Miracle-dz/UniFAR-FTUs huggingface dataset:
Iodidimonas, a bacterium unable to degrade hydrocarbons, thrives in a bioreactor treating oil and gas produced water

Iodidimonas is a genus recently described in bioreactors treating oil and gas produced water and in iodide rich brines. Besides the ability to oxidize iodine, little is known about the metabolic capabilities that enable Iodidimonas sp. to occupy this unique ecological niche. We isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor treating produced water. We describe the genomic features of these isolates and compare them with the only other four isolate genomes reported from this genus, as well as a metagenome-assembled genome from the source bioreactor. To survive in the produced water, Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal and organic compound stress. While the isolates could utilize a wide variety of carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines. Importance Occupying a niche habitat and having few representative isolates, genus Iodidimonas is a relatively understudied Alphaproteobacterial group. This genus has garnered attention due to its ability to corrode pipes in iodine production facilities and generate iodinated organic compounds during treatment of oil and gas produced water. The iodinated organic compounds are likely to be carcinogenic and may pose issues with recycling the treated water. Hence, detailed characterization of the metabolic potential of these isolates is not only of economic importance, but also sheds light on adaptation of this microbe to its environmental niche.
Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation

Core promoters are stretches of DNA at the beginning of genes that contain information that facilitates the binding of transcription initiation complex. Different functional subsets of genes have core promoters with distinct architectures and characteristic motifs. Some of these motifs inform the selection of transcription start sites (TSS). By discovering motifs with fixed distances from known TSS positions, we could in principle classify promoters into different functional groups. Due to the variability and overlap of architectures, promoter classification is a difficult task that requires new approaches. In this study, we present a new method based on non-negative matrix factorisation (NMF) and the associated software called seqArchR that clusters promoter sequences based on their motifs at near-fixed distances from a reference point, such as TSS. When combined with experimental data from CAGE, seqArchR can efficiently identify TSS-directing motifs, including known ones like TATA, DPE, and nucleosome positioning signal, as well as novel lineage-specific motifs and the function of genes associated with them. By using seqArchR on developmental time courses, we reveal how relative use of promoter architectures changes over time with stage-specific expression. seqArchR is a powerful tool for initial genome-wide classification and functional characterization of promoters. Its use cases are more general: it can also be used to discover any motifs at near-fixed distances from a reference point, even if they are present in only a small subset of sequences. seqArchR is available at http://www.bioconductor. org/packages/seqArchR.
Widespread sex ratio polymorphism in Caenorhabditis nematodes

Although equal sex ratio is ubiquitous and represents an equilibrium in evolutionary theory, biased sex ratios are predicted for certain local conditions. Cases of sex ratio bias have been mostly reported for single species, but little is known about its evolution above the species level. Here, we surveyed progeny sex ratios in 23 species of the nematode genus Caenorhabditis, including 19 for which we tested multiple strains. For the species with multiple strains, 5 species had female-biased and 2 had non-biased sex ratios in all strains, respectively. The other 12 species showed polymorphic sex ratios across strains. Female-biased sex ratios could be due to sperm competition whereby X-bearing sperm outcompete nullo-X sperm during fertilization. In this model, when sperm are limited allowing all sperm to be used, sex ratios are expected to be equal. However, in assays limiting mating to a few hours, most strains showed similarly biased sex ratios compared to unlimited mating experiments, except that one C. becei strain showed significantly reduced female bias compared to unlimited mating. Our study shows frequent polymorphism in sex ratios within Caenorhabditis species and that sperm competition alone cannot explain the sex ratio bias.
Shotgun metagenomics unravels higher antibiotic resistome profile in Bangladeshi gut microbiome

