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1.
Proc Natl Acad Sci U S A ; 120(26): e2218218120, 2023 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-37339213

RESUMEN

The criticality of the jamming transition responsible for amorphous solidification has been theoretically linked to the marginal stability of a thermodynamic Gardner phase. While the critical exponents of jamming appear independent of the preparation history, the pertinence of Gardner physics far from equilibrium is an open question. To fill this gap, we numerically study the nonequilibrium dynamics of hard disks compressed toward the jamming transition using a broad variety of protocols. We show that dynamic signatures of Gardner physics can be disentangled from the aging relaxation dynamics. We thus define a generic dynamic Gardner cross-over regardless of the history. Our results show that the jamming transition is always accessed by exploring increasingly complex landscape, resulting in anomalous microscopic relaxation dynamics that remains to be understood theoretically.

2.
Gastroenterology ; 158(3): 664-678.e24, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31678303

RESUMEN

BACKGROUND & AIMS: Immune checkpoint inhibitors have some efficacy in the treatment of hepatocellular carcinoma (HCC). Programmed cell death 1 ligand 1 (PD-L1), expressed on some cancer cells, binds to the receptor programmed cell death 1 (PDCD1, also called PD1) on T cells to prevent their proliferation and reduce the antigen-tumor immune response. Immune cells that infiltrate some types of HCCs secrete interferon gamma (IFNG). Some HCC cells express myocyte enhancer factor 2D (MEF2D), which has been associated with shorter survival times of patients. We studied whether HCC cell expression of MEF2D regulates expression of PD-L1 in response to IFNG. METHODS: We analyzed immune cells from 20 fresh HCC tissues by flow cytometry. We analyzed 225 fixed HCC tissues (from 2 cohorts) from patients in China by immunohistochemistry and obtained survival data. We created mice with liver-specific knockout of MEF2D (MEF2DLPC-KO mice). We knocked out or knocked down MEF2D, E1A binding protein p300 (p300), or sirtuin 7 (SIRT7) in SMMC-7721, Huh7, H22, and Hepa1-6 HCC cell lines, some incubated with IFNG. We analyzed liver tissues from mice and cell lines by RNA sequencing, immunoblot, dual luciferase reporter, and chromatin precipitation assays. MEF2D protein acetylation and proteins that interact with MEF2D were identified by coimmunoprecipitation and pull-down assays. H22 cells, with MEF2D knockout or without (controls), were transplanted into BALB/c mice, and some mice were given antibodies to deplete T cells. Mice bearing orthotopic tumors grown from HCC cells, with or without knockout of SIRT7, were given injections of an antibody against PD1. Growth of tumors was measured, and tumors were analyzed by immunohistochemistry and flow cytometry. RESULTS: In human HCC specimens, we found an inverse correlation between level of MEF2D and numbers of CD4+ and CD8+ T cells; level of MEF2D correlated with percentages of PD1-positive or TIM3-positive CD8+ T cells. Knockout of MEF2D from H22 cells reduced their growth as allograft tumors in immune-competent mice but not in immune-deficient mice or mice with depletion of CD8+ T cells. When MEF2D-knockout cells were injected into immune-competent mice, they formed smaller tumors that had increased infiltration and activation of T cells compared with control HCC cells. In human and mouse HCC cells, MEF2D knockdown or knockout reduced expression of PD-L1. MEF2D bound the promoter region of the CD274 gene (encodes PD-L1) and activated its transcription. Overexpression of p300 in HCC cells, or knockout of SIRT7, promoted acetylation of MEF2D and increased its binding, along with acetylated histones, to the promoter region of CD274. Exposure of HCC cells to IFNG induced expression of p300 and its binding MEF2D, which reduced the interaction between MEF2D and SIRT7. MEF2D-induced expression of PD-L1 upon IFNG exposure was independent of interferon-regulatory factors 1 or 9. In HCC cells not exposed to IFNG, SIRT7 formed a complex with MEF2D that attenuated expression of PD-L1. Knockout of SIRT7 reduced proliferation of HCC cells and growth of tumors in immune-deficient mice. Compared with allograft tumors grown from control HCC cells, in immune-competent mice, tumors grown from SIRT7-knockout HCC cells expressed higher levels of PD-L1 and had reduced infiltration and activation of T cells. In immune-competent mice given antibodies to PD1, allograft tumors grew more slowly from SIRT7-knockout HCC cells than from control HCC cells. CONCLUSIONS: Expression of MEF2D by HCC cells increases their expression of PD-L1, which prevents CD8+ T-cell-mediated antitumor immunity. When HCC cells are exposed to IFNG, p300 acetylates MEF2D, causing it to bind the CD274 gene promoter and up-regulate PD-L1 expression. In addition to promoting HCC cell proliferation, SIRT7 reduced acetylation of MEF2D and expression of PD-L1 in HCC cells not exposed to IFNG. Strategies to manipulate this pathway might increase the efficacy of immune therapies for HCC.


