Reconstruction of the medial patellofemoral ligament through a double bundle of a single patellar tract and quadriceps tendons combined with medial displacement of lateral hemi-tibial tuberosity for treating low-grade recurrent patella dislocation.

PURPOSE: The present study aimed to assess the clinical efficacy and imaging results of reconstruction of the medial patellofemoral ligament through a double bundle of single patellar tract and quadriceps tendons combined with medial displacement of lateral hemi-tibial tuberosity for treating low-grade recurrent patella dislocation. METHODS: Twenty-three patients with recurrent patellar dislocation, including ten males and 13 females, with 23 knee joints were enrolled according to the relevant criteria. Reconstruction of the medial patellofemoral ligament was performed through a double bundle of a single patellar tract and quadriceps tendons combined with medial displacement of lateral hemi-tibial tuberosity. Knee function was evaluated using visual analog scale (VAS) score, International Knee Documentation Committee (IKDC) score, Lysholm score, Tegner score, and Kujala score at pre- and postoperative stages. Patellar stability was assessed by CT scans measuring tibial tuberosity-trochlear groove (TT-TG) distance, lateral patella displacement (LPD), congruence angle (CA), and patellar tilt angle (PTA). RESULTS: All 23 patients were effectively followed up for 13-28 months (mean: 21.91 ± 4.14 months). At the last follow-up, the postoperative VAS score, IKDC score, Lysholm score, Tegner score, and Kujala score of 23 patients were 1.13 ± 0.82, 87.35 ± 3.17, 90.22 ± 1.28, 4.35 ± 0.65, and 89.26 ± 1.96, respectively, as compared to the preoperative values of 5.91 ± 1.13, 30.96 ± 5.09, 30.30 ± 2.98, 1.26 ± 0.62, and 27.87 ± 3.46, respectively, and these differences were statistically significant (P < 0.001). At the last follow-up, the postoperative TT-TG, LPD, CA, and PTA values of the 23 patients were 8.80 ± 1.85 mm, 6.01 ± 1.77 mm, 11.32 ± 6.18°, and 9.35 ± 2.88°, respectively, compared to the preoperative values of 18.77 ± 1.74 mm, 14.90 ± 4.07 mm, 37.82 ± 5.71°, and 23.58 ± 3.24°, respectively, and the differences were statistically significant (P < 0.001). No relevant complications were observed in the 23 patients. CONCLUSIONS: Reconstruction of the medial patellofemoral ligament through a double bundle of a single patellar tract and quadriceps tendons combined with medial displacement of lateral hemi-tibial tuberosity for treating low-grade recurrent patella dislocation showed satisfactory medium-term efficacy, and further investigations are required to confirm the long-term efficacy of this approach.

Anti-angiogenic effect of exo-LncRNA TUG1 in myocardial infarction and modulation by remote ischemic conditioning.

The successful use of exosomes in therapy after myocardial infarction depends on an improved understanding of their role in cardiac signaling and regulation. Here, we report that exosomes circulating after myocardial infarction (MI) carry LncRNA TUG1 which downregulates angiogenesis by disablement of the HIF-1α/VEGF-α axis and that this effect can be counterbalanced by remote ischemic conditioning (RIC). Rats with MI induced through left coronary artery ligation without (MI model) and with reperfusion (ischemia/reperfusion I/R model) were randomized to RIC, or MI (I/R) or sham-operated (SO) control. Data from one cohort study and one randomized-controlled trial of humans with MI were also utilized, the former involving patients who had not received percutaneous coronary intervention (PCI) and the latter patients with PCI. Exosome concentrations did not differ between intervention groups (RIC vs. control) in rats (MI and I/R model) as well as humans (with and without PCI). However, MI and I/R exosomes attenuated HIF-1α, VEGF-α, and endothelial function. LncRNA TUG1 was increased in MI and I/R exosomes, but decreased in SO and RIC exosomes. HIF-1α expression was downregulated with MI and I/R exosomes but increased with RIC exosomes. Exosome inhibition suppressed HIF-1α upregulation through RIC exosomes. VEGF-α was identified as HIF-1α-regulated target gene. Knockdown of HIF-1α decreased VEGF-α, endothelial cell capability, and tube formation. Overexpression of HIF-1α exerted opposite effects. Transfection and co-transfection of 293 T cells with exosome-inhibitor GW4869 and HIF-1α inhibitor si-HIF-1α confirmed the exosomal-LncRNA TUG1/HIF-1α/VEGF-α pathway. LncRNA TUG1 is a potential therapeutic target after MI with or without reperfusion through PCI.

