Miracle-dz/UniFAR-FTUs huggingface dataset:
Concurrent Expression of Latent and a Limited Number of Lytic Genes with Immune Modulation and Antiapoptotic Function by Kaposi's Sarcoma-Associated Herpesvirus Early during Infection of Primary Endothelial and Fibroblast Cells and Subsequent Decline of Lytic Gene Expression

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) infection of in vitro target cells is characterized by the expression of the latency-associated open reading frame (ORF) 73 gene (LANA-1) and the absence of progeny virus production. This default latent infection can be switched into lytic cycle by phorbol ester and by the lytic cycle ORF 50 (RTA) protein. In this study, the kinetics of latent and lytic gene expression immediately following KSHV infection of primary human dermal microvascular endothelial (HMVEC-d) and foreskin fibroblast (HFF) cells were examined by real-time reverse transcriptase PCR and whole-genome array. Within 2 h postinfection (p.i.), high levels of ORF 50 transcripts were detected in both cell types, which declined sharply by 24 h p.i. In contrast, comparatively low levels of ORF 73 expression were detected within 2 h p.i. , increased subsequently, were maintained at a steady state, and declined slowly by 120 h p.i. The RTA and LANA-1 proteins were detected in the majority of infected cells by immunoperoxidase assays. In genome array, only 29 of 94 (31%) KSHV genes were expressed, which included 11 immediate-early/early, 8 early, and 5 late lytic genes and 4 latency-associated genes. While the expression of latent ORF 72, 73, and K13 genes continued, nearly all of the lytic genes declined or were undetectable by 8 and 24 h p.i. in HMVEC-d and HFF cells, respectively. Only a limited number of RTA-activated KSHV genes were expressed briefly, and the majority of KSHV genes involved in viral DNA synthesis and structural proteins were not expressed. However, early during infection, the lytic K2, K4, K5, K6, and vIRF2 genes with immune modulation functions and the K7 gene with antiapoptotic function were expressed. Expression of K5 was detected for up to 5 days of observation, and vIRF2 was expressed up to 24 h p.i. The full complement of lytic cycle genes were expressed when 12-O-tetradecanoylphorbol-13-acetate was added to the HMVEC-d cells after 48 h p.i. These data suggest that in contrast to alpha- and betaherpesviruses and some members of gammaherpesviruses, gamma-2 KSHV in vitro infection is characterized by the concurrent expression of latent and a limited number of lytic genes immediately following infection and a subsequent decline and/or absence of lytic gene expression with the persistence of latent genes. Expression of its limited lytic cycle genes could be a “strategy” that evolved in KSHV allowing it to evade the immune system and to provide the necessary factors and time to establish and/or maintain latency during the initial phases of infection. These are unique observations among in vitro herpesvirus infections and may have important implications in KSHV biology and pathogenesis.
Food Insecurity and Hunger in Rich Countries—It Is Time for Action against Inequality

Household food insecurity is a serious public health concern in rich countries with developed economies closely associated with inequality. The prevalence of household food insecurity is relatively high in some developed countries, ranging from 8 to 20% of the population. Human rights approaches have the potential to address the structural causes, not just the symptoms of food insecurity. Despite most developed countries ratifying the Covenant on Economic, Social and Cultural Rights over 40 years ago, food insecurity rates suggest current social protections are inadequate. The contemporary framing of the solution to food insecurity in developed countries is that of diverting food waste to the hungry to meet the United Nations Sustainable Development Goals agenda (Goals 2 and 12.3). An estimated 60 million people or 7.2% of the population in high income countries used food banks in 2013. Although providing food assistance to those who are hungry is an important strategy, the current focus distracts attention away from the ineffectiveness of government policies in addressing the social determinants of food insecurity. Much of the action needed to improve household food security falls to actors outside the health sector. There is evidence of promising actions to address the social determinants of food insecurity in some developed countries. Learning from these, there is a strong case for government leadership, for action within and across government, and effective engagement with other sectors to deliver a coordinated, collaborative, and cooperative response to finding pathways out of food insecurity.
Connected and Automated Vehicles: Chances for Elderly Travellers

