Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Analysis of the Cross-Reactivity of Pacific White Shrimp (<i>Litopenaeus vannamei</i>) Allergens with Other Arthropod Species

This study provided new data in the area of cross-reactivity for Pacific white shrimp (Litopenaeus vannamei). Although the cross-reactivity between the most prominent allergenic proteins of shrimp and other crustaceans has been extensively studied, few data are showing the frequency of arthropod-shrimp Litopenaeus vannamei cosensitization in an in silico analysis. A comparative analysis of “typical and non-typical” shrimp L. vannamei allergens with other species was achieved, revealing new allergens and previously characterized shrimp allergens, which validated the comprehensive identification approach used in this study. Importantly, up to 192, amino acid sequences were identified that had matches to shrimp L. vannamei allergens that matched allergenic proteins in mites, insects, fish, bacteria, mammals, birds, and plants.
Benefits of IMU-based Wearables in Sports Medicine: Narrative Review

Background: Inertial Measurement Unit (IMU) based wearables have been the focus of many recent sports medicine research efforts. Objective: The goal of this narrative-driven literature review is to provide the current state of IMU-based wearable technology in Sports Medicine for the benefit of practitioners and athletic trainers. Method: A search was performed using university library resources; specifically, PubMed, EBSCO Discovery and Google Scholar search engines were used to identify appropriate peer-reviewed studies in this field. Results: IMU wearables have shown to be a cost-effective way to measure biomechanical and physiological data for athletic training and rehabilitation compared to laboratory gold standards. While IMU wearables show potential, barriers such as IMU drift and complicated calibrations limit the technology’s ability to flourish in the commercial market. Conclusion: IMU-based wearables provide kinematic information without the constraints and costs of gold standard laboratory equipment such as video-based motion capture and force plates; however, further innovation is required to overcome their major obstacles.
Generative Adversarial Networks for Creating Synthetic Nucleic Acid Sequences of Cat Genome

Nucleic acids are the basic units of deoxyribonucleic acid (DNA) sequencing. Every organism demonstrates different DNA sequences with specific nucleotides. It reveals the genetic information carried by a particular DNA segment. Nucleic acid sequencing expresses the evolutionary changes among organisms and revolutionizes disease diagnosis in animals. This paper proposes a generative adversarial networks (GAN) model to create synthetic nucleic acid sequences of the cat genome tuned to exhibit specific desired properties. We obtained the raw sequence data from Illumina next generation sequencing. Various data preprocessing steps were performed using Cutadapt and DADA2 tools. The processed data were fed to the GAN model that was designed following the architecture of Wasserstein GAN with gradient penalty (WGAN-GP). We introduced a predictor and an evaluator in our proposed GAN model to tune the synthetic sequences to acquire certain realistic properties. The predictor was built for extracting samples with a promoter sequence, and the evaluator was built for filtering samples that scored high for motif-matching. The filtered samples were then passed to the discriminator. We evaluated our model based on multiple metrics and demonstrated outputs for latent interpolation, latent complementation, and motif-matching. Evaluation results showed our proposed GAN model achieved 93.7% correlation with the original data and produced significant outcomes as compared to existing models for sequence generation.
Peningkatan Kualitas Program Pascasarjana Magister Manajemen Reguler Di Universitas Telkom Menggunakan Metode Quality Function Deployment

