Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome

During replication, RNA viruses accumulate genome alterations, such as mutations and deletions. The interactions between individual variants can determine the fitness of the virus population and, thus, the outcome of infection. To investigate the effects of defective interfering genomes (DI) on wild-type (WT) poliovirus replication, we developed an ordinary differential equation model. We experimentally determined virus and DI replication during co-infection, and use these data to infer model parameters. Our model predicts, and our experimental measurements confirm, that DI replication and encapsidation are the most important determinants for the outcome of the competition. WT replication inversely correlates with DI replication. Our model predicts that genome replication and effective DI genome encapsidation are critical to effectively inhibit WT production, but an equilibrium can be established which enables WT to replicate, albeit to reduce levels.
Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections

Uropathogenic Escherichia coli (UPEC) proliferate within superficial bladder umbrella cells to form intracellular bacterial communities (IBCs) during early stages of urinary tract infections. However, the dynamic responses of IBCs to host stresses and antibiotic therapy are difficult to assess in situ. We develop a human bladder-chip model wherein umbrella cells and bladder microvascular endothelial cells are co-cultured under flow in urine and nutritive media respectively, and bladder filling and voiding mimicked mechanically by application and release of linear strain. Using time-lapse microscopy, we show that rapid recruitment of neutrophils from the vascular channel to sites of infection leads to swarm and neutrophil extracellular trap formation but does not prevent IBC formation. Subsequently, we tracked bacterial growth dynamics in individual IBCs through two cycles of antibiotic administration interspersed with recovery periods which revealed that the elimination of bacteria within IBCs by the antibiotic was delayed, and in some instances, did not occur at all. During the recovery period, rapid proliferation in a significant fraction of IBCs reseeded new foci of infection through bacterial shedding and host cell exfoliation. These insights reinforce a dynamic role for IBCs as harbours of bacterial persistence, with significant consequences for non-compliance with antibiotic regimens.
Antifungal activities of artesunate, chloramphenicol, and cotrimoxazole against Basidiobolus species, the causal agents of gastrointestinal basidiobolomycosis

Basidiobolus species (n =13) isolated from human gastrointestinal basidiobolomycosis and lizards were tested against artesunate, chloramphenicol, and cotrimoxazole. The three agents exhibited inhibitory actions against Basidiobolus species comparable to the known antifungals. The combined effects of artesunate + voriconazole and cotrimoxazole + voriconazole have significant synergic effects, p = 0.003 and p = 0.021, respectively. These are promising results that enhance accelerated combined treatment of GIB in humans particularly the combination of artesunate and voriconazole.
The three-dimensional landscape of chromatin accessibility in Alzheimer’s disease

Much is still unknown about the neurobiology of Alzheimer’s disease (AD). To better understand AD, we generated 636 ATAC-seq libraries from cases and controls to construct detailed genomewide chromatin accessibility maps of neurons and non-neurons from two AD-affected brain regions, the entorhinal cortex and superior temporal gyrus. By analyzing a total of 19.6 billion read pairs, we expanded the known repertoire of regulatory sequences in the human brain. Multi-omic data integration associated global patterns of chromatin accessibility with gene expression and identified cell-specific enhancer-promoter interactions. Using inter-individual variation in chromatin accessibility, we define cis-regulatory domains capturing the 3D structure of the genome. Multifaceted analyses uncovered disease associated perturbations impacting chromatin accessibility, transcription factor regulatory networks and the 3D genome, and implicated transcriptional dysregulation in AD. Overall, we applied a systematic approach to understand the role of the 3D genome in AD and to illuminate novel disease biology that can advance diagnosis and therapy.
Transcriptomic Analyses of MYCN-Regulated Genes in Anaplastic Wilms’ Tumour Cell Lines Reveals Oncogenic Pathways and Potential Therapeutic Vulnerabilities

The MYCN proto-oncogene is deregulated in many cancers, most notably in neuroblastoma where MYCN gene amplification identifies a clinical subset with very poor prognosis. Gene expression and DNA analyses have also demonstrated over-expression of MYCN mRNA, as well as focal amplifications, copy number gains and presumptive change of function mutations of MYCN in Wilms’ tumours with poorer outcome, including tumours with diffuse anaplasia. Surpisingly, however, the expression and functions of the MYCN protein in Wilms’ tumours still remain obscure. In this study, we assessed MYCN protein expression in primary Wilms’ tumours using immunohistochemistry of tissue microarrays. We found MYCN protein to be expressed in tumour blastemal cells, and absent in stromal and epithelial components. For functional studies, we used two anaplastic Wilms’ tumour cell-lines, WiT49 and 17.94, to study the biological and transcriptomic effects of MYCN depletion. We found that MYCN knockdown consistently led to growth suppression but not cell death. RNA sequencing identified 561 MYCN-regulated genes shared by WiT49 and 17.94 cell-lines. As expected, numerous cellular processes were downstream of MYCN. MYCN positively regulated the miRNA regulator and known Wilms’ tumour oncogene LIN28B, the genes encoding methylosome proteins PRMT1, PRMT5 and WDR77, and the mitochondrial translocase genes TOMM20 and TIMM50. MYCN repressed genes included the developmental signalling receptor ROBO1 and the stromal marker COL1A1. Importantly, we found that MYCN also repressed the presumptive Wilms’ tumour suppressor gene REST, with MYCN knockdown resulting in increased REST protein and concomitant repression of REST target genes. Together, our study identifies regulatory axes that interact with MYCN, providing novel pathways for potential targeted therapeutics for poor prognosis Wilms’ tumour.
Yield strengths and stress induced crackles in copper films: effects of substrate and passivated layer

