Miracle-dz/UniFAR-FTUs huggingface dataset:
Applying knowledge-driven mechanistic inference to toxicogenomics

Government regulators and others concerned about toxic chemicals in the environment hold that a mechanistic, causal explanation of toxicity is strongly preferred over a statistical or machine learning-based prediction by itself. Elucidating a mechanism of toxicity is, however, a costly and time-consuming process that requires the participation of specialists from a variety of fields, often relying on animal models. We present an innovative mechanistic inference framework (MechSpy), which can be used as a hypothesis generation aid to narrow the scope of mechanistic toxicology analysis. MechSpy generates hypotheses of the most likely mechanisms of toxicity, by combining a semantically-interconnected knowledge representation of human biology, toxicology and biochemistry with gene expression time series on human tissue. Using vector representations of biological entities, MechSpy seeks enrichment in a manually-curated list of high-level mechanisms of toxicity, represented as biochemically- and causally-linked ontology concepts. Besides predicting the canonical mechanism of toxicity for many well-studied compounds, we experimentally validated some of our predictions for other chemicals without an established mechanism of toxicity. This framework can be modified to include additional mechanisms of toxicity, and is generalizable to other types of mechanisms of human biology. Author summary Several recent computational methods have displayed excellent performance in predicting toxicity outcomes [1–3] of chemicals. Yet, to our knowledge, there is to date no computational approach to generate mechanistic hypotheses to answer why these chemicals elicit a toxic response. There is great value in understanding the mechanism of toxicity for a chemical that appears to elicit an adverse response. Novel small molecule development is one example, where a chemical that failed initial toxicological screenings could be assessed to evaluate the actual mechanism of toxicity, greatly reducing research time and expenses on subsequent ones. The value of a mechanistic awareness of toxicity also applies to pharmacovigilance, when researching rare adverse effects of a drug in subsets of the population. The development of oncological chemotherapeutics is another example, where certain mechanisms of cytotoxicity can actually be desirable to eliminate different types of tumor cells. More importantly, the costs, time expenditure, and ethical concerns of toxicity animal models, make in vitro and in silico approaches an enticing alternative. We present a solution that uses a combination of gene expression assays and biomedical knowledge to address the gap of answering the why question.
Designing interactive virtual environments with feedback in health applications.

DESIGNING INTERACTIVE VIRTUAL ENVIRONMENTS WITH FEEDBACK IN HEALTH APPLICATIONS Yi Li April 6, 2018 One of the most important factors to influence user experience in human-computer interaction is the user emotional reaction. Interactive environments including serious games that are responsive to user emotions improve their effectiveness and user satisfactions. Testing and training for user emotional competence is meaningful in healthcare field, which has motivated us to analyze immersive affective games using emotional feedbacks. In this dissertation, a systematic model of designing interactive environment is presented, which consists of three essential modules: affect modeling, affect recognition, and affect control. In order to collect data for analysis and construct these modules, a series of experiments were conducted using virtual reality (VR) to evoke user emotional reactions and monitoring the reactions by physiological data. The analysis results lead to the novel approach of a framework to design affective gaming in virtual reality, including the descriptions on the aspects of interaction mechanism, graph-based structure, and user modeling. Oculus Rift was used in the experiments to provide immersive virtual reality with affective scenarios, and a sample application was implemented as cross-platform VR physical training serious game for elderly people to demonstrate the essential parts of the framework. The measurements of playability and effectiveness are discussed. The introduced framework should be used as a guiding principle for designing affective VR serious games. Possible healthcare applications include emotion competence training, educational softwares, as well as therapy methods.
Multimodal Biometric Authentication Systems Using Convolution Neural Network Based on Different Level Fusion of ECG and Fingerprint

A multimodal biometric system integrates information from more than one biometric modality to improve the performance of each individual biometric system and make the system robust to spoof attacks. In this paper, we propose a secure multimodal biometric system that uses convolution neural network (CNN) and Q-Gaussian multi support vector machine (QG-MSVM) based on a different level fusion. We developed two authentication systems with two different level fusion algorithms: a feature level fusion and a decision level fusion. The feature extraction for individual modalities is performed using CNN. In this step, we selected two layers from CNN that achieved the highest accuracy, in which each layer is regarded as separated feature descriptors. After that, we combined them using the proposed internal fusion to generate the biometric templates. In the next step, we applied one of the cancelable biometric techniques to protect these templates and increase the security of the proposed system. In the authentication stage, we applied QG-MSVM as a classifier for authentication to improve the performance. Our systems were tested on several publicly available databases for ECG and fingerprint. The experimental results show that the proposed multimodal systems are efficient, robust, and reliable than existing multimodal authentication systems.
Design of a Chamfering Tool Diagnosis System Using Autoencoder Learning Method