Antibiotic resistance management is a challenging task in Low and Middle-Income Countries (LMICs) such as Bangladesh. Improper regulation and uncontrolled spreading of Antibiotic Resistant Genes (ARGs) from LIMCs pose a great threat to global public health. The human gut microbiome is a massive reservoir of Antibiotic Resistant Genes (ARGs). In this study, we unraveled the ARGs in the gut microbiome of the Bangladeshi population and compared them with several other countries around the world. Here, 31 fecal samples from different ethnic groups living in Bangladesh namely Bengali (n=9), Chakma (n=6), Khyang (n=5), Marma (n=6), and Tripura (n=5) were collected. Shotgun metagenomic sequencing method was implemented for revealing the ARGs. The resistome profiling was executed on three levels-the total microbiome, the plasmidome, and the virome. In all three levels, samples from Bangladeshi cohorts showed higher ARG profiles compared to foreign samples. On average, the number of ARGs in the Bangladeshi samples ranged between 75.11 and 88. Among them, class C beta-lactamases, quinolone resistance genes, and tetracycline efflux pumps were relatively more abundant. Additionally, the MexPQ-OpmE drug resistance pathway was found to be more prevalent. Findings from our study suggest that the spread of antibiotic resistance within the Bangladeshi population is being facilitated by the gut microbiome especially via the mobilome. Therefore, strict regulation on antibiotic usage is necessary to halt the spread of ARGs.
Hierarchical and fine-scale mechanisms of binocular rivalry for conscious perception

Conscious perception alternates between the two eyes’ images during binocular rivalry. How hierarchical processes in our brain interact to resolve visual competition to generate conscious perception remains unclear. Here we investigated the mesoscale neural circuitry for binocular rivalry in human cortical and subcortical areas using high-resolution functional MRI at 7 Tesla. Eye-specific response modulation in binocular rivalry was strongest in the superficial layers of V1 ocular dominance columns (ODCs), and more synchronized in the superficial and deep layers. The intraparietal sulcus (IPS) generated stronger eye-specific response modulation and increased effective connectivity to the early visual cortex during binocular rivalry compared to monocular “replay” simulations. Although there was no evidence of eye-specific rivalry modulation in the lateral geniculate nucleus (LGN) of the thalamus, strong perceptual rivalry modulation can be found in its parvocellular (P) subdivision. Finally, IPS and ventral pulvinar showed robust perceptual rivalry modulation and increased connectivity to the early visual cortex. These findings demonstrate that local interocular competition arises from lateral mutual inhibition between V1 ODCs, and feedback signals from IPS to visual cortex and visual thalamus further synchronize and resolve visual competition to generate conscious perception. Graphical abstract Highlights Eye-specific rivalry modulation is strongest in the superficial layers of V1 ODCs and more synchronized in superficial and deep layers IPS generates stronger eye-specific response modulation and increases connectivity to V1 during rivalry compared to replay LGN activity shows no evidence of eye-specific rivalry modulation but strong perceptual rivalry modulation in its P subdivision IPS and ventral pulvinar show robust perceptual rivalry modulation and increased connectivity to the early visual cortex
Human Vascularized Bile Duct-on-a Chip: A multi-cellular micro-physiological system for studying Primary Sclerosing Cholangitis

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease in which the bile ducts of the liver become inflamed and scarred. Scarred bile ducts eventually narrow and obstruct and can cause additional liver pathology including liver failure, repeated infections, and tumors. The pathogenesis of PSC remains largely unknown, partly due to difficulty in obtaining cholangiocytes and partly due to a paucity of in vitro models that capture the various factors contributing to disease progression. Here we report the development of a human vascularized bile duct-on-a-chip that models blood vessels and bile ducts structurally and functionally in three dimensions and includes cholangiocytes derived from control and PSC patient tissue and bile. The flow of blood and bile was modeled by perfusion of cell-lined channels, and cholangiocytes and endothelial cells displayed differential responses to perfusion. Normal and PSC cholangiocytes polarized normally, formed mature tight junctions and displayed similar permeability, comparable to ex vivo measurements. The model with PSC cholangiocytes, however, became more inflammatory than the normal under the stimulation of IL-17A, which induced PBMC and differentiated Th17 cells in the vascular channel to transmigrate more through the endothelial layer of the vascular compartment. In sum, this human vascularized bile duct-on-a-chip recapitulated the vascular-biliary interface structurally and functionally and represents a novel multicellular platform to study inflammatory and fibrotic cholangiopathies such as PSC.
Genetic Inactivation of β-Catenin Attenuates and Its Activation Aggravates Desmoplakin Cardiomyopathy

