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1.
Opt Express ; 32(8): 13583-13596, 2024 Apr 08.
Artículo en Inglés | MEDLINE | ID: mdl-38859325

RESUMEN

What we believe to be a new architecture based on dual-branch photon-number-resolving (DB-PNR) detectors for the receiver in the hybrid quantum key distribution (QKD) is introduced. DB-PNR scheme empowers the receiver to detect both quadratures of the coherent state simultaneously. Our results show that using DB-PNR detectors, the key generation rate (KGR) is almost doubled as compared to homodyne detection which detects only one quadrature at a time. The mutual information is enhanced by around 0.85 bits/symbol using DB-PNR as compared to heterodyne detection. DB-PNR is also found to outperform the heterodyne detection against Eve's individual and collective attacks. PNR-based detection schemes require less local oscillator (LO) power compared to homodyne/heterodyne detection schemes and thereby, the power efficiency of the receiver is enhanced.

2.
Sensors (Basel) ; 23(5)2023 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-36905061

RESUMEN

This article discusses the concept and applications of cognitive dynamic systems (CDS), which are a type of intelligent system inspired by the brain. There are two branches of CDS, one for linear and Gaussian environments (LGEs), such as cognitive radio and cognitive radar, and another one for non-Gaussian and nonlinear environments (NGNLEs), such as cyber processing in smart systems. Both branches use the same principle, called the perception action cycle (PAC), to make decisions. The focus of this review is on the applications of CDS, including cognitive radios, cognitive radar, cognitive control, cyber security, self-driving cars, and smart grids for LGEs. For NGNLEs, the article reviews the use of CDS in smart e-healthcare applications and software-defined optical communication systems (SDOCS), such as smart fiber optic links. The results of implementing CDS in these systems are very promising, with improved accuracy, performance, and lower computational costs. For example, CDS implementation in cognitive radars achieved a range estimation error that is as good as 0.47 (m) and a velocity estimation error of 3.30 (m/s), outperforming traditional active radars. Similarly, CDS implementation in smart fiber optic links improved the quality factor by 7 dB and the maximum achievable data rate by 43% compared to those of other mitigation techniques.


Asunto(s)
Encéfalo , Radar , Inteligencia
3.
Sensors (Basel) ; 23(13)2023 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-37447800

RESUMEN

This work proposes an efficient and easy-to-implement single-layer artificial neural network (ANN)-based equalizer with improved compensation performance. The proposed equalizer is used for effectively mitigating the distortions induced in the short-haul fiber-optic communication systems based on intensity modulation and direct detection (IMDD). The compensation performance of the ANN equalizer is significantly improved, exploiting an introduced advanced training scheme. The efficiency and robustness of the proposed ANN equalizer are illustrated through 10- and 28-Gbaud short-reach optical-fiber communication systems. Compared to the efficient but computationally expensive maximum likelihood sequence estimator (MLSE), the proposed ANN equalizer not only significantly reduces its computational equalization cost and storage memory requirements, but it also outperforms its bit error rate performance.


Asunto(s)
Tecnología de Fibra Óptica , Fibras Ópticas , Comunicación , Redes Neurales de la Computación
4.
Ann Surg ; 276(5): 838-845, 2022 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-35894443

