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Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance. Author summary: Antiretroviral drugs have achieved great success in controlling the HIV pandemic. However, the therapy fails sometimes owing to the low drug adherence and/or the emergence of resistance associated mutations on viral genome. The persistence of drug resistance poses challenges in using antiretroviral drugs for long term control or pre-exposure prophylaxis. To understand the mechanisms of resistance evolution and persistence, we profiled the replication fitness of over 1000 HIV-1 mutants with combinations of resistance associated mutations on its protease gene. We found that although resistance associated mutations greatly reduce replication fitness, they interact positively to alleviate the mutational load. These genetic interactions, termed epistasis, increase the ruggedness along the evolution paths, restricting resistance associated mutations from reversal. Our data support the clinical observations that drug resistance mutations tend to persist even when antiretroviral drug is discontinued. [ABSTRACT FROM AUTHOR]

Purpose: Pharmacokinetic models facilitate assessment of properties of the micro-vascularization based on DCE-MRI data. However, accurate pharmacokinetic modeling in the liver is challenging since it has two vascular inputs and it is subject to large deformation and displacement due to respiration. Methods: We propose an improved pharmacokinetic model for the liver that (1) analytically models the arrival-time of the contrast agent for both inputs separately; (2) implicitly compensates for signal fluctuations that can be modeled by varying applied flip-angle e.g. due to B1-inhomogeneity. Orton’s AIF model is used to analytically represent the vascular input functions. The inputs are independently embedded into the Sourbron model. B1-inhomogeneity-driven variations of flip-angles are accounted for to justify the voxel’s displacement with respect to a pre-contrast image. Results: The new model was shown to yield lower root mean square error (RMSE) after fitting the model to all but a minority of voxels compared to Sourbron’s approach. Furthermore, it outperformed this existing model in the majority of voxels according to three model-selection criteria. Conclusion: Our work primarily targeted to improve pharmacokinetic modeling for DCE-MRI of the liver. However, other types of pharmacokinetic models may also benefit from our approaches, since the techniques are generally applicable. [ABSTRACT FROM AUTHOR]

After publication of this article [[1]], the following concerns were raised: Some I PHYB i accession numbers reported in Table 1 of this article [[1]] were also reported in another article (Table S8 of [[2]]), but the locations and geographical coordinates cited for the same GenBank accession numbers are different in the two articles (see S1 File). In [[1]], I PHYB i GenBank accession numbers KX059488 and KX059485 are reported as associated with two different ID numbers each. The corrected accession numbers and related information are as follows: GenBank accession number: MW930629 ID: P. gramineus1 Location: Luhuo, Sichuan 100° 13'N, 31° 37'E GenBank accession number: KX059488 ID: P. gramineus2 Location: Hongyuan, Sichuan 102°30'55.5", 32°46'43.6" GenBank accession number: MW930630 ID: P. distinctus1 Location: Tengchong, Yunnan 98° 40'N, 25° 37'E GenBank accession number: KX059485 ID: P. distinctus2 Location: Chayu, Xizang 97°21'26.6", 28°37'21" Supporting information S1 File. [Extracted from the article]

A numerical model of single-particle fog-dust collision coupling in a high-speed airflow based on three-phase flow theory. The effect of the fog-to-dust particle size ratio, relative velocity between the fog and dust particles, collision angle and contact angle at the wetting humidity function of dust particles is investigated. Different particle size ratios are determined for achieving the optimal wetting humidity for the interaction of high-velocity aerosols with dust particles of different sizes, for differ, that is, kPM2.5 = 2:1, kPM10 = 3.5:1 and kPM20 = 1.5:1. The optimal humidity increases with the relative velocity U between the fog and dust particles in the high-speed airflow. The larger the collision angle is, the lower the wetting rate is.The smaller the contact angle between the solid and liquid is, the better droplet wetting on dust is. The fine kinetic mechanism of single-particle fog-dust collision-coupling in a high-speed airflow is elucidated in this study. [ABSTRACT FROM AUTHOR]

Schizophrenia (SCZ) is a severe psychiatric disorder with evidence of a strong genetic component in the complex etiologies. Some studies indicated that gamma-aminobutyric acid (GABA)A receptor β2 subunit gene (GABRB2) was associated with SCZ. Other studies reported a negative association. Moreover, the results of two previous meta-analyses of GABRB2 with SCZ were inconsistent and the sample sizes were limited. Therefore, an updated meta-analysis combined with genome-wide association study (GWAS) data of the Han Chinese population and Psychiatric Genomics Consortium (PGC) was performed. Available case–control and family-based genetic data were extracted from association studies, and the GWAS data were included. The findings showed no association between six single-nucleotide polymorphisms of GABRB2 (rs6556547, rs1816071, rs1816072, rs194072, rs252944, and rs187269) and SCZ in a total of 51,491 patients and 74,667 controls. The ethnic subgroup analysis revealed no significant association in Asian populations. Since the PGC data of SCZ (SCZ-PGC, 2014) contained 3 studies of Asian populations (1866 patients and 3418 controls), only the data of European samples in SCZ-PGC were used for the meta-analysis of the Caucasian population in the present study. The result still showed no association in the Caucasian population. In conclusion, the present meta-analysis on combined data from GWASs of the Han Chinese population and PGC suggested that GABRB2 polymorphisms might not be associated with SCZ. [ABSTRACT FROM AUTHOR]