In this paper, the autoencoder learning method is proposed for the system diagnosis of chamfering tool equipment. The autoencoder uses unsupervised learning architecture. The training dataset that requires only a positive sample is quite suitable for industrial production lines. The abnormal tool can be diagnosed by comparing the output and input of the autoencoder neural network. The adjustable threshold can effectively improve accuracy. This method can effectively adapt to the current environment when the data contain multiple signals. In the experimental setup, the main diagnostic signal is the current of the motor. The current reflects the torque change when the tool is abnormal. Four-step conversions are developed to process the current signal, including (1) current-to-voltage conversion, (2) analog-digital conversion, (3) downsampling rate, and (4) discrete Fourier transform. The dataset is used to find the best autoencoder parameters by grid search. In training results, the testing accuracy, true positive rate, and precision approach are 87.5%, 83.33%, and 90.91%, respectively. The best model of the autoencoder is evaluated by online testing. The online test means loading the diagnosis model in the production line and evaluating the model. It is shown that the proposed tool can effectively detect abnormal conditions. The online assessment accuracy, true positive rate, and precision are 75%, 90%, and 69.23% in the original threshold, respectively. The accuracy can be up to 90% after adjusting the threshold, and the true positive rate and precision are up to 80% and 100%, respectively.
Javanese medaka (Oryzias javanicus Bleeker, 1854) as potential model organism for aeromoniasis and vibriosis study in fish

Javanese medaka is a small tropical fish that has been widely used as a test organism in ecology, toxicology and ecotoxicology, but less in fish-pathogen related study. This study evaluates the capability of Javanese medaka as an alternative model organism for aeromoniasis and vibriosis study in fish. Javanese medakas were infected with different concentrations of Aeromonas hydrophila, Vibrio alginolyticus and V. harveyi via intraperitoneal (IP) and immersion (IMM) routes. Following the infections, the LD50- 240h of all bacteria to Javanese medaka were observed lower in IP, compared with IMM route. In IP route, the LD50-240h ranged from 2.1 × 104 CFU/mL for V. harveyi to 2.5 × 107 CFU/mL for A. hydrophila. However, for IMM route, the range was from 6.6 × 107 CFU/mL for V. harveyi to 1.1 × 109 CFU/ mL for V. alginolyticus. The clinical signs, gross lesions and histopathological changes of Javanese medakas infected by either IP or IMM routes of all the pathogens were similarly observed in the real host of the pathogen. Moreover, in IP route, most of the fish mortalities (88.9%) were observed within ≤ 120 hours post infection (hpi), while for IMM, most of the mortalities (50.6%) were witnessed beyond 120 hpi, indicating the acute infection for IP compared to IMM route. This study highlights the potential utilization of Javanese medaka as another valuable in vivo model organism for bacterial diseases study in fish.
Identification of sequences encoding for ncr-peptides and defensins in the ‘meta-assembly’ of transcriptome of pea (pisum sativum l.) Nitrogen-fixing nodules

Background. The active and careless applying of antibiotics in medicine and agriculture leads to the emergence of resistance to the existing antimicrobial drugs, which reduces the effectiveness of their use. One of the ways to solve this problem is the development of new antibiotics based on plant peptides with antimicrobial activity, for example plant defensins (which identified in all plants) and NCR peptides that are specifically synthesized in nodules of some leguminous plants. Materials and methods. In the present study, a meta-assembly of a transcriptome was constructed based on publicly available RNA-sequencing transcriptomes of pea nodules (Pisum sativum L.). This meta-assembly was used to search for sequences encoding antimicrobial peptides. Results. As a result, 55 and 908 unique sequences encoding defensins and NCR peptides, respectively, were identified. The recognition site for the signal peptidase was predicted and sequences were divided into the signal and mature part of the peptide. Among mature defensins, 22 peptides possess in silico predicted antimicrobial activity, and for the NCR peptides family their number was 422. Conclusion. Sequences encoding defensins and NCR peptides expressed in nitrogen-fixing pea nodules were identified. They are candidates for testing their antimicrobial activity in vitro.
Research on traversability of tracked vehicle on slope with unfixed obstacles: derivation of climbing-over, tipping-over, and sliding-down conditions

When a tracked robot explores a volcanic environment, it faces difficulty in climbing over unfixed obstacles such as loose rocks on the ground. Such unfixed obstacles sometimes cause the sliding-down or tipping-over of the robot. Although such phenomena should be avoided for the success of the mission, they have not been sufficiently studied yet. Therefore, this research aims at understanding the phenomena for a tracked vehicle climbing an unfixed obstacle on a slope, and considers the conditions of climbing-over, tipping-over, and sliding-down. To simplify the problem, a model of a single track and circular cross-section obstacle is used in this research. The climbing-over and tipping-over conditions are derived from the geometric relationship, and the sliding-down condition is derived from statics. Moreover, some experiments using an actual robot are conducted to verify the validity of the conditions. The results show that the derived conditions are reasonable. Furthermore, it is revealed that unfixed obstacles typically tend to slide down more than fixed obstacles because of the number of contact points that can support a robot. GRAPHICAL ABSTRACT
Switching and Conduction Loss Reduction of Dual-Buck Full-Bridge Inverter Through ZVT Soft-Switching Under Full-Cycle Modulation

