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Colorectal cancer vaccines: in silico identification of tumor-specific antigens associated with frequent HLA-I alleles in the costa rican Central Valley population 结直肠癌疫苗:哥斯达黎加中央谷人群中与频繁hla - 1等位基因相关的肿瘤特异性抗原的计算机鉴定
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6458
Diego Morazán-Fernández, J. Molina-Mora
Colorectal cancer is a complex disease in which uncontrolled growth of abnormal cells occurs in the large intestine (colon or rectum). The study of tumor-specific antigens (neoantigens), molecules that interact with the immune system, has been extensively explored as a possible therapy called in silico cancer vaccine. Cancer vaccine studies have been triggered by the current high-throughput DNA sequencing technologies. However, there is no universal bioinformatic protocol to study tumor-antigens with DNA sequencing data. We propose a bioinformatic protocol to detect tumor-specific antigens associated with single nucleotide variants (SNVs) or “mutations” in colorectal cancer and their interaction with frequent HLA alleles (complex that present antigens to immune cells) in the Costa Rican Central Valley population. We used public data of human exome (DNA regions that produce functional products, including proteins). A variant calling analysis was implemented to detect tumorspecific SNVs, in comparison to healthy tissue. We then predicted and analyzed the peptides (protein fragments, the tumor specific antigens) derived from these variants, in the context of its affinity with frequent alleles of HLA type I of the Costa Rican population. We found 28 non-silent SNVs, present in 26 genes. The protocol yielded 23 strong binders peptides derived from the SNVs for frequent alleles (greater than 8%) for the Costa Rican population at the HLA-A, B and C loci. It is concluded that the standardized protocol was able to identify neoantigens and this can be considered a first step for the eventual design of a colorectal cancer vaccine for Costa Rican patients. To our knowledge, this is the first study of an in silico cancer vaccine using DNA sequencing data in the context of the Costa Rican HLA alleles.
结直肠癌是一种复杂的疾病,在大肠(结肠或直肠)发生不受控制的异常细胞生长。肿瘤特异性抗原(新抗原)的研究,与免疫系统相互作用的分子,已经被广泛探索作为一种可能的治疗方法,称为硅癌疫苗。目前的高通量DNA测序技术已经引发了癌症疫苗的研究。然而,目前还没有通用的生物信息学方案来研究肿瘤抗原的DNA测序数据。我们提出了一种生物信息学方案,用于检测哥斯达黎加中央山谷人群中与结直肠癌单核苷酸变异(snv)或“突变”相关的肿瘤特异性抗原,以及它们与频繁的HLA等位基因(向免疫细胞呈递抗原的复合物)的相互作用。我们使用了人类外显子组(产生功能产物的DNA区域,包括蛋白质)的公开数据。与健康组织相比,实施了一种变体调用分析来检测肿瘤特异性snv。然后,我们预测并分析了从这些变异中衍生的肽(蛋白质片段,肿瘤特异性抗原),在其与哥斯达黎加人群HLA I型频繁等位基因的亲和力的背景下。我们在26个基因中发现了28个非沉默snv。该方案从哥斯达黎加人群HLA-A, B和C位点的频繁等位基因(大于8%)的snv中获得23个强结合肽。结论是,标准化方案能够识别新抗原,这可以被认为是最终为哥斯达黎加患者设计结直肠癌疫苗的第一步。据我们所知,这是首次在哥斯达黎加人HLA等位基因的背景下使用DNA测序数据进行的计算机癌症疫苗研究。
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引用次数: 0
Assessing the effectiveness of diarization algorithms in costa rican children-adult speech according to age group and gender 根据年龄和性别评估哥斯达黎加儿童-成人语言的词频化算法的有效性
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6443
Alejandro Chacón-Vargas, Daniel Pérez-Conejo, Marvin Coto-Jiménez
Speaker diarization is the task of automatically identifying speaker identities and detecting their speaking times in an audio recording. Several algorithms have shown improvements in the performance of this task during the past years. However, it still has performance challenges in interaction scenarios, such as between a child and adult, where interruptions, fillers, laughs and other elements may affect the detection and clustering of the segments. In this work, we perform an exploratory study with two diarization algorithms in children-adult interactions within a recording studio and assess the effectiveness of the algorithms in different age groups and genders. All participants are native Costa Rican Spanish speakers. The children have ages between 3 to 14 years, and the interaction combines guided repetition of words or short phrases, as well as natural speech. The results demonstrate how the age affects the diarization performance, both in cluster purity and speaker purity, in a direct but non-linear fashion.