RESUMEN

OBJECTIVE: Living donor liver transplantation (LDLT) using small grafts, especially left lobe grafts (H1234-MHV) (LLG), continues to be a challenge due to small-for-size syndrome (SFSS). We herein demonstrate that with surgical modifications, outcomes with small grafts can be improved. METHODS: Between 2012 and 2020, we performed 130 adult LDLT using 61 (47%) LLG (H1234-MHV) in a single Enterprise. The median graft-to-recipient weight ratio was 0.84%, with graft-to-recipient weight ratio <0.7% accounting for 22%. Splenectomy was performed in 72 (56%) patients for inflow modulation before (n=50) or after (n=22) graft reperfusion. In LLG-LDLT, venous outflow was achieved using all three recipient hepatic veins. In right lobe graft (H5678) (RLG)-LDLT, the augmented graft right hepatic vein was anastomosed to the recipient's cava with a large cavotomy. Outcome measures include SFSS, early allograft dysfunction (EAD), and survival. RESULTS: Graft survival rates at 1, 3, and 5 years were 94%, 90%, and 83%, respectively, with no differences between LLG (H1234-MHV) and RLG (H5678). Splenectomy significantly reduced portal flow without increasing the complication rate. Despite the aggressive use of small grafts, SFSS and EAD developed in only 1 (0.8%) and 18 (13.8%) patients, respectively. Multivariable logistic regression revealed model for end-stage liver disease score and LLG (H1234-MHV) as independent risk factors for EAD and splenectomy as a protective factor (odds ratio: 0.09; P =0.03). For LLG (H1234-MHV)-LDLT, patients who underwent prereperfusion splenectomy tended to have better 1-year graft survival than those receiving postreperfusion splenectomy. CONCLUSIONS: LLG (H1234-MHV) are feasible in adult LDLT with excellent outcomes comparable to RLG (H5678). Venous outflow augmentation and splenectomy help lower the threshold of using small-for-size grafts without compromising graft survival.


Asunto(s)
Enfermedad Hepática en Estado Terminal , Trasplante de Hígado , Adulto , Enfermedad Hepática en Estado Terminal/etiología , Venas Hepáticas/cirugía , Humanos , Hígado/irrigación sanguínea , Hígado/cirugía , Donadores Vivos , Índice de Severidad de la Enfermedad , Esplenectomía
5.
Opt Express ; 30(10): 16264-16288, 2022 May 09.
Artículo en Inglés | MEDLINE | ID: mdl-36221473

RESUMEN

This work proposes a novel and powerful adaptive digital back propagation (A-DBP) method with a fast adaption process. Given that the total transmission distance is known, the proposed A-DBP algorithm blindly compensates for the linear and nonlinear distortions of optical fiber transmission systems and networks, without knowing the launch power and channel parameters. An adjoint-based optimization (ABO) technique is proposed to significantly accelerate the parameters estimation of the A-DBP. The ABO algorithm utilizes a sequential quadratic programming (SQP) method coupled with an adjoint sensitivity analysis (ASA) approach to rapidly solve the A-DBP training problem. The design parameters are optimized using the minimum overhead of only one extra system simulation. Regardless of the number of A-DBP design parameters, the derivatives of the training objective function with respect to all parameters are estimated using only one extra adjoint system simulation per optimization iterate. This is contrasted with the traditional finite-difference (FD)-based optimization methods whose sensitivity analysis calculations cost per iterate scales linearly with the number of parameters. The robustness, performance, and efficiency of the proposed A-DBP algorithm are demonstrated through applying it to mitigate the distortions of 4-span and 20-span optical fiber communication systems. Coarse-mesh A-DBPs with less number of virtual spans are also used to significantly reduce the computational complexity of the equalizer, achieving compensation performance higher than that obtained using the coarse-mesh DBP with the exact channel parameters and full number of virtual spans.

6.
Sensors (Basel) ; 22(9)2022 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-35591125

RESUMEN

Coherent detection provides the optimum performance for free space optical (FSO) communication systems. However, such detection systems are expensive and require digital phase noise compensation. In this paper, the transmission performance of long-haul FSO system for ground-to-satellite communication based on a Kramers-Kronig (KK) transceiver is evaluated. KK transceivers utilize inexpensive direct detection receivers and the signal phase is retrieved from the received current using the well-known KK relations. KK transceivers are not sensitive to the laser phase noise and, hence, inexpensive lasers with large linewidths can be used at the transmitter. The transmission performance of coherent and KK transceivers is compared in various scenarios such as satellite-to-ground, satellite-to-satellite, and ground-to-satellite for weak, moderate, and strong turbulence. The results show that the transmission performance of a system based on the KK transceiver is comparable to that based on a coherent transceiver, but at a significantly lower system cost and complexity. It is shown that in the absence of turbulence, the coherent receiver has a ~3 dB performance advantage over the KK receiver. However, in the presence of strong turbulence, this performance advantage becomes negligible.

