Stabilized Co‐Free Li‐Rich Oxide Cathode Particles with An Artificial Surface Prereconstruction

Li‐rich metal oxide (LXMO) cathodes have attracted intense interest for rechargeable batteries because of their high capacity above 250 mAh g^?1. However, the side effects of hybrid anion and cation redox (HACR) reactions, such as oxygen release and phase collapse that result from global oxygen migration (GOM), have prohibited the commercialization of LXMO. GOM not only destabilizes the oxygen sublattice in cycling, aggravating the well‐known voltage fading, but also intensifies electrolyte decomposition and Mn dissolution, causing severe full‐cell performance degradation. Herein, an artificial surface prereconstruction (ASR) for Li_1.2Mn_0.6Ni_0.2O₂ particles with a molten‐molybdate leaching is conducted, which creates a crystal‐dense anion‐redox‐free LiMn_1.5Ni_0.5O₄ shell that completely encloses the LXMO lattice (ASR‐LXMO). Differential electrochemical mass spectroscopy and soft X‐ray absorption spectroscopy analyses demonstrate that GOM is shut down in cycling, which not only stabilizes HACR in ASR‐LXMO, but also mitigates the electrolyte decomposition and Mn dissolution. ASR‐LXMO displays greatly stabilized cycling performance as it retains 237.4 mAh g^?1 with an average discharge voltage of 3.30 V after 200 cycles. More crucially, while the pristine LXMO cycling cannot survive 90 cycles in a pouch full‐cell matched with a commercial graphite anode and lean (2 g A^?1 h^?1) electrolyte, ASR‐LXMO shows high capacity retention of 76% after 125 cycles in full‐cell cycling.     

Validation of delay‐multiply‐and‐standard‐deviation weighting factor for improved photoacoustic imaging of sentinel lymph node

Delay‐and‐sum (DAS) is one of the most common algorithms used to construct the photoacoustic images due to its low complexity. However, it results in images with high sidelobes and low resolution. Delay‐and‐standard‐deviation (DASD) weighting factor can improve the contrast of the images compared to DAS. However, it still suffers from high sidelobes. In this work, a new weighting factor, named delay‐multiply‐and‐standard‐deviation (DMASD) is introduced to enhance the contrast of the reconstructed images compared to other mentioned methods. In the proposed method, the SD of the mutual multiplied delayed signals are calculated, normalized and multiplied to DAS beamformed data. The results show that DMASD improves the signal‐to‐noise‐ratio about 19.29 and 7.3 dB compared to DAS and DASD, respectively, for in vivo imaging of the sentinel lymph node. Moreover, the contrast ratio is improved by the DMASD about 23.61 and 10.81 dB compared to DAS and DASD, respectively.      

Reconstructing grassy understories in south‐eastern Australia: Interview with Paul Gibson‐Roy

A marriage of ecology with agronomy is proving successful in restoring diverse herbaceous layers ‐ to the extent that some reconstructed grasslands on ex‐agricultural land and rural roadsides have been found eligible for federal protection as threatened ecological communities. Can lessons from this improve our management and expansion of grassy ecosystems more broadly?     

Bayesian sparse‐based reconstruction in bioluminescence tomography improves localization accuracy and reduces computational time

Bioluminescence tomography (BLT) provides fundamental insight into biological processes in vivo. To fully realize its potential, it is important to develop image reconstruction algorithms that accurately visualize and quantify the bioluminescence signals taking advantage of limited boundary measurements. In this study, a new 2‐step reconstruction method for BLT is developed by taking advantage of the sparse a priori information of the light emission using multispectral measurements. The first step infers a wavelength‐dependent prior by using all multi‐wavelength measurements. The second step reconstructs the source distribution based on this developed prior. Simulation, phantom and in vivo results were performed to assess and compare the accuracy and the computational efficiency of this algorithm with conventional sparsity‐promoting BLT reconstruction algorithms, and results indicate that the position errors are reduced from a few millimeters down to submillimeter, and reconstruction time is reduced by 3 orders of magnitude in most cases, to just under a few seconds. The recovery of single objects and multiple (2 and 3) small objects is simulated, and the recovery of images of a mouse phantom and an experimental animal with an existing luminescent source in the abdomen is demonstrated. Matlab code is available at https://github.com/jinchaofeng/code/tree/master .      

Phylogeographical and cross‐species transmission dynamics of SAT1 and SAT2 foot‐and‐mouth disease virus in Eastern Africa

Understanding the dynamics of foot‐and‐mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (p = 0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (p = 0.72). Salient (Bayes factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities.     