Perkembangan ilmu pengetahuan di Indonesia cukup pesat begitu juga angka partisipasi sekolah (APS) untuk umur 19-24 tahun meningkat sebanyak 38% di tahun 2013. Hal ini mengakibatkan perlunya pengelolaan lembaga pendidikan yang baik agar dapat meluluskan mahasiswa-mahasiswa yang sesuai dengan kompetensi nya masing-masing. Pengelolaan lembaga pendidikan yang dimaksud adalah layanan pendidikan yang sedang dikelola oleh salah satu perguruan tinggi Di Kabupaten Bandung yaitu Pascasarjana Magister Manajemen Telkom University yang termasuk kedalam Yayasan Pendidikan Telkom (YPT). Pascasarjana Telkom melayani Graduate School dan berfokus pada kualitas dan pengembangan program Pascasarjana. Dengan Meningkatnya APS setiap tahunnya dan ketatnya persaingan dalam menyediakan lembaga pendidikan, Pascasarjana Magister Manajemen Telkom University perlu memerlukan perancangan kualitas layanan pendidikan yang sesuai dengan kebutuhan dan keinginan mahasiswa. Penelitian ini bertujuan untuk merumuskan rekomendasi perancangan kualitas layanan pendidikan Pascasarjana Magister Manajemen sesuai dengan true customer needs untuk meningkatkan kepuasan mahasiswa dalam menimba ilmu. Quality Function Deployment (QFD) merupakan metode yang digunakan dalam penelitian ini untuk menerjemahkan kemampuan lembaga pendidikan dalam mewujudkan kebutuhan tersebut. Untuk melakukan peracangan kualitas layanan pendidikan Pascasarjana Magister manajemen, diperlukan true customer needs yang didapat dari hasil penelitian sebelumnya. Terdapat 15 true customer needs yang dijadikan masukan ke dalam QFD iterasi 1, yang selanjutnya terindentifikasi 22 karakteristik teknis. Berdasarkan nilai rank dan pemenuhan target karakteristik teknis, terdapat 9 karakteristik teknis yang menjadi prioritas pengembangan dan menjadi masukan ke dalam QFD iterasi 2, teridentifikasi 18 critical part yang menjadi dasar perumusan rekomendasi. Perumusan rekomendasi dilakukan berdasarkan hasil pengolahan data, analisis, brainstorming dengan penyelenggara pendidikan yaitu Pascasarjana Magister Manajemen Telkom University serta melakukan benchmark dengan lembaga pendidikan pesaing yaitu Pascasarjana Magister Manajemen Universitas Padjajaran. Rekomendasi yang diusulkan dalam penelitian ini adalah Menyediakan layanan untuk mahasiswa yang membutuhkan jurnal hardcopy, menyediakan media tambahan sebagai alat publikasi hasil penelitian mahasiswa, menyediakan akses channel Tambahan jurnal internasional gratis, menyediakan channel publikasi tambahan untuk jurnal internasional, menyediakan waktu untuk responsi dan membahas materi secara dalam, penambahan jumlah waktu pertemuan dosen dan menyediakan training kepada tenaga pengajar atau dosen yang sesuai dengan bidang yang diajarkan. Kata Kunci: QFD, Quality Function Deployment, Kualitas pelayanan Pendidikan.
Investigating Plant–Bird Co-Occurrence Patterns in Mediterranean Wetlands: Can They Reveal Signals of Ecosystem Connectivity?

Interspecific biotic interaction is believed to be a fundamental phenomenon in ecology. However, despite the increasing efforts, interaction mechanisms are still not clearly understood. We compiled a database of 323 birds and 844 vascular plants in 30 wetlands from Sardinia. This was complemented with seed dispersal features and plant structures (suitability for nesting), and with site-level traits, such as wetland surface area, distance from the sea, percentage of open water, protection level, and number of human impacts. The percentage of non-random co-occurrences was then measured, and the relative importance of each trait in determining it was modelled. We found that non-random co-occurrences among sites decreased with the site extent and increase with the percentage of open water, bird zoochory was positively correlated with co-occurrences, nesting birds showed higher rates of co-occurrence than non-nesting birds, and plants with habits suitable for nesting displayed more co-occurrences than the rest of the plants. These results are a small contribution to the complex topic of species co-occurrence and connectivity within an ecosystem. Species co-occurrence is a promising but debatable approach that may provide insightful clues to species interactions within ecological systems.
Estimating the marginal cost of different vehicle types on rail infrastructure

In this paper we combine engineering and economic methods to estimate the relative cost of damage mechanisms on the Swedish rail infrastructure. The former method is good at predicting damage from traffic, while the latter is suitable for establishing a relationship between damage and cost. We exploit the best features of both methods in a two-stage approach and demonstrate its applicability for rail infrastructure charging. Our estimations are based on 143 track sections comprising about 11 000 km of tracks. We demonstrate how the estimated relative costs of damage mechanisms can be used in order to calculate the marginal wear and tear cost of different vehicle types. The results are relevant for infrastructure managers in Europe who desire to differentiate their track access charges such that each vehicle pays its short run-marginal wear and tear cost, which can create a more efficient use of the rail infrastructure.
Software process measurement utilisation from the project risk perspective