7.
Am J Transplant ; 21(1): 382-390, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-32865321

RESUMEN

Limited data exist regarding the impact of donation after circulatory death (DCD) allografts on outcomes following liver transplantation in fulminant hepatic failure (FHF). Utilizing the Scientific Registry of Transplant Recipients (SRTR), we compared outcomes after DCD in FHF to donation after brain death (DBD) in FHF and DCD in non-FHF over a 15-year period. Primary outcome measures were graft and patient survival. A total of 117, 3437, and 4379 recipients underwent DCD-FHF, DBD-FHF and DCD-non-FHF, respectively. One-year graft survival in DCD-FHF was inferior to DBD-FHF (72.9% vs. 83.8%, p = .002), but comparable to DCD-non-FHF (72.9% vs. 82.7%, p = .23). However, 3- and 5-year graft survival in DCD-FHF were comparable to DBD-FHF (67.9 vs. 77.6%, p = .63; 57.8% vs. 73.2%, p = .27) and DCD-non-FHF (67.9% vs. 72.9%, p = .44; 57.8% vs. 66.6%, p = .06). One-, 3-, and 5-year patient survival were also comparable among the three groups. Graft and patient survival in DCD-FHF improved over the study period. Multivariable analysis identified recipient age, male gender, African American ethnicity, donor age, and cold ischemia time as predictors of graft and patient survival in FHF, while DCD status was only predictive of graft survival. Long-term graft survival and patient survival in DCD-FHF are comparable to DBD-FHF and DCD-non-FHF. Consideration of DCD in FHF could help expand the donor pool in this subset of critically ill patients.


Asunto(s)
Fallo Hepático Agudo , Trasplante de Hígado , Obtención de Tejidos y Órganos , Aloinjertos , Muerte Encefálica , Muerte , Supervivencia de Injerto , Humanos , Fallo Hepático Agudo/cirugía , Masculino , Estudios Retrospectivos , Donantes de Tejidos , Estados Unidos/epidemiología
8.
J Neurooncol ; 152(1): 107-114, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33502679

RESUMEN

BACKGROUND: While autopsy-repository programs with a variety of pediatric central nervous system (CNS) tumor types are a critical resource for preclinical neuro-oncology research, few exist and there is no published guidance on how to develop one. The goal of this prospective Pediatric Brain Tumor Repository (PBTR) study was to develop such a program at Cincinnati Children's Hospital Medical Center (CCHMC) and then publish the quantitative and experiential data as a guide to support the development of similar programs. METHODS: Protocols and infrastructure were established-to educate oncologists and families, establish eligibility, obtain consent, address pre- and post-autopsy logistics (e.g., patient and tissue transportation), process and authenticate tissue samples, and collect and analyze data. RESULTS: Of the 129 pediatric CNS tumor patients at CCHMC who died between 2013 and 2018, 109 were eligible for our study. Of these, 74% (81 of 109) were approached for PBTR donation, and 68% (55 of 81) consented. In the final year of the study, approach and consent rates were 93% and 85%, respectively. Median time from death to autopsy (postmortem interval, PMI) was 10 h (range, 1.5-30). In the outpatient setting, PMI increased with distance (from the hospice/home where the patient died to CCHMC). In all patients, PMI appeared to be lower, when consent was obtained more than 24 h before death. CONCLUSIONS: Procurement of autopsy specimens need not be a barrier in neuro-oncology research. Regional centers, strict timing-of-consent, patient education, and dedicated staff are all needed to minimize PMI and, thereby, increase the value of the procured tissue for an array of basic and translational research applications.


Asunto(s)
Autopsia , Neoplasias del Sistema Nervioso Central , Obtención de Tejidos y Órganos/organización & administración , Adolescente , Adulto , Niño , Preescolar , Femenino , Humanos , Lactante , Masculino , Adulto Joven
9.
Opt Lett ; 45(17): 4682-4685, 2020 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-32870831

RESUMEN

We investigate the combination of a nonlinear frequency division multiplexed (NFDM) transmission scheme with midpoint optical phase conjugation (OPC), and show that midpoint OPC introduces power enhancement by compensating for nonlinear impairments. It offers a degree of freedom to have a flexible power normalization factor, Pn. Optimizing Pn helps minimize the signal-noise mixing in nonlinear Fourier transform processing for a specific launch power, resulting in improving the system performance significantly. The mid-OPC NFDM system can provide 4.5 dB and 5.6 dB advantages in Q-factor as compared to the conventional NFDM system when the transmission fiber is standard single-mode fiber and a fiber with optimum dispersion, respectively. Mid-OPC NFDM can also offer higher spectral efficiency at a longer transmission reach due to the shorter guard interval.

