In Bacillus subtilis, the RicA (YmcA), RicF (YlbF), and RicT (YaaT) proteins accelerate the phosphorylation of the transcription factor Spo0A, contributing to genetic competence, sporulation, and biofilm formation, and are also essential for the correct maturation of several protein-encoding and riboswitch RNAs. These proteins form a stable complex (RicAFT) that carries two [4Fe-4S]+2 clusters. We show here that the complex is a 1:1:1 heterotrimer, and we present the X-ray crystal structures of a RicAF heterotetramer and of a RicA dimer. We also demonstrate that one of the Fe-S clusters (cluster 1) is ligated by cysteine residues donated exclusively by RicT and can be retained when the RicT monomer is purified by itself. Cluster 2 is ligated by C167 from RicT, by C134 and C146 located near the C terminus of RicF, and by C141 at the C terminus of RicA. These findings imply the following novel arrangement: adjacent RicT residues C166 and 167 ligate clusters 1 and 2, respectively, while cluster 2 is ligated by cysteine residues from RicT, RicA, and RicF. Thus, the two clusters must lie close to one another and at the interface of the RicAFT protomers. We also show that the cluster-ligating cysteine residues, and therefore most likely both Fe-S clusters, are essential for cggR-gapA mRNA maturation, for the regulation of ricF transcript stability, and for several Ric-associated developmental phenotypes, including competence for transformation, biofilm formation, and sporulation. Finally, we present evidence that RicAFT, RicAF, and RicA and the RicT monomer may play distinct regulatory roles in vivoIMPORTANCE The RicA, RicF, and RicT proteins are widely conserved among the firmicute bacteria and play multiple roles in Bacillus subtilis Among the phenotypes associated with the inactivation of these proteins are the inability to be genetically transformed or to form biofilms, a decrease in sporulation frequency, and changes in the stability and maturation of multiple RNA species. Despite their importance, the molecular mechanisms of Ric protein activities have not been elucidated and the roles of the two iron-sulfur clusters on the complex of the three proteins are not understood. To unravel the mechanisms of Ric action, molecular characterization of the complex and of its constituent proteins is essential. This report represents a major step toward understanding the structures of the Ric proteins, the arrangement and roles of the Fe-S clusters, and the phenotypes associated with Ric mutations.

Laboratory strains of Bacillus subtilis encode many alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to being encoded on the large, low-copy-number plasmid pBS32, which was lost during domestication. DNA damage triggers pBS32 hyperreplication and cell death in a manner that depends on ZpdN, but how ZpdN mediates these effects is unknown. Here, we show that ZpdN is a bona fide sigma factor that can direct RNA polymerase to transcribe ZpdN-dependent genes, and we rename ZpdN SigN accordingly. Rend-seq (end-enriched transcriptome sequencing) analysis was used to determine the SigN regulon on pBS32, and the 5' ends of transcripts were used to predict the SigN consensus sequence. Finally, we characterize the regulation of SigN itself and show that it is transcribed by at least three promoters: PsigN1 , a strong SigA-dependent LexA-repressed promoter; PsigN2 , a weak SigA-dependent constitutive promoter; and PsigN3 , a SigN-dependent promoter. Thus, in response to DNA damage SigN is derepressed and then experiences positive feedback. How cells die in a pBS32-dependent manner remains unknown, but we predict that death is the product of expressing one or more genes in the SigN regulon.IMPORTANCE Sigma factors are utilized by bacteria to control and regulate gene expression. Some sigma factors are activated during times of stress to ensure the survival of the bacterium. Here, we report the presence of a sigma factor that is encoded on a plasmid that leads to cellular death after DNA damage.

Little is known about the national colonoscopy volume in Asian countries. This study aimed to assess the national colonoscopy volume in Korea over a 12-year period on the basis of a nationwide population-based database.

