Discriminating Codes in Geometric Setups

We study geometric variations of the discriminating code problem. In the \emph{discrete version} of the problem, a finite set of points $P$ and a finite set of objects $S$ are given in $\mathbb{R}^d$. The objective is to choose a subset $S^* \subseteq S$ of minimum cardinality such that for each point $p_i \in P$, the subset $S_i^* \subseteq S^*$ covering $p_i$ satisfies $S_i^*\neq \emptyset$, and each pair $p_i,p_j \in P$, $i \neq j$, we have $S_i^* \neq S_j^*$. In the \emph{continuous version} of the problem, the solution set $S^*$ can be chosen freely among a (potentially infinite) class of allowed geometric objects. In the 1-dimensional case ($d=1$), the points in $P$ are placed on a horizontal line $L$, and the objects in $S$ are finite-length line segments aligned with $L$ (called intervals). We show that the discrete version of this problem is NP-complete. This is somewhat surprising as the continuous version is known to be polynomial-time solvable. Still, for the 1-dimensional discrete version, we design a polynomial-time $2$-approximation algorithm. We also design a PTAS for both discrete and continuous versions in one dimension, for the restriction where the intervals are all required to have the same length. We then study the 2-dimensional case ($d=2$) for axis-parallel unit square objects. We show that both continuous and discrete versions are NP-complete, and design polynomial-time approximation algorithms that produce $(16\cdot OPT+1)$-approximate and $(64\cdot OPT+1)$-approximate solutions respectively, using rounding of suitably defined integer linear programming problems. We show that the identifying code problem for axis-parallel unit square intersection graphs (in $d=2$) can be solved in the same manner as for the discrete version of the discriminating code problem for unit square objects

Novel genetic modules encoding high-level antibiotic-free protein expression in probiotic lactobacilli

Lactobacilli are ubiquitous in nature, often beneficially associated with animals as commensals and probiotics, and are extensively used in food fermentation. Due to this close-knit association, there is considerable interest to engineer them for healthcare applications in both humans and animals, for which high-performance and versatile genetic parts are greatly desired. For the first time, we describe two genetic modules in Lactiplantibacillus plantarum that achieve high-level gene expression using plasmids that can be retained without antibiotics, bacteriocins or genomic manipulations. These include (i) a promoter, PtlpA, from a phylogenetically distant bacterium, Salmonella typhimurium, which drives up to 5-fold higher level of gene expression compared to previously reported promoters and (ii) multiple toxin-antitoxin systems as a self-contained and easy-to-implement plasmid retention strategy that facilitates the engineering of tuneable transient genetically modified organisms. These modules and the fundamental factors underlying their functionality that are described in this work will greatly contribute to expanding the genetic programmability of lactobacilli for healthcare applications

Análise comparativa das atividades antioxidantes e anti-inflamatórias dos chás vermelho, azul e preto para benefícios à saúde