10.
J Neurooncol ; 149(3): 511-522, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-33034839

RESUMEN

PURPOSE: Cyclin-dependent kinase-retinoblastoma (CDK-RB) pathway is dysregulated in some diffuse intrinsic pontine gliomas (DIPG). We evaluated safety, feasibility, and early efficacy of the CDK4/6-inhibitor ribociclib, administered following radiotherapy in newly-diagnosed DIPG patients. METHODS: Following radiotherapy, eligible patients received ribociclib in 28-day cycles (350 mg/m2; 21 days on/7 days off). Feasibility endpoints included tolerability for at least 6 courses, and a less than 2-week delay in restarting therapy after 1 dose reduction. Early efficacy was measured by 1-year and median overall survival (OS). Patient/parent-by-proxy reported outcomes measurement information system (PROMIS) assessments were completed prospectively. RESULTS: The study included 10 evaluable patients, 9 DIPG and 1 diffuse midline glioma (DMG)-all 3.7 to 19.8 years of age. The median number of courses was 8 (range 3-14). Three patients required dose reduction for grade-4 neutropenia, and 1 discontinued therapy for hematological toxicity following course 4. The most common grade-3/4 toxicity was myelosuppression. After 2 courses, MRI evaluations in 4 patients revealed increased necrotic volume, associated with new neurological symptoms in 3 patients. The 1-year and median OS for DIPG was 89% and 16.1 months (range 10-30), respectively; the DMG patient died at 6 months post-diagnosis. Five patients donated brain tissue and tumor; 3 were RB+ . CONCLUSIONS: Ribociclib administered following radiotherapy is feasible in DIPG and DMG. Increased tumor necrosis may represent a treatment effect. These data warrant further prospective volumetric analyses of tumors with necrosis. Feasibility and stabilization findings support further investigation of ribociclib in combination therapies. TRIAL REGISTRATION: NCT02607124.


Asunto(s)
Aminopiridinas/uso terapéutico , Neoplasias del Tronco Encefálico/terapia , Quimioradioterapia/métodos , Glioma Pontino Intrínseco Difuso/terapia , Purinas/uso terapéutico , Adolescente , Adulto , Aminopiridinas/farmacocinética , Neoplasias del Tronco Encefálico/patología , Niño , Preescolar , Glioma Pontino Intrínseco Difuso/patología , Femenino , Estudios de Seguimiento , Humanos , Masculino , Dosis Máxima Tolerada , Pronóstico , Purinas/farmacocinética , Distribución Tisular , Adulto Joven
11.
Molecules ; 25(23)2020 Nov 29.
Artículo en Inglés | MEDLINE | ID: mdl-33260422

RESUMEN

Sepsis aggregates undesirable immune response causing depression of ventricular myocardium and diastolic dysfunction. This present study examined the effect of a plant-derived flavone tangeretin (TG) on autophagy and reduction in myocardial dysfunction. The sepsis was induced by cecum ligation and puncture (CLP) in male Sprague-Dawley rats. Abnormal changes were seen in the heart after the sepsis induction. These abnormalities were analyzed based on the cardiac markers, namely Cardiac myosin light chain-1 (cMLC1) and Cardiac troponin I (cTnl), echocardiography, and plasma parameters, like Lactate dehydrogenase (LDH) and Creatinine kinase (CK). Microanatomy of the heart was studied using hematoxylin and eosin stained histopathological samples of cardiac tissue. Western blot technique was used to detect the nature and extent of protein with the amount of a specific RNA (gene expression) in the cardiac homogenate. Oxidative damage was analyzed using redox marker, reduced glutathione. This study successfully showed that TG attenuated sepsis-induced myocardial dysfunction by inhibiting myocardial autophagy via silencing the Phosphatase and tensin homolog (PTEN) expression and acting on the AKT/mTOR pathway. The present findings supported that TG is a novel cardioprotective therapeutic target for sepsis induced myocardial dysfunction.