Almost all dental diseases are caused by biofilms that consist of multispecies communities. DJK-5, which is a short D-enantiomeric, protease-resistant peptide with broad-spectrum anti-biofilm activity, was tested for its effect on oral multispecies biofilms. Peptide DJK-5 at 10 μg/mL effectively prevented the growth of these microbes in culture media in a time-dependent manner. In addition to the prevention of growth, peptide DJK-5 completely killed both Streptococcus mutans and Enterococcus faecalis suspended from biofilms after 30 minutes of incubation in liquid culture media. DJK-5 also led to the effective killing of microbes in plaque biofilm. The proportion of bacterial cells killed by 10 μg/mL of DJK-5 was similar after 1 and 3 days, both exceeding 85%. DJK-5 was able to significantly prevent biofilm formation over 3 days (P = 0.000). After 72 hours of exposure, DJK-5 significantly reduced and almost completely prevented plaque biofilm production by more than 90% of biovolume compared to untreated controls (P = 0.000). The proportion of dead biofilm bacteria at the 10 μg/mL DJK-5 concentration was similar for 1- and 3-day-old biofilms, whereby >86% of the bacteria were killed. DJK-5 was also able to kill >79% and >85% of bacteria, respectively, after one-time and three brief treatments of 3-day-old biofilms. The combination of DJK-5 and chlorhexidine showed the best bacterial killing among all treatments, with ~83% and >88% of bacterial cells killed after 1 and 3 minutes, respectively. No significant difference was found in the percentage of biofilm killing amongst three donor plaque samples after DJK-5 treatment. In particular, DJK-5 showed strong performance in inhibiting biofilm development and eradicating pre-formed oral biofilms compared to L-enantiomeric peptide 1018. DJK-5 was very effective against oral biofilms when used alone or combined with chlorhexidine, and may be a promising agent for use in oral anti-biofilm strategies in the future. [ABSTRACT FROM AUTHOR]

Potamogeton is one of the most difficult groups to clarify in aquatic plants, which has an extensive range of interspecific morphological and ecological diversity. Internal transcribed spacer (ITS) is prevalent for phylogenetic analysis in plants. However, most researches demonstrate that ITS has a high percentage of homoplasy in phylogenetic datasets. In this study, eighteen materials were collected in Potamogeton from China and incongruence was shown between the rbcL and ITS phylogenies. To solve the discrepancy, we employed a novel barcode PHYB to improve resolution and accuracy of the phylogenetic relationships. The PHYB phylogeny successfully resolved the incongruence between the rbcL and ITS phylogenies. In addition, six hybrids were confirmed using PHYB, including P. compressus × P. pusillus, P. octandrus × P. oxyphyllus, P. gramineus × P. lucens, P. distinctus × P. natans, P. distinctus × P. wrightii, and S. pectinata × S. amblyophylla. Whereas, only one hybrid was identified (P. compressus × P. pusillus) by ITS, indicating that ITS homoplasy was present in Potamogeton and ITS was completely homogenized to one parental lineage. Thus, ITS might have limited utility for phylogenetic relationships in Potamogeton. It is recommended that a three-locus combination of chloroplast DNA gene, ITS and PHYB is potential to effectively reveal more robust phylogenetic relationships and species identification. [ABSTRACT FROM AUTHOR]

Background: Rebleeding is a serious complication of aneurysmal subarachnoid hemorrhaging. To date, there are conflicting data regarding the factors contributing to rebleeding and their significance. Methods: A systematic review of PubMed and Embase databases was conducted for studies pertaining to aneurysmal subarachnoid hemorrhage (aSAH) and rebleeding in order to assess the associated risk factors. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were estimated from fourteen studies comprised of a total of 5693 patients that met the inclusion criteria. Results: Higher rebleeding rates were observed < 6 h after the initial aSAH (OR  = 3.22, 95% CI  = 1.46–7.12), and were associated with high systolic blood pressure (OR  = 1.93, 95% CI  = 1.31–2.83), poor Hunt-Hess grade (III–IV) (OR  = 3.43, 95% CI  = 2.33–5.05), intracerebral or intraventricular hematomas (OR  = 1.65, 95% CI  = 1.33–2.05), posterior circulation aneurysms (OR  = 2.15, 95% CI  = 1.32–3.49), and aneurysms >10 mm in size (OR  = 1.70, 95% CI  = 1.35–2.14). Conclusions: Aneurysmal rebleeding occurs more frequently within the first 6 hours after the initial aSAH. Risk factors associated with rebleeding include high systolic pressure, the presence of an intracerebral or intraventricular hematoma, poor Hunt-Hess grade (III-IV), aneurysms in the posterior circulation, and an aneurysm >10 mm in size. [ABSTRACT FROM AUTHOR]

