Miracle-dz/UniFAR-FTUs huggingface dataset:
From cold chain to ambient temperature: transport of viral specimens- a review

Abstract The diagnosis of an aetiology is dependent on the collection, transport, and storage of the infectious sample. The transport of the sample plays a crucial role in the chain of diagnosis. It is important to maintain the biological integrity of the pathogen during the transport of the sample to achieve an accurate diagnosis. This is important, particularly for labile organisms like viruses that are inactivated easily compared to other microorganisms. Many transport media have been utilised to ensure the integrity of the virus during transport. While most of the transport media are focused on preserving the infectious properties of the virus, progress has been made to develop virus transport media to inactivate the virus and obtain the stability of the viral nucleic acid, enabling better molecular diagnosis of the virus aetiologies. This review summarises the various media used for the transport of virus samples and focuses on the need to develop virus transport media that inactivates the virus and preserves the viral nucleic acid.
[11C]metoclopramide is a sensitive radiotracer to measure moderate decreases in P-glycoprotein function at the blood-brain barrier

The efflux transporter P-glycoprotein (P-gp) at the blood-brain barrier limits the cerebral uptake of various xenobiotics. To assess the sensitivity of [11C]metoclopramide to measure decreased cerebral P-gp function, we performed [11C]metoclopramide PET scans without (baseline) and with partial P-gp inhibition by tariquidar in wild-type, heterozygous Abcb1a/b(+/−) and homozygous Abcb1a/b(−/−) mice as models with controlled levels of cerebral P-gp expression. Brains were collected to quantify P-gp expression with immunohistochemistry. Brain uptake of [11C]metoclopramide was expressed as the area under the brain time-activity curve (AUCbrain) and compared with data previously obtained with (R)-[11C]verapamil and [11C]N-desmethyl-loperamide. Abcb1a/b(+/−) mice had intermediate P-gp expression compared to wild-type and Abcb1a/b(−/−) mice. In baseline scans, all three radiotracers were able to discriminate Abcb1a/b(−/−) from wild-type mice (2.5- to 4.6-fold increased AUCbrain, p ≤ 0.0001). However, only [11C]metoclopramide could discriminate Abcb1a/b(+/−) from wild-type mice (1.46-fold increased AUCbrain, p ≤ 0.001). After partial P-gp inhibition, differences in [11C]metoclopramide AUCbrain between Abcb1a/b(+/−) and wild-type mice (1.39-fold, p ≤ 0.001) remained comparable to baseline. There was a negative correlation between baseline [11C]metoclopramide AUCbrain and ex-vivo-measured P-gp immunofluorescence (r = −0.9875, p ≤ 0.0001). Our data suggest that [11C]metoclopramide is a sensitive radiotracer to measure moderate, but (patho-)physiologically relevant decreases in cerebral P-gp function without the need to co-administer a P-gp inhibitor.
The evolution of complex and higher organisms

The evolution of Phanerozoic life has probably been influenced by extraterrestrial events and properties of the Earth-Moon system that have not, until now, been widely recognized. Tide range, gravitational strength, the Earth's axial tilt, and other planetary properties provide background conditions whose effects on evolution may be difficult to distinguish. Solar flares, asteroid impacts, supernovae, and passage of the solar system through galactic clouds can provide catastrophic changes on the Earth with consequent characteristic extinctions. Study of the fossil record and the evolution of complex Phanerozoic life can reveal evidence of past disturbances in space near the Earth. Conversely, better understanding of environmental influences caused by extraterrestrial factors and properties of the solar system can clarify aspects of evolution, and may aid in visualizing life on other planets with different properties.
gPPM: A Generalized Matrix Operation and Parallel Algorithm to Accelerate the Encoding/Decoding Process of Erasure Codes

