Miracle-dz/UniFAR-FTUs huggingface dataset:
Influenza Virus: A Master Tactician in Innate Immune Evasion and Novel Therapeutic Interventions

Influenza is a contagion that has plagued mankind for many decades, and continues to pose concerns every year, with millions of infections globally. The frequent mutations and recombination of the influenza A virus (IAV) cast a looming threat that antigenically novel strains/subtypes will rise with unpredictable pathogenicity and fear of it evolving into a pandemic strain. There have been four major influenza pandemics, since the beginning of twentieth century, with the great 1918 pandemic being the most severe, killing more than 50 million people worldwide. The mechanisms of IAV infection, host immune responses, and how viruses evade from such defensive responses at the molecular and structural levels have been greatly investigated in the past 30 years. While this has advanced our understanding of virus–host interactions and human immunology, and has led to the development of several antiviral drugs, they have minimal impact on the clinical outcomes of infection. The heavy use of these drugs has also imposed selective pressure on IAV to evolve and develop resistance. Vaccination remains the cornerstone of public health efforts to protect against influenza; however, rapid mass-production of sufficient vaccines is unlikely to occur immediately after the beginning of a pandemic. This, therefore, requires novel therapeutic strategies against this continually emerging infectious virus with higher specificity and cross-reactivity against multiple strains/subtypes of IAVs. This review discusses essential virulence factors of IAVs that determine sustainable human-to-human transmission, the mechanisms of viral hijacking of host cells and subversion of host innate immune responses, and novel therapeutic interventions that demonstrate promising antiviral properties against IAV. This hopefully will promote discussions and investigations on novel avenues of prevention and treatment strategies of influenza, that are effective and cross-protective against multiple strains/subtypes of IAV, in preparation for the advent of future IAVs and pandemics.
A balance of activity in brain control and reward systems predicts self-regulatory outcomes

Abstract Previous neuroimaging work has shown that increased reward-related activity following exposure to food cues is predictive of self-control failure. The balance model suggests that self-regulation failures result from an imbalance in reward and executive control mechanisms. However, an open question is whether the relative balance of activity in brain systems associated with executive control (vs reward) supports self-regulatory outcomes when people encounter tempting cues in daily life. Sixty-nine chronic dieters, a population known for frequent lapses in self-control, completed a food cue-reactivity task during an fMRI scanning session, followed by a weeklong sampling of daily eating behaviors via ecological momentary assessment. We related participants’ food cue activity in brain systems associated with executive control and reward to real-world eating patterns. Specifically, a balance score representing the amount of activity in brain regions associated with self-regulatory control, relative to automatic reward-related activity, predicted dieters’ control over their eating behavior during the following week. This balance measure may reflect individual self-control capacity and be useful for examining self-regulation success in other domains and populations.
Information Theoretic-Based Interpretation of a Deep Neural Network Approach in Diagnosing Psychogenic Non-Epileptic Seizures

The use of a deep neural network scheme is proposed to help clinicians solve a difficult diagnosis problem in neurology. The proposed multilayer architecture includes a feature engineering step (from time-frequency transformation), a double compressing stage trained by unsupervised learning, and a classification stage trained by supervised learning. After fine-tuning, the deep network is able to discriminate well the class of patients from controls with around 90% sensitivity and specificity. This deep model gives better classification performance than some other standard discriminative learning algorithms. As in clinical problems there is a need for explaining decisions, an effort has been carried out to qualitatively justify the classification results. The main novelty of this paper is indeed to give an entropic interpretation of how the deep scheme works and reach the final decision.
Environmental Transport of Emerging Human-Pathogenic Cryptosporidium Species and Subtypes through Combined Sewer Overflow and Wastewater

