Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical Aspects of Viral Membrane Fusion

Enveloped viruses commonly employ membrane fusion during cell penetration in order to deliver their genetic material across the cell boundary. Large conformational changes in the proteins embedded in the viral membrane play a fundamental role in the membrane fusion process. Despite the tremendously wide variety of viruses that contain membranes, it appears that they all contain membrane fusion protein machinery with a remarkably conserved mechanism of action. Much of our current biochemical understanding of viral membrane fusion has been derived from high-resolution structural studies and solution-based in vitro assays in which viruses fuse with liposomes or cells. Recently, single-particle experiments have been used to provide measurements of details not available in the bulk assays. Here we focus our discussion on the key dynamical aspects of fusion protein structure, along with some of the experimental and computational techniques presently being used to investigate viral-mediated membrane fusion.
Understanding Practical Tradeoffs in HPC Checkpoint-Scheduling Policies

As the scale of High-Performance Computing (HPC) clusters continues to grow, their increasing failure rates and energy consumption levels are emerging as serious design concerns. Efficiently running systems at such large scales critically relies on deploying effective, practical methods for fault tolerance while having a good understanding of their respective performance and energy overheads. The most commonly used fault tolerance method is checkpoint/restart. Checkpoint scheduling policies, however, have been traditionally optimized and analysed from one angle: application performance. In this work, we provide an extensive analysis of the performance, energy and I/O costs associated with a wide array of checkpointing policies. We consider practical deployment issues and show that simple formulas can be used to accurately estimate wasted work in a system. We propose methods to optimize checkpoint scheduling for energy savings and evaluate the runtime-optimized and energy-optimized policies using simulations based on failure logs from 10 production HPC clusters. Our results show ample room for achieving high quality energy/performance tradeoffs when using methods that exploit characteristics of real world failures. We also analyze the impact of energy-optimized checkpointing on the storage subsystem and identify policies that are optimal for I/O savings.
miR-148a suppresses cell invasion and migration in gastric cancer by targeting DNA methyltransferase 1

Gastric cancer (GC) is the fourth most common malignant tumor globally. The highest incidence of GC is found in Eastern Asia, particularly in China. It is therefore imperative to further elucidate the molecular pathogenesis of GC in order to identify new biomarkers and targets for effective therapy. In the present study, we determined whether miR-148a was aberrantly downregulated in gastric cancer tissues and significantly correlated with aggressive clinicopathological characteristics in the MGC-803, HGC-27 and GES-1 cell lines using reverse transcription-quantitative PCR and western blot analysis. The cell lines were obtained from 60 patients who presented at our hospital between September 2010 and July 2015. The results showed that, miR-148a was aberrantly downregulated in GC tissues and its expression was relatively lower in the MGC-803 and HGC-27 GC cell lines than in the normal gastric epithelial cell line, GES-1. The clinicopathological analysis revealed that a decrease of miR-148a was significantly correlated with lymph-node metastasis (P<0.01) and tumor node metastasis (TNM) stage (P<0.05). The transwell assay showed that the re-expression of miR-148a significantly reduced cell migratory and invasive abilities in vitro (P<0.01). The luciferase assay confirmed that, DNA methyltransferase 1 (DNMT1) was a direct and functional target of miR-148a. The miR-148a inhibitor increased the expression of DNMT1 in HGC-27 cells and the re-expression of miR-148a reduced the expression of DNMT1 in MGC-803 cells as confirmed by western blot analysis. Furthermore, we found that the re-expression of DNMT1 reversed the inhibition of cell migration and invasion induced by miR-148a. Taken together, we demonstrated that miR-148a suppresses cell invasion and migration in gastric cancer by regulating DNMT1 expression. The miR-148a/DNMT1 axis may therefore be a new potential target for GC therapy.
A flash memory controller for 15μs ultra-low-latency SSD using high-speed 3D NAND flash with 3μs read time

In a memory hierarchy, there are various classes of memory systems depending on the access latency. A typical memory hierarchy consists of a CPU cache, DRAM, and an SSD or HDD. The DRAM has an access latency of 100ns, while flash memory has a latency of about 50μs [1]. Recently, new non-volatile memories with latencies of less than 10μs, including PRAM, MRAM, and ReRAM [2], are getting attention for business-critical systems such as big-data analysis and storage caches. To meet the low latency requirements, a new type of NAND flash, Z-NAND, with a read time (tR) of 3μs has also been introduced [3]. Figure 20.2. 1 shows a feature comparison between Z-NAND and conventional 3D NAND [4,5]. The Z-NAND achieves a read time of 3μs, which is 15–20 times faster than conventional NAND. Write throughput reaches up to 160MB/s with a 100μs program time. To further minimize read latency, I/O circuit support a DDR interface for both x8 and x16 mode. To take full advantage of such low-latency memory devices, reduction of memory access overhead is necessary. In this paper, we introduce an NVMe SSD controller which leverages the advantages of the low-latency NAND and enables the reduction of total memory access time, thereby minimizing overall system latency.
Management of community-acquired pneumonia in immunocompetent adults: updated Swedish guidelines 2017