Erasure codes are widely deployed in modern storage systems, leading to frequent usage of their encoding/decoding operations. The encoding/decoding process for erasure codes is generally carried out using the parity-check matrix approach. However, this approach is serial and computationally expensive, mainly due to dealing with matrix operations, which results in low encoding/decoding performance. These drawbacks are particularly evident for newer erasure codes, including SD and LRC codes. To address these limitations, this article introduces the Partitioned and Parallel Matrix (PPM) algorithm. This algorithm partitions the parity-check matrix, parallelizes encoding/decoding operations, and optimizes calculation sequence to facilitate fast encoding/decoding of these codes. Furthermore, we present a generalized PPM (gPPM) algorithm that surpasses PPM in performance by employing fine-grained dynamic matrix calculation sequence selection. Unlike PPM, gPPM is also applicable to erasure codes such as RS code. Experimental results demonstrate that PPM improves the encoding/decoding speed of SD and LRC codes by up to 210.81%. Besides, gPPM achieves up to 102.41% improvement over PPM and 32.25% improvement over RS regarding encoding/decoding speed.
A Case for Amplifying Row Hammer Attacks via Cell-Coupling in DRAM Devices

Main memory technologies have been largely dominated by Dynamic Random Access Memory (DRAM) for several decades. However, the recurring issue of higher latency has compelled researchers to propose In-DRAM based caching techniques. In-DRAM caches have become a popular research topic in recent years as they offer significant improvements over conventional DRAM devices. With every generation, DRAM devices are engineered to be denser. This has caused the emergence of electromagnetic interference within the device, known as row hammering, which causes flipping of bits without accessing the bits. Our work demonstrates the existence of a new and amplified row hammer attack, which, we term as double row hammer attack. It poses a simultaneous threat to both the DRAM array and the In-DRAM cache. We then propose an In-DRAM caching technique, called CRATAR, which can detect the aforementioned malicious memory pattern. Mitigating row hammer attacks impose some blocking time on the DRAM device. CRATAR is designed in a way that it mitigates double row hammer attacks in the most optimal time possible. Overall, we gain an average performance improvement of 6.74% over a conventional DDR4 DRAM. It reduces 24.71% blocking time previously imposed during mitigating row hammer attacks at the meager storage overhead of 3.88 KB.
DEVIL peptides control cell growth and differentiation in different developmental processes

The DEVIL/ROTUNDIFOLIA-LIKE (DVL/RTFL) family of plant peptides is present in all land plants, but their biological role and mode of action remains largely unknown, in part due to the lack of reported phenotypes associated to DVL/RTFL loss of function. In this work we have generated high order mutants and characterized their phenotypes in reproductive development. Our results indicate that dvl mutants are affected in cell elongation processes, mainly related to pollen tube growth, and they appear to provide robustness to these processes. We also show that DVL peptides may act in different domains to those where the corresponding genes are transcribed, suggesting a putative role in the coordination of organ growth by participating in cell-to-cell communication.
RapTCR: Rapid exploration and visualization of T-cell receptor repertoires

Motivation The acquisition of T-cell receptor (TCR) repertoire sequence data has become faster and cheaper due to advancements in high-throughput sequencing. However, fully exploiting the diagnostic and clinical potential within these TCR repertoires requires a thorough understanding of the inherent repertoire structure. Hence, visualizing the full space of TCR sequences could be a key step towards enabling exploratory analysis of TCR repertoire, driving their enhanced interrogation. Nonetheless, current methods remain limited to rough profiling of TCR V and J gene distributions. Addressing this need, we developed RapTCR, a tool for rapid visualization and post-analysis of TCR repertoires. Approach To overcome computational complexity, RapTCR introduces a novel, simple embedding strategy that represents TCR amino acid sequences as short vectors while retaining their pairwise alignment similarity. RapTCR then applies efficient algorithms for indexing these vectors and constructing their nearest neighbor network. It provides multiple visualization options to map and interactively explore a TCR network as a two-dimensional representation. Benchmarking analyses using epitope-annotated datasets demonstrate that these RapTCR visualizations capture TCR similarity features on a global level (e.g., J gene) and locally (e.g., epitope reactivity). RapTCR is available as a Python package, implementing the intuitive scikit-learn syntax to easily generate insightful, publication-ready figures for TCR repertoires of any size. Availability and Implementation RapTCR was written in Python 3. It is available as an anaconda package (https://anaconda.org/vincentvandeuren/raptcr), and on github (https://github.com/vincentvandeuren/RapTCR). Documentation and example notebooks are available at vincentvandeuren.github. io/rapTCR_docs/. Contact pieter.meysman@uantwerpen.be
Transcriptomic signatures of Aβ- and tau-induced neuronal dysfunction reveal inflammatory processes at the core of Alzheimer’s disease pathophysiology