Odorant binding proteins (OBPs) play a central role in transporting odorant molecules from the sensillum lymph to olfactory receptors to initiate behavioral responses. In this study, the OBP of Macrocentrus cingulum McinOBP1 was expressed in Escherichia coli and purified by Ni ion affinity chromatography. Real-time PCR experiments indicate that the McinOBP1 is expressed mainly in adult antennae, with expression levels differing by sex. Ligand-binding experiments using N-phenyl-naphthylamine (1-NPN) as a fluorescent probe demonstrated that the McinOBP1 can bind green-leaf volatiles, including aldehydes and terpenoids, but also can bind aliphatic alcohols with good affinity, in the order trans-2-nonenal>cis-3-hexen-1-ol>trans-caryophelle, suggesting a role of McinOBP1 in general odorant chemoreception. We chose those three odorants for further homology modeling and ligand docking based on their binding affinity. The Val58, Leu62 and Glu130 are the key amino acids in the binding pockets that bind with these three odorants. The three mutants, Val58, Leu62 and Glu130, where the valine, leucine and glutamic residues were replaced by alanine, proline and alanine, respectively; showed reduced affinity to these odorants. This information suggests, Val58, Leu62 and Glu130 are involved in the binding of these compounds, possibly through the specific recognition of ligands that forms hydrogen bonds with the ligands functional groups. [ABSTRACT FROM AUTHOR]

For the problem of coal dust pollution in the return air lane of the comprehensive mining working face of soft rock mines.Based on the principle of supersonic siphon pneumatic atomization dust control, mobile vehicle-mounted pneumatic spraying combined with full-section fog curtain dust control technology is proposed to address the coal dust pollution problem in the return air tunnel of the comprehensive mining working face of soft rock mines. This technology has a wider spraying range, stronger wind resistance and lower energy consumption.Using the k-ε turbulence module and the fluid flow particle tracking module of COMSOL simulation software, a three-dimensional numerical model of the return air tunnel was established. The effect of wind flow characteristics on the diffusion range of coal dust and fog droplets was analysed, and the dust transport pattern and dust control effect of the new technology were obtained for different cross-sectional return airways. The results show that the velocity of the wind flow is continuously decayed by the slope, and the dust of different particle sizes is distributed differently by the inertial force. Coal dust with particle sizes larger than 6.5 μm accumulates below the structure at a lower velocity, and coal dust with particle sizes smaller than 4.5 μm is mostly suspended above the structure at a higher velocity. The device effectively stops the transport of dust and covers the whole section of the roadway, and the dust removal efficiency reaches 96.53%~97.93%, which provides relevant theoretical support and treatment means for the control of dust pollution in the return airway of coal mines. [ABSTRACT FROM AUTHOR]

Text information mining is a key step to data-driven automatic/semi-automatic quality management (QM). For Chinese texts, a word segmentation algorithm is necessary for pre-processing since there are no explicit marks to define word boundaries. Because of intrinsic characteristics of QM-related texts, word segmentation algorithms for normal Chinese texts cannot be directly applied. Hence, based on the analysis of QM-related texts, we summarized six features, and proposed a hybrid Chinese word segmentation model by means of integrating transfer learning (TL), bidirectional long-short term memory (Bi-LSTM), multi-head attention (MA), and conditional random field (CRF) to construct the mTL-Bi-LSTM-MA-CRF model, considering insufficient samples of QM-related texts and excessive cutting of idioms. The mTL-Bi-LSTM-MA-CRF model is composed of two steps. Firstly, based on a word embedding space, the Bi-LSTM is introduced for context information learning, and the MA mechanism is selected to allocate attention among subspaces, and then the CRF is used to learn label sequence constraints. Secondly, a modified TL method is put forward for text feature extraction, adaptive layer weights learning, and loss function correction for selective learning. Experimental results show that the proposed model can achieve good word segmentation results with only a relatively small set of samples. [ABSTRACT FROM AUTHOR]