In the current decade, software organisations are, maybe more than ever, focusing their attention on measurement in software engineering. There is a growing need for the use of objective information in decision making as well as software project management. In the long-term, only realistic estimations are in the interests of both customer and supplier. However, in practice, organisations are forced to prioritise their measurement operations and targets. Measurement should be adequate and extensive, but at the same time consume little effort. This equation is rather difficult to realise in practice. Choosing the correct measurement entities and ranking the importance of measurement indicators is a challenging task in software engineering. This paper uses an empirical case study to examine how measurement was implemented in practice from the perspective of software. The possible risk sectors from the software project perspective are also evaluated based on the study results.
Investigation on the effects of cooking methods on anti-inflammatory and antioxidant activities of five mostly consumed vegetables in winter

The aim of this study is to investigate the effects of steaming and boiling on antioxidant and anti-inflammatory activity of five frequently consumed vegetables in winter. The vegetables were prepared by three different cooking methods including steaming, 5-minute boiling, 15-minute boiling to compare with their raw forms. Antioxidant capacity was measured with 1, 1-diphenyl–2 picrylhydrazyl (DPPH) radical scavenging method, anti-inflammatory activity was measured with 5-lipoxgenase inhibitory method, and the total phenolic content was detected after in vitro cooking process. The highest antioxidant activities among the raw vegetables were found in spinach (SR) (425.80 µg/mL, 12.83 mg/g) and broccoli (BR) (754.50 µg/mL, 7 mg/g). While boiling for 15 minutes and steaming slightly increased the antioxidant capacity in spinach and decreased it in broccoli; the highest activities among the mentioned cooking methods and vegetable samples were detected in these two vegetables. The lowest antioxidant activities were determined in leek (LR) (5662.0 µg/mL, 1.24 mg/g) and celery (CeR) (2796.0 µg/mL, 2.98 mg/g). In addition, the least affected vegetable from the cooking methods was spinach (S) (227.4-549.8 µg/mL). Cooking techniques have significative effects on the levels of phytochemical compounds and antioxidant capacities. It was observed that cooking methods increased the anti-inflammatory activity of the vegetables used in this study. Only broccoli (B) showed a decrease. The highest anti-inflammatory activity was found in the leek (L15) which was boiled for 15 minutes. Also, our results contribute to the databases that provide information about the effects of different cooking techniques on the antioxidant and anti-inflammatory potential of vegetables.
Numerical-based frequency domain controller design for stand-alone brushless doubly fed induction generator power system

Brushless doubly fed induction generator (BDFIG) shows high reliability in either grid-connected or stand-alone applications due to its brushless structure. However, the brushless structure results in a complicated electromagnetic feature. The BDFIG controller design is thus challenged. The recent controller design either ignores the usefully model information or requires the complicated feedforward terms. Besides, the bandwidth restriction exists if the dual-loop control is applied. To overcome these problems, this study proposes a numerical-based frequency domain design method and applies it to a CW-current-oriented stand-alone BDFIG system with dual-loop control. The control objects are developed as transfer function forms and derived from the complete BDFIG model. Then the PI controllers for inner current loops and outer voltage loop are designed step by step, and the previous design result is considered in the recent step. In this way, more model and controller information are considered, and the bandwidth limitation can be eliminated. The design steps are presented in this study. The results show that the good steady and dynamic performances of the voltage regulation can be obtained compared with the traditional methods, which is practically important for a stand-alone BDFIG system.
Automatic classification of MRI contrasts using a deep Siamese network and one-shot learning

