Miracle-dz/UniFAR-FTUs huggingface dataset:
High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

We investigated the role of 3D genome architecture in instructing functional properties of glioblastoma stem cells (GSCs) by generating the highest-resolution 3D genome maps to-date for this cancer. Integration of DNA contact maps with chromatin and transcriptional profiles identified specific mechanisms of gene regulation, including individual physical interactions between regulatory regions and their target genes. Residing in structurally conserved regions in GSCs was CD276, a gene known to play a role in immuno-modulation. We show that, unexpectedly, CD276 is part of a stemness network in GSCs and can be targeted with an antibody-drug conjugate to curb self-renewal, a key stemness property. Our results demonstrate that integrated structural genomics datasets can be employed to rationally identify therapeutic vulnerabilities in self-renewing cells. SIGNIFICANCE In adult GBM, GSCs act as therapy-resistant reservoirs to nucleate tumor recurrence. New therapeutic approaches that target these cell populations hold the potential of significantly improving patient care and overall prognosis for this always-lethal cancer. Our work describes new links between 3D genome architecture and stemness properties in GSCs. In particular, through integration of multiple genomics and structural genomics datasets, we found an unexpected connection between immune-related genes and self-renewal programs in GBM. Among these, we show that targeting CD276 with knockdown strategies or specific antibody-drug conjugates achieve suppression of self-renewal. Strategies to target CD276+ cells are currently in clinical trials for solid tumors. Our results indicate that CD276-targeting agents could be deployed in GBM to specifically target GSC populations. HIGHLIGHTS We generated high (sub-5 kb) resolution Hi-C maps for stem-like cells from GBM patients. Integration of Hi-C and genomics datasets dissects mechanisms of gene regulation. 3D genomes poise immune-related genes, including CD276, for expression. Targeting CD276 curbs self-renewal properties of GBM cells.
Ethylene Production and Physiological Parameters in Common Bean Plants Under Water Deficit

Common bean is a plant species cultivated around the globe. The objective of this study was to demonstrate how the physiological parameters associated with transpiration, photosynthesis and ethylene production vary in common bean plants under different periods without irrigation. Three experiments were carried out to assess leaf water potential, stomatal conductance, transpiration, carbon assimilation, and ethylene production as a function of different irrigation intervals. A fourth experiment with exogenous application of abscisic acid (ABA) in plants with daily irrigation was also carried out. In all experiments there was a reduction in stomatal conductance at the very early period without irrigation, which consequently influenced transpiration and carbon assimilation. It was also verified that the exogenous application of ABA caused a reduction on ethylene production in common bean plants. The relationship between increased ABA production and the reduction of ethylene production is discussed.
The architecture of cell differentiation in choanoflagellates and sponge choanocytes

Collar cells are ancient animal cell types which are conserved across the animal kingdom [1] and their closest relatives, the choanoflagellates [2]. However, little is known about their ancestry, their subcellular architecture, or how they differentiate. The choanoflagellate Salpingoeca rosetta [3] expresses genes necessary for animal multicellularity and development [4] and can alternate between unicellular and multicellular states [3,5], making it a powerful model to investigate the origin of animal multicellularity and mechanisms underlying cell differentiation [6,7]. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular “rosettes” and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with relatively high levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell-cell contact networks and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type. Intercellular bridges within choanoflagellate colonies displayed a variety of morphologies and connected some, but not all, neighbouring cells. Reconstruction of sponge choanocytes revealed both ultrastructural commonalities and differences in comparison to choanoflagellates. Choanocytes and colonial choanoflagellates are typified by high amoeboid cell activity. In both, the number of microvilli and volumetric proportion of the Golgi apparatus are comparable, whereas choanocytes devote less of their cell volume to the nucleus and mitochondria than choanoflagellates and more of their volume to food vacuoles. Together, our comparative reconstructions uncover the architecture of cell differentiation in choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of the animal kingdom.
Reading between the Lines: Using Text Analysis to Estimate the Loss Function of the ECB

We measure the tone (sentiment) of the ECB’s Governing Council regarding economic outlook at the time of each monetary policy meeting and use this information together with the Eurosystem/ECB staff macroeconomic projections to directly estimate the Governing Council’s loss function. Our results support earlier, more indirect findings, based on reaction function estimations, that the ECB has been either more averse to inflation above 2% ceiling or that the de facto inflation aim has been considerably below 2%. Our results suggest further that an inflation aim of 2% combined with asymmetry is a plausible specification of the ECB’s preferences.
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