Aim Mutations in the DSP gene encoding desmoplakin, a constituent of the desmosomes at the intercalated discs (IDs), cause a phenotype that spans arrhythmogenic cardiomyopathy (ACM) and dilated cardiomyopathy (DCM). It is typically characterized by biventricular enlargement and dysfunction, severe myocardial fibrosis, cell death, and arrhythmias. The canonical WNT (cWNT)/β-catenin signaling pathway is implicated in the pathogenesis of ACM. Given that β-catenin, an indispensable co-transcriptional regulator of the cWNT pathway, is also a member of the IDs, we genetically inactivated or activated β-catenin to determine its role in the pathogenesis of the desmoplakin cardiomyopathy. Methods and Results The Dsp gene was conditionally deleted in cardiac myocytes concomitant with the genetic inactivation or activation of β-catenin using the tamoxifen-inducible MerCreMer mice. Inactivation and activation of β-catenin were achieved upon deletion of its transcriptional domain and degrons, respectively. Analysis of cardiac myocytes transcripts and proteins showed marked dysregulation of the cWNT/β-catenin pathway in the DSP-deficient mouse cardiac myocytes (Myh6-McmTam:DspF/F), as indicated by increased expression of cWNT/β-catenin targets along with its inhibitors and isoforms of its key co-effectors. Genetic inactivation of β-catenin in the Myh6-McmTam:DspF/F mice prolonged survival, improved cardiac function, reduced cardiac arrhythmias, and attenuated myocardial fibrosis, and cell death caused by apoptosis, necroptosis, pyroptosis, i.e., PANoptosis, whereas its activation had the opposite effects. Inactivation of β-catenin was associated with partial restoration of the suppressed genes involved in OXPHOS, whereas its activation has the opposite effect. The beneficial effects were independent of the changes in the transcript levels of the cWNT target genes. Conclusion The cWNT/β-catenin was markedly dysregulated in the cardiac myocytes from a mouse model of DC. Inactivation of β-catenin attenuated the phenotype partly through the recovery of OXPHOS genes whereas its activation had deleterious effects. The findings suggest suppression of β-catenin might be beneficial in desmoplakin-cardiomyopathy. Summary Genetic inactivation of β-catenin improved desmoplakin cardiomyopathy, in part through the restoration of expression of genes involved in oxidative phosphorylation, whereas its activation was deleterious.
Biophysical Characterization and Interaction study of WhiB6 Protein of Mycobacterium tuberculosis with Nucleic Acid

Tuberculosis is an intractable disease because of the peculiar nature of the virulent properties of Mycobacterium tuberculosis. The WhiB6 protein, a transcriptional regulator, plays a crucial role in the virulence systems of Mtb. It regulates the expression of genes essential for the virulence pathways by binding to their promoter region; espA is one such gene. Herein, we have used biophysical methods, including steady-state intrinsic fluorescence spectroscopy, circular dichroism spectroscopy, Isothermal titration calorimetry (ITC), and Surface-Enhanced Raman Spectroscopy (SERS) to understand the interaction of WhiB6 protein with espA promoter DNA. For the first time, we report the conformational details and biophysical parameters related to the WhiB6-espA promoter DNA interaction. WhiB6 binds the DNA with moderate affinity, as revealed by ITC. CD and SERS studies suggest subtle perturbation in the secondary conformation of the protein on binding to the DNA. SERS provided detailed structural insights into the WhiB6 protein and the amino acids involved in the interaction, which could be harnessed to find suitable inhibitors of the protein-DNA interaction. Preventing the binding of WhiB6 with promoter DNA of the virulence genes can hinder the functioning of Mtb and hence can act as an effective therapeutic intervention for tuberculosis.
Brewster angles in reflection by uniaxial crystals