Asunto(s)
Antígeno B7-H1/genética , Carcinoma Hepatocelular/genética , Neoplasias Hepáticas/genética , Sirtuinas/genética , Adolescente , Adulto , Anciano , Animales , Recuento de Linfocito CD4 , Linfocitos T CD8-positivos/metabolismo , Carcinoma Hepatocelular/patología , Línea Celular Tumoral , Proliferación Celular/genética , Proteína p300 Asociada a E1A/genética , Proteína p300 Asociada a E1A/metabolismo , Femenino , Técnicas de Inactivación de Genes , Receptor 2 Celular del Virus de la Hepatitis A/metabolismo , Humanos , Inmunocompetencia , Interferón gamma/farmacología , Neoplasias Hepáticas/patología , Factores de Transcripción MEF2/genética , Factores de Transcripción MEF2/metabolismo , Masculino , Ratones , Ratones Endogámicos BALB C , Persona de Mediana Edad , Trasplante de Neoplasias , Receptor de Muerte Celular Programada 1/metabolismo , Sirtuinas/metabolismo , Transcripción Genética/efectos de los fármacos , Transcripción Genética/genética , Adulto Joven
3.
Opt Express ; 29(2): 604-614, 2021 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-33726293

RESUMEN

We report on the generation of a highly coherent broadband optical linear frequency sweep (LFS) using mode-spacing swept comb and multi-loop composite optical phase-locked loop (OPLL). We exploit a specially designed agile opto-electronic frequency comb as a sweeping reference, whose mode-spacing is capable of arbitrary frequency sweep while preserving a stable phase and power distribution per mode. By locking a continuous-wave (CW) laser to any of its modes using composite OPLL with a large loop bandwidth, it allows the extraction of the optical LFS at high-order modes in a coherent manner with a multiplied sweep range and rate. With such capability, only intermediate frequency LFS with smaller bandwidth is required to yield a broadband LFS while inheriting the coherence and precision from the comb. We achieve optical LFS of 60 GHz at 6 THz/s sweep rate with a nine-folded sweep bandwidth of the driving signal. Fourier transform-limited spatial resolution at more than 80 times of the intrinsic coherence length of the CW laser is demonstrated in an OFMCW interferometry, verifying the high coherence with more than 4 orders of magnitude improvement in spatial resolution. The characteristics in terms of agility, coherence, and precision are discussed together with the potential limitations. The proposed method is capable of generating arbitrary frequency-modulated optical waveforms with a multiplied bandwidth, showing attractive potential in future metrology applications.

4.
Opt Lett ; 46(23): 5782-5785, 2021 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-34851889

RESUMEN

We present a remote Michelson interferometric phase sensor based on dual-core fiber transmission and linear phase demodulation. The former allows for synchronous transmission of both sensing signal and reference lights, enabling efficient suppression for the environmental disturbances along the transmission link and for the incoherent phase noise between the two lights. The latter is conducted by two optical phase-locked loops, one of which consists of a fiber stretcher that is used to eliminate the residual phase noises, thus stabilizing the operation point while the other relies on a phase modulator that is used to track the remote phase changes, thus achieving a highly linearized phase demodulation. A remote phase sensing over a 20 km fiber link with less than 3% nonlinear phase error over 3π range has been readily realized, corresponding to more than 10 times extension in a linear phase demodulation range. The proposed system shows great potential in the field of remote phase sensing for a variety of physical quantities.

