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A substantial body of evidence points to the heritability of dietary preferences. While vegetarianism has been practiced for millennia in various societies, its practitioners remain a small minority of people worldwide, and the role of genetics in choosing a vegetarian diet is not well understood. Dietary choices involve an interplay between the physiologic effects of dietary items, their metabolism, and taste perception, all of which are strongly influenced by genetics. In this study, we used a genome-wide association study (GWAS) to identify loci associated with strict vegetarianism in UK Biobank participants. Comparing 5,324 strict vegetarians to 329,455 controls, we identified one SNP on chromosome 18 that is associated with vegetarianism at the genome-wide significant level (rs72884519, ß = -0.11, P = 4.997 x 10-8), and an additional 201 suggestively significant variants. Four genes are associated with rs72884519: TMEM241, RIOK3, NPC1, and RMC1. Using the Functional Mapping and Annotation (FUMA) platform and the Multi-marker Analysis of GenoMic Annotation (MAGMA) tool, we identified 34 genes with a possible role in vegetarianism, 3 of which are GWAS-significant based on gene-level analysis: RIOK3, RMC1, and NPC1. Several of the genes associated with vegetarianism, including TMEM241, NPC1, and RMC1, have important functions in lipid metabolism and brain function, raising the possibility that differences in lipid metabolism and their effects on the brain may underlie the ability to subsist on a vegetarian diet. These results support a role for genetics in choosing a vegetarian diet and open the door to future studies aimed at further elucidating the physiologic pathways involved in vegetarianism.
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Dieta Vegetariana , Estudio de Asociación del Genoma Completo , Humanos , Dieta , Dieta Vegana , EncéfaloRESUMEN
The abnormal aggregation of TDP-43 into cytoplasmic inclusions in affected neurons is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although how TDP-43 forms cytoplasmic aggregates and causes neurodegeneration in patients with ALS/FTD remains unclear, reducing cellular TDP-43 levels is likely to prevent aggregation and to rescue neurons from TDP-43 toxicity. To address this issue, here we developed gapmer-type antisense oligonucleotides (ASOs) against human TDP-43 using 2'-O,4'-C-ethylene nucleic acids (ENAs), which are modified nucleic acids with high stability, and tested the therapeutic potential of lowering TDP-43 levels using ENA-modified ASOs. We demonstrated that intracerebroventricular administration of ENA-modified ASOs into a mouse model of ALS/FTD expressing human TDP-43 results in the efficient reduction of TDP-43 levels in the brain and spinal cord. Surprisingly, a single injection of ENA-modified ASOs into TDP-43 mice led to long-lasting improvement of behavioral abnormalities and the suppression of cytoplasmic TDP-43 aggregation, even after TDP-43 levels had returned to the initial levels. Our results demonstrate that transient reduction of TDP-43 using ENA-modified ASOs leads to sustained therapeutic benefits in vivo, indicating the possibility of a disease-modifying therapy by lowering TDP-43 levels for the treatment of the TDP-43 proteinopathies, including ALS/FTD.
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Astrocyte abnormalities have received great attention for their association with various diseases in the brain but not so much in the eye. Recent independent genome-wide association studies of glaucoma, optic neuropathy characterized by retinal ganglion cell (RGC) degeneration, and vision loss found that single-nucleotide polymorphisms near the ABCA1 locus were common risk factors. Here, we show that Abca1 loss in retinal astrocytes causes glaucoma-like optic neuropathy in aged mice. ABCA1 was highly expressed in retinal astrocytes in mice. Thus, we generated macroglia-specific Abca1-deficient mice (Glia-KO) and found that aged Glia-KO mice had RGC degeneration and ocular dysfunction without affected intraocular pressure, a conventional risk factor for glaucoma. Single-cell RNA sequencing revealed that Abca1 deficiency in aged Glia-KO mice caused astrocyte-triggered inflammation and increased the susceptibility of certain RGC clusters to excitotoxicity. Together, astrocytes play a pivotal role in eye diseases, and loss of ABCA1 in astrocytes causes glaucoma-like neuropathy.