Introduction Gene homology type classification is a requisite for many types of genome analyses, including comparative genomics, phylogenetics, and protein function annotation. A large variety of tools have been developed to perform homology classification across genomes of different species. However, when applied to large genomic datasets, these tools require high memory and CPU usage, typically available only in costly computational clusters. To address this problem, we developed a new graph-based orthology analysis tool, SwiftOrtho, which is optimized for speed and memory usage when applied to large-scale data. Results In our tests, SwiftOrtho is the only tool that completed orthology analysis of 1,760 bacterial genomes on a computer with only 4GB RAM. Using various standard orthology datasets, we also show that SwiftOrtho has a high accuracy. SwiftOrtho enables the accurate comparative genomic analyses of thousands of genomes using low memory computers. Availability https://github.com/Rinoahu/SwiftOrtho
Moraxellaceae and Moraxella interact with the altered airway mycobiome in asthma

Airway microbial-microbial interaction plays an important role in chronic airway inflammatory diseases such as asthma. Moraxella is widely regarded as a human respiratory tract pathogen. We aimed to investigate the interactions among Moraxella, Moraxellaceae (to which Moraxella belongs) and the airway microbiome in asthma. Induced sputum samples were obtained from 116 asthma patients and 29 healthy individuals, and the bacterial/fungal communities were profiled using 16S rRNA and ITS1 DNA gene sequencing. We found that asthma patients harboured significantly greater airway bacterial and fungal α-diversity than that of healthy individuals. Moraxellaceae, Moraxella and Moraxella otu19 (bacteria), and Schizophyllaceae, Polyporaceae, Aspergillus, Schizophyllum and Candida (fungi) were increased in the airway of asthma. Moreover, Moraxellaceae, Schizophyllaceae, Polyporaceae and Candida were positively associated with airway fungal α-diversity. Correlation networks revealed Moraxellaceae and Moraxella as microbial “hubs” in asthma that had significant negative connections with multiple bacterial communities, such as Leptotrichiaceae, Lachnospiraceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotella, Veillonella, Rothia and Leptotrichia, but positive interactions with fungal communities such as Schizophyllaceae, Polyporaceae, Candida and Meyerozyma. Together, our finding revealed an altered microbiome and complex microbial-microbial interactions in the airway of asthma. Moraxellaceae and Moraxella showed significant interactions with the airway mycobiome, providing potential insights into the novel pathogenic mechanisms of asthma. IMPORTANCE With the advent of culture-independent techniques, growing evidence suggests that the airway microbiome is closely correlated with chronic respiratory diseases such as asthma. The complex microbial-microbial interaction exists in the airways of both healthy individuals and patients with respiratory diseases, which is of great significance for the pathogenesis and disease progression of asthma. In this study, we evaluated the airway dysbiosis in asthma patients, described the interaction between Moraxellaceae, Moraxella and airway bacterial/fungal communities, and it contributes to further understanding the pathogenic mechanisms of asthma.
Molecular characterization of myostatin gene in Malpura sheep of Rajasthan

Molecular characterization of myostatin gene in Malpura sheep of Rajasthan. -Genetika, Vol 52, No.2, 465-476. Objective of study was to characterize the complete sequence of Myostatin (MSTN) gene in Malpura sheep and to study its genetic variability across population. This study is the first ever report of complete Myostatin gene characterization among the Indian sheep breeds. MSTN (GDF-8) is found to be a negative regulator of skeletal muscle growth which is responsible for double muscling. The MSTN gene sequence was partitioned in 18 different overlapping fragments (P1 to P18). We obtained a sequence of 8002 bp (MH025940) for complete MSTN gene. Phylogenetic analysis revealed that MSTN gene of Malpura sheep breed is in close relation with that of Texel sheep and far related to pig. A total of 16 nucleotide substitutions were identified, revealing rich genetic diversity. Out of these 16 substitutions, none was observed in exonic region, 2 were observed to be present at promoter, 3 in the 5ꞌUTR, 6 in intron-1, 1 in intron-2 and 4 in 3ꞌUTR. Two substitutions c.373+1189 A or G and c. *202 A or G were found in intron-1 and 3′UTR, respectively and were new. The putative mutation for double muscling in sheep (c.*1232A) was not present in Malpura population (c.*12132G).
High Prevalence of Antimicrobial Resistance among Gram Negative Bacteria Isolated from Poultry