The current COVID-19 predicament necessitates a greater emphasis on developing immunity. Herbal teas are abundant in antioxidants which are important for strengthening the immune system. Hot water decoction of Hibiscus rosa sinensis flowers (red tea), Clitoria ternatea flowers (blue tea) and commercially available black tea were evaluated by comparing for in vitro antioxidant and anti-inflammatory properties. Anthocyanin pigment in red, blue, and black tea demonstrated Rf values of 0.52, 0.86 and 0.78 respectively. Blue and black teas exhibited dominance of polyphenols, flavonoids, tannins, glycosides, terpenoids, saponins as compared to red tea. The highest total phenolic (12.25 ± 0.245 mg GAE/gm extract-1) and flavonoid (15.84 ± 0.268mg QE/gm extract-1) content were observed with black and blue tea respectively. Blue tea, and black tea extracts exhibited FRPA values of 1.81 ± 0.413 mg and 1.93 ± 0.178 mg AAE per gram extract-1 respectively. Black tea exhibits the highest antioxidant capacity in reducing molybdate ions (1.94 ± 0.354 mg AAE per gram extract-1) followed by blue tea (1.56 ± 0.199 mg AAE per gram extract-1). Blue tea extract at a very low concentration showed highest percentage hemolytic inhibition (57.14 ± 0.567%). According to the study, blue tea is a rich source of antioxidants with significant anti-inflammatory properties. The research may offer a valuable supplementary strategyfor its therapeutic applications.La situación actual de COVID-19 requiere un mayor énfasis en desarrollar inmunidad. Los tés de hierbas son ricos en antioxidantes, que son importantes para fortalecer el sistema inmunológico. Se evaluó la decocción en agua caliente de flores de Hibiscus rosa sinensis (té rojo), flores de Clitoria ternatea (té azul) y té negro comercialmente disponible para determinar sus propiedades antioxidantes y antiinflamatorias in vitro. El pigmento de antocianina en el té rojo, azul y negro demostró valores de Rf de 0,52, 0,86 y 0,78, respectivamente. Los tés azul y negro exhibieron un predominio de polifenoles, flavonoides, taninos, glucósidos, terpenoides y saponinas en comparación con el té rojo. Los niveles más altos de fenoles totales (12,25 ± 0,245 mg EAG/g de extracto-1) y flavonoides (15,84 ± 0,268 mg QE/g de extracto-1) se observaron en los tés negro y azul, respectivamente. Los extractos de té azul y té negro exhibieron valores de FRPA de 1,81 ± 0,413 mg y 1,93 ± 0,178 mg de AAE por gramo de extracto-1, respectivamente. El té negro tiene la mayor capacidad antioxidante en la reducción de iones molibdato (1,94 ± 0,354 mg AAE por gramo de extracto-1), seguido del té azul (1,56 ± 0,199 mg AAE por gramo de extracto-1). El extracto de té azul a muy baja concentración presentó el mayor porcentaje de inhibición hemolítica (57,14 ± 0,567%). Según el estudio, el té azul es una rica fuente de antioxidantes con importantes propiedades antiinflamatorias. La investigación puede ofrecer una valiosa estrategia complementaria para sus aplicaciones terapéuticas.A situação atual do COVID-19 exige uma maior ênfase no desenvolvimento da imunidade. Os chás de ervas são abundantes em antioxidantes, importantes para fortalecer o sistema imunológico. A decocção de água quente de flores de Hibiscus rosa sinensis (chá vermelho), flores de Clitoria ternatea (chá azul) e chá preto comercialmente disponível, foi avaliada comparando as propriedades antioxidantes e anti-inflamatórias in vitro. O pigmento antocianina no chá vermelho, azul e preto, demonstrou valores de Rf de 0,52, 0,86 e 0,78, respectivamente. Os chás azul e preto, exibiram predominância de polifenóis, flavonoides, taninos, glicosídeos, terpenoides e saponinas em comparação com o chá vermelho. Os maiores teores de fenólicos totais (12,25 ± 0,245 mg EAG/gm extrato-1) e flavonoides (15,84 ± 0,268 mg QE/gm extrato-1) foram observados nos chás preto e azul, respectivamente. Os extratos de chá azul e chá preto exibiram valores de FRPA de 1,81 ± 0,413 mg e 1,93 ± 0,178 mg de AAE por grama de extrato-1, respectivamente. O chá preto apresenta a maior capacidade antioxidante na redução de íons molibdato (1,94 ± 0,354 mg AAE por grama de extrato-1), seguido pelo chá azul (1,56 ± 0,199 mg AAE por grama de extrato-1). O extrato de chá azul em concentração muito baixa, apresentou a maior porcentagem de inibição hemolítica (57,14 ± 0,567%). De acordo com o estudo, o chá azul é uma rica fonte de antioxidantes com propriedades anti-inflamatórias significativas. A pesquisa pode oferecer uma valiosa estratégia complementar para suas aplicações terapêuticas