In order to solve the problem of coal dust pollution at the transfer point, a three-dimensional numerical model of wind flow-coal dust at the loading point of underground rubber run was established by computational fluid dynamics (CFD) discrete particle model and finite element method and k-ε turbulence model, and the coal dust diffusion pollution phenomenon caused by the coal flow transfer under the intersection of wind flow in the cross tunnel was studied. Based on the simulation results of wind flow velocity contour, pressure contour and isochronous flow vector distribution, the influence mechanism of wind flow and coal dust characteristics on the distribution of wind flow and coal dust diffusion in the roadway is analysed, and a dust control and reduction system and treatment scheme with new pneumatic screw spray technology as the core is proposed to suppress coal dust pollution at the reloading point. The results of the study show that the wind flow distribution is mainly influenced by the intersection of tape traction and cross-roadway wind flow, showing a complex multi-layer distribution along the roadway and in the normal direction; the diffusion of coal dust of different particle sizes is influenced by the roadway wind flow, and coal dust with particle sizes in the range of 10μm~20μm is more easily diffused, and the dust with particle sizes in the range of 20μm~45μm is mainly collected and suspended near the vortex wind flow at the cross-roadway. The coal dust in the range of 20 μm~45 μm is more likely to gather in the vortex; the treatment system effectively controls the coal dust inside the dust cover, and the spiral-shaped transported droplet particle group formed by the pneumatic spiral spray combines with it efficiently, which verifies the dust control and reduction effect of the pneumatic spiral spray system at the transfer point, and the dust removal efficiency reaches 89.35%~93.06%, which provides relevant theoretical support for the treatment of dust pollution at the coal transfer point in underground coal mines It provides the theoretical support and means to control dust pollution at underground coal transfer points. [ABSTRACT FROM AUTHOR]

Macrophages restrict bacterial infection partly by stimulating phagocytosis and partly by stimulating release of cytokines and complement components. Here, we treat macrophages with LPS and a bacterial pathogen, and demonstrate that expression of cytokine IL-1β and bacterial phagocytosis increase to a transient peak 8 to 12 h post-treatment, while expression of complement component 3 (C3) continues to rise for 24 h post-treatment. Metabolomic analysis suggests a correlation between the cellular concentrations of succinate and IL-1β and of inosine and C3. This may involve a regulatory feedback mechanism, whereby succinate stimulates and inosine inhibits HIF-1α through their competitive interactions with prolyl hydroxylase. Furthermore, increased level of inosine in LPS-stimulated macrophages is linked to accumulation of adenosine monophosphate and that exogenous inosine improves the survival of bacterial pathogen-infected mice and tilapia. The implications of these data suggests potential therapeutic tools to prevent, manage or treat bacterial infections. Author summary: Bacterial infection is still one of the primary causes of death, especially in the context of exhausted antibiotic reservoir to the growing cases of antibiotic resistance. Novel approach to manage bacterial infection is required. Here, we report a metabolism-based approach to manage immune response to fight against bacterial infection. We find that innate immune response to bacterial infection is constituted with two phases, namely innate cellular immunity and innate humoral immunity. The two phases are interchangeably regulated by two metabolites, inosine and succinate. Succinate promotes the production of inflammatory cytokines IL-1β while inosine downregulates IL-1β expression but increases complement component 3 expression in a time-dependent manner. This is a novel phenomenon that this two-phases innate immune response is required to clear bacterial infection, and is confirmed by the in vivo challenge of mice and fish with pathogenic bacteria in combination of succinate or inosine. We also report a novel mechanism that succinate and inosine competitively regulate HIF-1α activation. Thus, our study presents a novel feedback mechanism of immune response, and inosine could be a potential metabolite in tuning immune response towards bacterial infection. [ABSTRACT FROM AUTHOR]

To solve the problem of the inability of traditional spray dust removal technology to efficiently restrain dust diffusion at the heading face, a multilayer spiral fog curtain dust control method based on spirally arranged pneumatic nozzles is proposed. In this paper, the k-ɛ turbulence model and K-H droplet breakage model are used. First, different airflow fields are analyzed by simulating the simultaneous injection of different numbers of nozzles, and the motion law of airflow interaction is obtained. Taking the two-layer fog curtain as an example, a multiphysical field coupling numerical simulation of the two-layer spiral fog curtain applied in the field is carried out, and the variation law of its velocity field distribution and particle motion characteristics is analyzed. A similar experimental platform is established to verify the effectiveness of the simulation results and the feasibility of the dust removal scheme. The simulation results show that the double helix arrangement will form a rotating airflow with the cutting arm as the axis to cover the whole roadway section and produce a double-layer spiral fog curtain. The water mist is fragmented into smaller fog droplets under the action of rotating airflow, which improves the dust catching effect of the fog curtain. Experiments show that the dust removal rate and efficiency of multilayer spiral fog curtains are obviously stronger than those of natural dust reduction and traditional spray. After 3 minutes, a dust concentration of approximately 470 mg/m3 can be reduced to less than 4 mg/m3. The average dust removal rates of total dust and exhaled dust were 2.600 mg/(m3.s) and 0.189 mg/(m3.s), respectively, and the dust removal efficiencies were 97.01% and 94.32%. [ABSTRACT FROM AUTHOR]