Abstract Based on expert group work, Swedish recommendations for the management of community-acquired pneumonia in adults are here updated. The management of sepsis-induced hypotension is addressed in detail, including monitoring and parenteral therapy. The importance of respiratory support in cases of acute respiratory failure is emphasized. Treatment with high-flow oxygen and non-invasive ventilation is recommended. The use of statins or steroids in general therapy is not found to be fully supported by evidence. In the management of pleural infection, new data show favourable effects of tissue plasminogen activator and deoxyribonuclease installation. Detailed recommendations for the vaccination of risk groups are afforded.
Joint Uplink and Downlink Resource Allocation in Data and Energy Integrated Communication Networks

In this paper, we propose a joint power control strategy for both the uplink and downlink transmission by considering the energy requirements of the user equipments’ uplink data transmissions in data and energy integrated communication networks (DEINs). In DEINs, the base station (BS) adopts the power splitting (PS) aided simultaneous wireless information and power transfer (SWIPT) technique in the downlink (DL) transmissions, while the user equipments (UEs) carry out their own uplink (UL) transmissions by exploiting the energy harvested during the BS’s DL transmissions. In our DEIN model, there are M UEs served by the BS in order to fulfil both of their DL and UL transmissions. The orthogonal frequency division multiple access (OFDMA) technique is adopted for supporting the simultaneous transmissions of multiple UEs. Furthermore, a transmission frame is divided into N time slots in the medium access control (MAC) layer. The mathematical model is established for maximizing the sum-throughput of the UEs’ DL transmissions and for ensuring their fairness during a single transmission frame T , respectively. In order to achieve these goals, in each transmission frame T , we optimally allocate the BS’s power for each subcarrier and the PS factor for each UE during a specific time slot. The original optimisation problems are transformed into convex forms, which can be perfectly solved by convex optimisation theories. Our numerical results compare the optimal results by conceiving the objective of maximising the sum-throughput and those by conceiving the objective of maximising the fair-throughput. Furthermore, our numerical results also reveal the inherent tradeoff between the DL and the UL transmissions.
Entomological impact and social participation in dengue control: a cluster randomized trial in Fortaleza, Brazil

Background This study intended to implement a novel intervention strategy, in Brazil, using an ecohealth approach and analyse its effectiveness and costs in reducing Aedes aegypti vector density as well as its acceptance, feasibility and sustainability. The intervention was conducted from 2012 to 2013 in the municipality of Fortaleza, northeast Brazil. Methodology A cluster randomized controlled trial was designed by comparing ten intervention clusters with ten control clusters where routine vector control activities were conducted. The intervention included: community workshops; community involvement in clean-up campaigns; covering the elevated containers and in-house rubbish disposal without larviciding; mobilization of schoolchildren and senior inhabitants; and distribution of information, education and communication (IEC) materials in the community. Results Differences in terms of social participation, commitment and leadership were present in the clusters. The results showed the effectiveness of the intervention package in comparison with the routine control programme. Differences regarding the costs of the intervention were reasonable and could be adopted by public health services. Conclusions Embedding social participation and environmental management for improved dengue vector control was feasible and significantly reduced vector densities. Such a participatory ecohealth approach offers a promising alternative to routine vector control measures.
Global, Regional, and Megacity Trends in the Highest Temperature of the Year: Diagnostics and Evidence for Accelerating Trends

Trends in short‐lived high‐temperature extremes record a different dimension of change than the extensively studied annual and seasonal mean daily temperatures. They also have important socioeconomic, environmental, and human health implications. Here, we present analysis of the highest temperature of the year for approximately 9000 stations globally, focusing on quantifying spatially explicit exceedance probabilities during the recent 50‐ and 30‐year periods. A global increase of 0.19°C per decade during the past 50 years (through 2015) accelerated to 0.25°C per decade during the last 30 years, a faster increase than in the mean annual temperature. Strong positive 30‐year trends are detected in large regions of Eurasia and Australia with rates higher than 0.60°C per decade. In cities with more than 5 million inhabitants, where most heat‐related fatalities occur, the average change is 0.33°C per decade, while some east Asia cities, Paris, Moscow, and Houston have experienced changes higher than 0.60°C per decade.
Improving Summarization of Biomedical Documents Using Word Sense Disambiguation