说话人拨号是在录音中自动识别说话人身份并检测其说话时间的任务。在过去的几年里,有几种算法在这项任务的性能上有所改进。然而,它在交互场景中仍然存在性能挑战,例如儿童和成人之间的交互场景,其中中断,填充,笑声和其他元素可能会影响片段的检测和聚类。在这项工作中,我们对录音棚内儿童与成人互动中的两种数字化算法进行了探索性研究,并评估了算法在不同年龄组和性别中的有效性。所有参与者均为母语西班牙语。这些孩子的年龄在3到14岁之间,这种互动结合了单词或短语的指导重复,以及自然语言。结果表明,在簇纯度和扬声器纯度方面,年龄如何以直接但非线性的方式影响拨号性能。
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引用次数: 0
An experimental study on footsteps sound recognition as biometric under noisy conditions 噪声条件下脚步声生物识别的实验研究
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6467
Marisol Zeledón-Córdoba, Carolina Paniagua Peñaranda, Marvin Coto-Jiménez
The experimentation of footsteps as a biometric has a short history of about two decades. The process of identification of a person is based on the study of footstep signals captured when walking over a sensing area, and the registering of sounds, pressure, vibration, or a combination of these measures. Application of this biometric can emerge in security systems, that identify persons who enter or leave a space, and in providing help to elderly and disabled persons. In this paper, we are focused in the exploration of pure audio signals of footsteps and the robustness of a person’s classification under noisy conditions. We present a comparison between four wellknown classifiers and three kinds of noise, applied at different signal to noise ratio. Results are reported in terms of accuracy in the detection an users, showing different levels of sensibility according to the kind and level of noise.
将脚步作为生物特征的实验只有大约20年的历史。识别一个人的过程是基于对走过感应区域时捕获的脚步声信号的研究,以及对声音、压力、振动或这些措施的组合的记录。这种生物识别技术的应用可以出现在安全系统中,用于识别进入或离开空间的人,以及为老年人和残疾人提供帮助。在本文中,我们专注于探索纯音频脚步声信号和噪声条件下人的分类的鲁棒性。我们比较了应用于不同信噪比下的四种常用分类器和三种噪声。结果报告的准确性方面的检测和用户,显示不同程度的敏感性根据噪音的种类和水平。
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引用次数: 0
GPU based approach for fast generation of robot capability representations 基于GPU的机器人能力表征快速生成方法
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6449
Daniel García Vaglio, Federico Ruiz Ugalde
Capability maps are an important tool for enabling robots to understand their bodies by providing a way of representing the dexterity of their arms. They are usually treated as static data structures be- cause of how computationally intensive they are to generate. We present a method for generating capability maps taking advantage of the parallelization that modern GPUs offer such that these maps are generated approximately 50 times faster than previous implementations. This system could be used in situations were the robot has to generate this maps fast, for example when using unknown tools.
能力图是一个重要的工具,通过提供一种表示手臂灵巧度的方法,使机器人能够理解自己的身体。它们通常被视为静态数据结构,因为它们的生成需要大量的计算。我们提出了一种利用现代gpu提供的并行性生成能力映射的方法,使这些映射的生成速度比以前的实现快大约50倍。该系统可用于机器人必须快速生成地图的情况,例如使用未知工具时。
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引用次数: 0
The impact of social media messages on Parkinson’s disease treatment: detecting genuine sentiment in patient notes 社交媒体信息对帕金森病治疗的影响:从病人的笔记中发现真实的情绪
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6441
Hanane Grissette, El Habib Nfaoui
Parkinson’s Disease(PD), one of the most serious neurodegenerative diseases that known huge controversy on social networks. Following medical lexicons, few approaches have been extended to leverage sentiment information that obviously reflects the patient’s health status in terms of related-narratives observations. It is been crucial to analyze online narratives and detect sentiment in patients’ self-reports. In this paper, we propose an automatic concept-level neural network method to distilling genuine sentiment in patients’ notes as medical polar facts into true positives and true negatives. Towards building emotional Parkinsonism assisted method from Parkinson’s Disease daily narratives di- gests, we characterize polar facts of defined medical configuration space through distributed biomedical representation at the concept-level as- sociated with real-world entities, which are operated to quantifying the emotional status of the speaker context. We conduct comparisons with state-of-art neural networks algorithms and biomedical distributed systems. Finally, as a result, we achieve an 85.3% accuracy performance, and the approach shows a well-understanding of medical natural language concepts.
