Research and Application Analysis of Risk Prediction Models for Prostate Cancer from a Data-driven Perspective / 医学信息学杂志

Purpose/Significance The paper retrospectively analyzes the research progress on risk prediction models for prostate cancer,and provides references for the construction of prostate cancer intelligent diagnosis and treatment system.Method/Process Through literature mining and analysis,the significance of molecular,imaging,individual,population and other omics level evaluation indexes in the diagnosis of prostate cancer is discussed,and the key characteristic variables and clinical application value of different cal-culation models are compared.Result/Conclusion The existing models have advantages of easy calculation and strong feasibility,but they also have limitations such as limited prediction accuracy and insufficient generalization ability.The integration of multi-omics data and artificial intelligence models is of great significance for medical informatics research and smart medical system construction of prostate cancer.

Localization of epileptogenic zone based on reconstruction of dynamical epileptic network and virtual resection / 生物医学工程学杂志

Drug-refractory epilepsy (DRE) may be treated by surgical intervention. Intracranial EEG has been widely used to localize the epileptogenic zone (EZ). Most studies of epileptic network focus on the features of EZ nodes, such as centrality and degrees. It is difficult to apply those features to the treatment of individual patients. In this study, we proposed a spatial neighbor expansion approach for EZ localization based on a neural computational model and epileptic network reconstruction. The virtual resection method was also used to validate the effectiveness of our approach. The electrocorticography (ECoG) data from 11 patients with DRE were analyzed in this study. Both interictal data and surgical resection regions were used. The results showed that the rate of consistency between the localized regions and the surgical resections in patients with good outcomes was higher than that in patients with poor outcomes. The average deviation distance of the localized region for patients with good outcomes and poor outcomes were 15 mm and 36 mm, respectively. Outcome prediction showed that the patients with poor outcomes could be improved when the brain regions localized by the proposed approach were treated. This study provides a quantitative analysis tool for patient-specific measures for potential surgical treatment of epilepsy.

Construction of patient-specific computational twins model based on low dose CT images / 中华放射医学与防护杂志

Objective:In order to make up for the gap in the digital model of twins in the study of fetal radiation dosimetry, this study intends to construct a computational twins phantom based on low-dose CT images.Methods:The low-dose CT images of a pregnant patient were segmented by the combination of threshold automatic segmentation and manual segmentation, which were derived into stereolithography files. The maternal contour, fetal contour and bone structure were constructed using 3D modeling software, and the organ mass was adjusted according to the reference values of ICRP Publication 89 and WHO report after the organs were scaled on a specific scale.Results:The first set of Non-Uniform Rational B-Splines (NURBS) surface phantom of twins in China was established. The external contours, bones, size, position and posture of the phantom were completely consistent with those of the real human body. Each fetus had 25 organs or tissues. After optimization and adjustment, the relative deviation between the twin phantom and the reference value of organ mass was less than 10%.Conclusions:In this study, a personalized computational phantom of twins based on low-dose CT images is constructed, which fills the gap in the twin model. It is helpful in estimating the dose by the fetus from ionizing radiation received in the process of radiation diagnosis of pregnant women with twins.

Numerical simulation of a self-propelled fish-like swimmer with rigid and flexible caudal fins

Aim: In this paper, numerical simulations were conducted to investigate the swimming performances, hydrodynamics performances and wake structures of a self-propelled swimmer with rigid and flexible caudal fins.Methodology: The kinematics model of the swimmer was constructed using thunniform swimming. Using computational fluid dynamics (CFD) method, the systematic study of swimmer with rigid and flexible caudal fins was carried out. Results: The results showed that the caudal fin flexibility is beneficial to the fast-start of fish but not conducive to the fast cruising of fish. The fish with rigid caudal fin has larger cruising velocity inquasi-steady swimming and smaller forward acceleration in fast-start stage. In addition, the caudal fin flexibility is also beneficial to the heading stability of fish’s self-propelled swimming. The pressure distribution on the fish surface indicates that most of the thrust is generated by the leading-edge region of the caudal fin. The visualization of wake structures showed the existence of the attached leading-edge vortex (LEV) in thunniform swimming. Interpretation: Based on the present simulations, the hydrodynamic performance of tuna during self-propelled swimming was analyzed in detail. Researchers can use these findings to design bionic robot fish with rigid and flexible tails.