We describe a concept-based summarization system for biomedical documents and show that its performance can be improved using Word Sense Disambiguation. The system represents the documents as graphs formed from concepts and relations from the UMLS. A degree-based clustering algorithm is applied to these graphs to discover different themes or topics within the document. To create the graphs, the MetaMap program is used to map the text onto concepts in the UMLS Metathe-saurus. This paper shows that applying a graph-based Word Sense Disambiguation algorithm to the output of MetaMap improves the quality of the summaries that are generated.
Utilization of a Wheat55K SNP Array for Mapping of Major QTL for Temporal Expression of the Tiller Number

Maximum tiller number and productive tiller number are important traits for wheat grain yield, but research involving the temporal expression of tiller number at different quantitative trait loci (QTL) levels is limited. In the present study, a population set of 371 recombined inbred lines derived from a cross between Chuan-Nong18 and T1208 was used to construct a high-density genetic map using a Wheat55K SNP Array and to perform dynamic QTL analysis of the tiller number at four growth stages. A high-density genetic map containing 11,583 SNP markers and 59 SSR markers that spanned 4,513.95 cM and was distributed across 21 wheat chromosomes was constructed. A total of 28 single environmental QTL were identified in the recombined inbred lines population, and among these, seven QTL were stable and used for multi-environmental and dynamic analysis. These QTL were mapped to chromosomes 2D, 4A, 4D, 5A, 5D, and 7D, respectively. Each QTL explained 1.63–21.22% of the observed phenotypic variation, with an additive effect from -20.51 to 11.59. Dynamic analysis showed that cqTN-2D.2 can be detected at four growth stages of tillering, explaining 4.92–17.16% of the observed phenotypic variations and spanning 13.71 Mb (AX-109283238-AX-110544009: 82189047-95895626) according to the physical location of the flanking markers. The effects of the stable QTL were validated in the recombined inbred lines population, and the beneficial alleles could be utilized in future marker-assisted selection. Several candidate genes for MTN and PTN were predicted. The results provide a better understanding of the QTL selectively expressing the control of tiller number and will facilitate future map-based cloning. 9.17% SNP markers showed best hits to the Chinese Spring contigs. It was indicated that Wheat55K Array was efficient and valid to construct a high-density wheat genetic map.
Biologically controlled crystal growth: the image-forming mirror in the eye of the scallop

Guanine crystals are found commonly in biological photonic systems (1) where they are responsible for the white color in certain spiders (2), the metallic silvery reflectance of fish scales (3, 4) and the brilliant iridescent colors of planktonic crustaceans (5, 6) and tropical fish (7). A wide range of different optical phenomena are produced by organisms "simply" by varying the size, morphology and arrangement of the guanine crystals. Organisms display an extraordinary ability to manipulate and control crystal growth producing crystal morphologies which are highly optimized for a particular optical function. The most complex of all these functions is in vision.
Reference Genes for Accurate Transcript Normalization in Citrus Genotypes under Different Experimental Conditions

Real-time reverse transcription PCR (RT-qPCR) has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus). We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family) and GAPC2 (GAPDH) was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin), TUB (tubulin) and CtP (cathepsin) were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein), GAPC2 and UPL7 (ubiquitin protein ligase 7) to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress.
The corpus‐predominant gastritis index can be an early and reversible marker to identify the gastric cancer risk of Helicobacter pylori‐infected nonulcer dyspepsia

Corpus‐predominant gastritis index (CGI) is an early histological marker to identify Helicobacter pylori‐infected gastric cancer relatives at risk of cancer. This study validated whether CGI is more prevalent in H. pylori‐infected nonulcer dyspepsia (NUD) subjects than in duodenal ulcer (DU) controls and whether it is reversible after H. pylori eradication or is correlated with noninvasive biomarkers.
Perampanel, an AMPA receptor antagonist: From clinical research to practice in clinical settings