BACKGROUND There is no previously published epidemiological study exploring the association between red blood cell distribution width (RDW) and mortality in patients with cardiogenic shock (CS). The aim of this study was to examine the association between RDW and the risk of all-cause mortality in these patients. MATERIAL AND METHODS We analyzed clinical data from the MIMIC-III V1.4 database. We collected data on each patient's demographic parameters, vital signs, laboratory parameters, vital signs, comorbidities, and scoring systems on ICU admission. Cox proportional hazards models were used to assess the association between RDW levels and the 30-day, 90-day, and 365-day mortality in patients with CS. RESULTS There were 1131 patients meeting inclusion criteria in our study. In multivariate analysis, following adjustment for age, sex, and ethnicity, higher RDW in tertiles and quintiles were all associated with increased risk of 30-day, 90-day, and 365-day all-cause mortality. Furthermore, after adjusting for more relevant confounders, RDW remained a significant predictor of risk of 30-day, 90-day, and 365-day mortality (tertile 3 versus tertile 1: HR, 95% CI: 1.66, 1.19-2.31; 1.73, 1.28-2.33; 1.80, 1.38-2.34). Similarly significant robust associations were found in RDW levels stratified by quintiles. CONCLUSIONS Higher RDW is associated with increased risk of all-cause mortality in critically ill patients with CS.

Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolithophore genus Gephyrocapsa with genomic analyses of extant species to assess the genetic processes underlying Pleistocene palaeontological patterns. We demonstrate that all modern diversity in Gephyrocapsa (including Emiliania huxleyi) originated in a rapid species radiation during the last 0.6 Ma, coincident with the latest of the three pulses of Gephyrocapsa diversification and extinction documented in the fossil record. Our evolutionary genetic analyses indicate that new species in this genus have formed in sympatry or parapatry, with occasional hybridisation between species. This sheds light on the mode of speciation during evolutionary radiation of marine phytoplankton and provides a model of how new plankton species form.

Cancer associated body wasting is the cause of physical disability, reduced tolerance to anticancer therapy and reduced survival of cancer patients and, similarly to cancer, its incidence is increasing. There is no cure for this clinical condition, and the pathophysiological process involved is largely unknown. Exercise training appears as the gold standard non-pharmacological therapy for the management of this wasting syndrome. Herein we used a lipidomics approach based on liquid chromatography coupled with high-resolution mass spectrometry (LC-HR-MS) to study the effect of exercise in the modulation of phospholipids profile of mitochondria isolated from gastrocnemius muscle of a pre-clinical model of urothelial carcinoma-related body wasting (BBN induced), submitted to 13 weeks of treadmill exercise after diagnosis. Multivariate analysis showed a close relationship between the BBN exercise group and both control groups (control sedentary and control exercise), while the BBN sedentary group was significantly separated from the control groups and the BBN exercise group. Univariate statistical analysis revealed differences mainly in phosphatidylserine (PS) and cardiolipin (CL), although some differences were also observed in phosphatidylinositol (PI, LPI) and phosphatidylcholine (PC) phospholipids. PS with shorter fatty acyl chains were up-regulated in the BBN sedentary group, while the other species of PS with longer FA and a higher degree of unsaturation were down-regulated, but the BBN exercise group was mostly similar to control groups. Remarkably, exercise training prevented these alterations and had a positive impact on the ability of mitochondria to produce ATP, restoring the healthy phospholipid profile. The remodelling of mitochondria phospholipid profile in rats with urothelial carcinoma allowed confirming the importance of the lipid metabolism in mitochondria dysfunction in cancer-induced skeletal muscle remodelling. The regulation of phospholipid biosynthetic pathways observed in the BBN exercise group supported the current perspective that exercise is an adequate therapeutic approach for the management of cancer-related muscle remodeling.

For cancers, such as common solid tumours, variants in the genome give a selective growth advantage to certain cells. It has recently been argued that the mean count of coding single nucleotide variants acting as disease-drivers in common solid tumours is frequently small in size, but significantly variable by cancer type (hypermutation is excluded from this study). In this paper we investigate this proposal through the use of integrative machine-learning-based classifiers we have proposed recently for predicting the disease-driver status of single nucleotide variants (SNVs) in the human cancer genome. We find that predicted driver counts are compatible with this proposal, have similar variabilities by cancer type and, to a certain extent, the drivers are identifiable by these machine learning methods. We further discuss predicted driver counts stratified by stage of disease and driver counts in non-coding regions of the cancer genome, in addition to driver-genes.

We apply novel analyses to images of superficial capillaries that are located near and around the optic disc of the human retina: the radial peri-papillary capillaries (RPCs). Due to their unique perfusion of the nerve fibre layer the RPCs are particularly significant for optic-neuropathies. The inputs to the analysis were z-stacks from 3D confocal fluorescence microscopy from 62 human retinas aged 9 to 84 years. Our aim was to find morphometric correlates of age. The retinas had no ophthalmic history. The analysis was undertaken in two stages: (1) converting the z-stacks to 3D tubular networks of vessels, and (2) characterizing the tubular networks using features derived from the Minkowski functionals (MFs). The MFs measure: the capillary volume, surface area, mean breadth, and Euler number. The mean breadth is related to tortuosity, wall shear stress and resistance to flow, and the Euler number is related to the density of loops (collaterals). Features derived from the surface area, mean breadth and Euler number were most related to age (all p ≤ 0.006). The results indicate the importance of pressure-equalizing loops and tortuosity as quantitative measures related to perfusion efficiency. The novel morphometric analysis could quantify disease-related accelerated aging and vessel malformation.