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Extracellular vesicles (EVs) have attracted much attention as potential diagnostic biomarkers for human diseases. Although both plasma and serum are utilized as a source of blood EVs, it remains unclear whether, how and to what extent the choice of plasma and serum affects the experimental results. To address this issue, in this study, we performed comprehensive characterization of EV fractions derived from plasma and serum, and investigated the differences between these blood EVs. We demonstrated by nanoparticle tracking analysis that EV fractions derived from serum contain more particles than those from plasma of mice. Proteomic analysis demonstrated that platelet-associated proteins are selectively enriched in serum EV fractions from both mice and humans. A literature review of proteomic data of human blood EVs reported by other groups further confirmed that selective enrichment of platelet-associated proteins is commonly observed in serum EVs, and confers different proteome profiles to plasma EVs. Our data provide experimental evidence that EV fractions derived from serum generally contain additional EVs that are released from platelets, which may qualitatively and quantitatively alter EV profiles when using serum as a source of blood EVs.
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Vesículas Extracelulares , Proteómica , Animales , Plaquetas , Vesículas Extracelulares/metabolismo , Ratones , Plasma , Proteómica/métodosRESUMEN
The reported case is of a 68-year-old man who was admitted to the ICU at our tertiary care medical center with severe COVID-19. He was admitted to the ICU due to a worsening respiratory condition during his hospitalization at the same medical center, which included the development of severe acute respiratory distress syndrome (ARDS). Ventilator management was started with alveolar protection in mind. On the ninth day of ventilator management, we judged that it was necessary to introduce extracorporeal membrane oxygenation (ECMO). Although the ninth day of ventilator management is considered relatively late for starting ECMO, there are no absolute contraindications for ECMO at this stage, and improvements in oxygenation can be expected. After introducing ECMO, the patient's oxygenation capacity improved, and ECMO was successfully withdrawn within 16 days. The patient required long-term rehabilitation but was discharged from the hospital to his home without lingering disease complications on the 150th day of illness and subsequently resumed his former work, daily activities, and quality of life. We conclude that, in regard to the introduction of ECMO for ARDS, it is necessary to reach a comprehensive judgment without being bound by any one index (such as the ventilation management period prior to ECMO introduction).
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OBJECTIVES: Subjective sleep quality (SSQ) is defined by the satisfaction of one's overall sleep experience and is composed of sleep depth and restfulness. It has not been clarified how poor SSQ is associated to changes in lifestyles. The purpose is to reveal the association of lifestyle pattern changes and poor SSQ. DESIGN: A cross-sectional study. SETTING: The data on basic attributes, SSQ and lifestyle such as presence/absence of smoking, exercise, physical activity, supper time close to bedtime, drinking habits and alcohol intake amount per day were obtained from database and questionnaire of specified medical check-ups in fiscal year 2014-2015 in Japan. The analysis was conducted in 2019. PARTICIPANTS: The subjects comprised 49 483 residents (26 087 men and 23 396 women), aged 40-74 years who had undergone an annual specified medical check-up from 2014 to 2015 in Fukushima Prefecture, Japan. OUTCOME MEASURE: Status of SSQ in 2015 was assessed using a question asking whether or not the subjects usually got enough sleep. Poor SSQ in 2015 and lifestyle pattern changes in 2014-2015 were compared between those who were in healthy status both in 2014 and 2015 (referent) and non-referent, using binary logistic regression analysis. RESULTS: Unhealthy lifestyle pattern for 2014-2015 was significantly associated to poor SSQ in 2015: 'absent to absent' in exercise for men (OR=1.472; 95% CI 1.316 to 1.647) and women (OR=1.428; 95% CI 1.285 to 1.587), physical activity for men (OR=1.420; 95% CI 1.270 to 1.588) and women (OR=1.471; 95% CI 1.322 to 1.638) and 'present to present' in supper time for men (OR=1.149; 95% CI 1.020 to 1.294) and women (OR=1.288; 95% CI 1.102 to 1.505). CONCLUSIONS: Healthcare workers may be able to contribute to the improvement of SSQ, focusing on changeable lifestyles.