Influence of polymorphisms in TNF-α and IL1β on susceptibility to alcohol induced liver diseases and therapeutic potential of miR-124-3p impeding TNF-α/IL1β mediated multi-cellular signaling in liver microenvironment

Background and aimsAlcoholic liver disease (ALD) is the leading cause of the liver cirrhosis related death worldwide. Excessive alcohol consumption resulting enhanced gut permeability which trigger sensitization of inflammatory cells to bacterial endotoxins and induces secretion of cytokines, chemokines leading to activation of stellate cells, neutrophil infiltration and hepatocyte injury followed by steatohepatitis, fibrosis and cirrhosis. But all chronic alcoholics are not susceptible to ALD. This study investigated the causes of differential immune responses among ALD patients and alcoholic controls (ALC) to identify genetic risk factors and assessed the therapeutic potential of a microRNA, miR-124-3p.Materials and methodsBio-Plex Pro™ Human Chemokine analysis/qRT-PCR array was used for identification of deregulated immune genes. Sequencing/luciferase assay/ELISA detected and confirmed the polymorphisms. THP1 co-cultured with HepG2/LX2/HUVEC and apoptosis assay/qRT-PCR/neutrophil migration assay were employed as required.ResultsThe combined data analysis of the GSE143318/Bio-Plex Pro™ Human Chemokine array and qRT-PCR array revealed that six genes (TNFα/IL1β/IL8/MCP1/IL6/TGFβ) were commonly overexpressed in both serum/liver tissue of ALD-patients compared to ALC. The promoter sequence analysis of these 6 genes among ALD (n=322)/ALC (n=168) samples revealed that only two SNPs, rs361525(G/A) at -238 in TNF-α/rs1143627(C/T) at -31 in IL1β were independently associated with ALD respectively. To evaluate the functional implication of these SNPs on ALD development, the serum level of TNF-α/IL1β was verified and observed significantly higher in ALD patients with risk genotypes TNF-α-238GA/IL1β-31CT+TT than TNF-α-238GG/IL1β-31CC. The TNF-α/IL1β promoter Luciferase-reporter assays showed significantly elevated level of luciferase activities with risk genotypes -238AA/-31TT than -238GG/-31CC respectively. Furthermore, treatment of conditioned medium of TNF-α/IL1β over-expressed THP1 cells to HepG2/LX2/HUVEC cells independently showed enhanced level of ER stress and apoptosis in HepG2/increased TGFβ and collagen-I production by LX2/huge neutrophil infiltration through endothelial layer. However, restoration of miR-124-3p in THP1 attenuated such inter-cellular communications and hepatocyte damage/collagen production/neutrophil infiltration were prohibited. Target analysis/luciferase-reporter assays revealed that both TNF-α/IL1β were inhibited by miR-124-3p along with multiple genes from TLR4 signaling/apoptosis/fibrogenesis pathways including MYD88, TRAF3/TRADD, Caspase8/PDGFRA, TGFβR2/MCP1, and ICAM1 respectively.ConclusionThus, rs361525(G/A) in TNF-α and rs1143627(C/T) in IL1β gene may be used as early predictors of ALD susceptibility among East Indian population. Impeding overexpressed TNF-α/IL1β and various genes from associated immune response pathways, miR-124-3p exhibits robust therapeutic potential for ALD patients

Novel genetic modules encoding high‐level antibiotic‐free protein expression in probiotic lactobacilli