Nonadiabatic Derivative Couplings Calculated Using Information of Potential Energy Surfaces without Wavefunctions: Ab Initio and Machine Learning Implementations.

In this work, we implemented an approximate algorithm for calculating nonadiabatic coupling matrix elements (NACMEs) of a polyatomic system with ab initio methods and machine learning (ML) models. Utilizing this algorithm, one can calculate NACMEs using only the information of potential energy surfaces (PESs), i.e., energies, and gradients as well as Hessian matrix elements. We used a realistic system, namely CH2NH, to compare NACMEs calculated by this approximate PES-based algorithm and the accurate wavefunction-based algorithm. Our results show that this approximate PES-based algorithm can give very accurate results comparable to the wavefunction-based algorithm except at energetically degenerate points, i.e., conical intersections. We also tested a machine learning (ML)-trained model with this approximate PES-based algorithm, which also supplied similarly accurate NACMEs but more efficiently. The advantage of this PES-based algorithm is its significant potential to combine with electronic structure methods that do not implement wavefunction-based algorithms, low-scaling energy-based fragment methods, etc., and in particular efficient ML models, to compute NACMEs. The present work could encourage further research on nonadiabatic processes of large systems simulated by ab initio nonadiabatic dynamics simulation methods in which NACMEs are always required.

Spatiotemporal dynamics and anthropologically dominated drivers of chlorophyll-a, TN and TP concentrations in the Pearl River Estuary based on retrieval algorithm and random forest regression.

Estimation of large-scale and high-precision water quality parameters is critical in explaining the spatiotemporal dynamics and the driving factors of water quality variability, especially in areas with environmental complexity (e.g., crisscrossing waterways, high flood risk in rainy season and seawater invasion). Thus, in this study, a retrieval algorithm was developed to predict chlorophyll-a (Chl-a), total nitrogen (TN) and total phosphorus (TP) concentrations in the Pearl River Estuary (PRE) based on a large amount of in situ measurements and Landsat 8 remote sensing images. Random Forest (RF) machine learning was conducted to identify the relationship between environmental indicators (pH, turbidity, conductivity, total dissolved solids and water temperature), Chl-a, TN and TP. The results showed that the NIR/R Binomial algorithm for Chl-a estimation presented appreciable reliability with R2 of 0.7429, root mean square error (RMSE) of 1.2089 and mean absolute percent error (MAPE) of 15.33%. The water quality variation in the PRE showed a characteristic of overall improvement and regional deterioration with average concentrations of 7.28 µg/L, 1.15 mg/L and 0.12 mg/L for Chl-a, TN, and TP respectively. Turbidity and pH were identified as the most important indicators to explain Chl-a (52.86%, 39.91%), TN (52.38%, 40.57%) and TP (55.23%, 40.03%) variation. Agricultural pollution was the main pollution source due to the intensive application of fertilizer and increased field size. Besides, land use patterns (e.g., increasing farmland but decreasing forest) greatly influenced water quality from 2010 to 2020. Moreover, light limitation caused by high turbidity reduced the algae productivity and further lowered the Chl-a concentration. The driving factors for regional water quality variations were anthropologically dominated and supplemented by climate change. This study improved the monitoring accuracy of regional water environment and provided quantitative early warning of water pollution events for environmental practitioners, so as to achieve long-term monitoring, precise pollution management and efficient water resources management.

Dynamic and driving evolution of lake basin pressure in cold and arid regions based on a new method: A case study of three lakes in Inner Mongolia, China.

