Data Reduction Method for Categorical Data Clustering

Categorical data clustering constitutes an important part of data mining; its relevance has recently drawn attention from several researchers. As a step in data mining, however, clustering encounters the problem of large amount of data to be processed. This article offers a solution for categorical clustering algorithms when working with high volumes of data by means of a method that summarizes the database. This is done using a structure called CM-tree. In order to test our method, the KModes and Click clustering algorithms were used with several databases. Experiments demonstrate that the proposed summarization method improves execution time, without losing clustering quality

Molecular changes underlying pulmonary emphysema and chronic bronchitis in Chronic Obstructive Pulmonary Disease: An updated review

The aim of this review is to update and synthesize the molecular mechanisms that lead to the heterogeneous effect on tissue remodeling observed in the two most important clinical phenotypes of chronic obstructive pulmonary disease (COPD), pulmonary emphysema (PE) and chronic bronchitis (CB). Clinical and experimental evidence suggests that this heterogeneous response to promote PE, CB, or both, is related to differentiated genetic, epigenetic, and molecular conditions. Specifically, a tendency toward PE could be related to a variant in the DSP gene, SIRT1 downregulation, macrophage polarization to M1, as well as the involvement of the noncanonical Wnt5A signaling pathway, among other alterations. Additionally, in advanced stages of COPD, PE development is potentiated by dysregulations in autophagy, which promotes senescence and subsequently cell apoptosis, through exacerbated inflammasome activation and release of caspases. On the other hand, CB or the pro-fibrotic phenotype could be potentiated by the downregulated activity of HDAC2, the activation of the TGF-β/Smad or Wnt/β-catenin signaling pathways, macrophage polarization to M2, upregulation of TIMP-1, and/or the presence of the epithelial-mesenchymal transition (EMT) mechanism. Interestingly, the upregulated activity of MMPs, especially MMP-9, is widely involved in the development of both phenotypes. Furthermore, MMP-9 and MMP-12 enhance the severity, perpetuation, and exacerbation of COPD, as well as the development of autoimmunity in this disease

Effect of oregano oil dietary supplementation on production parameters, height of intestinal villi and the antioxidant capacity in the breast of broiler

Oregano additives could contain growth stimulating compounds for poultry, however, a great variation attributed to their main components is observed. The aim of the present study was to investigate the effect of oregano oil dietary supplementationon the productive variables, the height of the intestinal villi and the accumulation of antioxidant compounds in the breast of broilers. In total, 480 broilers were reared from 1 to 42 d of age and since the first day of life were allocated into four treatments, each with four replications of 30 birds. The formulated diet was based on corn and soybean meal and 0, 100, 200 or 400 mg of oregano oilper kg of feed were incorporated in the diets of treatment 1, 2, 3 and 4, respectively. Feed intake, weight gain, feed conversion andmortality rates were weekly recorded. At 21 and 42 days of age the intestinal villi height and antioxidant capacity in the chicken breast were measured. Oregano oil used contained 43.17% and 29.16% of thymol and carvacrol, respectively. Feed intake, weight gain, feed conversion rate and mortality were not affected by oregano oil dietary supplementation. The height of intestinal villi increased with the level of oregano oil supplementation (P<0.05). However, the size of the intestinal villi was greater in the duodenum compared to the other parts (P<0.05), and jejunum and ileum had the same height. Antioxidant capacity of chicken breast at the 6th week was increased in the group that was dietary supplemented with 400 mg of oregano oil per kg of feed

Loss of FBXW7 and accumulation of MCL1 and PLK1 promote paclitaxel resistance in breast cancer