Yield strengths in unpassivated and 530 nm TiN passivated Cu films deposited on Ti, high-speed steel and Ni substrates have been measured by x-ray diffraction (XRD) in combination with the four-point bending method. The results show that, although the texture and average grain size, investigated by XRD and transmission electron microscopy respectively, do not vary with different substrate, the yield strength of the Cu film increases obviously when a thin passivated layer is present and varies slightly with substrates. Many crackles appear in the passivated Cu film on Ti substrate but do not appear in other samples. The experimental results have been explained satisfactorily with an expression for the yield strength of thin films given previously.
Inter- and intra-specific variation in hair cortisol concentrations of Neotropical bats

Quantifying hair cortisol has become popular in wildlife ecology for its practical advantages for evaluating health. Before hair cortisol levels can be reliably interpreted however, it is key to first understand the intrinsic factors explaining intra- and interspecific variation. Bats are an ecologically diverse group of mammals that allow studying such variation. Given that many bat species are threatened or have declining populations in parts of their range, non-invasive tools for monitoring colony health and identifying cryptic stressors are needed to efficiently direct conservation efforts. Here we describe intra- and interspecific sources of variation in hair cortisol levels in 18 Neotropical bat species from Mexico and Belize. We found that fecundity is an important ecological trait explaining interspecific variation in bat hair cortisol. Other ecological variables such as colony size, roost durability, and basal metabolic rate did not explain hair cortisol variation among species. At the individual level, females exhibited higher hair cortisol levels than males, and the effect of body mass varied among species. Overall, our findings help validate and accurately apply hair cortisol as a monitoring tool in free-ranging bats.
Characterization of a novel variant in the HR1 domain of MFN2 in a patient with ataxia, optic atrophy and sensorineural hearing loss

Pathogenic variants in MFN2 cause Charcot-Marie-Tooth disease (CMT) type 2A (CMT2A) and are the leading cause of the axonal subtypes of CMT. CMT2A is characterized by predominantly distal motor weakness and muscle atrophy, with highly variable severity and onset age. Notably, some MFN2 variants can also lead to other phenotypes such as optic atrophy, hearing loss and lipodystrophy. Despite the clear link between MFN2 and CMT2A, our mechanistic understanding of how dysfunction of the MFN2 protein causes human disease pathologies remains incomplete. This lack of understanding is due in part to the multiple cellular roles of MFN2. Though initially characterized for its role in mediating mitochondrial fusion, MFN2 also plays important roles in mediating interactions between mitochondria and other organelles, such as the endoplasmic reticulum and lipid droplets. Additionally, MFN2 is also important for mitochondrial transport, mitochondrial autophagy, and has even been implicated in lipid transfer. Though over 100 pathogenic MFN2 variants have been described to date, only a few have been characterized functionally, and even then, often only for one or two functions. Here, we describe a novel homozygous MFN2 variant, D414V, in a patient presenting with cerebellar ataxia, deafness, blindness, and diffuse cerebral and cerebellar atrophy. Characterization of patient fibroblasts reveals phenotypes consistent with impaired MFN2 functions and expands the phenotypic presentation of MFN2 variants to include cerebellar ataxia.
Bromodomain 4 inhibition leads to MYCN downregulation in Wilms’ tumor cells

Wilms’ tumor is the most common childhood kidney cancer. Two distinct histological subtypes of Wilms’ tumor have been described: tumors lacking anaplasia (the favorable subtype) and tumors displaying anaplastic features (the unfavorable subtype). Children with favorable disease generally have a very good prognosis, while those with anaplasia are oftentimes refractory to standard treatments and suffer poor outcomes. MYCN dysregulation has been associated with a number of pediatric cancers including the anaplastic subtype of Wilms’ tumor. In this context, we undertook a functional genomics approach to uncover novel therapeutic strategies for those patients with anaplastic Wilms’ tumor. Genomic analysis and in vitro experimentation demonstrate that Wilms’ tumor cell growth can be reduced by modulating MYCN overexpression via BRD4 inhibition. We observed a time dependent reduction of MYCN and MYC protein levels upon BRD4 inhibition in Wilms’ tumor cell lines which led to increased cell death and suppressed proliferation. We suggest that AZD5153, a novel dual-BRD4 inhibitor, can reduce MYCN levels and should be further explored for its therapeutic potential against Wilms’ tumor.
Why extinction estimates from extant phylogenies are so often zero