The distribution of multiscale pores and fractures in coal and rock is an important basis for reflecting the capacity of fluid flow in coal seam seepage passages. Accurate extraction and qualitative and quantitative analysis of pore-fracture structures are helpful in revealing the flow characteristics of fluid in seepage channels. The relationship between pore and fracture connectivity can provide a scientific reference for optimizing coal seam water injection parameters. Therefore, to analyse the change in permeability caused by the variability in the coal pore-fracture network structure, a CT scanning technique was used to scan coal samples from the Leijia District, Fuxin. A total of 720 sets of original images were collected, a median filter was used to filter out the noise in the obtained images, and to form the basis of a model, the reconstruction and analysis of the three-dimensional pore-fracture morphology of coal samples were carried out. A pore-fracture network model of the coal body was extracted at different scales. Using the maximum sphere algorithm combined with the coordination number, the effect of different quantitative relationships between pore size and pore throat channel permeability was studied. Avizo software was used to simulate the flow path of fluid in the seepage channels. The change trend of the fluid velocity between different seepage channels was discussed. The results of the pore-fracture network models at different scales show that the pore-fracture structure is nonuniform and vertically connected, and the pores are connected at connecting points. The pore size distribution ranges from 104 μm to 9425 μm. The pore throat channel length distribution ranges from 4206 μm to 48073 μm. The size of the coordination number determines the connectivity and thus the porosity of the coal seam. The more connected pore channels there are, the larger the pore diameters and the stronger the percolation ability. During flow in the seepage channels of the coal, the velocity range is divided into a low-speed region, medium-speed region and high-speed region. The fluid seepage in the coal seam is driven by the following factors: pore connectivity > pore and pore throat dimensions > pore and pore throat structure distribution. Ultimately, the pore radius and pore connectivity directly affect the permeability of the coal seam. [ABSTRACT FROM AUTHOR]

Evolutionarily conserved microRNAs (miRNAs) usually have high copy numbers in the genome. The redundant and specific roles of each member of a multimember miRNA gene family are poorly understood. Previous studies have shown that the miR156-SPL-miR172 axis constitutes a signaling cascade in regulating plant developmental transitions. Here, we report the feasibility and utility of CRISPR-Cas9 technology to investigate the functions of all 5 MIR172 family members in Arabidopsis. We show that an Arabidopsis plant devoid of miR172 is viable, although it displays pleiotropic morphological defects. MIR172 family members exhibit distinct expression pattern and exert functional specificity in regulating meristem size, trichome initiation, stem elongation, shoot branching, and floral competence. In particular, we find that the miR156-SPL-miR172 cascade is bifurcated into specific flowering responses by matching pairs of coexpressed SPL and MIR172 genes in different tissues. Our results thus highlight the spatiotemporal changes in gene expression that underlie evolutionary novelties of a miRNA gene family in nature. The expansion of MIR172 genes in the Arabidopsis genome provides molecular substrates for the integration of diverse floral inductive cues, which ensures that plants flower at the optimal time to maximize seed yields. This study uses CRISPR-Cas9 technology to investigate the functions of all five miR172 genes in Arabidopsis, finding that miRNA172 family members exhibit distinct expression pattern and exert functional specificity in regulating meristem size, trichome initiation, stem elongation, shoot branching and floral competence. [ABSTRACT FROM AUTHOR]

Background: To date, the missed diagnosis rate of pulmonary hypertension (PH) was high, and there has been limited development of a rapid, simple, and effective way to screen the disease. The purpose of this study is to develop a deep learning approach to achieve rapid detection of possible abnormalities in chest radiographs suggesting PH for screening patients suspected of PH. Methods: We retrospectively collected frontal chest radiographs and the pulmonary artery systolic pressure (PASP) value measured by Doppler transthoracic echocardiography from 762 patients (357 healthy controls and 405 with PH) from three institutes in China from January 2013 to May 2019. The wohle sample comprised 762 images (641 for training, 80 for internal test, and 41 for external test). We firstly performed a 8-fold cross-validation on the 641 images selected for training (561 for pre-training, 80 for validation), then decided to tune learning rate to 0.0008 according to the best score on validation data. Finally, we used all the pre-training and validation data (561+80 = 641) to train our models (Resnet50, Xception, and Inception V3), evaluated them on internal and external test dataset to classify the images as having manifestations of PH or healthy according to the area under the receiver operating characteristic curve (AUC/ROC). After that, the three deep learning models were further used for prediction of PASP using regression algorithm. Moreover, we invited an experienced chest radiologist to classify the images in the test dataset as having PH or not, and compared the prediction accuracy performed by deep learing models with that of manual classification. Results: The AUC performed by the best model (Inception V3) achieved 0.970 in the internal test, and slightly declined in the external test (0.967) when using deep learning algorithms to classify PH from normal based on chest X-rays. The mean absolute error (MAE) of the best model for prediction of PASP value was smaller in the internal test (7.45) compared to 9.95 in the external test. Manual classification of PH based on chest X-rays showed much lower AUCs compared to that performed by deep learning models both in the internal and external test. Conclusions: The present study used deep learning algorithms to classify abnormalities suggesting PH in chest radiographs with high accuracy and good generalizability. Once tested prospectively in clinical settings, the technology could provide a non-invasive and easy-to-use method to screen patients suspected of having PH. [ABSTRACT FROM AUTHOR]