5.
Environ Res ; 193: 110522, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33259785

RESUMEN

The stoichiometric characteristics of water-soluble ions (WSIs) in PM2.5, which can be used as an indicator socioeconomic development level, are mostly depending on the sources and formation mechanism of PM2.5. This work presents the stoichiometric characteristics and socioeconomic linkage of WSIs in PM2.5 from a resource-dependent city. The relationship between NO3-/SO42- and car parc indexes the contribution of mobile emission source. The equivalent ratio of WSIs suggested that aerosol particles were weak acidic due to the deficiency of cations in PM2.5, which was consistent with the average annual pH (6.27) of precipitation in Wuhai in 2015. NH4+ neutralizes PM2.5 acidity in clean and polluted days, while Ca2+ and NH4+ in dust storm days. Furthermore, the PCA analysis indicated the multi-sources pollution characteristics from Spring to Fall, which was related the small build-up area (only 62.30 km2) and the close-set of various industrial enterprises in Wuhai. The ratios of NO2/SO2 may not work effectively to identify the importance of mobile versus stationary pollution emission sources when the heavy emission from the secondary industry, especially the proportion of secondary industry higher than 65% and the ratios of NO2/SO2 lower than 0.4. This work contributes to more effective control strategies for PM2.5 in resource-dependent areas.


Asunto(s)
Contaminantes Atmosféricos , Material Particulado , Contaminantes Atmosféricos/análisis , Ciudades , Monitoreo del Ambiente , Iones/análisis , Material Particulado/análisis , Estaciones del Año , Agua
6.
Chaos ; 31(11): 113127, 2021 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-34881621

RESUMEN

Spatially distinct, self-sustained oscillations in artificial neural networks are fundamental to information encoding, storage, and processing in these systems. Here, we develop a method to induce a large variety of self-sustained oscillatory patterns in artificial neural networks and a controlling strategy to switch between different patterns. The basic principle is that, given a complex network, one can find a set of nodes-the minimum feedback vertex set (mFVS), whose removal or inhibition will result in a tree-like network without any loop structure. Reintroducing a few or even a single mFVS node into the tree-like artificial neural network can recover one or a few of the loops and lead to self-sustained oscillation patterns based on these loops. Reactivating various mFVS nodes or their combinations can then generate a large number of distinct neuronal firing patterns with a broad distribution of the oscillation period. When the system is near a critical state, chaos can arise, providing a natural platform for pattern switching with remarkable flexibility. With mFVS guided control, complex networks of artificial neurons can thus be exploited as potential prototypes for local, analog type of processing paradigms.


Asunto(s)
Redes Neurales de la Computación , Neuronas , Retroalimentación
7.
Zhonghua Nan Ke Xue ; 27(5): 426-432, 2021 May.
Artículo en Zh | MEDLINE | ID: mdl-34914318

RESUMEN

OBJECTIVE: To explore the role of transforming growth factor-ß (TGF-ß) in bladder neck contracture (BNC) after transurethral enucleation and resection of the prostate (TUERP). METHODS: This study included 300 BPH patients undergoing TUERP, aged 51-89 (69.19 ± 8.43) years, with the prostate volume of 14.4-355.8 (63.18 ± 47.63) ml and preoperative IPSS of 15-35 (26.07 ± 5.9), QOL score of 3-6 (4.43 ± 0.67), PSA content of 0.17-23.16 (2.94 ± 3.77) ug/L, urinary leukocyte increase in 50 cases, post-void residual urine volume (PVR) of 0-440 (83.53 ± 86.85) ml, and maximum urinary flow rate (Qmax) of 2.3-14.5 (7.77 ± 3.47) ml/s. During TUERP, we collected the tissues from the bladder neck at 5 and 7 o'clock as well as the BPH tissue and the tissue from the residual prostate for HE staining, immunohistochemistry (the SP method) and examination of the infiltration degree of inflammatory cells and expressions of TGF-ß1 and TGF-ß3. During the 6-24 months follow-up, 6 of the patients were confirmed with BNC based on the clinical symptoms and the results of uroflowmetry and cystoscopy, and underwent transurethral bladder neck incision and detection of the expressions of TGF-ß1 and TGF-ß3 in the bladder neck tissue with BNC. RESULTS: The bladder neck tissue without BNC was mainly composed of smooth muscle and fibrous tissues with local infiltration of inflammatory cells, and the residual prostate tissue primarily comprised fibrous and muscle tissues, mixed with a little prostatic epithelial tissue. The bladder neck tissue with BNC, compared with that harvested during the initial TUERP, exhibited significantly increased expression of TGF-ß1 (ï¼»68.20 ± 10.88ï¼½% vs ï¼»36.14 ± 7.62ï¼½%, P < 0.05), decreased expression of TGF-ß3 (ï¼»8.55 ± 4.73ï¼½% vs ï¼»20.77 ± 8.69ï¼½%, P < 0.05), and enhanced infiltration of inflammatory cells (P < 0.05). The bladder neck tissue without BNC, in comparison with the BPH tissue, showed dramatically up-regulated expressions of TGF-ß1 (ï¼»27.05 ± 8.21ï¼½% vs ï¼»1.61 ± 0.69ï¼½%, P < 0.001) and TGF-ß3 (ï¼»14.09 ± 4.19ï¼½% vs ï¼»0.32 ± 0.11ï¼½%, P < 0.001) and increased infiltration of inflammatory cells (P < 0.05). CONCLUSIONS: After TUERP, the expression of TGF-ß1 is increased, that of TGF-ß3 decreased and the infiltration of inflammatory cells enhanced in the bladder neck tissue with BNC, which suggests that BNC may be related to the expression of TGF-ß and that BNC after TUERP could be prevented by regulating the expression of TGF-ß.