Static single-path assessment methods usually underestimate the lake basin pressure (LBP). Considering the cumulative transmission of multiple paths, how to assess the dynamic changes of LBP and reveal the driving evolution is not clear. Here, taking Hulun, Daihai and Wuliangsuhai lake basins in the cold and arid region as the study case, we established an LBP assessment method that coupled multiple driving paths. For the first time, this study reveals the dynamic and driving evolution of LBP and found that rapid economic development and accelerated urbanization dramatically increased the LBPs in the three lakes. Specifically, the LBPs in the three lake basins has increased by 90%-270 % in the past 32 years, and they experienced a stable stage driven by climate (1987-1992), followed by a slight increasing stage driven by agriculture (1993-2004) and finally a significant increase stage (2005-2018) driven by industry and urbanization. Different degrees of warming, populations and development intensities of agriculture and livestock were the main factors driving the spatial differences in LBPs in the three lake basins. The LBPs in the Hulun, Daihai and Wuliangsuhai Lake Basins exhibited phase driving, continuous driving and ineffective driving characteristics to the water environment changes, respectively, which were related to lake basin governance. Compared with the driving paths of water quality and water quantity, the LBP was most strongly transmitted through the water ecological path. Rapid economic development and accelerated urbanization will bring greater LBPs to the lake basins. Lake management should promote the construction of water environmental protection mechanisms that correspond to urbanization, such as land use, and continue to strengthen watershed governance to alleviate the impact of LBP, especially the impact on the service functions of water ecosystem. Our method quantified the LBPs that were transmitted from different driving paths and provided action priorities for watershed management.

Prediction of harmful algal blooms in large water bodies using the combined EFDC and LSTM models.

Harmful algal blooms (HABs) is a worldwide water environmental problem. HABs usually happens in short time and is difficult to be controlled. Early warning of HABs using data-driven models is prospective in making time for taking precaution against HABs. High-frequency water quality monitoring data are necessary to improve the reliability of the model, but it is expensive. This research used environmental fluid dynamics code (EFDC) to extend one-point data obtained by only one instrument to the whole 249 ha water area instead of multi-instruments monitoring, followed by Long short-term memory (LSTM) to predict the HABs in the whole water body. Correlation analysis and principal component analysis were used to reduce the data dimension and improve model accuracy. Finally, the LSTM model was calibrated to predict chlorophyll-a (Chl-a) for the next 1 to 3 time steps. The Nash-Sutcliffe efficiency coefficient (NSE) and mean absolute percentage error (MAPE) of EFDC-LSTM were 0.797-0.991 and 2.74-13.16%, respectively, suggesting the promising utilization of this model in early warning systems for HABs. EFDC-LSTM achieves high-precision HABs forecasting in a cost-effective manner, providing a reliable way to detect HABs in advance.

Structurexplor: a platform for the exploration of structural features of RNA secondary structures.

SUMMARY: Discovering function-related structural features, such as the cloverleaf shape of transfer RNA secondary structures, is essential to understand RNA function. With this aim, we have developed a platform, named Structurexplor, to facilitate the exploration of structural features in populations of RNA secondary structures. It has been designed and developed to help biologists interactively search for, evaluate and select interesting structural features that can potentially explain RNA functions. AVAILABILITY AND IMPLEMENTATION: Structurxplor is a web application available at http://structurexplor.dinf.usherbrooke.ca. The source code can be found at http://jpsglouzon.github.io/structurexplor/. CONTACT: shengrui.wang@usherbrooke.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The super-n-motifs model: a novel alignment-free approach for representing and comparing RNA secondary structures.

MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations. The super-n-motifs model computes a vector representation of secondary structures as linear combinations of these motifs. RESULTS: We demonstrate the accuracy of our model for comparison of secondary structures from linear and circular RNA while also considering pseudoknot and G4 motifs. We show that the super-n-motifs representation effectively captures the most important structural features of secondary structures, as compared to other representations such as ordered tree, arc-annotated and string representations. Finally, we demonstrate the time efficiency of our model, which is alignment free and capable of performing large-scale comparisons of 10 000 secondary structures with an efficiency up to 4 orders of magnitude faster than existing approaches. AVAILABILITY AND IMPLEMENTATION: The super-n-motifs model was implemented in C ++. Source code and Linux binary are freely available at http://jpsglouzon.github.io/supernmotifs/ . CONTACT: Shengrui.Wang@Usherbrooke.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics o nline.

A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm.

Motivation: The identification of contaminating sequences in a de novo assembly is challenging because of the absence of information on the target species. For sample types where the target organism is impossible to isolate from its matrix, such as endoparasites, endosymbionts and soil-harvested samples, contamination is unavoidable. A few post-assembly decontamination methods are currently available but are based only on alignments to databases, which can lead to poor decontamination. Results: We present a new decontamination method based on a hierarchical clustering algorithm called MCSC. This method uses frequent patterns found in sequences to create clusters. These clusters are then linked to the target species or tagged as contaminants using classic alignment tools. The main advantage of this decontamination method is that it allows sequences to be tagged correctly even if they are unknown or misaligned to a database. Availability and Implementation: Scripts and documentation about the MCSC decontamination method are available at https://github.com/Lafond-LapalmeJ/MCSC_Decontamination . Contact: : benjamin.mimee@agr.gc.ca. Supplementary information: Supplementary data are available at Bioinformatics online.