Functional connectivity of the brain fluctuates even in resting-state condition. It has been reported recently that fluctuations of global functional network topology and those of individual connections between brain regions expressed multifractal scaling. To expand on these findings, in this study we investigated if multifractality was indeed an inherent property of dynamic functional connectivity (DFC) on the regional level as well. Furthermore, we explored if local DFC showed region-specific differences in its multifractal and entropy-related features. DFC analyses were performed on 62-channel, resting-state electroencephalography recordings of twelve young, healthy subjects. Surrogate data testing verified the true multifractal nature of regional DFC that could be attributed to the presumed nonlinear nature of the underlying processes. Moreover, we found a characteristic spatial distribution of local connectivity dynamics, in that frontal and occipital regions showed stronger long-range correlation and higher degree of multifractality, whereas the highest values of entropy were found over the central and temporal regions. The revealed topology reflected well the underlying resting-state network organization of the brain. The presented results and the proposed analysis framework could improve our understanding on how resting-state brain activity is spatio-temporally organized and may provide potential biomarkers for future clinical research.

Chronic obstructive pulmonary disease (COPD) is one of the most common respiratory diseases. Yihuo Huatan Formula (YHF), as a proven Chinese Herbal Medicine (CHM), has been verified to be effective in the treatment of stable COPD through years' of practice. Nevertheless, its working mechanism is still unclear. We sought to systematically decipher the mechanism of YHF for treating stable COPD using systems pharmacology-based method that integrates pharmacokinetic screening, target prediction, network analyses, GO and KEGG enrichment analyses. Firstly, a total of 1267 chemicals out of 15 herbal components were included in YHF chemical database. Among them, 180 potential active molecules were screened out through pharmacokinetic evaluation. Then 258 targets of the active molecules were predicted, of which 84 were chosen for further analyses. Finally, the network analyses and GO and KEGG enrichment methods suggested a therapeutic effect of YHF on the alleviation of airway inflammation, decrease of mucus secretion, maintenance of immune homeostasis and benefit of COPD comorbidities, by regulating multiple targets and pathways. The systems pharmacology-based approach helps to understand the underlying working mechanism of YHF in stable COPD from a holistic perspective, and offers an exemplification for systematically uncovering the action mechanisms of CHM.

As the largest portion of the terrestrial ecosystems, the arid and semi-arid grassland ecosystem is relatively sensitive and vulnerable to nitrogen (N) deposition. Mowing, the main management in Inner Mongolia grassland also has deep direct and indirect effect on N transformation by removing the nutrient from soils. However, the interaction effect of N addition and mowing on N transformation is still unclear, especially in semi-arid grassland. Here, we conducted a field-manipulated experiment to assess N addition (10 g N m-2 y-1) and mowing (in the middle of August) effects on soil net N mineralization rate across 4 growing seasons (2006-2009) in a semi-arid grassland in Inner Mongolia of northern China. We found that N addition with or without mowing led to significant effect on soil ammonification rate and net N mineralization rate, but had no significant effect on nitrification rates. Furthermore, mowing had no significant effect on soil net N mineralization, ammonification and nitrification rates. N addition and Mowing decreased microbial respiration and metabolic quotient, whereas the interaction of N addition and mowing had no significant effect on microbial respiration and metabolic quotient. Our results indicated that the effects of mowing and N addition did not interactively weaken soil net N mineralization rates in a semi-arid grassland of Northern China. Therefore, the anthropic management (i.e. mowing for hay once a year) with N addition may be a sustainable approach for restoration and reconstruction of vegetation in the abandoned grassland  of Northern China.