Asunto(s)
Contractura , Vejiga Urinaria , Anciano , Anciano de 80 o más Años , Contractura/etiología , Contractura/cirugía , Humanos , Masculino , Persona de Mediana Edad , Próstata/cirugía , Calidad de Vida , Factor de Crecimiento Transformador beta , Vejiga Urinaria/cirugía
8.
Biochem Biophys Res Commun ; 532(2): 258-264, 2020 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-32863002

RESUMEN

Anoikis is a programmed death of cell induced upon detachment from the extracellular matrix (ECM). Resistance to anoikis is a critical contributor to cancer invasion and metastasis. High frequency of metastatic recurrence is a huge challenge for current therapy of hepatocellular carcinoma (HCC). Our previous study had identified sulfhydryl oxidase 1 (QSOX1) as a suppressor of HCC metastasis. In the present study, we used the anchorage-independent growth condition to mimic the detachment of HCC cells from ECM. We found that QSOX1 was induced in HCC cells under the anchorage-independent growth condition and that could be blocked by endoplasmic reticulum stress (ERS) inhibitor. Overexpression and knockdown of QSOX1 gene were performed on HCC cells. QSOX1 inhibited de novo synthesis of fatty acids (FAs) and cholesterol (ChE) and reduced their content in the detached HCC cells, and thus mediated mitochondrial apoptosis of HCC cells. In conclusion, QSOX1 is induced under detached culture condition via ERS. QSOX1 promotes mitochondrial apoptosis by suppressing the lipid synthesis of HCC cells in detached condition. QSOX1 appears to accelerate anoikis of HCC cells. These findings offer a new insight into how to overcome anoikis resistance of HCC cells and provide a potential target for prevention of HCC metastasis.


Asunto(s)
Carcinoma Hepatocelular/patología , Lípidos/biosíntesis , Neoplasias Hepáticas/patología , Mitocondrias/patología , Oxidorreductasas actuantes sobre Donantes de Grupos Sulfuro/metabolismo , Anoicis/fisiología , Apoptosis , Carcinoma Hepatocelular/metabolismo , Línea Celular Tumoral , Proliferación Celular , Colesterol/metabolismo , Estrés del Retículo Endoplásmico , Ácidos Grasos/metabolismo , Regulación Neoplásica de la Expresión Génica , Humanos , Ácido Láctico/metabolismo , Neoplasias Hepáticas/metabolismo , Mitocondrias/metabolismo , Oxidorreductasas actuantes sobre Donantes de Grupos Sulfuro/genética
9.
Hepatology ; 70(4): 1197-1213, 2019 10.
Artículo en Inglés | MEDLINE | ID: mdl-30901096