Time-calibrated phylogenies comprising only extant lineages are widely used to estimate historical speciation and extinction rates. Such extinction rate estimates have long been controversial as many phylogenetic studies report zero extinction in many taxa, a finding in conflict with the fossil record. To date, the causes of this widely observed discrepancy remain unresolved. Here we provide a novel and simple explanation for these “zero-inflated” extinction rate estimates, based on the recent discovery that there exist many alternative “congruent” diversification scenarios that cannot possibly be distinguished on the sole basis of extant timetrees. Consequently, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may in principle exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to hit and stick to the boundary estimate of zero extinction. To test this explanation, we estimated extinction rates using maximum likelihood for a set of simulated trees and for 121 empirical trees, while either allowing or preventing negative extinction rates. We find that the existence of congruence classes and imposed bounds on extinction rates can explain the zero-inflation of previous extinction rate estimates, even for large trees (1000 tips) and in the absence of any detectable model violations. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.
A field-wide assessment of differential expression profiling by high-throughput sequencing reveals widespread bias

Here we assess inferential quality in the field of differential expression profiling by high throughput sequencing, based on analysis of datasets submitted 2008-2020 to the NCBI GEO data repository. We take advantage of the parallel differential expression testing over thousands of genes, whereby each experiment leads to a large set of p values, the distribution of which can indicate the validity of assumptions behind the test. Moreover, from a well-behaved p value set π0, the fraction of genes that are not differentially expressed, can be estimated. We found that only 25% of experiments resulted in theoretically expected p value histogram shapes, although there is a marked improvement over time. Uniform p value histogram shapes, indicative of < 100 true effects, were extremely few. Furthermore, although many HT-seq workflows assume that most genes are not differentially expressed we found 37% of experiments to have π0-s of less than 0.5, as if most genes changed their expression level. Restricting our analysis to studies involving cancer or transcription factors, expected to lead to real changes in expression of many genes, did not result in meaningfully different distributions of π0-s. Both the fractions of different p value histogram types and the π0 values are strongly associated with the differential expression analysis program used by the original authors. While we could double the proportion of theoretically expected p value distributions by removing low-count features from analysis, this treatment did not remove the association with the analysis program. Taken together, our results indicate widespread bias in differential expression profiling field.
In Vivo Sublayer Analysis of Human Retinal Inner Plexiform Layer Obtained by Visible-Light Optical Coherence Tomography

Purpose Growing evidence suggests, in glaucoma, the dendritic degeneration of subpopulation of the retinal ganglion cells (RGCs) may precede RGCs soma death. Since different RGCs synapse in different IPL sublayers, visualization of the lamellar structure of the IPL could enable both clinical and fundamental advances in glaucoma understanding and management. In this pilot study, we investigated whether visible-light optical coherence tomography (vis-OCT) could detect the difference in the inner plexiform layer (IPL) sublayers thicknesses between small cohorts of healthy and glaucomatous subjects. Method We investigated vis-OCT retinal images from nine healthy and five glaucomatous subjects. Four of the healthy subjects were scanned three times each in two separate visits, and five healthy and five glaucoma subjects were scanned three times during a single visit. Raster speckle-reduction scans (3 by 3 by 1.2 mm^3: horizontal; vertical; axial directions with 8192×8×1024 samplings, respectively) of the superior macular were acquired. IPL sublayers were then manually segmented using averaged A-line profiles. Results The mean ages of glaucoma and healthy subjects are 59.6 +/- 13.4 and 45.4 +/- 14.4 years (p =0.02, Wilcoxon rank-sum test), respectively. The visual field mean deviation (MD) are −26.4 to −7.7 dB in glaucoma patient and −1.6 to 1.1 dB in healthy subjects (p =0.002). The mean circumpapillary retinal nerve fiber layer (RNFL) thicknesses are 59.6 +/- 9.1 μm in glaucoma and 99.2 +/- 16.2 μm in healthy subjects (p=0.004). Median coefficients of variation (CVs) of intra-session repeatability for the entire IPL and three sublayers are 3.1%, 5.6%, 6.9%, and 5.6% in healthy subjects and 1.8%, 6.0%, 7.7%, and 6.2% in glaucoma patients, respectively. The mean entire IPL thicknesses are 36.2 +/- 1.5 μm in glaucomatous and 40.1 +/- 1.7 micrometer in healthy eyes (p=0.003, Mixed-effects model). We found that the middle sublayer thickness was responsible for the majority of the difference (14.2 +/- 1.8 μm in glaucomatous and 17.5 +/- 1.4 in healthy eyes, p<0.01). Conclusions IPL sublayer analysis revealed that the middle sublayer could be responsible for the majority of IPL thinning in glaucoma. Vis-OCT quantified IPL sublayers with good repeatability in both glaucoma and healthy subjects. Visualization of the IPL sublayers may enable the investigation of lamella-specific changes in the IPL in glaucoma and may help elucidate the response of different types of RGCs to the disease.
Structural and mechanistic insight into spectral tuning in flavin-binding fluorescent proteins