Fully automatic classification of magnetic resonance (MR) brain images into different contrasts is desirable for facilitating image processing pipelines, as well as for indexing and retrieving from medical image archives. In this paper, we present an approach based on a Siamese neural network to learn a discriminative feature representation for MR contrast classification. The proposed method is shown to outperform a traditional deep convolutional neural network method and a template matching method in identifying five different MR contrasts of input brain volumes with a variety of pathologies, achieving 98.59% accuracy. In addition, our approach permits one-shot learning, which allows generalization to new classes not seen in the training set with only one example of each new class. We demonstrate accurate one-shot learning performance on a sixth MR contrast that was not included in the original training.
Multidisciplinary Design Overview and Comparison for Two Case Studies of High Speed Permanent Magnet Machines

High-speed electrical machines have become more and more popular applications driven by electric vehicles and all-electric aircraft. Their design usually requires a high level of integration, including loss, thermal, cooling, and mechanical aspects. This article makes a comprehensive overview of the multidiscipline design method of high-speed permanent magnet (HSPM) machines. A 4-kW machine with the flexible rotor operating above the first bending critical speed is presented, and a 30-kW machine is also developed with consideration of the multidisciplinary design process for contrast. The constraint and the mechanism in the overview are investigated to clarify the influence of different design variables on the rotor structure and performance. Finally, two machines are fabricated and tested, and the values are compared with theoretical results.
Adult Memory T Cell Responses to the Respiratory Syncytial Virus Fusion Protein During a Single RSV Season (2018–2019)

Respiratory Syncytial Virus (RSV) is ubiquitous and re-infection with both subtypes (RSV/A and RSV/B) is common. The fusion (F) protein of RSV is antigenically conserved, induces neutralizing antibodies, and is a primary target of vaccine development. Insight into the breadth and durability of RSV-specific adaptive immune response, particularly to the F protein, may shed light on susceptibility to re-infection. We prospectively enrolled healthy adult subjects (n = 19) and collected serum and peripheral blood mononuclear cells (PBMCs) during the 2018–2019 RSV season. Previously, we described their RSV-specific antibody responses and identified three distinct antibody kinetic profiles associated with infection status: uninfected (n = 12), acutely infected (n = 4), and recently infected (n = 3). In this study, we measured the longevity of RSV-specific memory T cell responses to the F protein following natural RSV infection. We stimulated PBMCs with overlapping 15-mer peptide libraries spanning the F protein derived from either RSV/A or RSV/B and found that memory T cell responses mimic the antibody responses for all three groups. The uninfected group had stable, robust memory T cell responses and polyfunctionality. The acutely infected group had reduced polyfunctionality of memory T cell response at enrollment compared to the uninfected group, but these returned to comparable levels by end-of-season. The recently infected group, who were unable to maintain high levels of RSV-specific antibody following infection, similarly had decreased memory T cell responses and polyfunctionality during the RSV season. We observed subtype-specific differences in memory T cell responses and polyfunctionality, with RSV/A stimulating stronger memory T cell responses with higher polyfunctionality even though RSV/B was the dominant subtype in circulation. A subset of individuals demonstrated an overall deficiency in the generation of a durable RSV-specific adaptive immune response. Because memory T cell polyfunctionality may be associated with protection against re-infection, this latter group would likely be at greater risk of re-infection. Overall, these results expand our understanding of the longevity of the adaptive immune response to the RSV fusion protein and should be considered in future vaccine development efforts.
The Effect of Niacin and Melatonin Supplementation on the Antioxidant System and Lipid Peroxidation in Exercised Rats

Objective: The aim of this study was to examine the effect of niacin and melatonin supplementation on the antioxidant system and lipid peroxidation in exercised rats. Materials and Methods: The rats were divided into four groups. Running exercise was done for ten days. Niacin and melatonin were given before exercise. Results: The malondialdehyde levels of the melatonin group were lower than those of the other groups. Malondialdehyde levels of the niacin + melatonin group were higher than the control groups super oxide dismutase (SOD) levels of the melatonin group were higher than those of the other groups. SOD levels of the niacin + melatonin group were lower than those of the other groups. Catalase levels of the melatonin group were higher than those of the niacin groups. Glutathione peroxidase levels of the control group were lower than those of the other groups. Total oxidant levels of the control group were lower than those of the niacin groups. Total antioxidant level (TAS) levels of the control group were lower than those of the other groups. TAS levels of the niacin + melatonin group were lower than those of the niacin or melatonin groups. Melatonin levels of the melatonin groups were higher than those of the other groups. Conclusion: Melatonin supplementation decreased malondialdehyde levels and increased antioxidant parameters. It can be said that it has a higher antioxidant effect compared to niacin. Co-administration of niacin and melatonin increased oxidation parameters and decreased SOD and catalase levels. These enzymes indicated that they were used in response to increased oxidant status.
Store-Operated Ca2+ Entry in Skeletal Muscle Contributes to the Increase in Body Temperature during Exertional Stress