RESUMEN

Metabolic reprogramming endows cancer cells with the ability to adjust metabolic pathways to support heterogeneously biological processes. However, it is not known how the reprogrammed activities are implemented during differentiation of cancer stem cells (CSCs). In this study, we demonstrated that liver CSCs relied on the enhanced mitochondrial function to maintain stemness properties, which is different from aerobic glycolysis playing main roles in the differentiated non-CSCs. We found that liver CSCs exhibit increased mitochondrial respiratory capacity and that complex-I of mitochondria was necessary for stemness properties of liver CSCs through regulation of mitochondrial respiration. Bioinformatics analysis reveals that mitochondrial ribosomal protein S5 (MRPS5) is closely related with the function of complex-I. Further experiments confirmed that MRPS5 promoted the production of nicotinamide adenine dinucleotide (NAD+ ), which is necessary for enhanced mitochondrial function in liver CSCs. MRPS5 played a critical role for liver CSCs to maintain stemness properties and to participate in tumor progression. Mechanistically, the acetylation status of MRPS5 is directly regulated by NAD+ dependent deacetylase sirtuin-1 (SIRT1), which is abundant in liver CSCs and decreased during differentiation. Deacetylated MRPS5 locates in mitochondria to promote the function complex-I and the generation of NAD+ to enhance mitochondrial respiration. Conversely, the acetylated MRPS5 gathered in nuclei leads to increased expression of glycolytic proteins and promotion of the Warburg Effect. Therefore, liver CSCs transform mitochondrial-dependent energy supply to a Warburg phenotype by the dual function of MRPS5. Clinical analysis of SIRT1 and MRPS5 expression in tumor tissues showed the SIRT1High /Cytoplasmic-MRPS5High profile was associated with patients with hepatocellular carcinoma with poor prognosis. Conclusion: SIRT1/MRPS5 axis participates in metabolic reprogramming to facilitate tumor progression and may serve as a promising therapeutic target of liver cancer.


Asunto(s)
Carcinoma Hepatocelular/genética , Reprogramación Celular/genética , Neoplasias Hepáticas/genética , Proteínas Mitocondriales/genética , NAD/metabolismo , Proteínas Ribosómicas/genética , Sirtuina 1/metabolismo , Acetilación/efectos de los fármacos , Animales , Carcinoma Hepatocelular/patología , Diferenciación Celular/genética , Metilación de ADN/genética , Humanos , Neoplasias Hepáticas/patología , Ratones , Mitocondrias/metabolismo , Células Madre Neoplásicas/metabolismo , Sensibilidad y Especificidad , Células Tumorales Cultivadas
10.
Stem Cells ; 37(11): 1389-1400, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31322782

RESUMEN

Tcf7l1, which is a key effector molecule of the Wnt/ß-catenin signaling pathway, is highly expressed in various cancers, and it promotes tumor growth. In this study, we demonstrated that unlike its tumor-promoting effects in several other types of cancers, Tcf7l1 expression is downregulated in hepatocarcinoma compared with their adjacent nontumor counterparts. Underexpression of Tcf7l1 is correlated with poorer survival. In liver cancer stem cell (CSC) populations, Tcf7l1 expression is downregulated. Ectopic expression of Tcf7l1 attenuates the self-renewal abilities of liver CSCs. Mechanistically, Tcf7l1 regulates the self-renewal abilities of liver CSCs through transcriptional repression of the Nanog gene, and the effect is independent of ß-catenin. Moreover, we found that Tcf7l1 expression is controlled by extracellular insulin-like growth factor (IGF) signaling, and we demonstrated for the first time that IGF signaling stimulates Tcf7l1 phosphorylation and degradation through the mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway. Overall, our results provide some new insights into how extracellular signals modulate the self-renewal of liver CSCs and highlight the inhibitory roles of Tcf7l1 in cancer. Stem Cells 2019;37:1389-1400.