Abstract Lactobacilli are ubiquitous in nature, often beneficially associated with animals as commensals and probiotics, and are extensively used in food fermentation. Due to this close‐knit association, there is considerable interest to engineer them for healthcare applications in both humans and animals, for which high‐performance and versatile genetic parts are greatly desired. For the first time, we describe two genetic modules in Lactiplantibacillus plantarum that achieve high‐level gene expression using plasmids that can be retained without antibiotics, bacteriocins or genomic manipulations. These include (i) a promoter, PtlpA, from a phylogenetically distant bacterium, Salmonella typhimurium, which drives up to 5‐fold higher level of gene expression compared to previously reported promoters and (ii) multiple toxin‐antitoxin systems as a self‐contained and easy‐to‐implement plasmid retention strategy that facilitates the engineering of tuneable transient genetically modified organisms. These modules and the fundamental factors underlying their functionality that are described in this work will greatly contribute to expanding the genetic programmability of lactobacilli for healthcare applications

The RED-BLUE SEPARATION problem on graphs

We introduce the Red-Blue Separation problem on graphs, where we are given a graph G = (V, E) whose vertices are colored either red or blue, and we want to select a (small) subset S ⊆ V , called red-blue separating set, such that for every red-blue pair of vertices, there is a vertex s ∈ S whose closed neighborhood contains exactly one of the two vertices of the pair. We study the computational complexity of Red-Blue Separation, in which one asks whether a given red-blue colored graph has a red-blue separating set of size at most a given integer. We prove that the problem is NP-complete even for restricted graph classes. We also show that it is always approximable in polynomial time within a factor of 2 ln n, where n is the input graph's order. In contrast, for triangle-free graphs and for graphs of bounded maximum degree, we show that Red-Blue Separation is solvable in polynomial time when the size of the smaller color class is bounded by a constant. However, on general graphs, we show that the problem is W [2]-hard even when parameterized by the solution size plus the size of the smaller color class. We also consider the problem Max Red-Blue Separation where the coloring is not part of the input. Here, given an input graph G, we want to determine the smallest integer k such that, for every possible red-blue coloring of G, there is a red-blue separating set of size at most k. We derive tight bounds on the cardinality of an optimal solution of Max Red-Blue Separation, showing that it can range from logarithmic in the graph order, up to the order minus one. We also give bounds with respect to related parameters. For trees however we prove an upper bound of two-thirds the order. We then show that Max Red-Blue Separation is NP-hard, even for graphs of bounded maximum degree, but can be approximated in polynomial time within a factor of O(ln 2 n)

The Red-Blue Separation Problem on Graphs

International audienceWe introduce the Red-Blue Separation problem on graphs, where we are given a graph $G = (V, E)$ whose vertices are colored either red or blue, and we want to select a (small) subset $S\subseteq V$ , called red blue separating set , such that for every red-blue pair of vertices, there is a vertex $s\in S$ whose closed neighborhood contains exactly one of the two vertices of the pair.We study the computational complexity of Red-Blue Separation, in which one asks whether a given red-blue colored graph has a red-blue separating set of size at most a given integer. We prove that the problem is NP-complete even for restricted graph classes. We also show that it is always approximable in polynomial time within a factor of $2\ln n$, where $n$ is the input graph's order. In contrast, for triangle-free graphs and for graphs of bounded maximum degree, we show that Red-Blue Separation is solvable in polynomial time when the size of the smaller color class is bounded by a constant. However, on general graphs, we show that the problem is W[2] -hard even when parameterized by the solution size plus the size of the smaller color class.We also consider the problem Max Red-Blue Separation where the coloring is not part of the input. Here, given an input graph $G$, we want to determine the smallest integer $k$ such that, for every possible red-blue-coloring of $G$, there is a red-blue separating set of size at most $k$. We derive tight bounds on the cardinality of an optimal solution of Max Red-Blue Separation, showing that it can range from logarithmic in the graph order, up to the order minus one. We also give bounds with respect to related parameters. For trees however we prove an upper bound of two-thirds the order. We then show that Max Red-Blue Separation is NP-hard, even for graphs of bounded maximum degree, but can be approximated in polynomial time within a factor of $O(\ln^2 n)$