帕金森病(PD)是最严重的神经退行性疾病之一,在社交网络上引起了巨大的争议。在医学词汇之后,很少有方法被扩展到利用情感信息,这些信息明显反映了患者在相关叙述观察方面的健康状况。分析在线叙述和检测患者自我报告中的情绪至关重要。在本文中,我们提出了一种自动概念级神经网络方法,将患者笔记中的真实情感作为医学极性事实提炼为真阳性和真阴性。为了从帕金森病的日常叙述中建立情感帕金森辅助方法,我们通过概念层面上与现实世界实体相关的分布式生物医学表征来表征定义的医疗配置空间的极性事实,这些事实被用于量化说话者情境的情感状态。我们与最先进的神经网络算法和生物医学分布式系统进行了比较。最终,我们的准确率达到了85.3%,表明该方法对医学自然语言概念有很好的理解。
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引用次数: 0
Automatic diagnosis of lower back pain using gait patterns 使用步态模式的腰痛自动诊断
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6459
Chandrasen Pandey, Neeraj Baghel, Malay Kishore-Dutta, Carlos M. Travieso González
Back pain is a common pain that mostly affects people of all ages and results in different types of disorders such as Obesity, Slipped disc, Scoliosis, and Osteoporosis, etc. The diagnosis of back pain disorder is difficult due to the extent affected by the disorder and exact biomechanical factors. This work presents a machine learning method to diagnose these disorders using the Gait monitoring system. It involves support vector machines that classify between lower back pain and normal, on the bases of 3 Gait patterns that are integrated pressure, the direction of progression, and CISP-ML. The proposed method uses 13 different features such as mean and standard deviation, etc. recorded from 62 subjects (30 normal and 32 with lower back pain). The features alone resulted in higher leave-one-out classification accuracy (LOOCV) 92%. The proposed method can be used for automatically diagnosing the lower back pain and its gait effects on the person. This model can be ported to small computing devices for self-diagnosis of lower back pain in a remote area.
背痛是一种常见的疼痛,主要影响所有年龄段的人,并导致不同类型的疾病,如肥胖、椎间盘突出、脊柱侧凸和骨质疏松症等。由于疾病的影响程度和确切的生物力学因素,腰痛障碍的诊断是困难的。这项工作提出了一种机器学习方法来诊断这些疾病使用步态监测系统。它涉及支持向量机,根据综合压力、前进方向和CISP-ML三种步态模式对下背部疼痛和正常进行分类。所提出的方法使用了来自62名受试者(30名正常受试者和32名腰痛患者)的13种不同特征,如平均值和标准差等。单独的特征导致更高的留一分类准确率(LOOCV) 92%。该方法可用于下背部疼痛及其对人体步态的影响的自动诊断。该模型可以移植到小型计算设备上,用于偏远地区腰痛的自我诊断。
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引用次数: 0
A deep learning approach for epilepsy seizure detection using EEG signals 基于脑电图信号的深度学习癫痫发作检测方法
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6461
Manoj Kaushik, Divyanshu Singh, Malay Kishore-Dutta, Carlos M. Travieso
Electroencephalogram (EEG) is an effective non-invasive way to detect sudden changes in neural brain activity, which generally occurs due to excessive electric discharge in the brain cells. EEG signals could be helpful in imminent seizure prediction if the machine could detect changes in EEG patterns. In this study, we have proposed a one-dimensional Convolutional Neural network (CNN) for the automatic detection of epilepsy seizures. The automated process might be convenient in the situations where a neurologist is unavailable and also help the neurologists in proper analysis of EEG signals and case diagnosis. We have used two publicly available EEG datasets, which were collected from the two African countries, Guinea-Bissau and Nigeria. The datasets contain EEG signals of 318 subjects. We have trained and verify the performance of our model by testing it on both the datasets and obtained the highest accuracy of 82.818%.