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Ejercicio Físico , Estilo de Vida , Adulto , Anciano , Estudios Transversales , Femenino , Humanos , Japón/epidemiología , Masculino , Persona de Mediana Edad , Sueño , Encuestas y CuestionariosRESUMEN
We propose a new formulation of multiple-instance learning (MIL), in which a unit of data consists of a set of instances called a bag. The goal is to find a good classifier of bags based on the similarity with a "shapelet" (or pattern), where the similarity of a bag with a shapelet is the maximum similarity of instances in the bag. In previous work, some of the training instances have been chosen as shapelets with no theoretical justification. In our formulation, we use all possible, and thus infinitely many, shapelets, resulting in a richer class of classifiers. We show that the formulation is tractable, that is, it can be reduced through linear programming boosting (LPBoost) to difference of convex (DC) programs of finite (actually polynomial) size. Our theoretical result also gives justification to the heuristics of some previous work. The time complexity of the proposed algorithm highly depends on the size of the set of all instances in the training sample. To apply to the data containing a large number of instances, we also propose a heuristic option of the algorithm without the loss of the theoretical guarantee. Our empirical study demonstrates that our algorithm uniformly works for shapelet learning tasks on time-series classification and various MIL tasks with comparable accuracy to the existing methods. Moreover, we show that the proposed heuristics allow us to achieve the result in reasonable computational time.
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The polyglutamine (polyQ) diseases are a group of inherited neurodegenerative diseases that include Huntington's disease, various spinocerebellar ataxias, spinal and bulbar muscular atrophy, and dentatorubral pallidoluysian atrophy. They are caused by the abnormal expansion of a CAG repeat coding for the polyQ stretch in the causative gene of each disease. The expanded polyQ stretches trigger abnormal ß-sheet conformational transition and oligomerization followed by aggregation of the polyQ proteins in the affected neurons, leading to neuronal toxicity and neurodegeneration. Disease-modifying therapies that attenuate both symptoms and molecular pathogenesis of polyQ diseases remain an unmet clinical need. Here we identified arginine, a chemical chaperone that facilitates proper protein folding, as a novel compound that targets the upstream processes of polyQ protein aggregation by stabilizing the polyQ protein conformation. We first screened representative chemical chaperones using an in vitro polyQ aggregation assay, and identified arginine as a potent polyQ aggregation inhibitor. Our in vitro and cellular assays revealed that arginine exerts its anti-aggregation property by inhibiting the toxic ß-sheet conformational transition and oligomerization of polyQ proteins before the formation of insoluble aggregates. Arginine exhibited therapeutic effects on neurological symptoms and protein aggregation pathology in Caenorhabditis elegans, Drosophila, and two different mouse models of polyQ diseases. Arginine was also effective in a polyQ mouse model when administered after symptom onset. As arginine has been safely used for urea cycle defects and for mitochondrial myopathy, encephalopathy, lactic acid and stroke syndrome patients, and efficiently crosses the blood-brain barrier, a drug-repositioning approach for arginine would enable prompt clinical application as a promising disease-modifier drug for the polyQ diseases.
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Arginina/metabolismo , Arginina/farmacología , Péptidos/metabolismo , Animales , Caenorhabditis elegans/metabolismo , Modelos Animales de Enfermedad , Drosophila/metabolismo , Femenino , Trastornos Heredodegenerativos del Sistema Nervioso/genética , Enfermedad de Huntington/genética , Masculino , Ratones , Ratones Endogámicos , Chaperonas Moleculares/genética , Péptidos/genética , Agregación Patológica de Proteínas , Conformación Proteica/efectos de los fármacos , Pliegue de Proteína/efectos de los fármacos , Ataxias Espinocerebelosas/genéticaRESUMEN
Optimization of immunogen is crucial for induction of effective T-cell responses in the development of a human immunodeficiency virus (HIV) vaccine. Conventional T-cell-based vaccines have been designed to induce virus-specific CD4+ T as well as CD8+ T cells. However, it has been indicated that induction of HIV-specific CD4+ T cells, preferential targets for HIV infection, by vaccination may be detrimental and accelerate viral replication after HIV exposure. In the present study, we present a novel immunogen to selectively induce CD8+ T cells but not CD4+ T cells targeting viral antigens. The immunogen, CaV11, was constructed by tandem connection of overlapping 11-mer peptides spanning simian immunodeficiency virus (SIV) Gag capsid (CA) and Vif. Prime-boost immunization with DNA and Sendai virus (SeV) vectors expressing CaV11 efficiently induced Gag/Vif-specific CD8+ T-cell responses with inefficient Gag/Vif-specific CD4+ T-cell induction in rhesus macaques (n = 6). None of the macaques exhibited the enhancement of acute viral replication after an intravenous high-dose SIV challenge, which was observed in those immunized with DNA and SeV expressing the whole Gag protein in our previous study. Set point viral control postinfection was associated with SeV-specific