Connected and automated vehicles (CAV) are expected to improve the mobility of older people by compensating for the effects of a decreasing age-related fitness to drive. However, the technology is still under development and it is unclear how automated transport services will be implemented and which effects will be achievable. This paper aims to assess the potential of connected and automated transport to improve the mobility of older people. The discussion focuses on potentially disrupting highly automated services; in addition, general effects on the transport system and quality of life influenced by the increased mobility of older people are considered. Based on findings from mobility behavior research and studies exploring the mobility barriers of older people, the current mobility gaps are systematically analyzed on external barriers (availability of transport and related information) and 3 different internal barrier levels: access (physical limitations), ability (skills and know-how), and acceptance (experiences and symbolic meaning associated with a service). Subsequently, the potential of CAV to bridge these gaps is assessed. The results show that CAV can mitigate several of the barriers experienced by older people, especially barriers related to motor, sensory, and cognitive limitations. For other gaps, such as socioeconomic, usability, or acceptance issues, the potential benefits strongly depend on the way CAV are implemented and how the transformation takes place. Additionally, improvement of the mobility of older people by car can also have negative effects on their health and well-being, as physical activities like walking and social relations like receiving support from others may decline. In general, the introduction of CAV shows significant potential to improve the mobility of elderly travelers. However, the role automated services will take over in the future transport system can also bear some risks, especially if automated cars are used excessively. A comprehensive design of future transport systems is required to define the role of automated services in order to target the current supply gaps and improve the quality of life of transport-disadvantaged groups while avoiding unduly traffic growth.
Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network

Lactic acid bacteria are Gram-positive bacteria used throughout the world in many industrial applications for their acidification, flavor and texture formation attributes. One of the species, Lactococcus lactis, is employed for the production of fermented milk products like cheese, buttermilk and quark. It ferments lactose to lactic acid and, thus, helps improve the shelf life of the products. Many physiological and transcriptome studies have been performed in L. lactis in order to comprehend and improve its biotechnological assets. Using large amounts of transcriptome data to understand and predict the behavior of biological processes in bacterial or other cell types is a complex task. Gene networks enable predicting gene behavior and function in the context of transcriptionally linked processes. We reconstruct and present the gene co-expression network (GCN) for the most widely studied L. lactis strain, MG1363, using publicly available transcriptome data. Several methods exist to generate and judge the quality of GCNs. Different reconstruction methods lead to networks with varying structural properties, consequently altering gene clusters. We compared the structural properties of the MG1363 GCNs generated by five methods, namely Pearson correlation, Spearman correlation, GeneNet, Weighted Gene Co-expression Network Analysis (WGCNA), and Sparse PArtial Correlation Estimation (SPACE). Using SPACE, we generated an L. lactis MG1363 GCN and assessed its quality using modularity and structural and biological criteria. The L. lactis MG1363 GCN has structural properties similar to those of the gold-standard networks of Escherichia coli K-12 and Bacillus subtilis 168. We showcase that the network can be used to mine for genes with similar expression profiles that are also generally linked to the same biological process.
Aptasensor based optical detection of glycated albumin for diabetes mellitus diagnosis

Glycated albumin (GA) has been reported as an important biomarker for diabetes mellitus. This study investigates an optical sensor comprised of deoxyribonucleic acid (DNA) aptamer, semiconductor quantum dot and gold (Au) nanoparticle for the detection of GA. The system functions as a ‘turn on’ sensor because an increase in photoluminescence intensity is observed upon the addition of GA to the sensor. This is possibly because of the structure of the DNA aptamer, which folds to form a large hairpin loop before the addition of the analyte and is assumed to open up after the addition of target to the sensor in order to bind to GA. This pushes the quantum dot and the Au nanoparticle away causing an increase in photoluminescence. A linear increase in photoluminescence intensity and quenching efficiency of the sensor is observed as the GA concentration is varied between 0–14 500 nM. Time based photoluminescence studies with the sensor show the decrease in binding rate of the aptamer to the target within a specific time period. The sensor was found to have a higher selectivity towards GA than other control proteins. Further investigation of this simple sensor with greater number of clinical samples can open up avenues for an efficient diagnosis and monitoring of diabetes mellitus when used in conjunction with the traditional method of glucose level monitoring.
Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae)