Exertional heat stroke (HS) is a hyperthermic crisis triggered by an excessive accumulation of Ca2+ in skeletal muscle fibers. We demonstrated that exercise leads to the formation of calcium entry units (CEUs), which are intracellular junctions that reduce muscle fatigue by promoting the recovery of extracellular Ca2+ via store-operated Ca2+ entry (SOCE). Here, we tested the hypothesis that exercise-induced assembly of CEUs may increase the risk of HS when physical activity is performed in adverse environmental conditions (high temperature and humidity). Adult mice were: (a) first, divided into three experimental groups: control, trained-1 month (voluntary running in wheel cages), and acutely exercised-1 h (incremental treadmill run); and (b) then subjected to an exertional stress (ES) protocol, a treadmill run in an environmental chamber at 34 °C and 40% humidity. The internal temperature of the mice at the end of the ES was higher in both pre-exercised groups. During an ES ex-vivo protocol, extensor digitorum longus(EDL) muscles from the trained-1 month and exercised-1 h mice generated greater basal tension than in the control and were those that contained a greater number of CEUs, assessed by electron microscopy. The data collected suggest that the entry of Ca2+ from extracellular space via CEUs could contribute to exertional HS when exercise is performed in adverse environmental conditions.
Camu-Camu Reduces Obesity and Improves Diabetic Profiles of Obese and Diabetic Mice: A Dose-Ranging Study

Overweight, obesity, and their comorbidities are currently considered a major public health concern. Today considerable efforts are still needed to develop efficient strategies able to attenuate the burden of these diseases. Nutritional interventions, some with plant extracts, present promising health benefits. In this study, we evaluated the action of Camu-Camu (Myrciaria dubia), an Amazonian fruit rich in polyphenols and vitamin C, on the prevention of obesity and associated disorders in mice and the abundance of Akkermansia muciniphila in both cecum and feces. Methods: We investigated the dose-response effects of Camu-Camu extract (CCE) in the context of high-fat-diet (HFD)-induced obesity. After 5 weeks of supplementation, we demonstrated that the two doses of CCE differently improved glucose and lipid homeostasis. The lowest CCE dose (62.5 mg/kg) preferentially decreased non-HDL cholesterol and free fatty acids (FFA) and increased the abundance of A. muciniphila without affecting liver metabolism, while only the highest dose of CCE (200 mg/kg) prevented excessive body weight gain, fat mass gain, and hepatic steatosis. Both doses decreased fasting hyperglycemia induced by HFD. In conclusion, the use of plant extracts, and particularly CCE, may represent an additional option in the support of weight management strategies and glucose homeostasis alteration by mechanisms likely independent from the modulation of A. muciniphila abundance.
The Gut Microbiome May Help Address Mental Health Disparities in Hispanics: A Narrative Review

The gut–brain axis is the biological connection between the enteric and the central nervous systems. Given the expansion of the microbial sciences with the new human microbiome field facilitated by the decrease in sequencing costs, we now know more about the role of gut microbiota in human health. In this short review, particular focus is given to the gut–brain axis and its role in psychiatric diseases such as anxiety and depression. Additionally, factors that contribute to changes in the gut–brain axis, including the gut microbiome, nutrition, the host’s genome, and ethnic difference, are highlighted. Emphasis is given to the lack of studies on Hispanic populations, despite the fact this ethnic group has a higher prevalence of anxiety and depression in the US.