Omalizumab rescue therapy in refractory status asthmaticus

Introduction: Refractory status asthmaticus (RSA) is a severe, life-threatening form of asthma exacerbation that persists despite aggressive treatment with systemic corticosteroids, bronchodilators, and other supportive measures. Omalizumab, a monoclonal antibody that targets IgE, has been approved for treating severe allergic asthma and is effective in reducing the frequency of exacerbations and improving asthma control. Limited evidence exists regarding the use of Omalizumab in RSA, but some studies have suggested that it may have a role in its management. Case: A 39-year-old male with a decade-long history of asthma presented to the emergency department intubated and unresponsive to pharmacological therapy. The patient\u27s IgE levels were elevated, and Omalizumab was administered after a comprehensive evaluation. The patient made a dramatic recovery and was successfully weaned off the ventilator within 24 h of receiving Omalizumab. He made an uneventful recovery and was discharged home on Omalizumab once every two weeks with regular follow-ups. Discussion and conclusion: Per our literature search, only 3 cases have been reported where Omalizumab was administered to patients with RSA to wean them off ventilatory support successfully. This case study adds to the existing data on the potential benefits of Omalizumab in managing RSA. It suggests it may be a valuable treatment option for patients who do not respond to standard therapy. However, further research is needed to determine the efficacy and safety of Omalizumab in this population

Table_1_Influence of polymorphisms in TNF-α and IL1β on susceptibility to alcohol induced liver diseases and therapeutic potential of miR-124-3p impeding TNF-α/IL1β mediated multi-cellular signaling in liver microenvironment.docx

Background and aimsAlcoholic liver disease (ALD) is the leading cause of the liver cirrhosis related death worldwide. Excessive alcohol consumption resulting enhanced gut permeability which trigger sensitization of inflammatory cells to bacterial endotoxins and induces secretion of cytokines, chemokines leading to activation of stellate cells, neutrophil infiltration and hepatocyte injury followed by steatohepatitis, fibrosis and cirrhosis. But all chronic alcoholics are not susceptible to ALD. This study investigated the causes of differential immune responses among ALD patients and alcoholic controls (ALC) to identify genetic risk factors and assessed the therapeutic potential of a microRNA, miR-124-3p.Materials and methodsBio-Plex Pro™ Human Chemokine analysis/qRT-PCR array was used for identification of deregulated immune genes. Sequencing/luciferase assay/ELISA detected and confirmed the polymorphisms. THP1 co-cultured with HepG2/LX2/HUVEC and apoptosis assay/qRT-PCR/neutrophil migration assay were employed as required.ResultsThe combined data analysis of the GSE143318/Bio-Plex Pro™ Human Chemokine array and qRT-PCR array revealed that six genes (TNFα/IL1β/IL8/MCP1/IL6/TGFβ) were commonly overexpressed in both serum/liver tissue of ALD-patients compared to ALC. The promoter sequence analysis of these 6 genes among ALD (n=322)/ALC (n=168) samples revealed that only two SNPs, rs361525(G/A) at -238 in TNF-α/rs1143627(C/T) at -31 in IL1β were independently associated with ALD respectively. To evaluate the functional implication of these SNPs on ALD development, the serum level of TNF-α/IL1β was verified and observed significantly higher in ALD patients with risk genotypes TNF-α-238GA/IL1β-31CT+TT than TNF-α-238GG/IL1β-31CC. The TNF-α/IL1β promoter Luciferase-reporter assays showed significantly elevated level of luciferase activities with risk genotypes -238AA/-31TT than -238GG/-31CC respectively. Furthermore, treatment of conditioned medium of TNF-α/IL1β over-expressed THP1 cells to HepG2/LX2/HUVEC cells independently showed enhanced level of ER stress and apoptosis in HepG2/increased TGFβ and collagen-I production by LX2/huge neutrophil infiltration through endothelial layer. However, restoration of miR-124-3p in THP1 attenuated such inter-cellular communications and hepatocyte damage/collagen production/neutrophil infiltration were prohibited. Target analysis/luciferase-reporter assays revealed that both TNF-α/IL1β were inhibited by miR-124-3p along with multiple genes from TLR4 signaling/apoptosis/fibrogenesis pathways including MYD88, TRAF3/TRADD, Caspase8/PDGFRA, TGFβR2/MCP1, and ICAM1 respectively.ConclusionThus, rs361525(G/A) in TNF-α and rs1143627(C/T) in IL1β gene may be used as early predictors of ALD susceptibility among East Indian population. Impeding overexpressed TNF-α/IL1β and various genes from associated immune response pathways, miR-124-3p exhibits robust therapeutic potential for ALD patients.</p