ABSTRACT The environmental transport of Cryptosporidium spp. through combined sewer overflow (CSO) and the occurrence of several emerging human-pathogenic Cryptosporidium species in developing countries remain unclear. In this study, we collected 40 CSO samples and 40 raw wastewater samples from Shanghai, China, and examined them by PCR and DNA sequencing for Cryptosporidium species (targeting the small subunit rRNA gene) and Giardia duodenalis (targeting the triosephosphate isomerase, β-giardin, and glutamate dehydrogenase genes) and Enterocytozoon bieneusi (targeting the ribosomal internal transcribed spacer) genotypes. Human-pathogenic Cryptosporidium species were further subtyped by sequence analysis of the 60-kDa glycoprotein gene, with additional multilocus sequence typing on the emerging zoonotic pathogen Cryptosporidium ubiquitum. Cryptosporidium spp. , G. duodenalis, and E. bieneusi were detected in 12 and 15, 33 and 32, and 37 and 40 CSO and wastewater samples, respectively, including 10 Cryptosporidium species, 3 G. duodenalis assemblages, and 8 E. bieneusi genotypes. In addition to Cryptosporidium hominis and Cryptosporidium parvum, two new pathogens identified in industrialized nations, C. ubiquitum and Cryptosporidium viatorum, were frequently detected. The two novel C. ubiquitum subtype families identified appeared to be genetic recombinants of known subtype families. Similarly, the dominant group 1 E. bieneusi genotypes and G. duodenalis subassemblage AII are known human pathogens. The similar distribution of human-pathogenic Cryptosporidium species and E. bieneusi and G. duodenalis genotypes between wastewater and CSO samples reaffirms that storm overflow is potentially a significant contamination source of pathogens in surface water. The frequent identification of C. ubiquitum and C. viatorum in urban wastewater suggests that these newly identified human pathogens may be endemic in China. IMPORTANCE Cryptosporidium spp. , Giardia duodenalis, and Enterocytozoon bieneusi are major waterborne pathogens. Their transport into surface water through combined sewer overflow, which remains largely untreated in developing countries, has not been examined. In addition, the identification of these pathogens to genotypes and subtypes in urban storm overflow and wastewater is necessary for rapid and accurate assessment of pathogen transmission in humans and transport in the environment. Data from this study suggest that, like untreated urban wastewater, combined sewer overflow is commonly contaminated with human-pathogenic Cryptosporidium, G. duodenalis, and E. bieneusi genotypes and subtypes, and urban storm overflow potentially plays a significant role in the contamination of drinking source water and recreational water with human pathogens. They also indicate that Cryptosporidium ubiquitum and Cryptosporidium viatorum, two newly identified human pathogens, may be common in China, and genetic recombination can lead to the emergence of novel C. ubiquitum subtype families.
Surface Morphology of Silicon Induced by Laser Ablation in Flowing Water

Underwater laser machining process has a high potential over the typical laser ablation to remove materials with less thermal damage occurring along the cut. However, the formations of vapor bubble and cut debris in water can substantially disturb the incident laser beam, thereby reducing the ablation performance. Instead of performing the ablation in still water, the flowing water technique was applied to flush away the cut debris and bubble generated. In this study, the effects of laser pulse energy, traverse speed and water flow rate on the cut surface roughness and heat-affected zone in the laser grooving of silicon were experimentally investigated and analyzed. The findings revealed that the cut surface roughness decreased with the increases in laser pulse energy and laser traverse speed. Though a higher water flow rate resulted in a rougher cut surface, the heat-affected zone can be minimized when the increased flow rate was applied.
A CNN universal chip in CMOS technology

This paper describes the design of a CNN universal chip in a standard CMOS technology. The core of the chip consists of an array of 32/spl times/32 completely programmable CNN cells. Input image can be loaded in optical or electrical form. Accuracy is in the range of 7-8 bit and cell density is of 33 cells/mm/sup 2/. <<ETX>>
Evaluation of MIC Strip Isavuconazole Test for Susceptibility Testing of Wild-Type and Non-Wild-Type Aspergillus fumigatus Isolates