Simulation of the length of sugarcane (Saccharum spp. ) crop rows in the operational management of spraying / Simulação do comprimento das fileiras de cultivo de cana-de- açúcar ( saccharum spp. ) no gerenciamento operacional da pulverização

O Brasil é o maior produtor mundial de cana-de-açúcar destinada às usinas e tem produtividade média, superior aos demais países produtores dessa matéria-prima. A aplicação de defensivos agrícolas em canaviais das agroindústrias é realizada em extensas áreas de cultivo, com pulverizadoreshidráulicos autopropelidos, tratorizados e aéreo. Para tanto é necessário sistematizar as áreas de cultivo, tornando os talhões com longo comprimento de fileiras de cultivo, a fim de diminuir as manobras de cabeceira das máquinas. O objetivo do trabalho é avaliar o impacto causado pelo comprimento das fileiras de cultivo no custo operacional de pulverizadores hidráulicos para os tratos culturais de cana-de-açúcar. Pela dificuldade que existe em realizar o trabalho e atender o objetivo nas condições de campo, optou-se em desenvolver um modelo computacional denominado TratoCana, em planilha eletrônica e em linguagem de programação. O modelo foi verificado quanto a possíveis erros de rotina, validado, utilizado na análise dos fatores e na geração de cenários. Os resultados evidenciaram que o comprimento das fileiras de cultivo, impacta positivamente no desempenho operacional e econômico dos equipamentos.

Brazil is the world's largest producer of sugarcane destined for mills and has average productivity, higher than the other countries producing this raw material. The application of pesticides in sugar cane fields in agribusinesses is carried out in extensive cultivation areas, with self-propelled, sprayed and aerial hydraulic sprayers. Therefore, it is necessary to systematize the cultivation areas, making the plots with a long length of cultivation rows, in order to reduce the machines' headboard maneuvers. The objective of the work is to evaluate the impact caused by the length of the cultivation rows on the operational cost of hydraulic sprayers for the sugarcane crop treatments. Due to the difficulty in carrying out the work and meeting the objective in the field conditions, it was decided to develop a computational model called TratoCana, using an electronic spreadsheet and programming language. The model was checked for possible routine errors, validated, used in the analysis of factors and in the generation of scenarios. The results showed that the length of the cultivation rows has a positive impact on the operational and economic performance of the equipment. is Veja também be

3-D simulation of posterior fossa reduction in Chiari I / Simulação em 3D da redução da fossa posterior no Chiari do tipo I

ABSTRACT We proposed a 3D model to evaluate the role of platybasia and clivus length in the development of Chiari I (CI). Using a computer aided design software, two DICOM files of a normal CT scan and MR were used to simulate different clivus lengths (CL) and also different basal angles (BA). The final posterior fossa volume (PFV) was obtained for each variation and the percentage of the volumetric change was acquired with the same method. The initial normal values of CL and BA were 35.65 mm and 112.66º respectively, with a total PFV of 209 ml. Ranging the CL from 34.65 to 29.65 – 24.65 – 19.65, there was a PFV decrease of 0.47% – 1.12% – 1.69%, respectively. Ranging the BA from 122.66º to 127.66º – 142.66º, the PFV decreased 0.69% – 3.23%, respectively. Our model highlights the importance of the basal angle and clivus length to the development of CI.

RESUMO No presente estudo, propusemos a criação de um modelo computacional em 3D com elaboração de software onde dois arquivos em formato DICOM com uma TC e RNM de crânio foram usados para simular diferentes mensurações na extensão do clivus (EC) e no ângulo basal (AB). O volume final da fossa posterior (VFP) foi obtido em cada variação, bem como a percentagem de volume alterada. O tamanho inicial da EC era de 35,65 mm e o do AB era de 112.66º, com um VFP de 209 ml. Variando a EC de 34,65 para 29,65 – 24.65 e 19.65, houve uma diminuição do VFP de 0.47%, 1.12% e 1.69%, respectivamente. Variando o AB de 122,66º para 127,66º e 142,66º, o VFP diminui para 0.69% e 3.23%, respectivamente. Nosso modelo enfatiza a importância da patogênese do aumento do AB e do encurtamento do clivus no desenvolvimento do Chiari I.