CD4+ T-cell responses postimmunization, suggesting contribution of SeV-specific helper responses to effective Gag/Vif-specific CD8+ T-cell induction by vaccination. This immunogen design could be a promising method for selective induction of effective anti-HIV CD8+ T-cell responses.IMPORTANCE Induction of effective CD8+ T-cell responses is an important HIV vaccine strategy. Several promising vaccine delivery tools have been developed, and immunogen optimization is now crucial for effective T-cell induction. Conventional immunogens have been designed to induce virus-specific CD4+ T cells as well as CD8+ T cells, but induction of virus-specific CD4+ T cells that are preferential targets for HIV infection could enhance acute HIV proliferation. Here, we designed a novel immunogen to induce HIV-specific CD8+ T cells without HIV-specific CD4+ T-cell induction but with non-HIV antigen-specific CD4+ T-cell help. Our analysis in a macaque AIDS model showed that our immunogen can efficiently elicit effective CD8+ T but not CD4+ T cells targeting viral antigens, resulting in no enhancement of acute viral replication after virus exposure. This immunogen design, also applicable for other currently developed immunogens, could be a promising method for selective induction of effective anti-HIV CD8+ T-cell responses.
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Antígenos Virales/inmunología , Linfocitos T CD4-Positivos/inmunología , Linfocitos T CD8-positivos/inmunología , Infecciones por VIH/inmunología , Vacunas contra el SIDA/inmunología , Secuencia de Aminoácidos , Animales , Modelos Animales de Enfermedad , Inmunización , Macaca mulatta , Síndrome de Inmunodeficiencia Adquirida del Simio/inmunología , Virus de la Inmunodeficiencia de los Simios/inmunología , Vacunación , Carga Viral , Replicación Viral , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/inmunología , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/inmunologíaRESUMEN
The aim of this study was to determine what lifestyle changes can predict acute onset hypertension in the normotensive community-dwelling elderly.This study targeted elderly people enrolled in National Health Insurance in Fukushima Prefecture, Japan. The subjects were 24,490 people who took all of the specific health examination conducted by National Health Insurance in fiscal years 2013, 2014, and 2015 continuously and had a recorded systolic blood pressure (BP) <130 mm Hg and diastolic BP <85 mm Hg in the first 2 fiscal years. We examined their lifestyle changes for the first 2 fiscal years using the questionnaires given at the health examination. Multivariate Poisson regression analysis was conducted to examine the relationship between new-onset hypertension observed at the last examination and unhealthy lifestyle changes.The mean age of the subjects was 61.5â±â8.2 years old at baseline. We observed new-onset hypertension in 1.062 subjects at the last examination. Of the study subjects, 12,027 (49.1%) answered to having at least one of the items of unhealthy lifestyle change in the questionnaire. In the multivariate logistic regression, eating supper before bedtime showed a significant increase in the risk ratio for acute onset hypertension (risk ratio 1.27, 95% confidence interval, 1.01-1.58).This study indicated that eating before bedtime is a risk factor of new-onset hypertension in the normotensive community-dwelling elderly. Adequate health guidance to avoid unhealthy lifestyle changes is required even in normotensive people as this hypertension is preventable.
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Conducta Alimentaria , Hipertensión/etiología , Anciano , Femenino , Humanos , Hipertensión/epidemiología , Vida Independiente , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Factores de RiesgoRESUMEN
Excitotoxicity is well known in the neuronal death in the brain and is also linked to neuronal damages in the retina. Recent accumulating evidence show that microglia greatly affect excitotoxicity in the brain, but their roles in retina have received only limited attention. Here, we report that retinal excitotoxicity is mediated by microglia. To this end, we employed three discrete methods, that is, pharmacological inhibition of microglia by minocycline, pharmacological ablation by an antagonist for colony stimulating factor 1 receptor (PLX5622), and genetic ablation of microglia using Iba1-tTA::DTAtetO/tetO mice. Intravitreal injection of NMDA increased the number of apoptotic retinal ganglion cells (RGCs) followed by reduction in the number of RGCs. Although microglia did not respond to NMDA directly, they became reactive earlier than RGC damages. Inhibition or ablation of microglia protected RGCs against NMDA. We found up-regulation of proinflammatory cytokine genes including Il1b, Il6 and Tnfa, among which Tnfa was selectively blocked by minocycline. PLX5622 also suppressed Tnfa expression. Tumor necrosis factor α (TNFα) signals were restricted in microglia at very early followed by spreading into other cell types. TNFα up-regulation in microglia and other cells were significantly attenuated by minocycline and PLX5622, suggesting a central role of microglia for TNFα induction. Both inhibition of TNFα and knockdown of TNF receptor type 1 by siRNA protected RGCs against NMDA. Taken together, our data demonstrate that a phenotypic change of microglia into a neurotoxic one is a critical event for the NMDA-induced degeneration of RGCs, suggesting an importance of non-cell-autonomous mechanism in the retinal neuronal excitotoxicity.