脑电图(EEG)是一种有效的无创检测大脑神经活动突然变化的方法,这种变化通常是由于脑细胞过度放电引起的。如果机器能够检测到脑电图模式的变化,脑电图信号可能有助于预测即将发作的癫痫发作。在这项研究中,我们提出了一种用于癫痫发作自动检测的一维卷积神经网络(CNN)。自动化的过程可能会方便在没有神经科医生的情况下,也有助于神经科医生正确分析脑电图信号和病例诊断。我们使用了从几内亚比绍和尼日利亚两个非洲国家收集的两个公开可用的脑电图数据集。数据集包含318名受试者的脑电图信号。我们对模型的性能进行了训练和验证,并在两个数据集上进行了测试,获得了82.818%的最高准确率。
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引用次数: 0
Application of Fischer semi discriminant analysis for speaker diarization in costa rican radio broadcasts Fischer半判别分析在哥斯达黎加无线电广播中的应用
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6464
Roberto Sánchez Cárdenas, Marvin Coto-Jiménez
Automatic segmentation and classification of audio streams is a challenging problem, with many applications, such as indexing multi – media digital libraries, information retrieving, and the building of speech corpus or spoken corpus) for particular languages and accents. Those corpus is a database of speech audio files and the corresponding text transcriptions. Among the several steps and tasks required for any of those applications, the speaker diarization is one of the most relevant, because it pretends to find boundaries in the audio recordings according to who speaks in each fragment. Speaker diarization can be performed in a supervised or unsupervised way and is commonly applied in audios consisting of pure speech. In this work, a first annotated dataset and analysis of speaker diarization for Costa Rican radio broadcasting is performed, using two approaches: a classic one based on k-means clustering, and the more recent Fischer Semi Discriminant. We chose publicly available radio broadcast and decided to compare those systems’ applicability in the complete audio files, which also contains some segments of music and challenging acoustic conditions. Results show a dependency on the results according to the number of speakers in each broadcast, especially in the average cluster purity. The results also show the necessity of further exploration and combining with other classification and segmentation algorithms to better extract useful information from the dataset and allow further development of speech corpus.
音频流的自动分割和分类是一个具有挑战性的问题,在多媒体数字图书馆的索引、信息检索、特定语言和口音的语音语料库(口语语料库)的建立等方面有着广泛的应用。这些语料库是一个语音音频文件和相应文本转录的数据库。在这些应用程序所需的几个步骤和任务中,说话者拨号是最相关的一个,因为它假装根据每个片段中说话的人在录音中找到边界。说话人特征化可以以有监督或无监督的方式进行,通常应用于由纯语音组成的音频。在这项工作中,使用两种方法对哥斯达黎加无线电广播的第一个注释数据集和说话人特征进行了分析:一种基于k-means聚类的经典方法,以及最近的Fischer半判别法。我们选择了公开的无线电广播,并决定比较这些系统在完整音频文件中的适用性,其中还包含一些音乐片段和具有挑战性的声学条件。结果显示,根据每次广播中的扬声器数量,特别是在平均簇纯度上,结果依赖于结果。结果还表明,需要进一步探索并结合其他分类和分割算法,以便更好地从数据集中提取有用信息,从而进一步开发语音语料库。
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引用次数: 0
Artificial Intelligence based Multi-sensor COVID-19 Screening Framework 基于人工智能的多传感器COVID-19筛查框架
IF 0.1 Pub Date : 2022-11-16 DOI: 10.18845/tm.v35i8.6460
Rakesh Chandra-Joshi, Malay Kishore-Dutta, Carlos M. Travieso
Many countries are struggling for COVID-19 screening resources which arises the need for automatic and low-cost diagnosis systems which can help to diagnose and a large number of tests can be conducted rapidly. Instead of relying on one single method, artificial intelligence and multiple sensors based approaches can be used to decide the prediction of the health condition of the patient. Temperature, oxygen saturation level, chest X-ray and cough sound can be analyzed for the rapid screening. The multi-sensor approach is more reliable and a person can be analyzed in multiple feature dimensions. Deep learning models can be trained with multiple chest x-ray images belonging to different categories to different health conditions i.e. healthy, COVID-19 positive, pneumonia, tuberculosis, etc. The deep learning model will extract the features from the input images and based on that test images will be classified into different categories. Similarly, cough sound and short talk can be trained on a convolutional neural network and after proper training, input voice samples can be differentiated into different categories. Artificial based approaches can help to develop a system to work efficiently at a low cost.