Asunto(s)
Cardiomiopatías/tratamiento farmacológico , Cardiotónicos/farmacología , Flavonas/farmacología , Fosfohidrolasa PTEN/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Sepsis/complicaciones , Serina-Treonina Quinasas TOR/metabolismo , Animales , Autofagia/efectos de los fármacos , Cardiomiopatías/sangre , Cardiomiopatías/etiología , Cardiotónicos/administración & dosificación , Ciego/lesiones , Muerte Celular/efectos de los fármacos , Modelos Animales de Enfermedad , Flavonas/administración & dosificación , Glutatión/efectos de los fármacos , Glutatión/metabolismo , Corazón/efectos de los fármacos , Ligadura/métodos , Masculino , Miocardio/patología , Miocardio/ultraestructura , Proteína con Dominio Pirina 3 de la Familia NLR/efectos de los fármacos , Carbonilación Proteica/efectos de los fármacos , Punciones/métodos , Ratas Sprague-Dawley , Factor de Transcripción STAT3/efectos de los fármacos , Sepsis/metabolismo , Tirosina/análogos & derivados , Tirosina/efectos de los fármacos
12.
Artículo en Inglés | MEDLINE | ID: mdl-31332065

RESUMEN

Artemisinin-based combination therapy (ACT) has been used to treat uncomplicated Plasmodium falciparum infections in India since 2004. Since 2008, a decrease in artemisinin effectiveness has been seen throughout the Greater Mekong Subregion. The geographic proximity and ecological similarities of northeastern India to Southeast Asia may differentially affect the long-term management and sustainability of ACT in India. In order to collect baseline data on variations in ACT sensitivity in Indian parasites, 12 P. falciparum isolates from northeast India and 10 isolates from southwest India were studied in vitro Ring-stage survival assay (RSA) showed reduced sensitivity to dihydroartemisinin in 50% of the samples collected in northeast India in 2014 and 2015. Two of the 10 assayed samples from the southwest region of India from as far back as 2012 also showed decreased sensitivity to artemisinin. In both these regions, kelch gene sequences were not predictive of reduced artemisinin sensitivity, as measured by RSA. The present data justify future investments in integrated approaches involving clinical follow-up studies, in vitro survival assays, and molecular markers for tracking potential changes in the effectiveness of artemisinin against P. falciparum throughout India.


Asunto(s)
Artemisininas/farmacología , Estadios del Ciclo de Vida/efectos de los fármacos , Malaria Falciparum/epidemiología , Plasmodium falciparum/efectos de los fármacos , Proteínas Protozoarias/genética , Antimaláricos/farmacología , Secuencia de Bases , Resistencia a Medicamentos , Eritrocitos/efectos de los fármacos , Eritrocitos/parasitología , Expresión Génica , Geografía , Humanos , India/epidemiología , Secuencia Kelch , Estadios del Ciclo de Vida/genética , Malaria Falciparum/tratamiento farmacológico , Malaria Falciparum/parasitología , Mutación , Plasmodium falciparum/genética , Plasmodium falciparum/crecimiento & desarrollo , Plasmodium falciparum/metabolismo , Proteínas Protozoarias/metabolismo
13.
Opt Express ; 27(6): 8968-8982, 2019 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-31052707

RESUMEN

We introduce a new system configuration to reduce the nonlinear phase noise (NLPN) by splitting the digital back propagation (DBP) between transmitter and receiver, asymmetrically, along with using mid-line optical phase conjugation (OPC). Our analytical results show that the variance of NLPN reduces by a factor of 16 compared to the standard configuration which is the dispersion uncompensated fiber optic link with full DBP at the receiver, i.e., the back propagation for the fiber spans is done entirely at the receiver. Numerical simulations show the same trend as predicted by the analytical model, and show about 2.6 dB and 2 dB improvement in Q-factor, for single channel and 5-channel WDM systems, respectively.