Background: Multidrug resistant bacteria (MDR), such as Escherichia coli and Salmonella spp. are threat to the human health care system. In recent years, these MDR bacteria have been found increasingly inside and outside the hospital environment. Food animals (meat and poultry) are increasingly colonized with MDR bacteria, thus posing an additional concern. This study is intended to determine susceptibility and resistance pattern of pathogenic Gram negative bacteria isolated from rectal swabs of chicken against 16 antibiotics. Methods: A total of 216 cloacal swab samples (Gaza strip poultry farms) and 87 frozen and fresh meat samples (from slaughter houses and retails) from June 2017 to June 2018 were collected. Isolation and identification of organisms were achieved using standard bacteriological techniques. Antimicrobial susceptibility test was performed according to standard protocols. Results: 360 Enterobacteriaceae isolates, and 56 Gram-negative non fermenter were recovered. The predominant Enterobacteriaceae isolate was Citrobacter spp. (22.6%), followed by Enterobacter spp. (17.6%) and E. coli (16.5%). High rates of resistance against Ampicillin (85.4%) and Trimethoprim/ Sulfamethoxazole (80.1%) followed by Chloramphenicol (74%) were recorded. Six samples were positive for Salmonella spp. and Shigella spp. Of the tested Enterobacteriacae isolates, 94.7% were multidrug resistant (MDR), and 31.4% of None fermenting bacilli (NFB) were MDR. Carbapenem resistance was found to be high among isolates; 51.9% for imipenem and 1.8% for meropenem. Conclusion: Isolated bacteria in the study area were MDR and this suggests that chickens may be important reservoir of antimicrobial resistant organisms which is a major public health concern.
Knockdown of PTOV1 and PIN1 exhibit common phenotypic anti-cancer effects in MDA-MB-231 cells

Background Earlier, we have identified PTOV1 as a novel interactome of PIN1 in PC-3 cells. This study aims to explore the functional similarity and the common role of both genes in breast cancer cell proliferation. Methods CTG, crystal violet assay, clonogenic assay, wound healing assay, cell cycle analysis, Hoechst staining and ROS measurement were performed to assess cell viability were performed after knocking down of PTOV1 and PIN1 by siRNAs in MDA-MB-231 and MCF-7 cells. CO-IP, qPCR and western blot were performed for interaction, transcriptional and translational regulation of both genes. Results Knockdown of PTOV1 and PIN1 inhibited the cell proliferation, colony formation, migration cell cycle, and induces nuclear condensation as well as ROS production. Interaction of PTOV1 and PIN1 was validated by Co-IP in MDA-MB-231 cells. Genes involved in cell proliferation, migration, cell cycle, and apoptosis were regulated by PIN1 and PTOV1. PTOV1 knockdown inhibited Bcl-2, Bcl-xL and induces BAX, LC3 and Beclin-1. Overexpression of PIN1 increased the expression of PTOV1. Knockdown of both genes inhibited the expression of cyclin D1, c-Myc, and β-catenin. Conclusions PTOV1 and PIN1 interacts and exert oncogenic role in MDA-MB-231 cells by sharing the similar expression profile at transcriptional and translational level which can be a promising hub for therapeutic target.
Recent and rapid colonization of the Lesser Sundas Archipelago from adjacent Sundaland by seven amphibian and reptile species

The Lesser Sundas Archipelago is comprised of two parallel chains of islands that extend between the Asian continental shelf (Sundaland) and Australo-Papuan continental shelf (Sahul). These islands have served as stepping-stones for taxa dispersing between the Asian and Australo-Papuan biogeographic realms. While the oceanic barriers have prevented many species from colonizing the archipelago, a number of terrestrial vertebrate species have colonized the islands either by rafting/swimming or human introduction. Here we examine phylogeographic structure within the Lesser Sundas for three snake, two lizard, and two frog species that each have a Sunda Shelf origin. These species are suspected to have recently colonized the archipelago, though all have inhabited the Lesser Sundas for over 100 years. We sequenced mtDNA from 230 samples to test whether there is sufficiently deep genetic structure within any of these taxa to reject human-mediated introduction. Additionally, we tested for genetic signatures of population expansion consistent with recent introduction, and estimated the ages of Lesser Sundas clades, if any exist. Our results show little to no genetic structure between populations on different islands in five species, and moderate structure in two species. Nucleotide diversity is low for all species, and the ages of the most recent common ancestor for species with monophyletic Lesser Sundas lineages date to the Holocene or late Pleistocene. These results support the hypothesis that these species entered the archipelago relatively recently and either naturally colonized or were introduced by humans to most of the islands within the archipelago within a short time span.
Distributed Optimization Under Unbalanced Digraphs With Node Errors: Robustness of Surplus-Based Dual Averaging Algorithm

In this article, the robustness of distributed constrained optimization algorithms for weight-unbalanced directed multiagent networks is studied. Specifically, it is assumed that each agent is subject to additive random node errors, which are caused by the imperfect communication in networks. Under this framework, it is shown that a typical algorithm, called surplus-based dual averaging (SDA), can successfully achieve the convergence to the optimal value of the considered optimization problem, which exhibits the robustness to the node errors. Technically, in the proof of this result, an important augmentation of the node errors in the fusion and surplus variables is first introduced, and then by means of the random process theory and the attenuation effect of diminishing step size on node errors, the robustness of SDA is proved. In addition, inspired by the SDA, a robust algorithm is developed to solve the distributed online optimization problem with node errors. Finally, simulations are given to verify the theoretical results.
Substrate Integrated Waveguide Derived Novel Two-Way Rotation Sensor