Rice-crab culture is the characteristic rice ecological breeding model used in the Panjin area of Liaohe River Basin, China, and it can improve the ecological environment and create increased economic benefits. From a food perspective, both rice yield and quality, which are closely related to the fertilization mode, should be considered. However, the effect of different fertilization modes on rice quality has not been comprehensively investigated in this co-culture system. This study investigated the effects of three fertilization modes(FP1, FP2, and OPT) divided according to different fertilization types and methods on rice yield and quality, and set up a non-fertilized control group. In the rice-crab culture system, FP2 used fewer fertilizers and had a lower economic cost, and the yield was only slightly less than that of OPT(highest yield) but there was no statistical difference. FP2 elicited the best appearance quality and better cooking and eating quality among all treatment modes. Compared with CK, three fertilization modes significantly increased the protein content in rice and decreased the amylose content, which would lead to the deterioration of rice eating quality. However FP2 had the least protein increase and the least amylose reduction. There was no significant change in crude fat and starch content. Therefore, the FP2 fertilization mode was the best choice for the rice-crab culture system, as it significantly improved rice yield and increased rice quality at a relatively low cost. [ABSTRACT FROM AUTHOR]

The endoplasmic reticulum (ER) Ca2+ sensors stromal interaction molecule 1 (STIM1) and STIM2, which connect ER Ca2+ depletion with extracellular Ca2+ influx, are crucial for the maintenance of Ca2+ homeostasis in mammalian cells. Despite the recent progress in unraveling the role of STIM2 in Ca2+ signaling, the mechanistic underpinnings of its activation remain underexplored. We use an engineering approach to direct ER-resident STIMs to the plasma membrane (PM) while maintaining their correct membrane topology, as well as Förster resonance energy transfer (FRET) sensors that enabled in cellulo real-time monitoring of STIM activities. This allowed us to determine the calcium affinities of STIM1 and STIM2 both in cellulo and in situ, explaining the current discrepancies in the literature. We also identified the key structural determinants, especially the E470 residue, which define the distinct activation dynamics of STIM2. The E470G mutation could switch STIM2 from a slow and weak Orai channel activator into a fast and potent one like STIM1 and vice versa. The systemic dissection of STIM2 activation by protein engineering sets the stage for the elucidation of the regulation and function of STIM2-mediated signaling in mammals. [ABSTRACT FROM AUTHOR]

Certain Major Histocompatibility-I (MHC-I) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes (CTLs), but the mechanisms mediating this containment are difficult to elucidate in vivo. Here we provide controlled assessments of fitness landscapes and CTL-imposed constraints for immunodominant epitopes presented by two protective (B*57 and B*27) and one non-protective (A*02) MHC-I types. Libraries of HIV-1 with saturation mutagenesis of CTL epitopes are propagated with and without CTL selective pressure to define the fitness landscapes for epitope mutation and escape from CTLs via deep sequencing. Immunodominant B*57- and B*27- present epitopes are highly limited in options for fit mutations, with most viable variants recognizable by CTLs, whereas an immunodominant A*02 epitope-presented is highly permissive for mutation, with many options for CTL evasion without loss of viability. Generally, options for evasion overlap considerably between CTL clones despite highly distinct T cell receptors. Finally, patterns of variant recognition suggest population-wide CTL selection for the A*02-presented epitope. Overall, these findings indicate that these protective MHC-I types yield CTL targeting of highly constrained epitopes, and underscore the importance of blocking public escape pathways for CTL-based interventions against HIV-1. [ABSTRACT FROM AUTHOR]

Cardiosphere-derived cells (CDCs), one of the promising stem cell sources for myocardial repair, have been tested in clinical trials and resulted in beneficial effects; however, the relevant mechanisms are not fully understood. In this study, we examined the hypothesis that CDCs favor heart repair by switching the macrophages from a pro-inflammatory phenotype (M1) into a regulatory anti-inflammatory phenotype (M2). Macrophages from mice were cultured with CDCs-conditioned medium or with fibroblasts-conditioned medium as a control. Immunostaining showed that CDCs-conditioned medium significantly enhanced the expression of CD206 (a marker for M2 macrophages), but decreased the expression of CD86 (a marker for M1 macrophages) 3 days after culture. For animal studies, we used an acute myocardial infarction model of mice. We injected CDCs, fibroblasts, or saline only into the border zone of infarction. Then we collected the heart tissues for histological analysis 5 and 14 days after treatment. Compared with control animals, CDCs treatment significantly decreased M1 macrophages and neutrophils but increased M2 macrophages in the infarcted heart. Furthermore, CDCs-treated mice had reduced infarct size and fewer apoptotic cells compared to the controls. Our data suggest that CDCs facilitate heart repair by modulating M1/M2 macrophage polarization and neutrophil recruitment, which may provide a new insight into the mechanisms of stem cell-based myocardial repair. [ABSTRACT FROM AUTHOR]