Abstract This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of Pisum viz. P. fulvum and P. sativum and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of Pisum chloroplast genomes. It was found that GC content was lower than AT content in the genes. Low synonymous codon usage order (SCUO) values of genes indicated low CUB in chloroplast genes of Pisum species. Heatmaps showed positive correlations of GC3 with all the GC and AT ending codons. Neutrality plot analysis revealed that natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes in these two taxa. Positive correlation between SCUO and mRNA free energy (mFE) suggested that higher energy release by entire mRNA was related to high degree of CUB. Further, highly significant (p < .01) negative correlation was found between parameters in pair i.e. mFE-GC, mFE-GC1, mFE-GC2 and mFE for entire mRNA-GC3. This pointed out that higher GC content might have influenced lesser energy release by mRNA molecules of chloroplast genes.
New biphenanthrenes with butyrylcholinesterase inhibitory activitiy from Cremastra appendiculata

Abstract Encouraged by the in vitro potent inhibitory activity on butyrylcholinesterase (BChE) of 95% ethanol extract of Cremastra appendiculata (D. Don) Makino tubers, a further phytochemical investigation on C. appendiculata tubers was conducted, which led to the isolation of a pair of new biphenanthrene atropisomers, namely cremaphenanthrene F-G (1–2). Their structures were elucidated on the basis of extensive spectroscopic analyses and chemical method. It is the first time that biphenanthrene atropisomers have been isolated from the plant kingdom. Compound 1 showed potent BChE inhibitory effect with IC50 value of 14.62 ± 2.15 μM. Compound 2 exhibited weak BChE inhibitory effect with IC50 value of 79.56 ± 0.78 μM. Meanwhile, 1 and 2 were found to be inactive for acetylcholinesterase (AChE) inhibition. These findings suggested that compound 1 was a promising selective BChE inhibitor for AD prevention and treatment. Graphical Abstract
Risk Factors Influencing the Thickness and Stranding of Perinephric Fat of Mayo Adhesive Probability Score in Minimally Invasive Nephrectomy

Background Mayo adhesive probability (MAP) score, an accurate and reliable predictor of adherent perinephric fat (APF), consists of posterior perinephric fat thickness and perinephric fat stranding. The present study aimed to identify the potential clinical characteristics associated with these 2 variables to further our understanding of APF. Material/Methods Clinical data of 346 patients subjected to minimally invasive nephrectomy was collected within our prospectively maintained database, between January 2015 and December 2016. Radiological data was assessed by 2 readers in an independent blinded – to each other and APF patient status – fashion. Ordinal logistic regression analyses were performed to evaluate risk factors of posterior perinephric fat thickness and perinephric fat stranding. Results On multivariate analysis, posterior perinephric fat thickness was associated with older age (b=1.05 [range, 1.03–1.07], P<0.01); male gender (b=6.06 [3.18–11.54], P<0.01), and higher body mass index (BMI) (b=1.31 [1.21–1.41], P<0.01). Perinephric fat stranding was associated with older age (b=1.05 [1.02–1.07], P<0.01), male gender (b=3.64 [2.09–6.34], P<0.01) and history of diabetes (b=2.09 [1.24–3.52], P<0.01). MAP score was associated with older age (b=1.05 [1.03–1.07], P<0.01), male gender (b=5.07 [2.96–8.71], P<0.01), higher BMI (b=1.14 [1.07–1.21], P<0.01), history of diabetes (b=1.72 [1.06–2.78], P=0.03) and alcoholism (b=1.88 [1.10–3.20], P=0.02). Conclusions The current study highlights that different risk factors influence the posterior perinephric fat thickness and perinephric fat stranding. Posterior perinephric fat thickness was correlated with age, gender, and BMI, while perinephric fat stranding was associated with age, gender, and history of diabetes.
Klotho Protein Reduced the Expression of Matrix Metalloproteinase-1 (MMP-1) and Matrix Metalloproteinase-3 (MMP-3) in Fibroblasts from Patients with Pelvic Organ Prolapse (POP) by Down-Regulating the Phosphorylation of ERK1/2

