An improved global resilience assessment method for urban drainage systems: A case study of Haidian Island, south China.

Resilience assessment for urban drainage systems is a fundamental aspect of building resilient cities. Recently, some scholars have proposed the Global Resilience Analysis (GRA) method, which assesses resilience based on the functional performance of different system failure scenarios. Compared to traditional system dynamics methods, the GRA method considers the impact of internal structural failure on resilience but requires a large amount of computation. This research proposed an improved GRA method to enhance computational efficiency and practicality by reducing the number of system scenario simulations. Firstly, a hydrodynamic model of the drainage network of Haidian Island has been constructed using the Storm Water Management Model (SWMM) and Python. Secondly, the GRA method was improved using cluster analysis and convergence analysis to reduce the simulation scenarios. Thirdly, a resilience assessment index was established through system function functions, and two types of resilience enhancement measures, centralized and distributed, were proposed. The results show: (i) resilience assessment increases the computational efficiency by 25% compared to the traditional GRA method; (ii) the resilience index of the existing drainage network within Haidian Island is less than the design value (0.7) in all failure scenarios, indicating a lower level of recovery capability; (iii) compared to the centralized strategy, which is only effective when the system failure level is less than 9%, the distributed strategy enhances the resilience of the urban drainage system at a higher failure level (77%).

Singlet Fission in a New Series of Systematically Designed Through-space Coupled Tetracene Oligomers.

Singlet fission (SF) holds great promise for current photovoltaic technologies, where tetracenes, with their relatively high triplet energies, play a major role for application in silicon-based solar cells. However, the SF efficiencies in tetracene dimers are low due to the unfavorable energetics of their singlet and triplet energy levels. In the solid state, tetracene exhibits high yields of triplet formation through SF, raising great interest about the underlying mechanisms. To address this discrepancy, we designed and prepared a novel molecular system based on a hexaphenylbenzene core decorated with 2 to 6 tetracene chromophores. The spatial arrangement of tetracene units, induced by steric hindrance in the central part, dictates through-space coupling, making it a relevant model for solid-state chromophore organization. We then revealed a remarkable increase in SF quantum yield with the number of tetracenes, reaching quantitative (196 %) triplet pair formation in hexamer. We observed a short-lived correlated triplet pair and limited magnetic effects, indicating ineffective triplet dissociation in these through-space coupled systems. These findings emphasize the crucial role of the number of chromophores involved and the interchromophore arrangement for the SF efficiency. The insights gained from this study will aid designing more efficient and technology-compatible SF systems for applications in photovoltaics.

Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments.

To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of several months without aggregation or degradation, and with excellent reproducibility. The sedimentation and diffusion coefficients of linearized and nicked minicircle DNA demonstrated a highly homogeneous sample, and increased with temperature, indicating a decrease in friction. The sedimentation of linearized DNA was the slowest; supercoiled DNA sedimented the fastest. With increasing temperature, the supercoiled samples shifted to slower sedimentation, but sedimented faster than nicked minicircles. These results suggest that negatively supercoiled DNA becomes less compact at higher temperatures. The supercoiled minicircles, as purified from bacteria, displayed heterogeneity. Therefore, supercoiled DNA isolated from bacteria is unsuitable as a molecular standard. Linear and nicked samples are well suited as a molecular standard for AUC and have exceptional colloidal stability in an AUC cell. Even after sixty experiments at different speeds and temperatures, measured over the course of 4 months, all topological states of DNA remained colloidal, and their concentrations remained essentially unchanged.

Strong non-ideality effects at low protein concentrations: considerations for elongated proteins.

A recent investigation was aimed at obtaining structural information on a highly extended protein via SEC-MALS-SAXS. Significantly broadened elution peaks were observed, reminiscent of a phenomenon known as viscous fingering. This phenomenon is usually observed above 50 mg/mL for proteins like bovine serum albumin (BSA). Interestingly, the highly extended protein (Brpt5.5) showed viscous fingering at concentrations lower than 5 mg/mL. The current study explores this and other non-ideal behavior, emphasizing the presence of these effects at relatively low concentrations for extended proteins. BSA, Brpt5.5, and a truncated form of Brpt5.5 referred to as Brpt1.5 are studied systematically using size-exclusion chromatography (SEC), sedimentation velocity analytical ultracentrifugation (AUC), and viscosity. The viscous fingering effect is quantified using two approaches and is found to correlate well with the intrinsic viscosity of the proteins-Brpt5.5 exhibits the most severe effect and is the most extended protein tested in the study. By AUC, the hydrodynamic non-ideality was measured for each protein via global analysis of a concentration series. Compared to BSA, both Brpt1.5 and Brpt5.5 showed significant non-ideality that could be easily visualized at concentrations at or below 5 mg/mL and 1 mg/mL, respectively. A variety of relationships were examined for their ability to differentiate the proteins by shape using information from AUC and/or viscosity. Furthermore, these relationships were also tested in the context of hydrodynamic modeling. The importance of considering non-ideality when investigating the structure of extended macromolecules is discussed.

Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus.

Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.

A global analysis of literature on older adults and lifelong living with HIV.

With the growing number of older people living with HIV, "What is the most effective geriatric care and the research trend of existing literature?" is a compelling question after 30 years since the first paper related to aging and HIV/AIDS published. Our study aims to apply quantitative and qualitative analysis to explore the knowledge gaps and describes the research interest of gerontology research in the field of HIV. A bibliometric analysis was conducted based on the databased of the Web of Science from 1991 to 2019. The major domains of research areas were visualized by using VOSviewer software. Latent Dirichlet Allocation (LDA) was applied to classify the dataset into topics. There was a rising number of publications about this topic over time. Our findings indicated that antiretroviral treatment and evaluating quality of life and harm reduction were the major domains regarding care for OPLWH. In addition, the finding highlights the role of social competence in treatment outcomes. Further research needs to tailor multi-disciplinary programs and flexible interventions to reduce the burden and the mortality rate of HIV/AIDS.

Ultrafast Excited-State Decay Mechanisms of 6-Thioguanine Followed by Sub-20 fs UV Transient Absorption Spectroscopy.

Understanding the primary steps following UV photoexcitation in sulphur-substituted DNA bases (thiobases) is fundamental for developing new phototherapeutic drugs. However, the investigation of the excited-state dynamics in sub-100 fs time scales has been elusive until now due to technical challenges. Here, we track the ultrafast decay mechanisms that lead to the electron trapping in the triplet manifold for 6-thioguanine in an aqueous solution, using broadband transient absorption spectroscopy with a sub-20 fs temporal resolution. We obtain experimental evidence of the fast internal conversion from the S2(ππ*) to the S1(nπ*) states, which takes place in about 80 fs and demonstrates that the S1(nπ*) state acts as a doorway to the triplet population in 522 fs. Our results are supported by MS-CASPT2 calculations, predicting a planar S2(ππ*) pseudo-minimum in agreement with the stimulated emission signal observed in the experiment.

The Binding Pocket at the Interface of Multimeric Telomere G-quadruplexes: Myth or Reality?

Human telomeric DNA with hundreds of repeats of the 5'-TTAGGG-3' motif plays a crucial role in several biological processes. It folds into G-quadruplex (G4) structures and features a pocket at the interface of two contiguous G4 blocks. Up to now no structural NMR and crystallographic data are available for ligands interacting with contiguous G4s. Naphthalene diimide monomers and dyads were investigated as ligands of a dimeric G4 of human telomeric DNA comparing the results with those of the model monomeric G4. Time-resolved fluorescence, circular dichroism, isothermal titration calorimetry and molecular modeling were used to elucidate binding features. Ligand fluorescence lifetime and induced circular dichroism unveiled occupancy of the binding site at the interface. Thermodynamic parameters confirmed the hypothesis as they remarkably change for the dyad complexes of the monomeric and dimeric telomeric G4. The bi-functional ligand structure of the dyads is a fundamental requisite for binding at the G4 interface as only the dyads engage in complexes with 1 : 1 stoichiometry, lodging in the pocket at the interface and establishing multiple interactions with the DNA skeleton. In the absence of NMR and crystallographic data, our study affords important proofs of binding at the interface pocket and clues on the role played by the ligand structure.

Global changes in soil organic carbon and implications for land degradation neutrality and climate stability.

Soil organic carbon (SOC) is a critical indicator for healthy and fertile lands across the world. It is also the planet's largest terrestrial carbon pool, so any changes of this pool may have profound implications for both land productivity and climate stability. However, SOC changes have so far remained largely unexplored, although their understanding is essential for many international environmental policies. Here we investigate for the first time recent global SOC changes, based on some SOC stock interannual data that were processed for the 2001-2015 period on a planetary scale. We analysed the global SOC dynamics using the Mann-Kendall test and Sen's slope estimator, which are widely acknowledged to be reliable geostatistical tools for detecting various environmental trends from global to local scale. We explored SOC changes via three metrics (averages, quantities, areas) of negative and positive trends, but also of the balance between soil carbon trends, a key statistic for monitoring land quality stability and soil-atmosphere carbon fluxes in the global environmental policies. Globally, we estimated a net average decrease of -58.6 t C km2 yr-1, a total loss of ~3.1 Pg C, and an area affected by net SOC losses of ~1.9 million km2. Using this triple statistic, we found that 79% of countries worldwide have been affected by net declines of SOC after 2001, which suggests that halting land degradation and mitigating climate change through the SOC pathway are still far from being achieved by international policies.