Olfactory ensheathing cell (OEC) transplantation is a candidate cellular treatment approach for human spinal cord injury (SCI) due to their unique regenerative potential and autologous origin. The objective of this study was, through a meta-epidemiologic approach, (i) to assess the efficacy of OEC transplantation on locomotor recovery after traumatic experimental SCI and (ii) to estimate the likelihood of reporting bias and/or missing data. A study protocol was finalized before data collection. Embedded into a systematic review and meta-analysis, we conducted a literature research of databases including PubMed, EMBASE, and ISI Web of Science from 1949/01 to 2014/10 with no language restrictions, screened by two independent investigators. Studies were included if they assessed neurobehavioral improvement after traumatic experimental SCI, administrated no combined interventions, and reported the number of animals in the treatment and control group. Individual effect sizes were pooled using a random effects model. Details regarding the study design were extracted and impact of these on locomotor outcome was assessed by meta-regression. Missing data (reporting bias) was determined by Egger regression and Funnel-plotting. The primary study outcome assessed was improvement in locomotor function at the final time point of measurement. We included 49 studies (62 experiments, 1,164 animals) in the final analysis. The overall improvement in locomotor function after OEC transplantation, measured using the Basso, Beattie, and Bresnahan (BBB) score, was 20.3% (95% CI 17.8–29.5). One missing study was imputed by trim and fill analysis, suggesting only slight publication bias and reducing the overall effect to a 19.2% improvement of locomotor activity. Dose-response ratio supports neurobiological plausibility. Studies were assessed using a 9-point item quality score, resulting in a median score of 5 (interquartile range [IQR] 3–5). In conclusion, OEC transplantation exerts considerable beneficial effects on neurobehavioral recovery after traumatic experimental SCI. Publication bias was minimal and affirms the translational potential of efficacy, but safety cannot be adequately assessed. The data justify OECs as a cellular substrate to develop and optimize minimally invasive and safe cellular transplantation paradigms for the lesioned spinal cord embedded into state-of-the-art Phase I/II clinical trial design studies for human SCI. [ABSTRACT FROM AUTHOR]

Context: The preferred treatment for osteoporosis in men is debated, and pairwise meta-analysis cannot obtain hierarchies of these treatments. Objective: The objective of this study was to integrate the evidence and provide hierarchies of eight drugs based on their effect on the bone mineral density in the lumbar spine (BMD in LS) and the fracture rate. Data Sources: Eligible studies were identified by searching Amed, British Nursing Index, EMBASE, PubMed, the Cochrane Central Register of Controlled Trials (CENTRAL), Google Scholar, SIGLE, the National Technical Information Service, the National Research Register (UK), and the Current Controlled Trials databases. Study Selection: RCTs or quasi-RCTs reporting at least two drugs (two active drugs or one active drug and a placebo) used to treat osteoporosis in men were selected by two authors. Data Extraction: Two authors independently extracted the data. Data Synthesis: Thirteen studies involving 3647 patients were included. Compared with placebo therapy, zoledronate (SMDs 13.48, 95% credible intervals 11.88-15.08) yielded the most significant effect on increasing the BMD in LS, followed by alendronate (11.04, 9.68-12.41), teriparatide (20mcg) + risedronate (10.98, 8.55-13.48), risedronate (10.33, 8.68-12.01), teriparatide (20mcg) (9.33, 6.87-11.76), strontium ranelate (8.88, 7.51-10.24), ibandronate (5.49, 3.82-7.16), parathyroid hormone (1-84) (4.89, 3.12-6.62) and alfacalcidol (3.42, 1.7-5.2). Placebo therapy had a significantly higher fracture rate in contrast to risedronate (OR 2.51, 95% CrI 1.23-4.24) or zoledronate (2.92, 1.29-5.62) or teriparatide (20mcg) (4.04, 1.36-8.49) or teriparatide (40mcg) (3.5, 1.14-8.34). Zoledronate ranked first for increasing the BMD in LS, and teriparatide (20mg) was ranked first for decreasing the fracture rate. Conclusions: Zoledronate might be the best choice to increase the BMD in LS and teriparatide (20mg) might lead to the lowest fracture rate. [ABSTRACT FROM AUTHOR]