Image_1_Influence of polymorphisms in TNF-α and IL1β on susceptibility to alcohol induced liver diseases and therapeutic potential of miR-124-3p impeding TNF-α/IL1β mediated multi-cellular signaling in liver microenvironment.tif

Background and aimsAlcoholic liver disease (ALD) is the leading cause of the liver cirrhosis related death worldwide. Excessive alcohol consumption resulting enhanced gut permeability which trigger sensitization of inflammatory cells to bacterial endotoxins and induces secretion of cytokines, chemokines leading to activation of stellate cells, neutrophil infiltration and hepatocyte injury followed by steatohepatitis, fibrosis and cirrhosis. But all chronic alcoholics are not susceptible to ALD. This study investigated the causes of differential immune responses among ALD patients and alcoholic controls (ALC) to identify genetic risk factors and assessed the therapeutic potential of a microRNA, miR-124-3p.Materials and methodsBio-Plex Pro™ Human Chemokine analysis/qRT-PCR array was used for identification of deregulated immune genes. Sequencing/luciferase assay/ELISA detected and confirmed the polymorphisms. THP1 co-cultured with HepG2/LX2/HUVEC and apoptosis assay/qRT-PCR/neutrophil migration assay were employed as required.ResultsThe combined data analysis of the GSE143318/Bio-Plex Pro™ Human Chemokine array and qRT-PCR array revealed that six genes (TNFα/IL1β/IL8/MCP1/IL6/TGFβ) were commonly overexpressed in both serum/liver tissue of ALD-patients compared to ALC. The promoter sequence analysis of these 6 genes among ALD (n=322)/ALC (n=168) samples revealed that only two SNPs, rs361525(G/A) at -238 in TNF-α/rs1143627(C/T) at -31 in IL1β were independently associated with ALD respectively. To evaluate the functional implication of these SNPs on ALD development, the serum level of TNF-α/IL1β was verified and observed significantly higher in ALD patients with risk genotypes TNF-α-238GA/IL1β-31CT+TT than TNF-α-238GG/IL1β-31CC. The TNF-α/IL1β promoter Luciferase-reporter assays showed significantly elevated level of luciferase activities with risk genotypes -238AA/-31TT than -238GG/-31CC respectively. Furthermore, treatment of conditioned medium of TNF-α/IL1β over-expressed THP1 cells to HepG2/LX2/HUVEC cells independently showed enhanced level of ER stress and apoptosis in HepG2/increased TGFβ and collagen-I production by LX2/huge neutrophil infiltration through endothelial layer. However, restoration of miR-124-3p in THP1 attenuated such inter-cellular communications and hepatocyte damage/collagen production/neutrophil infiltration were prohibited. Target analysis/luciferase-reporter assays revealed that both TNF-α/IL1β were inhibited by miR-124-3p along with multiple genes from TLR4 signaling/apoptosis/fibrogenesis pathways including MYD88, TRAF3/TRADD, Caspase8/PDGFRA, TGFβR2/MCP1, and ICAM1 respectively.ConclusionThus, rs361525(G/A) in TNF-α and rs1143627(C/T) in IL1β gene may be used as early predictors of ALD susceptibility among East Indian population. Impeding overexpressed TNF-α/IL1β and various genes from associated immune response pathways, miR-124-3p exhibits robust therapeutic potential for ALD patients.</p