Transfer Mechanism, Uptake Kinetic Process, and Bioavailability of P, Cu, Cd, Pb, and Zn in Macrophyte Rhizosphere Using Diffusive Gradients in Thin Films.

The transfer-uptake-bioavailability of phosphorus (P), Cu, Cd, Zn, and Pb in rhizosphere of Zizania latifolia (ZL) and Myriophyllum verticiilaturn (MV) cultivated in rhizoboxes in Lake Erhai (China) is evaluated by DGT (diffusive gradients in thin films) technique. DGT induced fluxes in sediments (DIFS) model reveals that resupply ability (r), liable pool size in sediment solid (kd), kinetic parameter (k-1), or response time (Tc) control the diffusion-resupply characters of P and Cu (standing for four metals) in rhizosphere interface. The linear fitting curves of element content in ZL or MV roots (Croot) against DGT (CDGT), porewater (C0), or sediment concentration demonstrate that Croot for five elements can be predicted by CDGT more effectively than the other methods. (I) DOC (dissolved organic carbon) in porewater controlled by OM (organic matter) in solid plus pH for Cu and Cd or (II) DOP/DTP ratio in porewater (between dissolved organic P and dissolved total P) for P controlled by Fe-bound P and OM in solid, can affect phytoavailability in rhizosphere. They lead to (I) the larger slope (s) and the linear regression coefficient (R2) in the first part than those for the complete fitting curve (ZL or MV root against CDGT(Cu) or C0(Cu) and MV root against CDGT(Cd)) or (II) the outliers above or below the fitting curve (ZL root (P) against C0(P) or CDGT(P)) and the larger R2 without outliers. DGT-rhizobox-DIFS should be a reliable tool to research phytoremediation mechanism of macrophytes.

Accuracy and generalizability of using automated methods for identifying adverse events from electronic health record data: a validation study protocol.

BACKGROUND: Adverse events (AEs) in acute care hospitals are frequent and associated with significant morbidity, mortality, and costs. Measuring AEs is necessary for quality improvement and benchmarking purposes, but current detection methods lack in accuracy, efficiency, and generalizability. The growing availability of electronic health records (EHR) and the development of natural language processing techniques for encoding narrative data offer an opportunity to develop potentially better methods. The purpose of this study is to determine the accuracy and generalizability of using automated methods for detecting three high-incidence and high-impact AEs from EHR data: a) hospital-acquired pneumonia, b) ventilator-associated event and, c) central line-associated bloodstream infection. METHODS: This validation study will be conducted among medical, surgical and ICU patients admitted between 2013 and 2016 to the Centre hospitalier universitaire de Sherbrooke (CHUS) and the McGill University Health Centre (MUHC), which has both French and English sites. A random 60% sample of CHUS patients will be used for model development purposes (cohort 1, development set). Using a random sample of these patients, a reference standard assessment of their medical chart will be performed. Multivariate logistic regression and the area under the curve (AUC) will be employed to iteratively develop and optimize three automated AE detection models (i.e., one per AE of interest) using EHR data from the CHUS. These models will then be validated on a random sample of the remaining 40% of CHUS patients (cohort 1, internal validation set) using chart review to assess accuracy. The most accurate models developed and validated at the CHUS will then be applied to EHR data from a random sample of patients admitted to the MUHC French site (cohort 2) and English site (cohort 3)-a critical requirement given the use of narrative data -, and accuracy will be assessed using chart review. Generalizability will be determined by comparing AUCs from cohorts 2 and 3 to those from cohort 1. DISCUSSION: This study will likely produce more accurate and efficient measures of AEs. These measures could be used to assess the incidence rates of AEs, evaluate the success of preventive interventions, or benchmark performance across hospitals.

Adsorption of Lysine on Na-Montmorillonite and Competition with Ca(2+): A Combined XRD and ATR-FTIR Study.