许多国家正在努力争取COVID-19筛查资源,这就产生了对自动和低成本诊断系统的需求,这些系统可以帮助诊断并快速进行大量检测。可以使用人工智能和基于多个传感器的方法来预测患者的健康状况,而不是依赖单一的方法。体温、血氧饱和度、胸部x光片和咳嗽声可以进行快速筛查。多传感器方法更可靠,可以从多个特征维度分析一个人。深度学习模型可以使用多个属于不同类别的胸部x线图像来训练不同的健康状况,如健康、COVID-19阳性、肺炎、结核病等。深度学习模型将从输入图像中提取特征,并在此基础上将测试图像分类为不同的类别。同样,咳嗽声和简短的谈话也可以在卷积神经网络上进行训练,经过适当的训练后,输入的语音样本可以被区分为不同的类别。基于人工的方法可以帮助开发一个以低成本高效工作的系统。
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引用次数: 1
Análisis cualitativo y cuantitativo de fosfatos de calcio por difracción de rayos-X mediante los métodos de Scherrer, Williamson-Hall y refinamiento de Rietveld 用Scherrer、Williamson-Hall和Rietveld细化法对磷酸钙进行x射线衍射定性和定量分析
IF 0.1 Pub Date : 2022-09-30 DOI: 10.18845/tm.v35i4.5664
Alexánder Campos-Quirós, Kenneth Paniagua-Murillo, Gerardo Valladares-Castrillo, Jorge M. Cubero-Sesin, Luis Cordero-Arias
Los fosfatos de calcio son materiales biocerámicos de gran importancia utilizados en el área de recubrimientos bioactivos para implantes metálicos. En el presente estudio, una muestra de fosfatos de calcio fue sintetizada mediante el método de precipitación química a partir de Ca(NO3)2 y (NH4)2HPO4. La técnica de difracción de rayos-X fue utilizada para realizar un análisis cualitativo y cuantitativo de las fases cristalinas presentes en el material mediante los métodos de Scherrer, Williamson-Hall y Rietveld. Se determinó que la muestra está constituida en un 75 % en masa de monetita (CaHPO4) y un 25 % en masa de brushita (CaHPO4.H2O), con tamaños promedio de cristalito en el orden submicrométrico. El análisis mediante microscopia electrónica de barrido muestra que las partículas se encuentran altamente aglomeradas, con un tamaño promedio de 2,8 ± 1 µm y morfología variada. El análisis elemental por espectroscopia de energía dispersiva de rayos-X reveló una relación molar calcio/fósforo (Ca/P) promedio de 0,95, lo cual concuerda con las fases cristalinas de monetita y brushita. Por último, la presencia de ambas fases se debe principalmente a los bajos niveles de pH durante la reacción y al secado de la muestra posterior al proceso de síntesis.
磷酸钙是一种重要的生物陶瓷材料,用于金属植入物的生物活性涂层。本研究以Ca(NO3)2和(NH4)2HPO4为原料,采用化学沉淀法合成了磷酸钙样品。采用Scherrer、Williamson-Hall和Rietveld方法对材料中存在的晶体相进行了定性和定量分析。该样品由75%质量的monetite (CaHPO4)和25%质量的brushite (CaHPO4. h2o)组成,平均晶粒尺寸为亚微米级。扫描电子显微镜分析表明,颗粒高度团聚,平均粒径2.8±1µm,形貌不同。x射线能量色散光谱元素分析显示,钙磷摩尔比(Ca/P)平均为0.95,与monetite和brushite的结晶相一致。最后,这两种相的存在主要是由于反应过程中的低pH值和合成过程后样品的干燥。
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引用次数: 0
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Tecnologia en Marcha
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