Structurally Reconstructed CsPbI2Br Perovskite for Highly Stable and Square‐Centimeter All‐Inorganic Perovskite Solar Cells

Although all‐inorganic perovskite solar cells (PSCs) demonstrate high thermal stability, cesium‐lead halide perovskites with high iodine content suffer from poor stability of the black phase (α‐phase). In this study, it is demonstrated that incorporating InCl₃ into the host perovskite lattice helps to inhibit the formation of yellow phase (δ‐phase) perovskite and thereby enhances the long‐term ambient stability. The enhanced stability is achieved by a strategy for the structural reconstruction of CsPbI₂Br perovskite by means of In³⁺ and Cl^? codoping, which gives rise to a significant improvement in the overall spatial symmetry with a closely packed atom arrangement due to the crystal structure transformation from orthorhombic (Pnma) to cubic (Pm‐3m). In addition, a novel thermal radiation heating method that further improves the uniformity of the perovskite thin films is presented. This approach enables the construction of all‐inorganic InCl₃:CsPbI₂Br PSCs with a champion power conversion efficiency of 13.74% for a small‐area device (0.09 cm²) and 11.4% for a large‐area device (1.00 cm²).     

Novel organic dyes for multicolor localization‐based super‐resolution microscopy

Precise multicolor single molecule localization‐based microscopy (SMLM) requires bright probes with compatible photo‐chemical and spectral properties to resolve distinct molecular species at the nanoscale. The accuracy of multicolor SMLM is further challenged by color channel crosstalk and chromatic alignment errors. These constrains limit the applicability of known reversibly switchable organic dyes for optimized multicolor SMLM. Here, we tested 28 commercially available dyes for their suitability to super‐resolve a known cellular nanostructure. We identified eight novel dyes in different spectral regimes that enable high quality dSTORM imaging. Among those, the spectrally close dyes CF647 and CF680 comprise an optimal dye pair for spectral demixing‐based, registration free multicolor dSTORM with low crosstalk. Combining this dye pair with the separately excited CF568 we performed 3‐color dSTORM to image the relative nanoscale distribution of components of the endocytic machinery and the cytoskeleton.

A major limitation of multicolor single molecule localization based super‐resolution microscopy (SMLM) is the availability of suitable photo‐switchable fluorescent dyes. By screening 28 commercially available dyes, novel dyes in different spectral regimes were identified that are well suited for dual and triple color SMLM with low crosstalk. These novel dyes are employed to image the relative nanoscale distribution of sub‐cellular components.     

Estimating population size using single‐nucleotide polymorphism‐based pedigree data

Reliable population estimates are an important aspect of sustainable wildlife management and conservation but can be difficult to obtain for rare and elusive species. Here, we test a new census method based on pedigree reconstruction recently developed by Creel and Rosenblatt (2013). Using a panel of 96 single‐nucleotide polymorphisms (SNPs), we genotyped fecal samples from two Swedish brown bear populations for pedigree reconstruction. Based on 433 genotypes from central Sweden (CS) and 265 from northern Sweden (NS), the population estimates (N = 630 for CS, N = 408 for NS) fell within the 95% CI of the official estimates. The precision and accuracy improved with increasing sampling intensity. Like genetic capture–mark–recapture methods, this method can be applied to data from a single sampling session. Pedigree reconstruction combined with noninvasive genetic sampling may thus augment population estimates, particularly for rare and elusive species for which sampling may be challenging.     

Sparse‐graph manifold learning method for bioluminescence tomography

In preclinical researches, bioluminescence tomography (BLT) has widely been used for tumor imaging and monitoring, imaged‐guided tumor therapy, and so forth. For these biological applications, both tumor spatial location and morphology analysis are the leading problems needed to be taken into account. However, most existing BLT reconstruction methods were proposed for some specific applications with a focus on sparse representation or morphology recovery, respectively. How to design a versatile algorithm that can simultaneously deal with both aspects remains an impending problem. In this study, a Sparse‐Graph Manifold Learning (SGML) method was proposed to balance the source sparseness and morphology, by integrating non‐convex sparsity constraint and dynamic Laplacian graph model. Furthermore, based on the nonconvex optimization theory and some iterative approximation, we proposed a novel iteratively reweighted soft thresholding algorithm (IRSTA) to solve the SGML model. Numerical simulations and in vivo experiments result demonstrated that the proposed SGML method performed much superior to the comparative methods in spatial localization and tumor morphology recovery for various source settings. It is believed that the SGML method can be applied to the related optical tomography and facilitate the development of optical molecular tomography.     