Asunto(s)
Supervivencia Celular/fisiología , Hígado/citología , Hígado/metabolismo , Células Madre Neoplásicas/citología , Células Madre Neoplásicas/metabolismo , Somatomedinas/metabolismo , Proteína 1 Similar al Factor de Transcripción 7/metabolismo , beta Catenina/metabolismo , Línea Celular , Supervivencia Celular/genética , Inmunoprecipitación de Cromatina , Citometría de Flujo , Humanos , Inmunoensayo , Inmunohistoquímica , Inmunoprecipitación , Técnicas In Vitro , Lentivirus , Sistema de Señalización de MAP Quinasas/genética , Sistema de Señalización de MAP Quinasas/fisiología , Proteína Homeótica Nanog/genética , Proteína Homeótica Nanog/metabolismo , Fosforilación , Plásmidos/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Somatomedinas/genética , Proteína 1 Similar al Factor de Transcripción 7/genética , beta Catenina/genética
11.
Phys Rev Lett ; 124(24): 248301, 2020 Jun 19.
Artículo en Inglés | MEDLINE | ID: mdl-32639824

RESUMEN

We introduce two generalizations of core percolation in graphs to hypergraphs, related to the minimum hyperedge cover problem and the minimum vertex cover problem on hypergraphs, respectively. We offer analytical solutions of these two core percolations for uncorrelated random hypergraphs whose vertex degree and hyperedge cardinality distributions are arbitrary but have nondiverging moments. We find that for several real-world hypergraphs their two cores tend to be much smaller than those of their null models, suggesting that covering problems in those real-world hypergraphs can actually be solved in polynomial time.

12.
Ecotoxicol Environ Saf ; 191: 110232, 2020 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-31986457

RESUMEN

Air pollution has been considered as one of the most important factors associating with various birth outcomes. However, the seasonal response of maternal comorbidities effects associated with air pollution has not been investigated, especially in the city with distinguish seasonal pattern and long heating seasons. In this work, 69,945 live births were investigated from 2013 to 2016, and the seasonal relationship between air pollution and preterm birth and low birth weight were assessed, as well as the synergism of maternal comorbidities. Exposures of six pollutants were assigned to maternal residences during pregnancy. The potential effect modification by maternal comorbidities on the associations was evaluated between prenatal air pollution and preterm birth (PTB), as well as effects of seasons and trimesters. Adjusting for seasonality, all six pollutants presented seasonal relationship with preterm birth, which CO, PM10, NO2, and PM2.5 were with [odds ratio (OR) = 1.035 95% CI: 1.015, 1.055, OR = 1.039 95% CI: 1.034, 1.045, OR = 1.042, 95% CI: 1.029, 1.056 and OR = 1.085 95% CI 1.073, 1.097, respectively] for tenth quartile of 10 µg/m3 range increased in autumn (the beginning of heating season). For O3, it associated with PTB in winter and spring with OR = 1.113 95% CI: 1.104, 1.123, and OR = 1.155 95% CI: 1.145, 1.165, respectively. The OR increase of PTB for exposure to all six pollutants was higher among women with preeclampsia and gestational hypertension. The associations between ambient air pollution and preterm birth were modified by gestational hypertension and preeclampsia. The seasonal patterns of six studied air pollutants increases the risk of PTB in autumn and winter distinguishably, which may due to the sudden increased concentrations of pollutants emitted by traditional heating. The seasonal response of the synergism of maternal comorbidities and long-term air pollution exposure on birth outcomes is supported by the data sets of preterm birth.


Asunto(s)
Contaminantes Atmosféricos/toxicidad , Exposición Materna , Nacimiento Prematuro/epidemiología , Estaciones del Año , Contaminantes Atmosféricos/análisis , Contaminación del Aire , Comorbilidad , Femenino , Humanos , Hipertensión Inducida en el Embarazo , Recién Nacido de Bajo Peso , Recién Nacido , Oportunidad Relativa , Preeclampsia , Embarazo , Resultado del Embarazo , Trimestres del Embarazo
13.
Phys Biol ; 16(2): 026002, 2019 01 29.
Artículo en Inglés | MEDLINE | ID: mdl-30605896

RESUMEN

Direct coupling analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics. DCA can be expected to yield meaningful results when a population is in the quasi-linkage equilibrium (QLE) phase studied by Kimura and others, but not, for instance, in a phase of clonal competition. We discuss how the exponential (Potts model) distributions emerge in QLE, and compare couplings to correlations obtained in a study of about 3000 genomes of the human pathogen Streptococcus pneumoniae.