Reflection by anisotropic media is characterized by the four reflection amplitudes rpp, rss, rps, and rsp. We show that rpp can be zero at angles θpp, the anisotropic Brewster angles, and that a quantity related to θpp satisfies a quartic equation. When the refractive index of the medium of incidence lies between the ordinary and the extraordinary indices of the crystal, it is possible for rss to be zero at an angle θss, and there exist four equivalent orientations of the crystal optic axis for which rpp, rss, and either rps or rsp are simultaneously zero, at angle of incidence equal to arctan (no/n1).
A paper based microfluidic platform combining LAMP-CRISPR/Cas12a for fluorometric detection of nucleic acids

Nucleic acid isothermal amplification methods are advantageous for point-of-care (POC) diagnostics because of their precision, sensitivity, and low power requirements. Loop-mediated isothermal amplification (LAMP) is an established method, renowned for its nucleic acid amplification efficiency and robust amplification of semi purified target nucleic acids. However, LAMP may be prone to non-specific amplification causing false positives and therefore fails to replace PCR as the gold standard method in clinical testing. We show that LAMP combined with clustered regularly interspaced short palindromic repeats (CRISPR) technology is an effective alternative for overcoming the limitations of LAMP alone. Nucleic acids are first isothermally pre-amplified to enrich for targets, then specific amplification detection signals are generated by sequences of RNA guided recognition of amplicons. We are the first to demonstrate a paper based microfluidic system for detecting pathogen nucleic acids in samples by combining the power of LAMP and CRISPR technology. We show that although LAMP may produce non-specific amplification, the possibility of detecting a false positive can be eliminated by combining LAMP with CRISPR based detection. We demonstrate that a paper based microfluidic platform has the potential to compete with the conventional Nucleic acid testing (NAT) technologies not only in terms of robustness but also in terms of cost and complexity.
Sum-of-Squares Lower Bounds for the Minimum Circuit Size Problem

We prove lower bounds for the Minimum Circuit Size Problem (MCSP) in the Sum-of-Squares (SoS) proof system. Our main result is that for every Boolean function $f: \{0,1\}^n \rightarrow \{0,1\}$, SoS requires degree $\Omega(s^{1-\epsilon})$ to prove that $f$ does not have circuits of size $s$ (for any $s>\mathrm{poly}(n)$). As a corollary we obtain that there are no low degree SoS proofs of the statement NP $\not \subseteq $ P/poly. We also show that for any $0<\alpha<1$ there are Boolean functions with circuit complexity larger than $2^{n^{\alpha}}$ but SoS requires size $2^{2^{\Omega(n^{\alpha})}}$ to prove this. In addition we prove analogous results on the minimum \emph{monotone} circuit size for monotone Boolean slice functions. Our approach is quite general. Namely, we show that if a proof system $Q$ has strong enough constraint satisfaction problem lower bounds that only depend on good expansion of the constraint-variable incidence graph and, furthermore, $Q$ is expressive enough that variables can be substituted by local Boolean functions, then the MCSP problem is hard for $Q$.
Depth-3 Circuit Lower Bounds for k-OV

The 2-Orthogonal Vectors (2-OV) problem is the following: given two tuples A and B of n Boolean vectors, each of dimension d , decide if there exist vectors u ∈ A , and v ∈ B , such that u and v are orthogonal. This problem, and its generalization k -OV defined analogously for k tuples, are central problems in the area of fine-grained complexity. One of the major conjectures in fine-grained complexity is that k -OV cannot be solved by a randomised algorithm in n k − ϵ poly ( d ) time for any constant ϵ > 0. In this paper, we are interested in unconditional lower bounds against k -OV, but for weaker models of computation than the general Turing Machine. In particular, we are interested in circuit lower bounds to computing k -OV by Boolean circuit families of depth 3 of the form OR-AND-OR, or equivalently, a disjunction of CNFs . We show that for all k ≤ d , any disjunction of t -CNFs computing k -OV requires size Ω(( n/t ) k ). In particular, when k is a constant, any disjunction of k -CNFs computing k -OV needs to use Ω( n k ) CNFs. This matches the brute-force construction, and for each fixed k > 2, this is the first unconditional Ω( n k ) lower bound against k -OV for a computation model that can compute it in size O ( n k ). Our results partially resolve a conjecture by Kane and Williams [17] (page 12, conjecture 10) about depth-3 AC 0 circuits computing 2-OV. As a secondary result, we show an exponential lower bound on the size of AND ◦ OR ◦ AND circuits computing 2-OV when d is very large. Since 2-OV reduces to k -OV by projections trivially, this lower bound works against k -OV as well.
Robustness Aspects of Score Tests for Generalized Linear and Partially Linear Regression Models