Based on the no blanking time characteristic, voltage error does not occur in the pulsewidth modulated output stage of dual-buck full-bridge inverter (DBFBI), resulting in lower total harmonic distortion (THD) of the output current. The two main modulations applied in the topology are half-cycle modulation and full-cycle modulation. Compared with the half-cycle modulation, the full-cycle modulation does not have the zero-crossing problem, but the inverter requires a bias current to guarantee better output waveform. The circulation current loop caused by bias current has a great influence on inverter efficiency. This article proposes a novel zero voltage transition (ZVT) soft-switching topology to increase efficiency by reducing the switching losses and conduction losses resulting from low bias current. The advantages of the DBFBI are included in the proposed inverter. The soft-switching condition is achieved by the snubber cells, and the energy stored in the passive snubber capacitors can be transferred effectively. The topology deduction, operating principles, and design guidelines are presented in detail. An 800-W experimental prototype operating with a 100-kHz switching frequency is implemented to verify the theoretical result.
Cuticular Morphohogy of The Anoplius viaticus (Hymenoptera: Pompilidae) Collected From Different Altitudes of Kars Plateau

In this study we collected various samples of Anoplius viaticus (Pompilidae: Hymenoptera) from different locations found at different altitudes in Kars (1850 m), in Igdir (1400 m) and on Allahuekber Mountains (2800 m) and photographed them under the electron microscope. We investigated and discussed the differences in cuticle and morphology of the samples taken from various altitudes. We observed that as the altitude gets higher, there is an increase in coverage of hair found on the head, antenna, thorax, and abdomen.
Towards an adaptive and genomic understanding of an exaggerated secondary sexual trait in water striders

From the DNA molecule to the more complex phenotypes, variation is a universal process in life and living organisms. The innumerable differences that exist between species are probably one of the most manifest examples. Yet, all this diversity would never have occurred in nature without some pre-existing divergence within species. One of the most striking examples of intraspecies variation appears in sexual organisms, between males and females. Understanding the environmental and genetic factors influencing sexual divergence is a longstanding question in evolutionary biology. To this end, I focus here on a new insect model system, Microvelia longipes, which has the particularity to have evolved an extreme case of sexual dimorphism in the rear legs. Males display exaggerated long rear legs compared to females but also an extreme variability in these leg lengths from one male to another. We identified that M. longipes males use their exaggerated legs as weapons during male-male competition. Males with longer legs have more chance to access females on egg-laying sites and therefore increase their reproductive success. Moreover, fitness assays and comparative studies between Microvelia species revealed that the intensity of male competition was associated with the exaggeration and hypervariability of the rear legs in M. longipes males. In a second approach, we studied the developmental and genomic basis of this sexual dimorphism through a comparative transcriptomic analysis and identified genes and genomic regions associated with male exaggerated legs and ultimately with sexual selection. Overall, the integrative approach used in this work allows to establish Microvelia longipes as a promising new model system to study the influence of sexual selection in adaptive evolution.
Excess postexercise oxygen consumption decreases with swimming duration in a labriform fish: Integrating aerobic and anaerobic metabolism across time.

Many vertebrate animals employ anaerobic pathways during high-speed exercise, even if it imposes an energetic cost during postexercise recovery, expressed as excess postexercise oxygen consumption (EPOC). In ectotherms such a fish, the initial anaerobic contribution to exercise is often substantial. Even so, fish may recover from anaerobic pathways as swimming exercise ensues and aerobic metabolism stabilizes, thus total energetic costs of exercise could depend on swimming duration and subsequent physiological recovery. To test this hypothesis, we examined EPOC in striped surfperch (Embiotoca lateralis) that swam at high speeds (3.25 L s-1 ) during randomly ordered 2-, 5-, 10-, and 20-min exercise periods. We found that EPOC was highest after the 2-min period (20.9 mg O2 kg-1 ) and lowest after the 20-min period (13.6 mg O2 kg-1 ), indicating that recovery from anaerobic pathways improved with exercise duration. Remarkably, EPOC for the 2-min period accounted for 72% of the total O2 consumption, whereas EPOC for the 20-min period only accounted for 14%. Thus, the data revealed a striking decline in the total cost of transport from 0.772 to 0.226 mg O2 ·kg-1 ·m-1 during 2- and 20-min periods, respectively. Our study is the first to combine anaerobic and aerobic swimming costs to demonstrate an effect of swimming duration on EPOC in fish. Clarifying the dynamic nature of exercise-related costs is relevant to extrapolating laboratory findings to animals in the wild.
Reatores eletrônicos para lâmpadas de vapor de sódio de alta pressão de 70W