Asunto(s)
Epistasis Genética , Genoma Bacteriano , Modelos Genéticos , Modelos Estadísticos , Streptococcus pneumoniae/genética , Epigenómica
14.
Opt Express ; 27(19): 27062-27075, 2019 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-31674574

RESUMEN

We investigate the performance of coherent free-space optical (FSO) system in terms of bit error rate (BER) evaluation by adopting the modified Rician distribution based coherent channel model which allows taking into consideration the composite effects of both Rician turbulence, including amplitude fluctuation and optical phase distortion, and pointing errors (PEs). By expanding the Rician distribution, a mathematically traceable expression of the probability density function (PDF) for the composite channel is derived in the form of the Meijer-G function. Based on the composite channel PDF, the exact BER expression is obtained, allowing the analysis of BER performance for single-input single-output (SISO) links. This analysis is extended to single-input multi-output (SIMO) links with maximal ratio combining (MRC). With the help of the moment generating function (MGF), the exact BER expression can be simplified into a single integral, facilitating the analysis with high accuracy and reducing calculation complexity. Engineering insights including high-SNR approximated channel PDF, asymptotic BER expression, coding and diversity gains, are investigated and cross-validated for both SISO and SIMO links. Through both analytical and numerical verifications, the impairment due to PEs as well as the effect of modal compensation on the BER performance are discussed in detail, unveiling the fact that their inner relations should be taken into account for optimization. These verify the effectiveness of our models for both SISO and SIMO links with a wide range of different conditions and can be feasibly applied for different types of coherent FSO links.

15.
Phys Rev Lett ; 122(16): 160601, 2019 Apr 26.
Artículo en Inglés | MEDLINE | ID: mdl-31075020

RESUMEN

Spontaneous symmetry breaking (SSB) in statistical physics is a macroscopic collective phenomenon. For the paradigmatic Q-state Potts model it means a transition from the disordered color-symmetric phase to an ordered phase in which one color dominates. Existing mean field theories imply that SSB in the microcanonical statistical ensemble (with energy being the control parameter) should be a continuous process. Here we study microcanonical SSB on the random-graph Potts model and discover that the entropy is a kinked function of energy. This kink leads to a discontinuous phase transition at certain energy density value, characterized by a jump in the density of the dominant color and a jump in the microcanonical temperature. This discontinuous SSB in random graphs is confirmed by microcanonical Monte Carlo simulations, and it is also observed in bond-diluted finite-size lattice systems.

16.
Nanotechnology ; 30(27): 275602, 2019 Jul 05.
Artículo en Inglés | MEDLINE | ID: mdl-30901767

RESUMEN

This work reports a bioinspired anisotropic nanocomposite by polar solution assisted mechanical stretching method, consisting of polyvinyl alcohol (PVA) and silicon carbide nanowires (SiCNWs) with aligned morphology in one direction. Inspired by the structural mimicry of myofibers, in which the uniaxial mechanical property of materials can be improved evidently, highly-aligned SiCNWs and PVA chains that interact using intermolecular force can be obtained. Hysteresis is observed and reversible deformation occurs while tensile-relaxation cycles are applied to the 100% stretched SiCNWs/PVA nanocomposites. The nanocomposites exhibit excellent properties and the tensile strength of 100% stretched SiCNWs/PVA nanocomposites is 188.30 ± 4.2 MPa and elastic modulus is 6.95 GPa, which are increased by 421.90% and 581.37% compared with pure PVA. Finite element simulation of fracture mechanism shows good agreement with the experimental results. An improvement of thermal conductivity is also achieved in well-aligned SiCNWs/PVA. The work imitates the structure of mammal muscle and also has great potential for the macroscopic application of one-dimensional nanomaterials as super flexible heat dissipation materials.