Robustness aspects of score tests for the null hypothesis of no z effect on the mean response μ for some given subset of explanatory variables, z, are explored in the context of regression analysis. The model considered here is θ = θ(μ) = something else + f(β1z′), where θ is a given transformation of μ via some link function, and f, representing the form of the z effect on θ, is monotonic and twice differentiable. It is shown that the score test for H 0: β1 = 0 remains unchanged whatever the form chosen for f under the alternative, H 1: β1 ≠ 0. This type of robustness is desirable in testing how z might affect the mean response, when precise knowledge of the form for f under H 1 is lacking. Further robust score tests against extreme observations, either in the rank-test sense or in the Hampe–Huber sense, can be achieved for the location family with additive errors, as is pointed out in one of the examples, by replacing in the tests the score vector based on the observations by that based on the ranks or s.
Wave design and polarization optimization in the interference of four non-coplanar beams for making three-dimensional periodical microstructures

Abstract A systematic analysis of the interference of four non-coplanar beams for the purpose of making three-dimensional periodical microstructures is described. A general relationship between the four wavevectors, the required wavelength and the desired 3D lattice is formulated based on the reciprocal space theory. A concept of uniform contrast is introduced to evaluate the modulation depth of the resultant pattern as a whole by properly choosing the beam ratio and polarization. A calculation algorithm is developed to determine the optimized polarization of each beam for a given lattice to reach the maximum uniform contrast. Specifically, the effect of non-uniqueness of the wavevector solution for a given lattice on the final result is investigated. It is shown that one can improve the uniform contrast by using a set of waves with less angular divergence.
Thermodynamic analysis and phase field modeling of domain structures in bilayer ferroelectric thin films

The domain structure in bilayer ferroelectric films was studied by using an analytical thermodynamic theory and computer simulations utilizing the phase field model. It is demonstrated that in a low applied field, a self-poled state can be produced in a bilayer film with one layer in a polydomain state and the other layer in a single-domain state. The presence of the layer with a polydomain structure results in a higher dielectric constant and lower coercive field as compared to a bilayer in a single-domain state. The increase in the applied field results in the transition to a single-domain state in the whole bilayer. The thermodynamic potentials of the layers and the energies of electrostatic and elastic interactions determine the critical fields which can control the transitions between single-domain and polydomain states as well as polarization switching of bilayers. Different thermodynamic hysteresis loops are obtained depending on the relationship between these critical fields and the amplitude of t.
I. On the quadric inversion of plane curves

1. The method of inversion which forms the subject of the present paper is an immediate generalization of that now universally employed. In place of a fixed circle with the origin at its centre, any fixed conic (quadric) whatever is taken, as a fundamental curve, and the origin is placed anywhere in its plane. In this manner many descriptive relations which in the ordinary theory are masked, regain the generality and prominence to which they are entitled. Having long ago convinced myself of the utility of this generalized method of inversion, I deem it desirable to establish, for the sake of future reference, its chief general principles. With the view of securing the greatest possible familiarity with the effects of inversion, I employ purely geometrical considerations, and everywhere give preference to a direct and immediate contemplation of the several geometrical forms which present themselves.
ASE suppression in high-gain solid-state amplifiers by a leak method

A leak method was developed to suppress amplified spontaneous emission (ASE) in large-aperture high-gain solid-state amplifiers. The gain medium edges are processed into an arris. The ASE ray will undergo reflection several times at the arris surface when it propagates to the gain medium edges, and most of its power will leak out. This leak method was tested in an experiment, in which a piece of commonly used gain medium was processed for contrast. The maximal increase of the gain value was 5.26% with the maximal pump power.