FBXW7 is a component of SCF (complex of SKP1, CUL1 and F-box-protein)-type ubiquitin ligases that targets several oncoproteins for ubiquitination and degradation by the proteasome. FBXW7 regulates cellular apoptosis by targeting MCL1 for ubiquitination. Recently, we identified PLK1 as a new substrate of FBXW7 modulating the intra-S-phase DNA-damage checkpoint. Taxanes are frequently used in breast cancer treatments, but the acquisition of resistance makes these treatments ineffective. We investigated the role of FBXW7 and their substrates MCL1 and PLK1 in regulating the apoptotic response to paclitaxel treatment in breast cancer cells and their expression in breast cancer tissues. Paclitaxel-sensitive MDA-MB-468 and a paclitaxel-resistant MDA-MB-468R subclone were used to study the role of FBXW7 and substrates in paclitaxel-induced apoptosis. Forced expression of FBXW7 or downregulation of MCL1 or PLK1 restored sensitivity to paclitaxel in MDA-MB-468R cells. By contrary, FBXW7-silenced MDA-MB-468 cells became resistant to paclitaxel. The expression of FBXW7 and substrates were studied in 296 invasive carcinomas by immunohistochemistry and disease-free survival was analyzed in a subset of patients treated with paclitaxel. In breast cancer tissues, loss of FBXW7 correlated with adverse prognosis markers and loss of FBXW7 and MCL1 or PLK1 accumulation were associated with diminished disease-free survival in paclitaxel-treated patients. We conclude that FBXW7 regulates the response to paclitaxel by targeting MCL1 and PLK1 in breast cancer cells and thus targeting these substrates may be a valuable adjunct for paclitaxel treatment. Also, FBXW7, MCL1 and PLK1 may be relevant predictive markers of tumor progression and response to paclitaxel treatment.España, Ministerio de Economía y Competitividad SAF2014- 53799-C2-1/2-REspaña, Consejería de Salud AI-0025-2015España, Consejería de Innovación Ciencia y Empresa P10- CTS-624

BBB opening with focused ultrasound in nonhuman primates and Parkinson’s disease patients: Targeted AAV vector delivery and PET imaging

血液脳関門開放術による遺伝子治療法の開発 --身体を傷つけない脳疾患の治療を目指して--. 京都大学プレスリリース. 2023-04-20.Intracerebral vector delivery in nonhuman primates has been a major challenge. We report successful blood-brain barrier opening and focal delivery of adeno-associated virus serotype 9 vectors into brain regions involved in Parkinson’s disease using low-intensity focus ultrasound in adult macaque monkeys. Openings were well tolerated with generally no associated abnormal magnetic resonance imaging signals. Neuronal green fluorescent protein expression was observed specifically in regions with confirmed blood-brain barrier opening. Similar blood-brain barrier openings were safely demonstrated in three patients with Parkinson’s disease. In these patients and in one monkey, blood-brain barrier opening was followed by 18F-Choline uptake in the putamen and midbrain regions based on positron emission tomography. This indicates focal and cellular binding of molecules that otherwise would not enter the brain parenchyma. The less-invasive nature of this methodology could facilitate focal viral vector delivery for gene therapy and might allow early and repeated interventions to treat neurodegenerative disorders

Biotechnological production and application of fructooligosaccharides

Currently, prebiotics are all carbohydrates of relatively short chain length. An important group is the fructooligosaccharides, which are a special kind of prebiotics associated to their selective stimulation of the activity of certain groups of colonic bacteria that have a positive and beneficial effect on intestinal microbiota, reducing incidence of gastrointestinal infections, respiratory and also possessing a recognized bifidogenic effect. Traditionally, these prebiotic compounds have been obtained through extraction processes from some plants, as well as through enzymatic hydrolysis of sucrose. However, different fermentative methods have also been proposed for the production of fructooligosaccharides, such as solid-state fermentation utilizing various agroindustrial by-products. By optimizing the culture parameters, fructooligosaccharides yields and productivity can be improved. The use of immobilized enzymes and cells has also been proposed as being an effective and economic method for large-scale production of fructooligosaccharides. This paper is an overview on the results of recent studies on fructooligosacharides biosynthesis, physicochemical properties, sources, biotechnological production and applications.The authors thank the National Council of Science and Technology of Mexico (CONACYT) for funding this study. D. A. Flores-Maltos thank the CONACYT for the financial support provided for her postgraduate studies in the Food Science and Technology Program, Universidad Autonoma de Coahuila, Mexico

Trophic Ecology of Atlantic Bluefin Tuna (Thunnus thynnus) Larvae from the Gulf of Mexico and NW Mediterranean Spawning Grounds: A Comparative Stable Isotope Study

The present study uses stable isotopes of nitrogen and carbon (δ15Nandδ13C) as trophic indicators for Atlantic bluefin tuna larvae (BFT) (6–10mm standard length) in the highly contrasting environmental conditions of the Gulf of Mexico (GOM) and the Balearic Sea (MED). These regions are differentiated by their temperature regime and relative productivity, with the GOM being significantly warmer and more productive. MED BFT larvae showed the highest δ15N signatures, implying an elevated trophic position above the underlyingmicrozooplankton baseline. Ontogenetic dietary shifts were observed in the BFT larvae from the GOM and MED which indicates early life trophodynamics differences between these spawning habitats. Significant trophic differences between the GOM and MED larvae were observed in relation to δ15N signatures in favour of the MED larvae, which may have important implications in their growth during their early life stages. These low δ15N levels in the zooplankton from the GOM may be an indication of a shifting isotopic baseline in pelagic food webs due to diatrophic inputs by cyanobacteria. Lack of enrichment for δ15N in BFT larvae compared to zooplankton implies an alternative grazing pathway from the traditional food chain of phytoplankton— zooplankton—larval fish. Results provide insight for a comparative characterization of the trophic pathways variability of the two main spawning grounds for BFT larvaeVersión del editor4,411

Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores

The identification or design of biocatalysts to mitigate the accumulation of plastics, including sub-micro- and nano-sized polyethylene terephthalate (nPET), is becoming a global challenge. Here we computationally incorporated two hydrolytic active sites with geometries similar to that of Idionella sakaiensis PET hydrolase, to fragaceatoxin C (FraC), a membrane pore-forming protein. FraCm1/m2 could be assembled into octameric nanopores (7.0 nm high × 1.6–6.0 nm entry), which deconstructed (40 °C, pH 7.0) nPET from GoodFellow, commodities and plastic bottles. FraCm1 and FraCm2 degrade nPET by endo- and exo-type chain scission. While FraCm1 produces bis(2-hydroxyethyl) terephthalate as the main product, FraCm2 yields a high diversity of oligomers and terephthalic acid. Mechanistic and biochemical differences with benchmark PET hydrolases, along with pore and nPET dynamics, suggest that these pore-forming protein catalytic nanoreactors do not deconstruct macro-PET but are promising in nanotechnology for filtering, capturing and breaking down nPET, for example, in wastewater treatment plants. [Figure not available: see fulltext.]. © 2023, The Author(s).This study was conducted under the auspices of the FuturEnzyme Project funded by the European Union’s Horizon 2020 Research and Innovation Programme under the auspices of the FuturEnzyme Project (grant agreement no. 101000327) and the PlasticsFatE project (grant agreement no. 95921), and Horizon Europe Research and Innovation Programme under grant agreement no. GA101060625 (Nymphe project). We also acknowledge financial support under grants PID2020-112758RB-I00 (M.F.), PDC2021-121534-I00 (M.F.), TED2021-130544B-I00 (M.F.), PID2019-106370RB-I00 (V.G.) and PID2019-105838RB-C31 (F.J.P.) from the Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (AEI) (Digital Object Identifier MCIN/AEI/10.13039/501100011033), Fondo Europeo de Desarrollo Regional (ERDF) A way of making Europe and the European Union NextGenerationEU/PRTR, UCM-Banco Santander Grants PR87/19-22556 and PR108/20-26896 and UnaEuropa (Unano) SF2106 (to A.M.P.). S.G.-L. was supported by a Real Colegio Complutense Postdoctoral Fellowship for Distinguished Junior Scholars. S.R. thanks the Spanish Ministry of Science and Innovation for a PhD fellowship (FPU19/00608). D.H.-M. thanks Complutense University of Madrid and Banco Santander for a PhD fellowship (CT82/20/CT83/20). A.R.-M. thanks the Spanish Ministry of Science and Innovation for a PhD fellowship (PRE2020-091825) and the project PID2019-106370RB-I00. We thank M. J. Vicente for the ESI–MS analysis, performed at the Servicio Interdepartamental de Investigación (SIDI) from the Autonomous University of Madrid, Spain.Supplementary dataPeer reviewe

Dendritic cell deficiencies persist seven months after SARS-CoV-2 infection

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 infection induces an exacerbated inflammation driven by innate immunity components. Dendritic cells (DCs) play a key role in the defense against viral infections, for instance plasmacytoid DCs (pDCs), have the capacity to produce vast amounts of interferon-alpha (IFN-α). In COVID-19 there is a deficit in DC numbers and IFN-α production, which has been associated with disease severity. In this work, we described that in addition to the DC deficiency, several DC activation and homing markers were altered in acute COVID-19 patients, which were associated with multiple inflammatory markers. Remarkably, previously hospitalized and nonhospitalized patients remained with decreased numbers of CD1c+ myeloid DCs and pDCs seven months after SARS-CoV-2 infection. Moreover, the expression of DC markers such as CD86 and CD4 were only restored in previously nonhospitalized patients, while no restoration of integrin β7 and indoleamine 2,3-dyoxigenase (IDO) levels were observed. These findings contribute to a better understanding of the immunological sequelae of COVID-19