Context: Alendronate may relate to the incidence of cancers, especially esophageal and colon cancer. But the results are inconsistent in different studies. Objective: To quantify the association between the use of alendronate and the occurrence of different types of cancer. Data Sources: We searched Embase, Pubmed, CENTRAL, SIGLE and , up to 2014 June. Study Selection: Cohort studies reporting association between alendronate or bisphosphonate therapy including alendronate in patients with osteoporosis and risk of cancer were selected by two authors. Data Extraction: Two authors independently extracted the data. The Chi-square test and the I-square test were used for testing heterogeneity between studies. Data Synthesis: Eight cohort studies were included in the meta-analysis. Meta-analysis result manifested that alendronate significantly increased the incidence of lung cancer (HR 1.23, 95%CI 1.03 to 1.47, P value = 0.03), nevertheless, there was no significant difference after we excluded either Lee’s 2012 study (HR 1.17, 95%CI 0.95 to 1.44, P value = 0.13) or Chiang’s 2012 study (HR 1.47, 95%CI 1 to 2.17, P value = 0.05). For the incidence of colorectal cancer, no significant difference occurred (HR 0.91, 95%CI 0.74 to 1.13, P value = 0.39), but there was a positive relationship when we used fixed model (HR 0.85, 95%CI 0.78 to 0.93, P value = 0.004). For the incidence of liver cancer, there was no significant difference (HR 1.36, 95%CI 0.9 to 2.04, P value = 0.14), however, the result changed after we excluded Chiang’s 2012 study (HR 1.69, 95%CI 1.03 to 2.77, P value = 0.04). There was no significant difference in other types of cancer. Conclusion: Based on current evidences, alendronate therapy may be associated with a high risk of lung cancer, may with an excess risk of liver cancer, a low risk of colorectal and no related risk of other cancers. [ABSTRACT FROM AUTHOR]

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species. [ABSTRACT FROM AUTHOR]

Aims: The asymptomatic nature of early-stage esophageal squamous cell carcinoma (ESCC) results in late presentation and consequent dismal prognosis This study characterized 14-3-3σ protein expression in the multi-stage development of ESCC and determined its correlation with clinical features and prognosis. Materials and Methods: Western blot was used to examine 14-3-3σ protein expression in normal esophageal epithelium (NEE), low grade intraepithelial neoplasia (LGIN), high grade intraepithelial neoplasia (HGIN), ESCC of TNM I to IV stage and various esophageal epithelial cell lines with different biological behavior. Immunohistochemistry was used to estimate 14-3-3σ protein in 110 biopsy samples of NEE, LGIN or HGIN and in 168 ESCC samples all of whom had follow-up data. Support vector machine (SVM) was used to develop a classifier for prognosis. Results: 14-3-3σ decreased progressively from NEE to LGIN, to HGIN, and to ESCC. Chemoresistant sub-lines of EC9706/PTX and EC9706/CDDP showed high expression of 14-3-3σ protein compared with non-chemoresistant ESCC cell lines and immortalized NEC. Furthermore, the downregulation of 14-3-3σ correlated significantly with histological grade (P = 0.000) and worse prognosis (P = 0.004). Multivariate Cox regression analysis indicated that 14-3-3σ protein (P = 0.016) and T stage (P = 0.000) were independent prognostic factors for ESCC. The SVM ESCC classifier comprising sex, age, T stage, histological grade, lymph node metastasis, clinical stage and 14-3-3σ, distinguished significantly lower- and higher-risk ESCC patients (91.67% vs. 3.62%, P = 0.000). Conclusions: Downregulation of 14-3-3σ arises early in the development of ESCC and predicts poor survival, suggesting that 14-3-3σ may be a biomarker for early detection of high-risk subjects and diagnosis of ESCC. Our seven-feature SVM classifier for ESCC prognosis may help to inform clinical decisions and tailor individual therapy. [ABSTRACT FROM AUTHOR]

Interleukin-33 (IL-33) is associated with multiple diseases, including asthma, rheumatoid arthritis, tissue injuries and infections. Although IL-33 has been indicated to be involved in Staphylococcus aureus (S. aureus) wound infection, little is known about how IL-33 is regulated as a mechanism to increase host defense against skin bacterial infections. To explore the underlying intricate mechanism we first evaluated the expression of IL-33 in skin from S. aureus-infected human patients. Compared to normal controls, IL-33 was abundantly increased in skin of S. aureus-infected patients. We next developed a S. aureus cutaneous infection mouse model and found that IL-33 was significantly increased in dermal macrophages of infected mouse skin. The expression of IL-33 by macrophages was induced by staphylococcal peptidoglycan (PGN) and lipoteichoic acid (LTA) via activation of toll-like receptor 2(TLR2) –mitogen-activated protein kinase (MAPK)-AKT-signal transducer and activator of transcription 3(STAT3) signaling pathway as PGN and LTA failed to induce IL-33 in Tlr2-deficient peritoneal macrophages, and MAPK,AKT, STAT3 inhibitors significantly decreased PGN- or LTA-induced IL-33. IL-33, in turn, acted on macrophages to induce microbicidal nitric oxygen (NO) release. This induction was dependent on inducible nitric oxide synthase (iNOS) activation, as treatment of macrophages with an inhibitor of iNOS, aminoguanidine, significantly decreased IL-33-induced NO release. Moreover, aminoguanidine significantly blocked the capacity of IL-33 to inhibit the growth of S. aureus, and IL-33 silencing in macrophages significantly increased the survival of S. aureus in macrophages. Furthermore, the administration of IL-33-neutralizing antibody into mouse skin decreased iNOS production but increased the survival of S. aureus in skin. These findings reveal that IL-33 can promote antimicrobial capacity of dermal macrophages, thus enhancing antimicrobial defense against skin bacterial infections. [ABSTRACT FROM AUTHOR]