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Muerte Celular/fisiología , Citocinas/metabolismo , Microglía/fisiología , Células Ganglionares de la Retina/fisiología , Aminopiridinas/farmacología , Animales , Animales Recién Nacidos , Proteínas de Unión al Calcio/genética , Proteínas de Unión al Calcio/metabolismo , Muerte Celular/efectos de los fármacos , Células Cultivadas , Citocinas/genética , Agonistas de Aminoácidos Excitadores/farmacología , Regulación de la Expresión Génica/efectos de los fármacos , Regulación de la Expresión Génica/genética , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Proteínas de Microfilamentos/genética , Proteínas de Microfilamentos/metabolismo , Microglía/efectos de los fármacos , Microglía/ultraestructura , N-Metilaspartato/farmacología , Degeneración Nerviosa/inducido químicamente , Traumatismos del Nervio Óptico/inducido químicamente , Compuestos Orgánicos/farmacología , Pirroles/farmacología , Células Ganglionares de la Retina/efectos de los fármacos , Células Ganglionares de la Retina/ultraestructura , Transducción de Señal/efectos de los fármacos , Factor de Transcripción Brn-3A/genética , Factor de Transcripción Brn-3A/metabolismo , Factor de Necrosis Tumoral alfa/metabolismoRESUMEN
Although psychotropic drugs act on neurons and glial cells, how glia respond, and whether glial responses are involved in therapeutic effects are poorly understood. Here, we show that fluoxetine (FLX), an anti-depressant, mediates its anti-depressive effect by increasing the gliotransmission of ATP. FLX increased ATP exocytosis via vesicular nucleotide transporter (VNUT). FLX-induced anti-depressive behavior was decreased in astrocyte-selective VNUT-knockout mice or when VNUT was deleted in mice, but it was increased when astrocyte-selective VNUT was overexpressed in mice. This suggests that VNUT-dependent astrocytic ATP exocytosis has a critical role in the therapeutic effect of FLX. Released ATP and its metabolite adenosine act on P2Y11 and adenosine A2b receptors expressed by astrocytes, causing an increase in brain-derived neurotrophic factor in astrocytes. These findings suggest that in addition to neurons, FLX acts on astrocytes and mediates its therapeutic effects by increasing ATP gliotransmission.
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Depresión/tratamiento farmacológico , Fluoxetina/administración & dosificación , Proteínas de Transporte de Nucleótidos/genética , Receptor de Adenosina A2B/genética , Receptores Purinérgicos P2/genética , Adenosina Trifosfato/metabolismo , Animales , Antidepresivos/administración & dosificación , Astrocitos/efectos de los fármacos , Astrocitos/metabolismo , Astrocitos/patología , Depresión/genética , Depresión/metabolismo , Depresión/patología , Exocitosis/efectos de los fármacos , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , Ratones , Ratones Noqueados , Neuroglía/efectos de los fármacos , Neuroglía/metabolismo , Neuronas/efectos de los fármacos , Neuronas/metabolismoRESUMEN
Glaucoma is an optic neuropathy characterized by progressive degeneration of retinal ganglion cells (RGCs) and visual loss. Although one of the highest risk factors for glaucoma is elevated intraocular pressure (IOP) and reduction in IOP is the only proven treatment, the mechanism of IOP regulation is poorly understood. We report that the P2Y6 receptor is critical for lowering IOP and that ablation of the P2Y6 gene in mice (P2Y6KO) results in hypertensive glaucoma-like optic neuropathy. Topically applied uridine diphosphate, an endogenous selective agonist for the P2Y6 receptor, decreases IOP. The P2Y6 receptor was expressed in nonpigmented epithelial cells of the ciliary body and controlled aqueous humor dynamics. P2Y6KO mice exhibited sustained elevation of IOP, age-dependent damage to the optic nerve, thinning of ganglion cell plus inner plexiform layers, and a reduction of RGC numbers. These changes in P2Y6KO mice were attenuated by an IOP lowering agent. Consistent with RGC damage, visual functions were impaired in middle-aged P2Y6KO mice. We also found that expression and function of P2Y6 receptors in WT mice were significantly reduced by aging, another important risk factor for glaucoma. In summary, our data show that dysfunctional purinergic signaling causes IOP dysregulation, resulting in glaucomatous optic neuropathy.