Impact of lockdown during the COVID-19 outbreak on multi-scale air quality.

One of the multi-facet impacts of lockdowns during the unprecedented COVID-19 pandemic was restricted economic and transport activities. This has resulted in the reduction of air pollution concentrations observed globally. This study is aimed at examining the concentration changes in air pollutants (i.e., carbon monoxide (CO), nitrogen dioxide (NO2), sulfur dioxide (SO2), ozone (O3), and particulate matters (PM2.5 and PM10) during the period March-April 2020. Data from both satellite observations (for NO2) and ground-based measurements (for all other pollutants) were utilized to analyze the changes when compared against the same months between 2015 and 2019. Globally, space borne NO2 column observations observed by satellite (OMI on Aura) were reduced by approximately 9.19% and 9.57%, in March and April 2020, respectively because of public health measures enforced to contain the coronavirus disease outbreak (COVID-19). On a regional scale and after accounting for the effects of meteorological variability, most monitoring sites in Europe, USA, China, and India showed declines in CO, NO2, SO2, PM2.5, and PM10 concentrations during the period of analysis. An increase in O3 concentrations occurred during the same period. Meanwhile, four major cities case studies i.e. in New York City (USA), Milan (Italy), Wuhan (China), and New Delhi (India) have also shown a similar reduction trends as observed on the regional scale, and an increase in ozone concentration. This study highlights that the reductions in air pollutant concentrations have overall improved global air quality likely driven in part by economic slowdowns resulting from the global pandemic.

Primary processes in the bacterial reaction center probed by two-dimensional electronic spectroscopy.

In the initial steps of photosynthesis, reaction centers convert solar energy to stable charge-separated states with near-unity quantum efficiency. The reaction center from purple bacteria remains an important model system for probing the structure-function relationship and understanding mechanisms of photosynthetic charge separation. Here we perform 2D electronic spectroscopy (2DES) on bacterial reaction centers (BRCs) from two mutants of the purple bacterium Rhodobacter capsulatus, spanning the Q y absorption bands of the BRC. We analyze the 2DES data using a multiexcitation global-fitting approach that employs a common set of basis spectra for all excitation frequencies, incorporating inputs from the linear absorption spectrum and the BRC structure. We extract the exciton energies, resolving the previously hidden upper exciton state of the special pair. We show that the time-dependent 2DES data are well-represented by a two-step sequential reaction scheme in which charge separation proceeds from the excited state of the special pair (P*) to P+HA- via the intermediate P+BA- When inhomogeneous broadening and Stark shifts of the B* band are taken into account we can adequately describe the 2DES data without the need to introduce a second charge-separation pathway originating from the excited state of the monomeric bacteriochlorophyll BA*.

Responses of the Pheromone-Binding Protein of the Silk Moth Bombyx mori on a Graphene Biosensor Match Binding Constants in Solution.

An electronic biosensor for odors was assembled by immobilizing the silk moth Bombyx mori pheromone binding protein (BmorPBP1) on a reduced graphene oxide surface of a field-effect transistor. At physiological pH, the sensor detects the B. mori pheromones, bombykol and bombykal, with good affinity and specificity. Among the other odorants tested, only eugenol elicited a strong signal, while terpenoids and other odorants (linalool, geraniol, isoamyl acetate, and 2-isobutyl-3-methoxypyrazine) produced only very weak responses. Parallel binding assays were performed with the same protein and the same ligands, using the common fluorescence approach adopted for similar proteins. The results are in good agreement with the sensor's responses: bombykol and bombykal, together with eugenol, proved to be strong ligands, while the other compounds showed only poor affinity. When tested at pH 4, the protein failed to bind bombykol both in solution and when immobilized on the sensor. This result further indicates that the BmorPBP1 retains its full activity when immobilized on a surface, including the conformational change observed in acidic conditions. The good agreement between fluorescence assays and sensor responses suggests that ligand-binding assays in solution can be used to screen mutants of a binding protein when selecting the best form to be immobilized on a biosensor.

Combined FCS and PCH Analysis to Quantify Protein Dimerization in Living Cells.