A phenomenological model for the dynamics of cell cycle in responding to X-rays / 中华放射医学与防护杂志

Objective To establish a model to predict the cell-cycle process in response to ionizing radiation.Methods Human choroidal malignant melanoma 92-1 cells were used and the cell cycle distribution of cells was analyzed in 0-96 h after exposure to X-rays.A phenomenological model was constructed based on biological knowledge to describe the cell cycle dynamics in experiments.Results In the present study,a phenomenological model was constructed to describe the cellcycle dynamics of synchronized 92-1 cells in responding to various doses of ionizing radiation.The simulation results obtained with the model were consistent with the experimental data,demonstrating that the model had a good expansibility and could be used to predict the dynamics of cell cycle in responding to ionizing radiation.Further theoretical modeling of the cellcycle dynamics was made and the results were consistent with the simulation.Conclusions A phenomenological model was constructed which could be used to describe the dynamics of cell cycle of cells exposed to ionizing radiation and was supported by the experimental data.Because this model is easy to run by the written code,it has a good expansibility for studying the behaviors of cell populations under various conditions.

PARAMETRIC ANALYSIS OF DRUG DISTRIBUTION DURING INFUSIONS INTO THE BRAIN USING AN AXISYMMETRIC MODEL WITH BACKFLOW / ANÁLISIS PARAMÉTRICO DE LA DISTRIBUCIÓN DE DROGA DURANTE INFUSIONES EN EL CEREBRO CON UN MODELO AXISIMÉTRICO CON REFLUJO / A ANÁLISE PARAMÉTRICA DE DISTRIBUIÇÃO DE DROGAS NO CÉREBRO DURANTE INFUSÕES COM UM MODELO AXISYMMETRIC COM REFLUXO

Convection-enhanced delivery as a means to deliver therapeutic drugs directly to the brain has shown limited clinical efficacy, primarily attributed to the phenomena of backflow, in which the infused fluid flows preferentially along the shaft catheter rather than forward into the tissue. We have previously developed a finite element model of backflow that includes both material and geometric nonlinearities and the free boundary conditions associated with the displacement of the tissue away from the external surface of the catheter. However, that study was limited to predictions of the tissue deformation and resulting convective fluid velocity in the interstitial space. In this study, we use results from that model to solve for the distribution of the infused therapeutic agent. We demonstrate that a significant percentage of the infused drug is not transported into the region of tissue located forward from the catheter tip, but instead is transported into the region along the lateral sides of the catheter. For lower flow rates, this study suggests that the use of a catheter with a larger radius may be preferable since it will provide the higher amount of drug to be transported to the tissue in front of the catheter. In contrast, for higher flow rates consistent with clinical infusions, the radius of the infusion catheter had minimal effect on the distribution of the infused drug, with most being transported into the tissue around the shaft of the catheter.

Convection-enhanced delivery es una técnica que permite transportar drogas directamente en el cerebro para el tratamiento de enfermedades del sistema nervioso central. Este método ha mostrado una eficacia limitada debido principalmente al fenómeno de reflujo (backflow), según el cual, el fluido inyectado fluye preferiblemente a lo largo del catéter y no hacia el tejido delante de la punta. Previamente desarrollamos un modelo de elementos finitos para representar el reflujo, el cual incluye las no linealidades geométricas y del material y las condiciones de borde libre asociadas con el desplazamiento del tejido en la superficie externa del catéter. Sin embargo, ese modelo solo predice la deformación del tejido y el campo de velocidades en el espacio intersticial. En este estudio, hemos utilizado los resultados provenientes del mencionado modelo bifásico para resolver la ecuación de transporte de masa y predecir la distribución de droga suministrada. Se pudo demostrar que un porcentaje significativo de droga no penetra en el tejido ubicado delante de la punta del catéter, sino que es transportado hacia el tejido ubicado alrededor del catéter. Para bajo caudales, este estudio sugiere que el uso de un catéter con un radio mayor permitiría transportar una mayor cantidad de droga hacia el tejido al frente de la punta. Por otro lado, para los mayores caudales usados en la práctica clínica, el radio del catéter tiene un efecto marginal en la distribución del fármaco, y la mayor cantidad de droga se transporta hacia el tejido ubicado alrededor del catéter.

Convection-enhanced delivery é uma técnica para o transporte de drogas directamente no cérebro para tratar doenças do sistema nervoso central. Este método tem demonstrado eficácia limitada devido, principalmente, ao fenómeno de refluxo (refluxo), através do qual, de preferência, o fluido injectado flui através do cateter para o tecido e não à frente da ponta. Anteriormente desenvolvido um modelo de elementos finitos para representar a refluxo, que inclui geométricas e não-linearidades do material e as condições associadas com a extremidade livre de deslocamento da trama na superfície exterior do cateter. No entanto, este modelo apenas prevê deformação do tecido e campo de velocidades no espaço intersticial. Neste estudo, foram utilizados os resultados do modelo de duas fases acima referidas, para resolver a equação de transporte e prever a distribuição de massa de medicamentos fornecidos. Demonstrou-se que uma percentagem significativa da droga não penetra no tecido localizado em frente da ponta do cateter, que é transportado para o tecido que rodeia o cateter. Para as taxas de fluxo baixas, este estudo sugere que o uso de um cateter com um raio maior do que transportar uma maior quantidade de droga para o tecido em frente da ponta. Além disso, para taxas de fluxo mais elevadas utilizadas na prática clínica, o raio do cateter tem um efeito marginal sobre a distribuição da droga, e tanto fármaco é transportado para o tecido que rodeia o cateter.