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Glaucoma/complicaciones , Enfermedades del Nervio Óptico/etiología , Receptores Purinérgicos P2/fisiología , Envejecimiento/patología , Envejecimiento/fisiología , Animales , Humor Acuoso/metabolismo , Cuerpo Ciliar/metabolismo , Modelos Animales de Enfermedad , Relación Dosis-Respuesta a Droga , Glaucoma/tratamiento farmacológico , Glaucoma/metabolismo , Glaucoma/patología , Presión Intraocular/efectos de los fármacos , Presión Intraocular/fisiología , Ratones Noqueados , Enfermedades del Nervio Óptico/metabolismo , Enfermedades del Nervio Óptico/patología , Receptores Purinérgicos P2/deficiencia , Receptores Purinérgicos P2/genética , Células Ganglionares de la Retina/patología , Transducción de Señal/fisiología , Uridina Difosfato/administración & dosificación , Uridina Difosfato/farmacología , Uridina Difosfato/uso terapéuticoRESUMEN
OBJECTIVES: Several studies indicate that cyclosporin A has a protective effect against brain infarction. In this study, we aimed to determine if co-administration of cyclosporin A and ondansetron could reduce damage caused by cerebral ischemia. METHODS: ICR (Charles River Laboratories) mice were subjected to transient focal cerebral ischemia and divided into 4 groups (O, V, C, and Mix). Immediately after reperfusion, each ligand was administered intravenously through the external jugular vein. Group V animals received 0.9% saline alone, group O animals received 0.1 mg/kg ondansetron solution, group C animals received 10 mg/kg cyclosporin A solution, and group Mix received 0.1 mg/kg ondansetron solution and 10 mg/kg cyclosporin A solution. RESULTS: Our results showed that the volume of brain infarction induced by middle cerebral artery occlusion in group Mix was significantly smaller than that seen in group V. Forty-eight hours after ischemia, the neurological scores of rats from group Mix significantly improved when compared to group V. CONCLUSION: Overall, our study showed that a combination of cyclosporin A and ondansetron may be a practical clinical method to treat brain infarction. However, further studies are required to investigate the cerebroprotective mechanism of action, the possible side effects of co-administration of these drugs, and the ability of these ligands to cross the blood brain barrier.
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Ciclosporina/uso terapéutico , Ataque Isquémico Transitorio/tratamiento farmacológico , Fármacos Neuroprotectores/uso terapéutico , Ondansetrón/uso terapéutico , Animales , Circulación Cerebrovascular/efectos de los fármacos , Ciclosporina/farmacología , Modelos Animales de Enfermedad , Quimioterapia Combinada , Masculino , Ratones , Ratones Endogámicos ICR , Fármacos Neuroprotectores/farmacología , Ondansetrón/farmacología , Resultado del TratamientoRESUMEN
We propose a unified formulation of robust learning methods for classification and regression problems. In the learning methods, the hinge loss is used with outlier indicators in order to detect outliers in the observed data. To analyze the robustness property, we evaluate the breakdown point of the learning methods in the situation that the outlier ratio is not necessarily small. Although minimization of the hinge loss with outlier indicators is a non-convex optimization problem, we prove that any local optimal solution of our learning algorithms has the robustness property. The theoretical findings are confirmed in numerical experiments.