Lysine adsorption at clay/aqueous interfaces plays an important role in the mobility, bioavailability, and degradation of amino acids in the environment. Knowledge of these interfacial interactions facilitates our full understanding of the fate and transport of amino acids. Here, X-ray diffraction (XRD) and attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR) measurements were used to explore the dynamic process of lysine adsorption on montmorillonite and the competition with Ca(2+) at the molecular level. Density functional theory (DFT) calculations were employed to determine the peak assignments of dissolved lysine in the solution phase. Three surface complexes, including dicationic, cationic, and zwitterionic structures, were observed to attach to the clay edge sites and penetrate the interlayer space. The increased surface coverage and Ca(2+) competition did not affect the interfacial lysine structures at a certain pH, whereas an elevated lysine concentration contributed to zwitterionic-type coordination at pH 10. Moreover, clay dissolution at pH 4 could be inhibited at a higher surface coverage with 5 and 10 mM lysine, whereas the inhibition effect was inconspicuous or undetected at pH 7 and 10. The presence of Ca(2+) not only could remove a part of the adsorbed lysine but also could facilitate the readsorption of dissolved Si(4+) and Al(3+) and surface protonation. Our results provide new insights into the process of lysine adsorption and its effects on montmorillonite surface sites.

Molecular-Scale Study of Aspartate Adsorption on Goethite and Competition with Phosphate.

Knowledge of the interfacial interactions between aspartate and minerals, especially its competition with phosphate, is critical to understanding the fate and transport of amino acids in the environment. Adsorption reactions play important roles in the mobility, bioavailability, and degradation of aspartate and phosphate. Attenuated total reflectance Fourier-transform infrared (ATR-FTIR) measurements and density functional theory (DFT) calculations were used to investigate the interfacial structures and their relative contributions in single-adsorbate and competition systems. Our results suggest three dominant mechanisms for aspartate: bidentate inner-sphere coordination involving both α- and γ-COO(-), outer-sphere complexation via electrostatic attraction and H-bonding between aspartate NH2 and goethite surface hydroxyls. The interfacial aspartate is mainly governed by pH and is less sensitive to changes of ionic strength and aspartate concentration. The phosphate competition significantly reduces the adsorption capacity of aspartate on goethite. Whereas phosphate adsorption is less affected by the presence of aspartate, including the relative contributions of diprotonated monodentate, monoprotonated bidentate, and nonprotonated bidentate structures. The adsorption process facilitates the removal of bioavailable aspartate and phosphate from the soil solution as well as from the sediment pore water and the overlying water.

Multi-metals Measured at Sediment-Water Interface (SWI) by Diffusive Gradients in Thin Films (DGT) Technique for Geochemical Research.

Diffusive gradients in thin films (DGT) technique was used to determine pore water profile and to assess remobilization character of metals at sediment/water interface. The remobilization of Mn was due to redox reaction in profile, which engendered two large peaks: one with DGT concentration of 1355 µg L(-1) at depth of -4.75 cm in sediment and the other with DGT concentration of 1040 µg L(-1) at depth of -3.25 cm in sediment pore water. Fe reduction zone had a large peak of Fe (3209 µg L(-1)) at depth of -4.75 cm in sediment. Fe DGT-profile also indicated the little peaks and low values of dissolved Fe concentration in Fe-reduction/S-reduction boundary zone in sediment. Detailed correspondence of trace metals with Fe or Mn features in DGT-profiles suggested that their release is related to the reductive dissolution of Fe- or Mn-oxide.

[Compositional Characteristics of Sediment Dissolved Organic Nitrogen in Typical Lakes and Its Relationship on Water Trophic Status].