Molecular mechanisms enabling pathology-induced neuronal dysfunction in Alzheimer’s disease (AD) remain elusive. Here, we use mechanistic computational models to infer the combined influence of PET-measured Aβ and tau burdens on fMRI-derived neuronal activity and to subsequently identify the transcriptomic spatial correlates of AD pathophysiology. Our results reveal overrepresented genes and biological processes that participate in synaptic degeneration and interact with Aβ and tau deposits. Furthermore, we confirmed the central role of the immune system and neuroinflammatory pathways within AD pathogenesis; microglia were significantly enriched in the gene set associated with Aβ and tau synergistic influences on neuronal activity. Lastly, our computational approach unveiled drug candidates with the potential to halt or reduce the observed pathological effects on neuronal activity, including existing medication for cancer, immune disorders, and cardiovascular diseases, many currently under clinical evaluation in AD. Overall, these findings support the notion that the AD brain experiences functional changes intricately associated with a diverse spectrum of molecular processes.
Practical Implementation of Computational Tactical Metrics for the Football Game Towards an Augmenting Perception of Coaches and Sport Analysts

Novel estimation, detection and identification techniques have been recently applied on sports, providing the cartesian positional information of players over time. This information has been seen as vital within sports sci- ence's literature, so as to propose new computational tactical metrics that may allow to inspect the spatio-temporal relationship between teammates. Such technological approaches can improve the understanding of the collective match, providing to coaches and analysts a real-time augmented perception of the game. In spite of this, this study aims to identify, and computational de- scribe, the most promising tactical metrics developed over the last few years and characterize their practical applications. Moreover, a technological ap- proach that integrates these metrics will be discussed, focusing on the data re- trieval, processing and visualization. Therefore, concepts such as Augmented Reality, Cloud Computing and Human-computer Interaction are considered to give the first steps toward a football game analysis system.
NOLLA: Non-Linear Outer Loop Link Adaptation for Enhancing Wireless Link Transmission

Modern wireless systems require strict key performance indicators (KPIs), such as very high reliability and throughput. Link adaptation (LA) is a core technology used to achieve these targets, with outer loop link adaptation (OLLA) being the most commonly used algorithm due to its feasibility and simplicity. OLLA uses a term called backoff factor to correct the signal to interference and noise ratio (SINR) estimate mapped from channel state information (CSI) to obtain an effective SINR. Based on the effective SINR, modulation and coding scheme (MCS) will be selected. OLLA adjusts the backoff factor with respect to hybrid automatic repeat request (HARQ) in a linear manner. However, this leads to effective SINR fluctuation and quite often results in overestimation. Hence, the performance of the system will be degraded. In this work, we propose a novel algorithm which introduces an adaptive adjustment step size for the backoff factor using an exponentially decaying factor to alleviate this issue. Since the backoff factor is not adjusted in a linear manner like OLLA, we call the proposed novel algorithm non-linear outer loop link adaptation (NOLLA). NOLLA can be regarded as an extension of OLLA that retains low complexity and high feasibility, providing the possibility to improve the link transmission in an uncomplicated way. Numerical evaluations demonstrate that NOLLA achieves higher reliability and throughput in scenarios with and without interference.
Hydroxyapatite/superparamagnetic iron oxide nanoparticles nanocomposite for Congo red adsorption