Determining the molecular origin of spectral tuning in photoactive biological systems is instrumental for understanding their function. Spectral-tuning efforts for flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, are limited by their dependency on protein-bound flavins, whose structure and hence electronic properties, cannot be altered by mutation. To address those shortcomings, we here present the photophysical, computational and structural characterization of structurally uncharacterized blue-shifted FbFPs, carrying a previously described lysine substitution within their flavin-binding pocket. X-ray structures reveal displacement of the lysine away from the chromophore and opening up of the structure as cause for the blue shift. Site-saturation mutagenesis and high-throughput screening, yielded a red-shifted variant, in which the lysine side chain of the blue-shifted variant is stabilized in close distance to the flavin by a secondary mutation, mechanistically accounting for the red shift. Thus, a single secondary mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools that should find application in life sciences.
Antioxidant activity of some wild edible plants of Meghalaya state of India: A comparison using two solvent extraction systems

The objective of the present study was to find out the antioxidant potential of some wild edible plants, traditionally used by the local people of Meghalaya state in India and also to investigate the effect of solvent extraction system (aq. methanol and acetone) on the total phenolic, flavonoids and flavonols content, reducing power and antioxidant activity of the plants. The total phenol content varied from 3.31±0.10 to 27.67±0.16 mg/g in the aqueous methanol extract and 2.61±0.13 to 6.85±0.13 mg/g in the acetone extract of the plants. Flavonoids content were between 8.11±0.071 and 52.14±0.004 mg/g in aqueous methanol extract and varied from 1.22± 0.01 to 52.17± 0.01 mg/g in the acetone extract. 1,1diphenyl-2-picryl hydrazyl (DPPH) radical scavenging effect of the extracts were determined spectrophotometrically. The highest radical scavenging was observed in the aq. methanol extract of Gentiana pedicellata with IC50 = 0.23±0.0007 mg dry material. The greater amount of phenolic compounds, flavonoids and flavonol content leads to more potent radical scavenging effect as shown by the aq. methanol extract of G. pedicellata. Flavonol content was observed highest in the aq. methanol extract of G. pedicellata (23.12 ±0.006 mg/g) and least in the acetone extract of Gynocardia odorata (0.09±0.008 mg/g). The reducing power of the extracts of the plants were also evaluated as mg AAE (ascorbic acid equivalent)/g dry material and highest reducing power (16.11 ± 0.03) observed in the aq. methanol extract of Bauhinia purpurea, which contain maximum amount of phenolic compounds (27.67±0.16 mg/g GAE). The results indicate that the type of extragent significantly influenced the antioxidant activity of these wild edible plants and could be utilized as potential source of natural antioxidant in the food or in pharmaceutical industry.
The Dorsolateral Prefrontal Cortex Presents Structural Variations Associated with Empathic Capacity in Psychotherapists

Empathic capacity has been shown to be correlated with brain structural variations, such as cortical thickness. Since psychotherapists have a constant demand to modulate their empathic response, in this study we compared cortical thickness between a group of psychotherapists and a control group at prefrontal and cingulate brain regions, and investigated how this is correlated with their empathic skills. Eighteen psychotherapists and eighteen healthy controls underwent 3-Tesla MRI scanning and completed empathy-related psychometric assessments. Cortical thickness (CT) measures were estimated for each participant. We evaluated how these measures differed between groups, and if they were associated with individual empathy-related scores in a series of regions of interest. Our analysis shows that psychotherapists display a significantly greater CT at a region in the left dorsolateral prefrontal cortex (dlPFC; p < 0.05, FDR corrected). Moreover, psychotherapists’ CT in this region is correlated with the tendency to feel empathically concerned for others (p < 0.01, FDR corrected). This finding is relevant because the dlPFC region participates strongly in the cognitive components of the empathic response, such as emotion regulation and perspective-taking processes. Thus, our findings support the idea that empathic capacity is reflected by brain structural variations while also studying for the first time a sample of subjects for whom empathic responding is crucial in their profession.