Modulation of synaptic potentials and cell excitability by dendritic KIR and KAs channels in nucleus accumbens medium spiny neurons: A computational study.

The nucleus accumbens (NAc), a critical structure of the brain reward circuit, is implicated in normal goal-directed behaviour and learning as well as pathological conditions like schizophrenia and addiction. Its major cellular substrates, the medium spiny (MS) neurons, possess a wide variety of dendritic active conductances that may modulate the excitatory post synaptic potentials (EPSPs) and cell excitability. We examine this issue using a biophysically detailed 189-compartment stylized model of the NAc MS neuron, incorporating all the known active conductances. We find that, of all the active channels, inward rectifying K+ (KIR) channels play the primary role in modulating the resting membrane potential (RMP) and EPSPs in the down-state of the neuron. Reduction in the conductance of KIR channels evokes facilitatory effects on EPSPs accompanied by rises in local input resistance and membrane time constant. At depolarized membrane potentials closer to up-state levels, the slowly inactivating A-type potassium channel (KAs) conductance also plays a strong role in determining synaptic potential parameters and cell excitability. We discuss the implications of our results for the regulation of accumbal MS neuron biophysics and synaptic integration by intrinsic factors and extrinsic agents such as dopamine.

Modelos computacionales de diferenciación y adaptación ósea / Computational models of bone differentiation and adaptation

Se realizó una revisión de los modelos computaciones de diferenciación y adaptación ósea existentes, haciendo énfasis en el desarrollo alcanzado en esta área durante los últimos años. El estudio del tejido óseo ha venido en aumento en las últimas décadas gracias al renacimiento de la mecanobiología, cuyo paradigma principal es la influencia que tienen las cargas mecánicas sobre el desarrollo, adaptación y mantenimiento de los tejidos. El objetivo principal del trabajo es resaltar la importancia de la mecanobiología computacional en el modelado del tejido óseo y la necesidad de seguir desarrollando la mecanobiología experimental para poder medir con exactitud las propiedades de los tejidos y las características celulares de mayor sensibilidad en los modelos computacionales

Authors review the available computational models of bone differentiation and adaptation, emphasizing on the development achieved in this area during pas years. The bone tissue study has increased in past decades due to rebirth of mechanobiology, whose main paradigm is the influence of mechanical loads on the tissues development, adaptation and maintenance. The major objective of present paper is to emphasize la significance of computational mechanobiology in the bone tissue modeling and the need to keep on developing the experimental mechanobiology to measure accurately the tissues properties and the more sensible cellular features of computational models

Predicción computacional de estructura terciaria de las proteínas humanas Hsp27, αB-cristalina y HspB8 / Computational prediction of tertiary structure of the human proteins Hsp27, αB-crystalline and HspB8 / Predição computacional da estrutura terciária das proteínas humanas Hsp27, αB-cristalina e HspB8

Objetivo. Realizar predicciones computacionales de estructura de las proteínas humanas Hsp27, αB cristalina y HspB8. Materiales y métodos. La predicción de la estructura secundaria se obtuvo mediante un consenso de los programas de predicción secundaria GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN y Psi-Pred. Los modelos de estructura terciaria se elaboraron a partir de fragmentos homólogos de proteínas con estructura terciaria conocida que fueron obtenidos por múltiples alineamientos. Empleando la secuencia primaria se obtuvieron perfiles de antigenicidad de las proteínas nativas y fueron analizados los perfiles de hidrofobicidad, polaridad, flexibilidad, accesibilidad tanto de las proteínas nativas como de las mutadas. Resultados. Las predicciones de estructura secundaria y terciaria de las proteínas estudiadas muestran que en los tres casos, más del 65% son regiones en coil, 20-25% en hoja plegada y menos del 10% en alfa hélice. Los análisis de estructura primaria muestran que al menos uno de los perfiles estudiados, en cada mutación está alterado. Conclusiones. Los análisis comparativos de estructura sugieren que las mutaciones afectan la solubilidad de las proteínas mutadas y con ello su función como chaperonas moleculares.

