights into therapeutic interventions for Alzheimer’s disease.