Epileptic seizures are refractory to treatment in approximately one‐third of patients despite the recent introduction of many newer antiepileptic drugs (AEDs). Development of novel AEDs therefore remains a high priority. Perampanel is a first‐in‐class non‐competitive selective AMPA receptor antagonist with a unique mechanism of action. Clinical efficacy and safety of perampanel as adjunctive treatment for focal seizures with/without secondary generalization (±SG) and primary generalized tonic‐clonic (PGTC) seizures have been established in five phase 3 randomized controlled trials (RCTs), and a long‐term extension study, and perampanel is approved as monotherapy for focal seizures ±SG in the USA. In patients with focal seizures ±SG, add‐on perampanel resulted in median percent reduction in seizure frequency 23.3%‐34.5% and ≥50% responder rate 28.5%‐37.6%; in PGTC seizures, these results were 76.5% and 64.2%, respectively. Efficacy among adolescents (reduction in seizure frequency 34.8%‐35.6%; ≥50% responder rate 40.9%‐45.0%) and elderly people (reduction in seizure frequency 12.5%‐16.9%; ≥50% responder rate 22.2%‐42.9%) is similar to those in adults, and results remain comparable between Asian (reduction in seizure frequency 17.3%‐38.0%) and global populations. Perampanel has been extensively studied in real‐world clinical practice, with similar efficacy and safety results to the RCTs (≥50% responder rate 12.8%‐75.0%; adverse events of somnolence/sedation, dizziness, ataxia, and behavioral changes). Real‐world observational studies suggest that perampanel tolerability can be improved by slow titration (2 mg every 2‐4 weeks), and bedtime administration can mitigate somnolence and dizziness. Counseling about the potential for behavioral changes and close monitoring are recommended.
Methods to generate variable keys with noise burst bit in modern cryptosystem for achieving perfect security

Time variant key is a concept to generate new keys which vary during data transmission over time. Automatic Variable Key (AVK) is a time variant key generation technique. In this manuscript, we have proposed new key generation techniques with Noise Burst Bit based on already established variable key generation techniques. The proposed techniques provide maximum level of security as compared to those related existing techniques as the newly generated keys are more random. To verify the true randomness of the proposed techniques, we have tested the randomness of successive generated keys by using National Institute of Standards and Technology (NIST) statistical tool and proved that the generated keys are truly random.
Response by Lee et al to Letter Regarding Article, "Pioglitazone for Secondary Stroke Prevention: A Systematic Review and Meta-Analysis".

Liraglutide, semaglutide, and empagliflozin are antidiabetic drugs that have been proven in randomized controlled trials to have a beneficial effect at reducing the composite primary end point of major cardiovascular events (nonfatal myocardial infarction, nonfatal stroke, and cardiovascular death). 1–3 The benefits of long-acting glucagon-like peptide 1 (GLP-1) receptor agonists, such as liraglutide and semaglutide, are perhaps related to the modified progression of atherosclerotic vascular disease,4 whereas benefits of sodium-glucose cotransporter 2 (SGLT-2) inhibitors, such as empagliflozin, may be more closely linked to hemodynamic changes. These differences in postulated mechanisms of action may explain, …
Comparative Studies on the Physicochemical Characteristics of Popcorn And Groundnut Flour Fermented Using Pure Strains Of Rhizopus nigricans and Saccharomyces cerevisae

Proximate, elemental and anti-nutrient composition of fermented using Sacchromyces cerevisae and Rhizopus nigricans for 72 hours and unfermented groundnut and popcorn were carried out using standard methods of analysis. The proximate analysis results showed that crude protein, fat and crude fibre increased in fermented samples. Sodium, potassium and phosphorus were also found to increase in the fermented sample while anti-nutrient was found to decrease after fermentation. The result from the research work revealed that fermentation could be a very good method of enhancing nutritional benefit of food materials and could be utilized in food formulation.
Loss of Mhc and Neutral Variation in Peary Caribou: Genetic Drift Is Not Mitigated by Balancing Selection or Exacerbated by Mhc Allele Distributions

Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by comparing historical and contemporary samples. We observed that similar proportions of genetic variation were lost over time at each type of marker despite strong evidence for selection at Mhc genes. These results suggest that microsatellites can be used to estimate genome-wide levels of variation, but also that adaptive potential is likely to be lost following population bottlenecks. However, gene conversion and recombination at Mhc loci may act to increase variation following bottlenecks.
Physical activity and obesity in children

Globally, obesity is affecting an increasing proportion of children. Physical activity plays an important role in the prevention of becoming overweight and obese in childhood and adolescence, and reducing the risk of obesity in adulthood. Puberty and the following adolescent period are acknowledged as particularly vulnerable times for the development of obesity due to sexual maturation and, in many individuals, a concomitant reduction in physical activity. In many Western settings, a large proportion of children and adolescents do not meet recommended physical activity guidelines and, typically, those who are more physically active have lower levels of body fat than those who are less active. Active behaviours have been displaced by more sedentary pursuits which have contributed to reductions in physical activity energy expenditure. Without appropriate activity engagement there is an increased likelihood that children will live less healthy lives than their parents. Owing to the high risk of overweight adolescents becoming obese adults, the engagement of children and adolescents in physical activity and sport is a fundamental goal of obesity prevention.