Protein dimerization plays a crucial role in the regulation of numerous biological processes. However, detecting protein dimers in a cellular environment is still a challenge. Here we present a methodology to measure the extent of dimerization of GFP-tagged proteins in living cells, using a combination of fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis of single-color fluorescence fluctuation data. We named this analysis method brightness and diffusion global analysis (BDGA) and adapted it for biological purposes. Using cell lysates containing different ratios of GFP and tandem-dimer GFP (diGFP), we show that the average brightness per particle is proportional to the fraction of dimer present. We further adapted this methodology for its application in living cells, and we were able to distinguish GFP, diGFP, as well as ligand-induced dimerization of FKBP12 (FK506 binding protein 12)-GFP. While other analysis methods have only sporadically been used to study dimerization in living cells and may be prone to errors, this paper provides a robust approach for the investigation of any cytosolic protein using single-color fluorescence fluctuation spectroscopy.

Modelling excitation energy transfer and trapping in the filamentous cyanobacterium Anabaena variabilis PCC 7120.

The phycobilisome (PBS) serves as the major light-harvesting system, funnelling excitation energy to both photosystems (PS) in cyanobacteria and red algae. The picosecond kinetics involving the excitation energy transfer has been studied within the isolated systems and intact filaments of the cyanobacterium Anabaena variabilis PCC 7120. A target model is proposed which resolves the dynamics of the different chromophore groups. The energy transfer rate of 8.5 ± 1.0/ns from the rod to the core is the rate-limiting step, both in vivo and in vitro. The PBS-PSI-PSII supercomplex reveals efficient excitation energy migration from the low-energy allophycocyanin, which is the terminal emitter, in the PBS core to the chlorophyll a in the photosystems. The terminal emitter of the phycobilisome transfers energy to both PSI and PSII with a rate of 50 ± 10/ns, equally distributing the solar energy to both photosystems. Finally, the excitation energy is trapped by charge separation in the photosystems with trapping rates estimated to be 56 ± 6/ns in PSI and 14 ± 2/ns in PSII.

Global perspectives on the three criteria for premature ejaculation: An observational study of ejaculatory latency, ejaculatory control and bother/distress.

Criteria for premature ejaculation (PE) were established using Western-based samples, yet these criteria are applied worldwide for its diagnosis. This study (a) determined whether men from various world regions differ/agree on their views of ejaculation latency (ELT) and their perceptions of ejaculatory control and bother/distress, the three criteria for PE, and (b) compared PE and non-PE men across worldwide regions on these measures. 1,065 participants were recruited via social media to respond to a survey about men's typical, ideal and PE ELTs, about their own ELT, and about perceptions of ejaculatory control and bother/distress related to PE. Responses from men from four worldwide regions were compared to a reference group of North American/European men, and PE men were compared with non-PE men across three world regions. Results showed that most world region groups showed similarity in ELT estimations. The Sub-Saharan group focused more heavily on the importance of ejaculatory control. Both ELT and ejaculatory control differed between PE and non-PE groups in all regions assessed. In conclusion, perceived ELTs and ejaculatory control show substantial consistency across world regions despite geo-cultural variations and traditions. Such findings argue for the universality of the concepts of ELT, control and bother/distress related to PE.

Dynamics and Control of Peptide Self-Assembly and Aggregation.

The aggregation of proteins into fibrillar structures is a central process implicated in the onset and development of several devastating neuro-degenerative diseases, but can, in contrast to these pathological roles, also fulfil important biological functions. In both scenarios, an understanding of the mechanisms by which soluble proteins convert to their fibrillar forms represents a fundamental objective for molecular sciences. This chapter details the different classes of microscopic processes responsible for this conversion and discusses how they can be described by a mathematical formulation of the aggregation kinetics. We present easily accessible experimental quantities that allow the determination of the dominant pathways of aggregation, as well as a general strategy to obtain detailed solutions to the kinetic rate laws that yield the microscopic rate constants of the individual processes of nucleation and growth. This chapter discusses a framework for a structured approach to address key questions regarding the dynamics of protein aggregation and shows how the use of chemical kinetics to tackle complex biophysical systems can lead to a deeper understanding of the underlying physical and chemical principles.

Mechanisms of drought-induced dissipation of excitation energy in sun- and shade-adapted drought-tolerant mosses studied by fluorescence yield change and global and target analysis of fluorescence decay kinetics.