Objective: To make computational predictions of the structure of the human proteins Hsp27, αB-crystalline and HspB8. Materials and methods. The prediction of the secondary structure was obtained by a consensus of the programs for secondary prediction GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN and Psi-Pred. The models of tertiary structure were built from fragments homologous to proteins with tertiary known structure that were obtained by multiple alignments. Using the primary sequence we obtained the antigenicity profiles of native proteins and we analyzed the profiles of hydrophobicity, polarity, flexibility and accessibility of both native and mutant proteins. Results. Predictions of the secondary and tertiary structures of the studied proteins show that in the three cases, more than 65% are coil regions, 20-25% are folded sheet and less than 10% are alpha helix. Analyses of the primary structure show that at least one of the studied profiles in every mutation is altered. Conclusions. The comparative analyses of structure suggest that mutations affect the solubility of the mutated proteins and hence affect their function as molecular chaperones.

Objetivo. Realizar predições computacionais da estrutura das proteínas humanas Hsp27, αB-cristalina e HspB8. Materiais e métodos. A predição da estrutura secundária foi obtida através de um consenso dos programas de predição secundária GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN e Psi-Pred. Os modelos de estrutura terciária foram desenvolvidos a partir de fragmentos homólogos de proteínas com estrutura terciária conhecida que foram obtidos por alinhamentos múltiplos. Utilizando a seqüência primária foram obtidos perfis de antigenicidade das proteínas nativas e foram analisados os perfis de hidrofobicidade, polaridade, flexibilidade e acessibilidade, tanto da proteína nativa, como das mutantes. Resultados. As predições de estrutura secundária e terciária das proteínas estudadas mostram que nos três casos, mais de 65% são regiões em coil, 20-25% de folha pregueada e inferior a 10% em alfa-hélice. A análise da estrutura primária mostra que pelo menos um dos perfis estudados, em cada mutação está alterado. Conclusões. A análise comparativa da estrutura sugere que as mutações afetam a solubilidade das proteínas mutantes e, assim, sua função como chaperones moleculares.

A Computational Model of Cytosolic and Mitochondrial Ca2+ in Paced Rat Ventricular Myocytes

We carried out a series of experiment demonstrating the role of mitochondria in the cytosolic and mitochondrial Ca2+ transients and compared the results with those from computer simulation. In rat ventricular myocytes, increasing the rate of stimulation (1~3 Hz) made both the diastolic and systolic [Ca2+] bigger in mitochondria as well as in cytosol. As L-type Ca2+ channel has key influence on the amplitude of Ca2+-induced Ca2+ release, the relation between stimulus frequency and the amplitude of Ca2+ transients was examined under the low density (1/10 of control) of L-type Ca2+ channel in model simulation, where the relation was reversed. In experiment, block of Ca2+ uniporter on mitochondrial inner membrane significantly reduced the amplitude of mitochondrial Ca2+ transients, while it failed to affect the cytosolic Ca2+ transients. In computer simulation, the amplitude of cytosolic Ca2+ transients was not affected by removal of Ca2+ uniporter. The application of carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) known as a protonophore on mitochondrial membrane to rat ventricular myocytes gradually increased the diastolic [Ca2+] in cytosol and eventually abolished the Ca2+ transients, which was similarly reproduced in computer simulation. The model study suggests that the relative contribution of L-type Ca2+ channel to total transsarcolemmal Ca2+ flux could determine whether the cytosolic Ca2+ transients become bigger or smaller with higher stimulus frequency. The present study also suggests that cytosolic Ca2+ affects mitochondrial Ca2+ in a beat-to-beat manner, however, removal of Ca2+ influx mechanism into mitochondria does not affect the amplitude of cytosolic Ca2+ transients.

Application of Moving Average Method in Formation of Hospital Drug Purchase Plan / 中国药房

OBJECTIVE:To provide a method for a scientific and rational formation of hospital drug purchase plan.METHODS:Based on the major factors influencing the drug purchase plans,a moving-average method(mathematical principle)was used to establish computational formula for hospital drug purchase plan model,which was then put into practice.RESULTS:The predicted amount calculated using the computation model could be used to track the actual consumption quantity rapidly;this model could auto-adjust the inventory and dynamically forecast the drug purchase amount.CONCLUSION:The computation model contributes to the scientific and reasonable formation of hospital drug purchase plan thus meeting the needs of majority clinical drugs.