14.
Opt Lett ; 44(16): 3940-3943, 2019 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-31415517

RESUMEN

This Letter proposes a novel adjoint sensitivity analysis approach for the nonlinear Schrödinger equation, which describes the light wave propagation in optical fiber communication systems. Using only one extra adjoint system simulation, all the sensitivities of a general objective function with respect to all fiber design parameters are estimated. We provide a full description of the solution to the derived adjoint problem. The accuracy and efficiency of our proposed algorithm are illustrated through optical fiber examples.

15.
Sensors (Basel) ; 19(9)2019 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-31083397

RESUMEN

Brain-inspired intelligence using the cognitive dynamic system (CDS) concept is proposed to control the quality-of-service (QoS) over a long-haul fiber-optic link that is nonlinear and with non-Gaussian channel noise. Digital techniques such as digital-back-propagation (DBP) assume that the fiber optic link parameters, such as loss, dispersion, and nonlinear coefficients, are known at the receiver. However, the proposed CDS does not need to know about the fiber optic link physical parameters, and it can improve the bit error rate (BER) or enhance the data rate based on information extracted from the fiber optic link. The information extraction (Bayesian statistical modeling) using intelligent perception processing on the received data, or using the previously extracted models in the model library, is carried out to estimate the transmitted data in the receiver. Then, the BER is sent to the executive through the main feedback channel and the executive produces actions on the physical system/signal to ensure that the BER is continuously under the forward-error-correction (FEC) threshold. Therefore, the proposed CDS is an intelligent and adaptive system that can mitigate disturbance in the fiber optic link (especially in an optical network) using prediction in the perceptor and/or doing proper actions in the executive based on BER and the internal reward. A simplified CDS was implemented for nonlinear fiber optic systems based on orthogonal frequency division multiplexing (OFDM) to show how the proposed CDS can bring noticeable improvement in the system's performance. As a result, enhancement of the data rate by 12.5% and the Q-factor improvement of 2.74 dB were achieved in comparison to the conventional system (i.e., the system without smart brain).

17.
Fish Shellfish Immunol ; 76: 324-332, 2018 May.
Artículo en Inglés | MEDLINE | ID: mdl-29518558

RESUMEN

The laboratory acclimatized Clarias gariepinus (80 ±â€¯10 g) were divided into six groups and five subgroups each containing 10 fish. A fish feed was reconstituted by adding 33% powder of Leucaena leucocephala seed in place of fish trash. Group B, C and E were fed on reconstituted feed and group A, D and F were fed on artificial feed containing animal protein for 7 days prior to start of experiments. Then Group B was challenged with BSA while other groups were challenged with Vibrio harveyi (Group C, D) and Pseudomonas aeruginosa (Group E, F). Group A was used as negative control (not challenged with antigen). The fish were challenged on weekly intervals till 28th day. Blood was collected from one subgroup of each group on day 7, 14, 21 & 28 and finally sacrificed on day 35. Change in body weight, liver function tests (SGOT, SGPT) and serum ALP levels were monitored. The phagocytic index, percentage phagocytosis and nitric oxide levels were measured in macrophages isolated from spleen and head kidney. The levels of total fish immunoglobulin were also measured following indirect ELISA. The results showed improved immune response in fish fed on 33% L. leucocephala pod seed reconstituted feed; however their specific growth rate was low.


Asunto(s)
Bagres , Fabaceae/química , Enfermedades de los Peces/prevención & control , Extractos Vegetales/farmacología , Proteínas de Plantas/metabolismo , Infecciones por Pseudomonas/veterinaria , Vibriosis/veterinaria , Inmunidad Adaptativa/efectos de los fármacos , Alimentación Animal/análisis , Animales , Dieta/veterinaria , Suplementos Dietéticos/análisis , Enfermedades de los Peces/inmunología , Inmunidad Innata/efectos de los fármacos , Extractos Vegetales/administración & dosificación , Proteínas de Plantas/administración & dosificación , Infecciones por Pseudomonas/inmunología , Infecciones por Pseudomonas/prevención & control , Pseudomonas aeruginosa/fisiología , Semillas/química , Vibrio/fisiología , Vibriosis/inmunología , Vibriosis/prevención & control
18.
BMC Genomics ; 18(1): 823, 2017 Oct 24.
Artículo en Inglés | MEDLINE | ID: mdl-29065857