Pseudomonas aeruginosa is an opportunistic pathogen with a capacity to develop antibiotic resistance, which underlies a larger proportion of hospital-acquired infections and higher morbidity and mortality, compared to other bacterial infections. Effective novel approaches for treatment of infections induced by this pathogen are therefore necessary. Phage therapy represents a promising alternative solution to eradicate antibiotic-resistant pathogens. Here, we investigated phage protein efficacy against multi-drug resistant (MDR) P. aeruginosa PAR21 and PAR50 strains isolated from diabetic foot ulcer patients. The results obtained using spot assay, zymography, spectrophotometry and scanning electron microscopy at low voltage (SEM-LV) indicate that the phage protein, PA-PP, exerts activity against P. aeruginosa PAR50 while having no impact on the PAR21 strain. Using LC-MS-MS/MS and comparative analysis of the peptide molecular mass with the protein sequence database, PA-PP was identified as a member of the serine protease family, a result corroborated by its ability to digest casein. We additionally showed a capacity of PA-PP to digest porin protein on the bacterial outer membrane (OM). Moreover, synergistic activity between PA-PP protein and piperacillin led to higher sensitivity of bacterial cells to this antibiotic. Our collective findings suggest that PA-PP targets porin protein on PAR50 OM, thereby increasing its sensitivity to specific antibiotics. The adverse effects observed on bacterial cells using SEM-LV suggest further roles of this protein that remain to be established.

Preclinical models and clinical studies have shown that anti-CD20-based treatment has multifaceted consequences on T-cell immunity. We have performed a prospective study of peripheral T-cell compartment in FL patients, all exhibiting high tumor burden and receiving rituximab-chemotherapy-based regimen (R-CHOP). Before treatment, FL patients harbor low amounts of peripheral naive T cells, but high levels of CD4+ TEM, CD4+ Treg and CD8+ TEMRA subsets and significant amounts of CD38+ HLA-DR+ activated T cells. A portion of these activated/differentiated T cells also expressed PD-1 and/or TIGIT immune checkpoints. Hierarchical clustering of phenotyping data revealed that 5/8 patients with only a partial response to R-CHOP induction therapy or with disease progression segregate into a group exhibiting a highly activated/differentiated T cell profile and a markedly low proportion of naive T cells before treatment. Rituximab-based therapy induced a shift of CD4+ and CD8+ T cells toward a central memory phenotype and of CD8+ T cells to a naive phenotype. In parallel, a decrease in the number of peripheral T cells expressing both PD-1 and TIGIT was detected. These observations suggest that the standard rituximab-based therapy partially reverts the profound alterations observed in T-cell subsets in FL patients, and that blood T-cell phenotyping could provide a better understanding of the mechanisms of rituximab-based treatment.

We report detection of Baculoviral inhibitor of apoptosis repeat containing-5 (BIRC5) protein biomarker in dog serum by label-free surface plasmon resonance (SPR) immunosensor. Initially, overexpression of BIRC5 in canine mammary tumour (CMT) tissues was confirmed by real-time PCR. Recombinant BIRC5 was produced and protein specific antibodies developed in guinea pig specifically reacted with native protein in immunohistochemistry and immunocytochemistry. SPR immunosensor was developed by fabricating anti-BIRC5 antibodies on gold sensor disc. The equilibrium dissociation constant, (KD = kd/ka) was 12.1 × 10-12 M; which indicates that antibodies are of high affinity with sensitivity in picomolar range. The SPR assay could detect as low as 6.25 pg/ml of BIRC5 protein in a calibration experiment (r2 = 0.9964). On testing real clinical samples, 95% specificity and 73.33% sensitivity were recorded. The average amount of serum BIRC5 in dogs with CMT was 110.02 ± 9.77 pg/ml; whereas, in non-cancerous disease conditions, 44.79 ± 4.28 pg/ml and in healthy dog sera 30.28 ± 2.99 pg/ml protein was detected. The SPR immunosensor for detection of BIRC5 in dog sera is reported for the first time and this may find prognostic and diagnostic applications in management of CMT. In future, 'on-site' sensors can be developed using this technique for near-patient testing.

Tumors affect the immune system, locally and systemically. The frequencies of specific circulating immune cell populations correlate with disease progression as well as prognosis of the patients. Although largely neglected, conventional antitumoral therapies often possess immunomodulatory properties and affect the levels of specific immune cell populations. Most information, however, derive from animal or in vitro studies. As this could impact prognosis as well as response to therapy, further studies of the effects of treatment on circulating immune cells in patients are warranted. In this pilot study, we evaluated a wide panel of circulating immune cells over time (up to six months) in ten patients with metastatic breast cancer receiving standard antitumoral regimens. Overall, endocrine therapy tends to enrich for natural killer (NK) and natural killer T (NKT) cells in the circulation, whereas both chemotherapy and endocrine therapy reduce the levels of circulating monocytic myeloid-derived suppressor cells (Mo-MDSCs). This indicates that the systemic immunosuppressive profile observed in patients tends to revert over the course of systemic therapy and holds promise for future combination treatment with standard antitumoral agents and immunotherapy.