ABSTRACT We evaluated the MIC Strip Isavuconazole test against EUCAST E.Def 9.3 by using 40 wild-type and 39 CYP51A mutant Aspergillus fumigatus strains. The strip full inhibition endpoint (FIE) and 80% growth inhibition endpoint were determined by two independent readers, reader 1 (R1) and R2. The essential (within ±0, ±1, and ±2 twofold dilutions) and categorical agreements were best with the FIE (for R1/R2, 42%/41%, 75%/73%, and 90%/89% for essential agreement, and 91.1%/92.4% categorical agreement, with 6.3/8.9% very major errors and 0/1.3% major errors, respectively). The MIC Strip Isavuconazole test with the FIE appears to be useful.
Autophagy and mitochondrial biogenesis impairment contribute to age‐dependent liver injury in experimental sepsis: dysregulation of AMP‐activated protein kinase pathway

Age is an independent risk factor of multiple organ failure in patients with sepsis. However, the age‐related mechanisms of injury are not known. AMPK is a crucial regulator of energy homeostasis, which controls mitochondrial biogenesis by activation of peroxisome proliferator‐activated receptor‐γ coactivator‐α (PGC‐1α) and disposal of defective organelles by autophagy. We investigated whether AMPK dysregulation might contribute to age‐dependent liver injury in young (2–3 mo) and mature male mice (11–13 mo) subjected to sepsis. Liver damage was higher in mature mice than in young mice and was associated with impairment of hepatocyte mitochondrial function, structure, and biogenesis and reduced autophagy. At molecular analysis, there was a time‐dependent nuclear translocation of the active phosphorylated catalytic subunits AMPKα1/α2 and PGC‐1α in young, but not in mature, mice after sepsis. Treatment with the AMPK activator 5‐amino‐4‐imidazolecarboxamide riboside‐1‐β‐D‐ribofuranoside (AICAR) improved liver mitochondrial structure in both age groups compared with vehicle. In loss‐of‐function studies, young knockout mice with systemic deficiency of AMPKα1 exhibited greater liver injury than did wild‐type mice after sepsis. Our study suggests that AMPK is important for liver metabolic recovery during sepsis. Although its function may diminish with age, pharmacological activation of AMPK may be of therapeutic benefit. —Inata, Y. , Kikuchi, S. , Samraj, R. S. , Hake, P. W. , O'Connor, M. , Ledford, J. R. , O'Connor, J., Lahni, P., Wolfe, V. , Piraino, G. , Zingarelli, B. Autophagy and mitochondrial biogenesis impairment contribute to age‐dependent liver injury in experimental sepsis: dysregulation of AMP‐activated protein kinase pathway. FASEB J. 32, 728–741 (2018). www.fasebj. org
Robust Visual Tracking via Semiadaptive Weighted Convolutional Features

In recent years, hierarchical features extracted from convolutional neural network (CNN) for robust visual tracking have been developed by several methods. As features from different layers characterize different information of target and are set fixed weighted parameters, the performance of traditional visual tracking methods based on CNN can be further improved. In this letter, we propose a novel online visual tracking method by using hierarchical convolutional features with semiadaptive weights. The responses from different layers are assessed by a novel loss function. It considers the log likelihood and the entropy term of each response. The layer with the lower loss value is set to a higher weight parameter and the layer with the higher loss value is set to a lower one. We further develop a target appearance pyramid to deal with the scale change and an online classifier to redetect targets in case of tracking failures. Extensive experiments on challenging videos demonstrate that our method can achieve better tracking results in terms of lower center location error and higher overlap rate.
Soybean-fragmented proteoglycans against skin aging

ABSTRACT Objective: The majority of age-dependent skin changes happen in the dermis layer inducing changes in skin collagen and in the proteoglycans. The main aim of this work is to study the efficacy of a Proteum serum, containing soybean-fragmented proteoglycans, against skin aging. Materials and methods: In vitro tests were performed to evaluate the Proteum serum ability on activating the production of collagen and proteoglycans. An in vivo long-term study was performed to determine the efficacy of the Proteum serum when applied on skin. Protection of healthy skin against detergent-induced dermatitis and the antioxidant properties of the applied Proteum serum were also studied. Results and discussion: The in vitro tests demonstrated that the Proteum serum was able to elevate the production of molecules which are essential for supporting the dermal extracellular matrix organization. These results were correlated by the in vivo measurements where a clear trend on improving the measured skin parameters due to the Proteum serum application was found. Conclusions: A beneficial effect of the Proteum serum was demonstrated with an improvement in the skin roughness and a reinforcement of the skin barrier function. Moreover, a significant protector effect on human stratum corneum against lipids peroxides (LPO) was demonstrated.
Convex Combined Adaptive Filtering Algorithm for Acoustic Echo Cancellation in Hostile Environments