In this work, a nanostructural composite based on the superparamagnetic iron oxide nanoparticles (SPIONs) coated with hydroxyapatite (HAp) was demonstrated as an effective adsorbent for the removal of the Congo red (CR) from aqueous solutions. Prior to its application on the model pollutant, the morphology, crystallinity, specific surface area, chemical composition, and magnetic properties were characterized with several techniques, including scanning electron microscopy, transmission electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, Brunauer–Emmett– Teller, and vibrating sample magnetometer. Amongst composites synthesized in different ratios of SPION’s weight, the composite containing 35 wt. % of SPION was chosen to adsorb CR. The magnetization saturation of the latter was about 20.39 emu·g –1 , still enough for magnetic separation. The effect of adsorbent mass, pH, initial concentration, temperature, and contact time on the adsorption efficiency and capacity of CR was evaluated using UV-Vis spectrometry. It was shown that the most effective results of CR removal were achieved for 0.10 g dosage of SPION/HAp to absorb 50 mL of CR solution of 50 mg·L –1 at pH 0 and a contact time of 4 h. The CR adsorption process on SPION/ HAp composite is matched with the pseudo-second-order kinetic model and the Langmuir model. The obtained thermodynamic parameters (Δ G ° > 0, Δ H ° = –39.02 kJ·mol –1 , Δ S ° = –0.134 kJ·mol –1 ·K –1 ) suggest that the adsorption of CR onto the composite is non-spontaneous, exothermic, with a rising of randomness at the adsorbate–adsorbent interface. The maximum CR adsorption capacity using the SPION/HAp adsorbent was determined to be 158.98 mg·g –1 , suggesting that the adsor-bent has a satisfactory potential to adsorb CR. The chosen composite can be easily separated using magnets, making it a promising material for wastewater treatment.
Badantam Traditions in Marriage in Korong Koto Rajo Nagari Sunur Tengah, Nan Sabaris District, Padang Pariaman Regency

This thesis is entitled "Badantam Traditions in Marriage in Korong Koto Rajo Nagari Sunur Tengah, Nan Sabaris District, Padang Pariaman Regency". The purpose of this study was to find out the background to the emergence of the Badantam tradition and the function of the Badantam tradition in Korong Koto Rajo Nagari Sunur Tengah, Nan Sabaris District, Padang Pariaman Regency. The theory used in this final project is Malinowski's theory of functionalism. The method that the writer uses is a qualitative method, with data collection techniques namely observation, interviews and documentation. The results of the study found that the background to the emergence of the Badantam tradition was economic limitations. Due to the low economic status of the community, this led to the birth of the Badantam in the life of the Korong Koto Rajo Nagari Sunur Tengah community which aims to help with the cost of carrying out the wedding. The functions of this Badantam tradition are as follows: 1) economic function, 2) function as a gathering place, 3) function of cultural inheritance.
Bony Fish Arachidonic Acid 15-Lipoxygenases Exhibit Different Catalytic Properties than Their Mammalian Orthologs, Suggesting Functional Enzyme Evolution during Vertebrate Development

The human genome involves six functional arachidonic acid lipoxygenase (ALOX) genes and the corresponding enzymes (ALOX15, ALOX15B, ALOX12, ALOX12B, ALOXE3, ALOX5) have been implicated in cell differentiation and in the pathogenesis of inflammatory, hyperproliferative, metabolic, and neurological disorders. In other vertebrates, ALOX-isoforms have also been identified, but they occur less frequently. Since bony fish represent the most abundant subclass of vertebrates, we recently expressed and characterized putative ALOX15 orthologs of three different bony fish species (Nothobranchius furzeri, Pundamilia nyererei, Scleropages formosus). To explore whether these enzymes represent functional equivalents of mammalian ALOX15 orthologs, we here compared a number of structural and functional characteristics of these ALOX-isoforms with those of mammalian enzymes. We found that in contrast to mammalian ALOX15 orthologs, which exhibit a broad substrate specificity, a membrane oxygenase activity, and a special type of dual reaction specificity, the putative bony fish ALOX15 orthologs strongly prefer C20 fatty acids, lack any membrane oxygenase activity and exhibit a different type of dual reaction specificity with arachidonic acid. Moreover, mutagenesis studies indicated that the Triad Concept, which explains the reaction specificity of all mammalian ALOX15 orthologs, is not applicable for the putative bony fish enzymes. The observed functional differences between putative bony fish ALOX15 orthologs and corresponding mammalian enzymes suggest a targeted optimization of the catalytic properties of ALOX15 orthologs during vertebrate development.
Potencial genético de populações de milho tropicais, mistas e temperadas avaliadas em ambientes tropicais