Background Pelvic organ prolapse (POP) is due to age-related atrophy and the weakening of the tissues of the pelvic floor, with degradation of collagen and extracellular matrix (ECM) by metalloproteinases (MMPs). This study aimed to investigates the role of the age-related enzyme klotho, encoded by the KL gene, in cultured fibroblasts obtained from patients with POP and the levels of reactive oxygen species (ROS), interleukin-6 (IL-6), and MMPs. Material/Methods Pelvic floor fibroblasts were obtained from connective tissue from three patients with POP and three normal subjects. Cell proliferation and ROS production were measured using a cell counting kit-8 (CCK-8) assay and flow cytometry. Levels of interleukin-6 (IL-6), klotho, metalloproteinase-1 (MMP-1), MMP-3, extracellular signal-regulated kinases 1/2 (ERK1/2), and p-ERK1/2 were measured by enzyme-linked immunoassay (ELISA), quantitative real-time polymerase chain reaction (qRT-PCR), and Western blot. Results In cultured pelvic floor fibroblasts from patients with POP, the expression of klotho protein and klotho mRNA were significantly down-regulated in fibroblasts from patients with POP compared with normal fibroblasts. Klotho supplementation in cultured fibroblasts for patients with POP included increased cell growth, reduced expression of ROS reduction, and reduced the secretion of IL-6. Using qRT-PCR and Western blot, klotho supplementation of fibroblasts from patients with POP increased cell growth and reduced the levels of IL-6 and ROS in a dose-dependent way. Conclusions Klotho protein reduced the expression of MMP-1 and MMP-3 in fibroblasts from patients with POP by down-regulating the phosphorylation of ERK1/2.
Isolation of simian retroviruses closely related to human T‐cell leukemia virus by establishment of lymphoid cell lines from various non‐human primates

Simian retroviruses closely related to human T‐cell leukemia virus (HTLV) were isolated by establishing virus‐producing lymphoid cell lines from 7 species of non‐human primates. By co‐cultivation with human umbilical cord‐blood cells and/or in the presence of interleukin‐2, lymphoid cell lines were successfully established from the chimpanzee, African green monkey, pig‐tailed macaque, red‐faced macaque, Formosan monkey, Japanese monkey and bonnet monkey that had antibodies against HTLV antigens. These cell lines reacted with human sera of ATL patients and monoclonal antibodies against p19 and p24 of HTLV antigens. Cellular DNAs contained the provirus sequences homologous to HTLV‐I by Southern blot hybridization. Moreover, they produced extracellular type‐C virus particles and RNA‐dependent DNA polymerase. All of these lymphoid line cells had Tac antigen, interleukin‐2 receptor, and those of chimpanzee and red‐faced macaque had helper/inducer T‐cell markers, while those derived from African green monkey had suppressor/cytotoxic T‐cell markers. Furthermore, simian HTLV‐related viruses of pig‐tailed macaque, red‐faced macaque and Japanese monkey were transmitted to human lymphocytes on co‐cultivation.
Robust Transcriptional Response to Heat Shock Impacting Diverse Cellular Processes despite Lack of Heat Shock Factor in Microsporidia