Research into combined adaptive filters has been attracting considerable attention; the performance of which is generally superior to that of the individual component filters. Formulating an adaptive filtering algorithm to handle a range of cases can be very difficult, particularly in complicated scenarios. This paper applies a robust convex combination method to the problem of acoustic echo cancellation. According to the minimum mean square error criterion, we first derive the optimal combination factor for a combination adaptive filter with two component filters. Next, we provide an approximation method to the inaccessible optimal combination factor. Finally, we extend this approximated factor to a robust one so that it is applicable even in situations with strong a ambient impulsive noise (IN) and abrupt changes in the echo channel. To do this, we non-linearly transfer the approximated combination factor so that this combination factor exhibits less transient time during the adaptation process of the combination factor and a fewer fluctuations in its steady state. Moreover, we detect the presence of the strong ambient IN and force the combined system output mainly contributed by one of the two component adaptive filters which is less sensitive to the the strong IN. We adopted computer simulations combining two affine projection sign algorithms with different step sizes as an example. Simulation results show that the proposed method is superior to comparable algorithms in terms of the normalized mean squared deviation and echo return loss enhancement.
RAD‐seq linkage mapping and patterns of segregation distortion in sedges: meiosis as a driver of karyotypic evolution in organisms with holocentric chromosomes

Meiotic drive, the class of meiotic mechanisms that drive unequal segregation of alleles among gametes, may be an important force in karyotype evolution. Its role in holocentric organisms, whose chromosomes lack localized centromeres, is poorly understood. We crossed two individuals of Carex scoparia (Cyperaceae) with different chromosome numbers (2n = 33II = 66 × 2n = 32II = 64) to obtain F1 individuals, which we then self‐pollinated to obtain second‐generation (F2) crosses. RAD‐seq was performed for 191 individuals (including the parents, five F1 individuals and 184 F2 individuals). Our F2 linkage map based on stringent editing of the RAD‐seq data set yielded 32 linkage groups. In the final map, 865 loci were located on a linkage map of 3966.99 cM (linkage groups ranged from 24.39 to 193.31 cM in length and contained 5–51 loci each). Three linkage groups exhibit more loci under segregation distortion than expected by chance; within linkage groups, loci exhibiting segregation distortion are clustered. This finding implicates meiotic drive in the segregation of chromosome variants, suggesting that selection of chromosome variants in meiosis may contribute to the establishment and fixation of chromosome variants in Carex, which is renowned for high chromosomal and species diversity. This is an important finding as previous studies demonstrate that chromosome divergence may play a key role in differentiation and speciation in Carex.
Identification of genes related to chlamydospore formation in Clonostachys rosea 67‐1

Chlamydospores are specific structures that are of great significance to the commercialization of fungal biopesticides. To explore the genes associated with chlamydospore formation, a biocontrol fungus Clonostachys rosea 67‐1 that is capable of producing resistant spores under particular conditions was investigated by transcriptome sequencing and analysis. A total of 549,661,174 clean reads were obtained, and a series of differentially expressed genes potentially involved in fungal chlamydospore formation were identified. At 36 hr, 67 and 117 genes were up‐ and downregulated in C. rosea during chlamydospore production, compared with the control for conidiation, and 53 and 24 genes were up‐ and downregulated at 72 hr. GO classification suggested that the differentially expressed genes were related to cellular component, biological process, and molecular function categories. A total of 188 metabolism pathways were linked to chlamydospore production by KEGG analysis. Sixteen differentially expressed genes were verified by reverse transcription quantitative PCR, and the expression profiles were consistent with the transcriptome data. To the best of our knowledge, it is the first report on the genes associated with chlamydospore formation in C. rosea. The results provide insight into the molecular mechanisms underlying C. rosea sporulation, which will assist the development of fungal biocontrol agents.
Power Allocation in MISO Interference Channels with Stochastic CSIT