RESUMEN

BACKGROUND: Interpretation of large-scale data is very challenging and currently there is scarcity of web tools which support automated visualization of a variety of high throughput genomics and transcriptomics data and for a wide variety of model organisms along with user defined karyotypes. Circular plot provides holistic visualization of high throughput large scale data but it is very complex and challenging to generate as most of the available tools need informatics expertise to install and run them. RESULT: We have developed CGDV (Circos for Genomics and Transcriptomics Data Visualization), a webtool based on Circos, for seamless and automated visualization of a variety of large scale genomics and transcriptomics data. CGDV takes output of analyzed genomics or transcriptomics data of different formats, such as vcf, bed, xls, tab limited matrix text file, CNVnator raw output and Gene fusion raw output, to plot circular view of the sample data. CGDV take cares of generating intermediate files required for circos. CGDV is freely available at https://cgdv-upload.persistent.co.in/cgdv/ . CONCLUSION: The circular plot for each data type is tailored to gain best biological insights into the data. The inter-relationship between data points, homologous sequences, genes involved in fusion events, differential expression pattern, sequencing depth, types and size of variations and enrichment of DNA binding proteins can be seen using CGDV. CGDV thus helps biologists and bioinformaticians to visualize a variety of genomics and transcriptomics data seamlessly.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Genómica/métodos , Programas Informáticos , Reproducibilidad de los Resultados , Interfaz Usuario-Computador , Navegador Web
19.
Opt Express ; 25(17): 19923-19945, 2017 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-29041679

RESUMEN

With the aid of a discrete nonlinear Schrödinger equation (NLSE), the nonlinear interaction among the periodically placed ultrashort pulses is analyzed. If the amplitudes of these pulses are chosen to be secant-hyperbolic, it is found that they propagate without exchanging energy and hence the envelope of the peak of the short pulses is termed the discrete soliton in analogy with its counterpart in the spatial domain. In addition, we develop the concept of discrete chirp transform (DChT) and its inverse, and show that the weights of the pulses can be extracted from the field envelope using the discrete chirp transform (DChT). The computational cost of evaluating the output of a linear dispersive fiber using DChT approach is nearly half of the conventional frequency domain approach based on fast Fourier transform (FFT). We found that an isolated pump sinc pulse is not stable and it generates temporally separated sinc pulses if the dispersion of the transmission fiber is anomalous. By choosing a proper time separation between signal pulse and pump pulse, it is possible to amplify the signal pulse. The nonlinear interaction between signal pulse and pump pulse generates an idler pulse that is a phase-conjugated copy of the signal pulse. Hence, this result could have potential applications for time domain optical amplification and phase-conjugation.

20.
Opt Express ; 25(5): 5031-5043, 2017 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-28380769

RESUMEN

We have investigated an optical back propagation (OBP) method to compensate for propagation impairments in fiber optic networks with lumped Erbium doped fiber amplifier (EDFA) and/or distributed Raman amplification. An OBP module consists of an optical phase conjugator (OPC), optical amplifiers and dispersion varying fibers (DVFs). We derived a semi-analytical expression that calculates the dispersion profile of DVF. The OBP module acts as a nonlinear filter that fully compensates for the nonlinear distortions due to signal propagation in a transmission fiber, and is applicable for fiber optic networks with reconfigurable optical add-drop multiplexers (ROADMs). We studied a wavelength division multiplexing (WDM) network with 3000 km transmission distance and 64-quadrature amplitude modulation (QAM) modulation. OBP brings 5.8 dB, 5.9 dB and 6.1 dB Q-factor gains over linear compensation for systems with full EDFA amplification, hybrid EDFA/Raman amplification, and full Raman amplification, respectively. In contrast, digital back propagation (DBP) or OPC-only systems provide only 0.8 ~ 1.5 dB Q-factor gains.

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