Some mosses stay green and survive long even under desiccation. Dissipation mechanisms of excess excitation energy were studied in two drought-tolerant moss species adapted to contrasting niches: shade-adapted Rhytidiadelphus squarrosus and sun-adapted Rhytidium rugosum in the same family. (1) Under wet conditions, a light-induced nonphotochemical quenching (NPQ) mechanism decreased the yield of photosystem II (PSII) fluorescence in both species. The NPQ extent saturated at a lower illumination intensity in R. squarrosus, suggesting a larger PSII antenna size. (2) Desiccation reduced the fluorescence intensities giving significantly lower F 0 levels and shortened the overall fluorescence lifetimes in both R. squarrosus and R. rugosum, at room temperature. (3) At 77 K, desiccation strongly reduced the PSII fluorescence intensity. This reduction was smaller in R. squarrosus than in R. rugosum. (4) Global and target analysis indicated two different mechanisms of energy dissipation in PSII under desiccation: the energy dissipation to a desiccation-formed strong fluorescence quencher in the PSII core in sun-adapted R. rugosum (type-A quenching) and (5) the moderate energy dissipation in the light-harvesting complex/PSII in shade-adapted R. squarrosus (type-B quenching). The two mechanisms are consistent with the different ecological niches of the two mosses.

Energy transfer and trapping in Synechococcus WH 7803.

Excitation energy transfer (EET) and trapping in Synechococcus WH 7803 whole cells and isolated photosystem I (PSI) complexes have been studied by time-resolved emission spectroscopy at room temperature (RT) and at 77 K. With the help of global and target analysis, the pathways of EET and the charge separation dynamics have been identified. Energy absorbed in the phycobilisome (PB) rods by the abundant phycoerythrin (PE) is funneled to phycocyanin (PC645) and from there to the core that contains allophycocyanin (APC660 and APC680). Intra-PB EET rates have been estimated to range from 11 to 68/ns. It was estimated that at RT, the terminal emitter of the phycobilisome, APC680, transfers its energy at a rate of 90/ns to PSI and at a rate of 50/ns to PSII. At 77 K, the redshifted Chl a states in the PSI core were heterogeneous, with maximum emission at 697 and 707 nm. In 72% of the PSI complexes, the bulk Chl a in equilibrium with F697 decayed with a main trapping lifetime of 39 ps.

A functional compartmental model of the Synechocystis PCC 6803 phycobilisome.

In the light-harvesting antenna of the Synechocystis PCC 6803 phycobilisome (PB), the core consists of three cylinders, each composed of four disks, whereas each of the six rods consists of up to three hexamers (Arteni et al., Biochim Biophys Acta 1787(4):272-279, 2009). The rods and core contain phycocyanin and allophycocyanin pigments, respectively. Together these pigments absorb light between 400 and 650 nm. Time-resolved difference absorption spectra from wild-type PB and rod mutants have been measured in different quenching and annihilation conditions. Based upon a global analysis of these data and of published time-resolved emission spectra, a functional compartmental model of the phycobilisome is proposed. The model describes all experiments with a common set of parameters. Three annihilation time constants are estimated, 3, 25, and 147 ps, which represent, respectively, intradisk, interdisk/intracylinder, and intercylinder annihilation. The species-associated difference absorption and emission spectra of two phycocyanin and two allophycocyanin pigments are consistently estimated, as well as all the excitation energy transfer rates. Thus, the wild-type PB containing 396 pigments can be described by a functional compartmental model of 22 compartments. When the interhexamer equilibration within a rod is not taken into account, this can be further simplified to ten compartments, which is the minimal model. In this model, the slowest excitation energy transfer rates are between the core cylinders (time constants 115-145 ps), and between the rods and the core (time constants 68-115 ps).

Accuracy and Utility of Estimating Lean Body Mass and Nutritional Status in Patients with Chronic Kidney Disease on Long-Term Hemodialysis Using Anthropometric Skinfold Thickness Measurements.

Malnutrition is common in patients on hemodialysis (prevalence of 30% to 50%) and is associated with higher mortality. Lean body mass (LBM) assessment is an accurate way of assessing nutritional status. The dual-energy X-ray absorptiometry (DEXA) scan is a reliable method in assessing body compositions and LBM; however, it is expensive and largely inaccessible. Anthropometric skinfold thickness measurement (ASFM) is useful in assessing LBM. It is cheaper and accessible, but underutilized clinically. The subjective global score (SGA) is a well-established method of assessing nutritional status. All three methods of assessing nutritional status were compared. In this pilot observational study, there was a significant correlation between LBM% estimated by DEXA and ASFM (mean difference -1.46% [95% CI -4.09 to 1.18]; LOA -14.0 to 11.1). Nutritional status by SGA could only detect those severely malnourished when using LBM% by ASFM as comparison. Our study demonstrated that ASFM is a useful method of assessing LBM and nutritional status, which can be easily utilized clinically.