UV-Vis absorbance, fluorescence, and Gas Chromatography Mass Spectrometry (GC-MS) were applied to the comparative study on sediment dissolved organic nitrogen (DON) in five typical lakes (Erhai lake, Dianchilake, Poyang lake, Wuhan Dong lake, and Taihu lake) in different lake regions with different nutrition status, revealing the relationship between structural and compositional characteristics of sediment DON and trophic level of lakes. The obtained results showed that: ①Structure of lake sediment DON in Yungui Plateau region is more stable, compared with those in Eastern Plain region, indicating its lower bioavailability. ②In Yungui Plateau region, the source and compositional characteristics of sediment DON weremore complex in Dianchi lake (a seriously polluted lake), and its sediment DON bioavailabilitywas relatively higher. While, with respect to the less polluted Erhai lake, the source of sediment DON is more simple with a higher stability in DON structure and composition, which is beneficial for maintaining its good water quality. ③In Eastern Plain region, nutrition status of Taihu lake was similer to Donghu lake. The structure and composition of sediment DON was complex. But the lower aromaticityand fewer Aromatic ring substituents abundance made their relatively weak nutrient retention ability, posing risk to water quality. With regard to Poyang Lake, the structure and composition of sediment DON was relatively simple, but nutrient retention ability was relatively strong, which played a positive role in maintaining good water quality. ④P(Ⅲ+Ⅴ, n)/P(Ⅰ+Ⅱ, n) values(the content ratio of humic-like substanceto protein-like substances)were in sequence of Dianchi Lake (33.14)>Erhai Lake(21.49)>Taihu Lake(9.06)>Donghu Lake(7.04)>Poyang Lake(4.83), while E(4)/E(6) values (the ratio of UV-Vis absorbance at 465 and 665 nm) were in sequence of Dianchi Lake (27.00)>Donghu Lake(6.65)>Poyang Lake(5.47)>Taihu(3.50)>Erhai Lake(2.31). In addition, P(Ⅲ+Ⅴ, n)/P(Ⅰ+Ⅱ, n) and E(4)/E(6) valueswere positively correlated with thecontents of the different nitrogen (N) forms in the sediments. The above information suggested that P(Ⅲ+Ⅴ, n)/P(Ⅰ+Ⅱ, n) and E(4)/E(6) values exhibited good discrimination degree among different trophic status lakes, and they were considered to indirectly indicate the nutrition levels of lakes to a certain extent.

Protective effects of puerarin against tetrabromobisphenol a-induced apoptosis and cardiac developmental toxicity in zebrafish embryo-larvae.

Tetrabromobisphenol A (TBBPA), a brominated flame retardant, is detected commonly in aquatic environments, where it is thought to be highly toxic to the development of aquatic life. In this study, zebrafish embryos and larvae were used to investigate the protective effects of puerarin after exposure to TBBPA. Malformation, blood flow disorders, pericardial edema, and spawn coagulation rates increased, whereas survival decreased significantly after exposure to 0.5 and 1.0 mg L(-1) TBBPA. The measured indices of morphological toxicity improved after treatment with puerarin. TBBPA also induced reactive oxygen species (ROS) production in a dose-dependent manner. Acridine orange staining results revealed that TBBPA exposure caused cardiomyocyte apoptosis and induced the expression of three proapoptotic genes: P53, Bax, and Caspase9. In contrast, the expression of the antiapoptotic gene Bcl2 was down-regulated. When genes related to cardiac development were assessed, the expression of Tbx1, Raldh2, and Bmp2b changed after exposure to the combination of TBBPA and puerarin. These results suggest that TBBPA induces cardiomyocyte apoptosis and ROS production, resulting in cardiac developmental toxicity in zebrafish embryos or larvae. Therefore, puerarin regulates the expression of cardiac developmental genes, such as Tbx1, Bmp2b, and Raldh2 by inhibiting ROS production, and subsequently modulates cardiac development after the exposure of zebrafish larvae to TBBPA.

Resolving the influence of nitrogen abundances on sediment organic matter in macrophyte-dominated lakes, using fluorescence spectroscopy.

A controlled experiment was designed to resolve the influence of nitrogen abundance on sediment organic matters in macrophyte-dominated lakes using fluorescence analysis. Macrophyte biomass showed coincident growth trends with time, but different variation rates with nitrogen treatment. All plant growth indexes with nitrogen addition (N, NH4Cl 100, 200, 400mg/kg, respectively) were lower than those of the control group. Four humic-like components, two autochthonous tryptophan-like components, and one autochthonous tyrosine-like component were identified using the parallel factor analysis model. The results suggested that the relative component changes of fluorescence in the colonized sediments were in direct relation to the change of root biomass with time. In the experiment, the root formation parameters of the plants studied were significantly affected by adding N in sediments, which may be related to the reason that the root growth was affected by N addition. Adding a low concentration of N to sediments can play a part in supplying nutrients to the plants. However, the intensive uptake of NH4(+) may result in an increase in the intracellular concentration of ammonia, which is highly toxic to the plant cells. Hence, our experiment results manifested that organic matter cycling in the macrophyte-dominated sediment was influenced by nitrogen enrichment through influencing vegetation and relevant microbial activity.