As populações de milho possuem grande importância para o melhoramento genético, como fonte de alelos e variabilidade genética. Dessa forma, a introdução e adaptação de germoplasma exótico é uma estratégia para aumentar a base genética do programa. O objetivo deste estudo foi avaliar o potencial genético de populações de milho tropicais, mistas e temperadas em ambientes tropicais de cultivo. Para isso, 15 populações de milho tropicais, mistas e temperadas foram avaliadas per se e com base em progênies em dois locais de Minas Gerais. Na avaliação per se, utilizou-se o delineamento experimental de blocos ao acaso, com três repetições e na avaliação de progênies, o delineamento experimental de blocos incompletos (alfa látice), com duas repetições. Na avaliação de populações per se cada parcela foi constituída por duas linhas de 5m, e na avaliação de progênies, por uma linha de 4m, espaçadas em 0,80m. Os caracteres avaliados foram: dias até o florescimento masculino (FM, dias) e feminino (FF, dias) , altura de planta (AP, cm), espiga (AE, cm) e produtividade de grãos (PG, kg ha-1). Os dados da avaliação per se foram submetidos a análise de variância e as médias das populações comparadas pelo teste de Fisher. Em relação as progênies, usou-se modelos mistos implementado no pacote do R “lme4” para estimar os componentes de variância e predizer os valores genotípicos de cada progênie. Foi predito o ganho genético pela seleção das 20 melhores progênies através da seleção truncada para PG e seleção simultânea para FF e PG. A seleção foi realizada com base na média dos dois ambientes e com base no valor individual de cada ambiente. Houve efeito de populações (P<0,01) no experimento per se. As populações tropicais apresentaram desempenho superior às populações mistas, seguidas pelas populações tropicais adaptadas aos ambientes temperados e temperadas. Nos experimentos de progênies, observou-se efeito de progênies (P<0,01) para todos os caracteres em todas as populações. A interação progênies por ambientes (GxA) foi não significativa para todos os caracteres na maioria dos experimentos. Os ganhos preditos pela seleção truncada para PG foram de alta magnitude para o caractere em seleção para todos os experimentos. Enquanto, os ganhos preditos pelo índice, foram altos para PG e equilibrados para os demais caracteres. Conclui-se que as populações apresentam variabilidade genética e que a seleção pelo índice é a melhor estratégia para reduzir ciclo e aumentar PG. Além disso, as populações FS8A(S) e FS8B(S) apresentam potencial para melhoramento per se, enquanto as populações tropicais adaptadas ao ambiente temperado e as temperadas devem ser avaliadas em cruzamentos. Palavras-chave: Zea mays L. Seleção recorrente. Introdução de germoplasma.
Modeling and Evaluation of Oxy-Combustion and In Situ Oxygen Production in a Two-Stroke Marine Engine

Considering the concerns for emissions reduction in the maritime sector, the present paper evaluates, through modeling and simulation, oxy-fuel combustion in a two-stroke ship engine (2SE) and the best production system configuration to obtain the required oxygen (O2). An initial model of a ship engine is calibrated with the engine manufacturer’s data and then adapted to work with O2 as the oxidant to eliminate nitrogen oxide (NOx) emissions and with exhaust gas recirculation (EGR) to control the in-cylinder combustion temperature. Mixed Ionic–Electronic Conducting (MIEC) membranes produce the necessary O2 from the ambient air, which is heated up and pressurized by a heat exchanger and turbocharging coupled system to provide the air conditions required for the proper operation of the MIEC. Several layouts of this system are evaluated for the full load engine operating point to find the optimum O2 production system configuration. Results reveal that the engine operating under oxy-fuel combustion conditions avoids NOx emissions at the expense of higher brake-specific fuel consumption (BSFC) to obtain the original brake torque, and also expels a stream composed exclusively of CO2 and H2O, which facilitates the separation of CO2 from exhaust gases.
World's Science, Technology & Medicine Open Access book publisher

This book presents new aspects and technologies for the applicability of soybean and soybean products in industry (human food, livestock feed, oil and biodiesel production, textile, medicine) as well as for future uses of some soybean sub-products. The contributions are organized in two sections considering soybean in aspects of food, nutrition and health and modern processing technologies. Each of the sections covers a wide range of topics. The authors are from many countries all over the world and this clearly shows that the soybean research and applications are of global significance.