This paper considers multiuser interference channels in which the transmitters have imperfect channel state information (CSI) where CSI perturbations are modeled stochastically. Transmitters are assumed to be equipped with multiple antennas serving single-antenna receivers. Transmitters use pre-designed discrete codebooks for beamforming directions and dynamically (based on the available CSI) select the best set of beamformers from the given codebook. The objective is to perform optimal power allocation to different users while certain quality of service (QoS) guarantees are ensured for the users. Imposed by stochastic CSI uncertainties, guarantees provided for the QoS measures have a stochastic nature too. The primary focus is placed on the interference channels for which two power allocation problems are considered. The first problem minimizes power consumption subject to serving users at certain data rates and the second problem considers max-min rate allocation subject to given power budgets for the transmitters. The core step in formalizing these problems in mathematically tractable forms relies on using Bernstein approximation, which approximates and convexifies the non-convex stochastic guarantees by conservative convex and deterministic counterparts. For solving this resulting convex and deterministic optimization problem, a specialized version of the long-step logarithmic barrier cutting plane (LLBCP) algorithm is used. Effectiveness of the proposed solutions and comparisons with other existing methods are assessed via extensive simulation results.
Macrophage-Derived Extracellular Vesicles Induce Long-Lasting Immunity Against Hepatitis C Virus Which Is Blunted by Polyunsaturated Fatty Acids

Extracellular vesicles (EVs) are increasingly recognized as important mediators of intercellular communication. In this study, we aimed to further characterize the role of macrophage-derived EVs in immune responses against hepatitis C virus (HCV) and the potential of polyunsaturated fatty acids (PUFAs) to modulate this modality of innate immunity. To this end, EVs were isolated from interferon-stimulated macrophage cultures or from serum of patients with acute or chronic hepatitis C. EVs were characterized by electron microscopy, flow cytometry, RNA-sequencing, and Western blot analysis. The effect of EVs on replication of HCV was assessed in coculture models. Functional analyses were performed to assess the impact of PUFAs on EV-mediated antiviral immunity. We found that macrophages secreted various cytokines shortly after stimulation with type I and II IFN, which orchestrated a fast but short-lasting antiviral state. This rapid innate immune answer was followed by the production of macrophage-derived EVs, which induced a late, but long-lasting inhibitory effect on HCV replication. Of note, exposure of macrophages to PUFAs, which are important regulators of immune responses, dampened EV-mediated antiviral immune responses. Finally, EVs from patients with hepatitis C exhibited long-lasting antiviral activities during IFN therapy as well. The antiviral effect of EVs from Caucasian and Japanese patients differed, which may be explained by different nutritional uptake of PUFAs. In conclusion, our data indicate that macrophage-derived EVs mediate long-lasting inhibitory effects on HCV replication, which may bridge the time until efficient adaptive immune responses are established, and which can be blunted by PUFAs.
Cingulate Cortical Thickness and Dopamine Transporter (DAT1) Genotype in Children and Adolescents With ADHD

Objective: This study aimed to examine the influence of dopamine transporter gene (DAT1) 3’UTR genotype on cingulate cortical thickness in a large sample of children and adolescents with ADHD. Method: Brain MRIs were acquired from 46 ADHD patients with homozygosity for the 10-repeat allele and 52 ADHD patients with a single copy or no copy of the allele. The cingulate cortex of each MRI scan was automatically parceled into sulci and gyri as well as into Brodmann areas (BA). Results: There were no group differences in age, gender, full-scale intelligence quotient, symptom severity, treatment status, comorbidity, or mean overall cortical thickness. Sulcus/gyrus- and BA-based analyses revealed that patients homozygous for the 10-repeat allele showed significantly greater thickness in right cingulate gyrus and right BA 24 compared with 9-repeat carriers. Conclusion: These findings suggest that thickness of cingulate cortex is influenced by the presence of the 10-repeat allele in ADHD.