A novel two-way rotation sensor is proposed in this work deploying substrate integrated waveguide (SIW) for the first time instead of traditional microstrip and coplanar waveguide. The SIW is designed for the fundamental TE $_{\sf 10}$ propagation mode with the cut-off frequency at 3 GHz. The designed rotation sensor is comprised of a stator which in this case is the SIW itself with a circular metallic disc etched from the top of it. The other part of the sensor is its rotor which is made of a circular cylindrical disc to be mounted over the stator and with the same diameter as that of the etched part of stator. The top and bottom surfaces of the rotor are having complimentary split ring resonator (CSRR) etched on it which causes a resonance dip to be introduced in the passband of the SIW at a frequency of nearly 6.5 GHz when the CSRR is aligned with the propagation direction of the SIW. As the rotor rotates in either the clockwise or counter-clockwise direction, the resonance frequency starts shifting along with the decrease in the notch dip indicating reduction in coupling. The proposed rotation sensor is exhibiting a wide dynamic range till 90° along with high linearity from 0° - 80°. The sensitivity of the sensor in terms of resonance frequency is 5 MHz/° while 0.21 dB/° in terms of notch dip magnitude. A detailed comparison with the available literature confirms that the proposed rotation sensor provides quite high sensitivity with a high linearity.
Lightweight Misbehavior Detection Management of Embedded IoT Devices in Medical Cyber Physical Systems

We propose a lightweight specification-based misbehavior detection management technique to efficiently and effectively detect misbehavior of an IoT device embedded in a medical cyber physical system through automatic model checking and formal verification. We verify our specification-based misbehavior detection technique with a patient-controlled analgesia (PCA) device embedded in a medical health monitoring system. Through extensive ns3 simulation, we verify its superior performance over popular machine learning anomaly detection methods based on support vector machine (SVM) and k-nearest neighbors (KNN) techniques in both effectiveness and efficiency performance metrics.
Optimal biochemical information processing at criticality

How cells utilize surface receptors for chemoreception is a recurrent question spanning between physics and biology over the past few decades. However, the dynamical mechanism for processing time-varying signals is still unclear. Using dynamical systems formalism to describe criticality in non-equilibrium systems, we propose generic principle for temporal information processing through phase-space trajectories using dynamic transient memory. In contrast to short-term memory, dynamic memory generated via ghost attractor enables signal integration depending on stimulus history, and thus balance between stability and plasticity in receptor responses. We propose that self-organization at criticality can arise through fluctuation-sensing mechanism, illustrated for the experimentally established epidermal growth factor sensing system. This framework applies irrespective of the intrinsic node dynamics or network size, as we show using also a basic neuronal model. Processing of non-stationary signals, a feature previously attributed only to neuronal networks, thus uniquely emerges for biochemical networks organized at criticality.
Chromatography purification of the promising biomaterial: elastin-like protein genetically expressed in Escherichia coli

Inverse transition cycling is the most popular purification method for elastin-like polypeptides, a promising biomaterial with high biocompatibility and functional properties. However this mean depends on the high concentration of elastin-like protein in solution, large molecule weight or high-salt concentration. To overcome the defects of inverse transition cycling, we successfully developed a chromatographic method to effectively purify the recombinant elastin-like proteins expressed in Escherichia coli BL21(DE3), with formulation of MGRS ((VPGVG)10S)5 and a transition temperature higher than 40°C. Ion-exchange chromatography was carried out to remove the most charged proteins from cell lysis prior to hydrophobic proteins were isolated using reverse phase chromatography. A maximum quantity of 303.92 ± 10.17 mg per liter of culture was obtained for the recombinant elastin-like proteins and the purity of the recombinant ELP50 was more than 95%.
Asynchronous Grid Connection of a Cage Induction Generator Excited by a Power Electronic Converter

This article presents an analysis of grid connection of an excited induction generator, where an inrush current is significantly reduced and voltage drop in the local grid is eliminated. In the proposed method, generator connection to the grid is done at the moment when the generator voltage vector equals the grid voltage vector, but the generator frequency differs from the grid frequency. Excitation of the induction generator is provided by a power electronic converter, which is rated only on the rated reactive power of the generator. Moreover, when the generator is connected to the grid, the converter satisfies reactive power demand of an induction generator, according to the requirements from the distribution system operator. The simulation and laboratory tests were conducted with a 7.5 kW induction generator.