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Redes Neurales de la Computación , Máquina de Vectores de SoporteRESUMEN
Nonconvex variants of support vector machines (SVMs) have been developed for various purposes. For example, robust SVMs attain robustness to outliers by using a nonconvex loss function, while extended [Formula: see text]-SVM (E[Formula: see text]-SVM) extends the range of the hyperparameter by introducing a nonconvex constraint. Here, we consider an extended robust support vector machine (ER-SVM), a robust variant of E[Formula: see text]-SVM. ER-SVM combines two types of nonconvexity from robust SVMs and E[Formula: see text]-SVM. Because of the two nonconvexities, the existing algorithm we proposed needs to be divided into two parts depending on whether the hyperparameter value is in the extended range or not. The algorithm also heuristically solves the nonconvex problem in the extended range. In this letter, we propose a new, efficient algorithm for ER-SVM. The algorithm deals with two types of nonconvexity while never entailing more computations than either E[Formula: see text]-SVM or robust SVM, and it finds a critical point of ER-SVM. Furthermore, we show that ER-SVM includes the existing robust SVMs as special cases. Numerical experiments confirm the effectiveness of integrating the two nonconvexities.
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[This corrects the article on p. 30 in vol. 6, PMID: 25717326.].
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BACKGROUND: In high-throughput experimental biology, it is widely acknowledged that while expression levels measured at the levels of transcriptome and the corresponding proteome do not, in general, correlate well, messenger RNA levels are used as convenient proxies for protein levels. Our interest is in developing data-driven computational models that can bridge the gap between these two levels of measurement at which different mechanisms of regulation may act on different molecular species causing any observed lack of correlations. To this end, we build data-driven predictors of protein levels using mRNA levels and known proxies of translation efficiencies as covariates. Previous work showed that in such a setting, outliers with respect to the model are reliable candidates for post-translational regulation. RESULTS: Here, we present and compare two novel formulations of deriving a protein concentration predictor from which outliers may be extracted in a systematic manner. The first approach, outlier rejecting regression, allows explicit specification of a certain fraction of the data as outliers. In a regression setting, this is a non-convex optimization problem which we solve by deriving a difference of convex functions algorithm (DCA). With post-translationally regulated proteins, one expects their concentrations to be affected primarily by disruption of protein stability. Our second algorithm exploits this observation by minimizing an asymmetric loss using quantile regression and extracts outlier proteins whose measured concentrations are lower than what a genome-wide regression would predict. We validate the two approaches on a dataset of yeast transcriptome and proteome. Functional annotation check on detected outliers demonstrate that the methods are able to identify post-translationally regulated genes with high statistical confidence.
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Biología Computacional/métodos , Proteoma/metabolismo , ARN Mensajero/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Transcriptoma , Algoritmos , Biomarcadores/análisis , Regulación Fúngica de la Expresión Génica , Genoma Fúngico , Saccharomyces cerevisiae/metabolismoRESUMEN
Splenic transitional B-cells (T1 and T2) are selected to avoid self-reactivity and to safeguard against autoimmunity, then differentiate into mature follicular (FO-I and FO-II) and marginal zone (MZ) subsets. Transcriptomic analysis by RNA-seq of the five B-cell subsets revealed T1 cell signature genes included RAG suggesting a potential for receptor revision. T1 to T2 B-cell differentiation was marked by a switch from Myb to Myc, increased expression of the PI3K adapter DAP10 and MHC class II. FO-II may be an intermediate in FO-I differentiation and may also become MZ B-cells as suggested by principle component analysis. MZ B-cells possessed the most distinct transcriptome including down-regulation of CD45 phosphatase-associated protein (CD45-AP/PTPRC-AP), as well as upregulation of IL-9R and innate molecules TLR3, TLR7, and bactericidal Perforin-2 (MPEG1). Among the endosomal TLRs, stimulation via TLR3 further enhanced Perforin-2 expression exclusively in MZ B-cells. Using gene-deleted and overexpressing transgenic mice we show that IL-9/IL-9R interaction resulted in rapid activation of STAT1, 3, and 5, primarily in MZ B-cells. Importantly, CD45-AP mutant mice had reduced transitional and increased mature MZ and FO B-cells, suggesting that it prevents premature entry of transitional B-cells to the mature B-cell pool or their survival and proliferation. Together, these findings suggest, developmental plasticity among splenic B-cell subsets, potential for receptor revision in peripheral tolerance whereas enhanced metabolism coincides with T2 to mature B-cell differentiation. Further, unique core transcriptional signatures in MZ B-cells may control their innate features.