Coronary artery disease (CAD) is a progressive cardiovascular syndrome characterized by cholesterol-induced focal arterial lesions that impair oxygen delivery to the heart. As both innate and adaptive immune cells play critical roles in the formation and progression of arterial plaques and endothelial cell dysfunction, CAD is commonly viewed as a chronic inflammatory disorder. Our lab has previously discovered that 5-HT2A receptor activation with the 5-HT2 receptor selective agonist (R)-2,5-dimethoxy-4-iodoamphetamine [(R)-DOI] has potent anti-inflammatory activity in both cell culture and whole animal models. Here we have examined the putative therapeutic effects of (R)-DOI in the ApoE-/- high fat model of cardiovascular disease. Subcutaneously implanted osmotic minipumps were used to infuse sustained low rates (0.15 μg / hr) of (R)-DOI∙HCl to mice fed a high-fat "Western" diet. (R)-DOI treated mice had significant reductions in expression levels of mRNA for inflammatory markers like Il6 in vascular tissue, normalized glucose homeostasis, and reduced circulating cholesterol levels. As cardiovascular disease is a leading cause of death both globally and in the Western world, activation of 5-HT2A receptors at sub-behavioral levels may represent a new strategy to treat inflammation-based cardiovascular disease.

VX-770 (ivacaftor) is approved for clinical use in CF patients bearing multiple CFTR mutations. VX-770 potentiated wildtype CFTR and several disease mutants expressed in oocytes in a manner modulated by PKA-mediated phosphorylation. Potentiation of some other mutants, including G551D-CFTR, was less dependent upon the level of phosphorylation, likely related to the severe gating defects in these mutants exhibited in part by a shift in PKA sensitivity to activation, possibly due to an electrostatic interaction of D551 with K1250. Phosphorylation-dependent potentiation of wildtype CFTR and other variants also was observed in epithelial cells. Hence, the efficacy of potentiators may be obscured by a ceiling effect when drug screening is performed under strongly phosphorylating conditions. These results should be considered in campaigns for CFTR potentiator discovery, and may enable the expansion of VX-770 to CF patients bearing ultra-orphan CFTR mutations.

Patients with stage II or III colorectal cancer (CRC) exhibit various clinical outcomes after radical treatments. The 5-year survival rate was between 50 and 87%. However, the underlying mechanisms of the variation remain unclear. Here we show that AMPKα1 is overexpressed in CRC patient specimens and the high expression is correlated with poor patient survival. We further reveal a previously unrecognized function of AMPKα1, which maintains high level of reduced glutathione to keep reduction-oxidation reaction (redox) homeostasis under stress conditions, thus promoting CRC cell survival under metabolic stress in vitro and enhancing tumorigenesis in vivo. Mechanistically, AMPKα1 regulate the glutathione reductase (GSR) phosphorylation possibly through residue Thr507 which enhances its activity. Suppression of AMPKα1 by using nano-sized polymeric vector induces a favorable therapeutic effect, especially when in combination with oxaliplatin. Our study uncovers a novel function of AMPKα1 in redox regulation and identifies a promising therapeutic strategy for treatment of CRC.

Occupational therapy and occupational science are founded on the theoretical core assumption that occupation and quality of life (QoL) are closely related. However, such theoretical core assumptions must be supported through empirically based research.

Deep learning is the crucial technology in intelligent question answering research tasks. Nowadays, extensive studies on question answering have been conducted by adopting the methods of deep learning. The challenge is that it not only requires an effective semantic understanding model to generate a textual representation but also needs the consideration of semantic interaction between questions and answers simultaneously. In this paper, we propose a stacked Bidirectional Long Short-Term Memory (BiLSTM) neural network based on the coattention mechanism to extract the interaction between questions and answers, combining cosine similarity and Euclidean distance to score the question and answer sentences. Experiments are tested and evaluated on publicly available Text REtrieval Conference (TREC) 8-13 dataset and Wiki-QA dataset. Experimental results confirm that the proposed model is efficient and particularly it achieves a higher mean average precision (MAR) of 0.7613 and mean reciprocal rank (MRR) of 0.8401 on the TREC dataset.