We do not fully understand why some fungal species are able to grow at temperatures approaching mammalian body temperature. Nosema ceranae, a microsporidium, is a type of fungal parasite that infects honey bees and grows optimally at the colony temperature of 35°C despite possessing cellular machinery for responding to heat stress that is notably simpler than that of other fungi. We find that N. ceranae demonstrates a robust and broad response to heat shock. These results provide important insight into the stress responses of this type of fungus, allow new comparisons with other pathogenic fungi, and potentially enable the discovery of novel treatment strategies for this type of fungus. ABSTRACT The majority of fungal species prefer the 12° to 30°C range, and relatively few species tolerate temperatures higher than 35°C. Our understanding of the mechanisms underpinning the ability of some species to grow at higher temperatures is incomplete. Nosema ceranae is an obligate intracellular fungal parasite that infects honey bees and can cause individual mortality and contribute to colony collapse. Despite a reduced genome, this species is strikingly thermotolerant, growing optimally at the colony temperature of 35°C. In characterizing the heat shock response (HSR) in N. ceranae, we found that this and other microsporidian species have lost the transcriptional regulator HSF and possess a reduced set of putative core HSF1-dependent HSR target genes. Despite these losses, N. ceranae demonstrates robust upregulation of the remaining HSR target genes after heat shock. In addition, thermal stress leads to alterations in genes involved in various metabolic pathways, ribosome biogenesis and translation, and DNA repair. These results provide important insight into the stress responses of microsporidia. Such a new understanding will allow new comparisons with other pathogenic fungi and potentially enable the discovery of novel treatment strategies for microsporidian infections affecting food production and human health. IMPORTANCE We do not fully understand why some fungal species are able to grow at temperatures approaching mammalian body temperature. Nosema ceranae, a microsporidium, is a type of fungal parasite that infects honey bees and grows optimally at the colony temperature of 35°C despite possessing cellular machinery for responding to heat stress that is notably simpler than that of other fungi. We find that N. ceranae demonstrates a robust and broad response to heat shock. These results provide important insight into the stress responses of this type of fungus, allow new comparisons with other pathogenic fungi, and potentially enable the discovery of novel treatment strategies for this type of fungus.
Effects of an increased concentrate diet on rumen pH and the bacterial community in Japanese Black beef cattle at different fattening stages

This study evaluated the effects of increasing the proportion of concentrate in the diet on the rumen pH and bacterial community in Japanese Black beef cattle at different fattening stages. Six rumen-cannulated beef cattle were studied in the middle (Mid group, n=3, age 21–22 months) and late (Late group, n=3, age 31 months) fattening stages. The cattle were fed rice straw with control (CON period) or high-concentrate (HC period) diets for 14 consecutive days in each period. Rumen pH was measured continuously and the rumen fluids were collected on the last day of each period. The 24-hr mean and minimum rumen pH in the Mid group were significantly (P<0.05) lower during the HC period compared with the CON period, whereas those in the Late group were continuously low during both periods. In the Late group, the ruminal volatile fatty acid and lactic acid concentrations were significantly (P<0.05) higher during the HC period. During the HC period, the proportions of Prevotella and Caloramator were significantly (P<0.05) higher and lower, respectively, in the Mid group. From these findings, significant changes in the rumen pH and bacterial community induced by dietary changes were mainly observed in the Mid group. Therefore, the ruminal fermentative function in response to a higher concentrate diet might adapt differently in Japanese Black beef cattle at the two different fattening stages.
Optimal Outcome Measures, Research Priorities, and International Cooperation

&NA; The participants in the Eriksholm Workshop on “Measuring Outcomes in Audiological Rehabilitation Using Hearing Aids” debated three issues that are reported in this article. First, it was agreed that the characteristics of an optimal outcome measure vary as a function of the purpose of the measurement. Potential characteristics of outcome self‐report tools for four common goals of outcome measurement are briefly presented to illustrate this point. Second, 10 important research priorities in outcome measurement were identified and ranked. They are presented with brief discussion of the top five. Third, the concept of generating a brief universally applicable outcome measure was endorsed. This brief data set is intended to supplement existing outcome measures and to promote data combination and comparison across different social, cultural, and health‐care delivery systems. A set of seven core items is proposed for further study.
Empirical Characteristic Function Based Estimation of Multiple Scattering Channel Parameters

Multiple scattering propagation channel is a physically motivated generic model whose special cases include Rayleigh, Rice, double-Rayleigh and "leaky keyhole" channels. Estimation of the parameters of its amplitude distribution is still largely an unexplored problem. In this paper, several novel estimators based on the empirical characteristic (ECF) function are derived. The mathematical form of the considered signal model makes the ECF approach ideally suited for the estimation problem at hand, whereas the maximum-likelihood (ME) estimator is analytically and computationally intractable. Furthermore, it can be easily extended to other similar signal models. By simulations it is shown that the derived ECF estimators have at least as small mean square error as the previously proposed moment-based approaches