NGS++: a library for rapid prototyping of epigenomics software tools.

MOTIVATION: The development of computational tools to enable testing and analysis of high-throughput-sequencing data is essential to modern genomics research. However, although multiple frameworks have been developed to facilitate access to these tools, comparatively little effort has been made at implementing low-level programming libraries to increase the speed and ease of their development. RESULTS: We propose NGS++, a programming library in C++11 specialized in manipulating both next-generation sequencing (NGS) datasets and genomic information files. This library allows easy integration of new formats and rapid prototyping of new functionalities with a focus on the analysis of genomic regions and features. It offers a powerful, yet versatile and easily extensible interface to read, write and manipulate multiple genomic file formats. By standardizing the internal data structures and presenting a common interface to the data parser, NGS++ offers an effective framework for epigenomics tool development. AVAILABILITY: NGS++ was written in C++ using the C++11 standard. It requires minimal efforts to build and is well-documented via a complete docXygen guide, online documentation and tutorials. Source code, tests, code examples and documentation are available via the website at http://www.ngsplusplus.ca and the github repository at https://github.com/NGS-lib/NGSplusplus. CONTACT: nicolas.gevry@usherbrooke.ca or arnaud.droit@crchuq.ulaval.ca.

[Optical signatures of chromophoric dissolved organic matter in water body of Tien Lake].

The water samples of the Tien Lake were collected for the three-dimensional fluorescence spectrum detected. And parallel factor analysis (PARAFAC) and principal component analysis (PCA) were used for the spectra analyzing to know the main factor and relative contribution of the chromophoric dissolved organic matter (CDOM). PARAFAC decomposed CDOM into four components, the humic-like: C1 (240, 415), C3 (265, 525), C4 (255, 505) and the protein-like: C2(230/280, 330). The fluorescence intensity of CDOM components was high in north and estuary of the lake, but low in the other region. All the four components show significant positive correlations (p < 0.01), this result means they may have the same sources. Principal component analysis shows that these four components of the Tien Lake are all from terrestrial organic matter, meanwhile its DTN, DTP, DON may also come with the terrestrial substance. These components of Tien Lake can well be connected with dissolved nutrient salts by nonlinear multiple regression, which means we can use the three-dimensional fluorescence spectrum results of CDOM to indicate the eutrophication degree of Tien Lake.

Nuclear Quantum Effects on Nonadiabatic Dynamics of a Green Fluorescent Protein Chromophore Analogue: Ring-Polymer Surface-Hopping Simulation.

Herein, we have used the "on-the-fly" ring-polymer surface-hopping simulation method with the centroid approximation (RPSH-CA), in combination with the multireference OM2/MRCI electronic structure calculations to study the photoinduced dynamics of a green fluorescent protein (GFP) chromophore analogue in the gas phase, i.e., o-HBI, at 50, 100, and 300 K with 1, 5, 10, and 15 beads (3600 1 ps trajectories). The electronic structure calculations identified five new minimum-energy conical intersection (MECI) structures, which, together with the previous one, play crucial roles in the excited-state decay dynamics of o-HBI. It is also found that the excited-state intramolecular proton transfer (ESIPT) occurs in an ultrafast manner and is completed within 20 fs in all the simulation conditions because there is no barrier associated with this ESIPT process in the S1 state. However, the other excited-state dynamical results are strongly related to the number of beads. At 50 and 100 K, the nuclear quantum effects (NQEs) are very important; therefore, the excited-state dynamical results change significantly with the bead number. For example, the S1 decay time deduced from time-dependent state populations becomes longer as the bead number increases. Nevertheless, an essentially convergent trend is observed when the bead number is close to 10. In contrast, at 300 K, the NQEs become weaker and the above dynamical results converge very quickly even with 1 bead. Most importantly, the NQEs seriously affect the excited-state decay mechanism of o-HBI. At 50 and 100 K, most trajectories decay to the S0 state via perpendicular keto MECIs, whereas, at 300 K, only twisted keto MECIs are responsible for the excited-state decay. The present work not only comprehensively explores the temperature-dependent photoinduced dynamics of o-HBI, but also demonstrates the importance and necessity of NQEs in nonadiabatic dynamics simulations, especially at relatively low temperatures.