The present work deals with the study of electronic ballasts with high power factor used for supplying power to high pressure sodium vapor lamps. Primarily, a study of the characteristics of this type of lamp is shown, which made possible the obtainment of a simulation model for the lamp. Afterwards, a study of a passive rectifier for power factor correction, chosen due to its simplicity and robustness, is presented. A description of two inverters, a symmetrical one and an asymmetrical one, each with different command strategies, used to supply power to the lamp, follows. It is important to emphasize the simplicity of the command circuits and the soft-switching of both of the inverters’ switches throughout their entire operation. The asymmetric inverter is microcontrolled, which allows the luminosity of the lamp to be varied according to the microcontroller’s program. Finally, a conclusion stating the advantages and disadvantages of the chosen structures and some suggestions for the continuation of studies in this area is presented.
Date Palm Biotechnology: Recent Research an Overview

Date palm (Phoenix dactylifera L.) is among the earliest fruit crops cultivated in the arid Arab Peninsula, North Africa, and Middle East territories. Dates are a significant source of food and revenue for Middle East and North Africa's local communities. It has distinctive features of biology and development that require special methods of reproduction, culture and governance. In varying date-growing regions, there are thousands of date plant cultivars and varieties. The lengthy life cycle, long juvenile lifespan, and date palm dioecism produce cultivation difficult. Every year, the percentage of crop genomes sequenced has continued to increase. The incredible rate at which DNA samples become accessible is mainly due to the enhancement in cost-and speed-related sequencing techniques. Modern sequencing techniques enable the sequencing at realistic price of various cultivars of tiny plant genomes. Although many of the published genomes are deemed incomplete, they have nevertheless proven to be useful instruments for understanding significant plant characteristics such as fruit maturation, grain characteristics and adaptation of flowering time, here we review date palm genomic studies and determine its genomics element.
Transposable elements in individual genotypes of Drosophila simulans

Transposable elements are mobile DNA sequences that are able to copy themselves within a host’s genome. Within insects they often make up a substantial proportion of the genome. While they are the subject of intense research, often times when copy number is estimated it is estimated only at the population level, or in a limited number of individuals within a population. I was interested in whether or not transposable elements accumulate at different rates in different genetic backgrounds – the variance between individual genotypes in transposable element accumulation. Using two populations of Drosophila simulans from California and Africa I estimated transposable element copy number in individual genotypes. Some active transposable elements seem to be a property of the species, while others of the populations. I find that in addition to population level differences in transposable element load certain genotypes accumulate transposable elements at a much higher rate than others. Most likely active transposable elements are fairly rare, and were inherited only by specific genotypes that were used to create the inbred lines. Whether or not this reflects dynamics in natural populations, where transposable elements may accumulate in specific genotypes and maintain themselves in the population rather than being active at low levels population wide, is an open question.
Expanding floral multimodality : floral temperature and floral humidity

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Real Time Facial Recognition Using Principal Component Analysis (PCA) And EmguCV

Facial recognition is a challenging research in the field of image processing and computer vision, especially for security systems, weight determiner, and emotional determination based on the face image recognition. Some of the methods that can be used in facial recognition are holistic, feature extraction, hybrids and intelligent systems. This paper used the method of characteristic extraction that used Principal Component Analysis (PCA) which was built using EmguCV application. The purpose of this research is to assess the accuracy of Principal Component Analysis (PCA) method when combined with Emgu CV in face recognition in real time. Based on the results of training and testing, it can be concluded that the PCA method combined with EmguCV has better accuracy, if the data used has the same characteristics, PCA and EmguCV can also be developed to make image processing application especially for security system, because it applies simple statistic method and easy- applied algorithm.
Crystal Structure of the Active Site Mutant Form of Soluble Fumarate Reductase, Osm1

Soluble fumarate reductase is essential for survival under anaerobic conditions. This enzyme can maintain the redox balance in the cell by catalyzing the reduction of fumarate to succinate. Although the overall reaction mechanism of soluble fumarate reductase in yeast, Osm1, has been proposed by a previous structural study, the details of the underlying mechanism are not completely elucidated. The present study provides the structural information regarding the active site mutant form of Osm1 (R326A), thus, revealing that R326A mutation does not affect the substrate binding. Structural alterations of the residues surrounding the active site, and the missing 2nd flavin adenine dinucleotide (FAD) in the previously defined 2nd FAD binding site, were observed as characteristic features of the Osm1 R326A crystal structure. Based on these findings, we provided a clue that can explain the loss of activity of Osm1 R326A.