17.
Ecotoxicol Environ Saf ; 167: 317-323, 2019 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-30343146

RESUMEN

To interpret the relationship of the seasonal pattern of air pollution exposure associated with increased risk of congenital anomalies (CA) and the trimester-specific effects. In this work, 55,428 hospital records with 847 doctor-diagnosed CA from July 2013 to December 2016 were collected in Hohhot, China. Maternal exposure to critical air pollutants (SO2, CO, PM10, O3, NO2 and PM2.5) were estimated using an inverse distance weighted (IDW) method on the basis of the ambient air quality monitoring stations. Logistic regression analysis was employed to determine the association of CA (in terms of odds ratio (OR) and 95% confidence interval (CI)) in three trimesters with heating/none heating season exposure. The results showed that CO exposure was found a significant association with ORs (95% CI) 1.58 (1.09, 2.27) changing from IQR2-3 and 1.40 (1.01, 1.93) changing from IQR3-IQR4 in 1st trimester and 1.51 (1.12, 2.04) changing from IQR2-3 in 2nd trimester, respectively. PM10 also presented significant association with ORs (95% CI) 1.42(1.08, 1.86) changing from IQR3-4 in 2nd trimester. Exposure effects were found more obvious in heating season, i.e. CO exposure levels were associated with the risks of CA with IQR changing ORs (95% CI) of 5.21(2.02, 7.44), 2.24 (1.21, 4.15) and 1.84 (1.10, 3.11) in 1st trimester, respectively; PM2.5 exposure levels were associated with the risks of CA with IQR changing ORs (95% CI) of 3.76 (1.48, 6.55), 2.45 (1.10, 5.44) and 3.30 (1.63, 6.67) in 2nd trimester, respectively. Our findings suggested some positive associations of pregnancy and CA with maternal exposure to ambient CO and PM2.5 during the 1st and 2nd trimester after controlling for maternal comorbidities general covariates and other pollutants. PM10 was also found significantly associated with increased risk of CA in 2nd trimester besides seasons. There was no association found in 3rd trimester.


Asunto(s)
Contaminantes Atmosféricos/toxicidad , Contaminación del Aire/efectos adversos , Anomalías Congénitas/diagnóstico , Estaciones del Año , Monóxido de Carbono/toxicidad , China , Anomalías Congénitas/etiología , Femenino , Humanos , Modelos Logísticos , Exposición Materna/efectos adversos , Dióxido de Nitrógeno/toxicidad , Ozono/toxicidad , Material Particulado/toxicidad , Embarazo , Medición de Riesgo , Factores de Riesgo , Dióxido de Azufre/toxicidad
18.
Phys Rev Lett ; 121(21): 210602, 2018 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-30517800

RESUMEN

Lower temperature leads to a higher probability of visiting low-energy states. This intuitive belief underlies most physics-inspired strategies for addressing hard optimization problems. For instance, the popular simulated annealing (SA) dynamics is expected to approach a ground state if the temperature is lowered appropriately. Here, we demonstrate that this belief is not always justified. Specifically, we employ the cavity method to analyze the minimum strong defensive alliance problem and discover a bifurcation in the solution space, induced by an inflection point in the entropy-energy profile. While easily accessible configurations are associated with the lower-free-energy branch, the low-energy configurations are associated with the higher-free-energy branch within the same temperature range. There is a discontinuous phase transition between the high-energy configurations and the ground states, which generally cannot be followed by SA. We introduce an energy-clamping strategy to obtain superior solutions by following the higher-free-energy branch, overcoming the limitations of SA.

19.
PLoS Comput Biol ; 13(2): e1005384, 2017 02.
Artículo en Inglés | MEDLINE | ID: mdl-28192429

RESUMEN

The brain is highly energy consuming, therefore is under strong selective pressure to achieve cost-efficiency in both cortical connectivities and activities. However, cost-efficiency as a design principle for cortical activities has been rarely studied. Especially it is not clear how cost-efficiency is related to ubiquitously observed multi-scale properties: irregular firing, oscillations and neuronal avalanches. Here we demonstrate that these prominent properties can be simultaneously observed in a generic, biologically plausible neural circuit model that captures excitation-inhibition balance and realistic dynamics of synaptic conductance. Their co-emergence achieves minimal energy cost as well as maximal energy efficiency on information capacity, when neuronal firing are coordinated and shaped by moderate synchrony to reduce otherwise redundant spikes, and the dynamical clusterings are maintained in the form of neuronal avalanches. Such cost-efficient neural dynamics can be employed as a foundation for further efficient information processing under energy constraint.


Asunto(s)
Potenciales de Acción/fisiología , Relojes Biológicos/fisiología , Encéfalo/fisiología , Cognición/fisiología , Modelos Neurológicos , Red Nerviosa/fisiología , Animales , Simulación por Computador , Metabolismo Energético/fisiología , Humanos , Almacenamiento y Recuperación de la Información/métodos , Modelos Estadísticos
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