Lattice‐Matching Structurally‐Stable 1D@3D Perovskites toward Highly Efficient and Stable Solar Cells

The stability of perovskite solar cells (PSCs) has been identified to be the bottleneck toward their industrialization. With the aim of tackling this challenge, a 1D PbI₂‐bipyridine (BPy)(II) perovskite is fabricated, which is shown to be capable of in situ assembly of a 1D@3D perovskite that is promoted by a PbI₂‐dimethyl sulfoxide complex with a skeletal linear chain structure. The as‐prepared 1D@3D perovskite is observed to demonstrate extremely high stability under external large electric fields in humid environments by means of an in situ characterization technique. This stability is associated with its well lattice‐matching heterojunction structure between 1D and 3D heterojunction domains. Importantly, ion migration is alleviated through blocking of the ion‐migration channels. Accordingly, the 1D@3D hybrid PSC shows a power conversion efficiency of 21.18% maintaining remarkably high long‐term stability in the presence of water, illumination, and external electric fields. This rational design and microstructure study of 1D@3D perovskites provides a new paradigm that may enable higher efficiency and stability of PSCs.     

A pre‐Miocene Irano‐Turanian cradle: Origin and diversification of the species‐rich monocot genus Gagea (Liliaceae)

The Irano‐Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species‐rich monocot genus Gagea Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro‐Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA‐trnH, trnL‐trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro‐Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro‐Siberia. Most of the currently existing species originated during the last 3 Ma.     

The chironomid‐temperature relationship: expression in nature and palaeoenvironmental implications

Fossils of chironomid larvae (non‐biting midges) preserved in lake sediments are well‐established palaeotemperature indicators which, with the aid of numerical chironomid‐based inference models (transfer functions), can provide quantitative estimates of past temperature change. This approach to temperature reconstruction relies on the strong relationship between air and lake surface water temperature and the distribution of individual chironomid taxa (species, species groups, genera) that has been observed in different climate regions (arctic, subarctic, temperate and tropical) in both the Northern and Southern hemisphere. A major complicating factor for the use of chironomids for palaeoclimate reconstruction which increases the uncertainty associated with chironomid‐based temperature estimates is that the exact nature of the mechanism responsible for the strong relationship between temperature and chironomid assemblages in lakes remains uncertain. While a number of authors have provided state of the art overviews of fossil chironomid palaeoecology and the use of chironomids for temperature reconstruction, few have focused on examining the ecological basis for this approach. Here, we review the nature of the relationship between chironomids and temperature based on the available ecological evidence. After discussing many of the surveys describing the distribution of chironomid taxa in lake surface sediments in relation to temperature, we also examine evidence from laboratory and field studies exploring the effects of temperature on chironomid physiology, life cycles and behaviour. We show that, even though a direct influence of water temperature on chironomid development, growth and survival is well described, chironomid palaeoclimatology is presently faced with the paradoxical situation that the relationship between chironomid distribution and temperature seems strongest in relatively deep, thermally stratified lakes in temperate and subarctic regions in which the benthic chironomid fauna lives largely decoupled from the direct influence of air and surface water temperature. This finding suggests that indirect effects of temperature on physical and chemical characteristics of lakes play an important role in determining the distribution of lake‐living chironomid larvae. However, we also demonstrate that no single indirect mechanism has been identified that can explain the strong relationship between chironomid distribution and temperature in all regions and datasets presently available. This observation contrasts with the previously published hypothesis that climatic effects on lake nutrient status and productivity may be largely responsible for the apparent correlation between chironomid assemblage distribution and temperature. We conclude our review by summarizing the implications of our findings for chironomid‐based palaeoclimatology and by pointing towards further avenues of research necessary to improve our mechanistic understanding of the chironomid‐temperature relationship.     

Engineering of pre‐vascularized urethral patch with muscle flaps and hypoxia‐activated hUCMSCs improves its therapeutic outcome

Tissue engineering has brought new hopes for urethral reconstruction. However, the absence of pre‐vascularization and the subsequent degradation of materials often lead to the failure of in vivo application. In this study, with the assistance of hypoxia‐activated human umbilical cord mesenchymal stem cells (hUCMSCs), pedicled muscle flaps were used as materials and pre‐incubated in ventral penile subcutaneous cavity of rabbit for 3 weeks to prepare a pre‐vascularized urethral construct. We found that small vessels and muscle fibres were scattered in the construct after 3 weeks' pre‐incubation. The construct presented a fibrous reticular structure, which was similar to that of the corpus spongiosum under microscope examination. The produced constructs were then used as a patch graft for reconstruction of the defective rabbit urethra (experimental group), natural muscular patch was used as control (control group). Twelve weeks after the reconstructive surgery, urethrography and urethroscope inspections showed wide calibres of the reconstructed urethra in the experimental group. Histopathological studies revealed that fibrous connective tissues and abundant muscle fibres constituted the main body of the patch‐grafted urethra. In contrast, in the control group, only adipose tissue was found in the stenosis‐reconstructed urethra, replacing the originally grafted muscular tissue. To our knowledge, this is the first report that successfully constructed a pre‐vascularized urethral construct by using hypoxia‐activated hUCMSC and pedicled muscle flaps. More importantly, the pre‐vascularized construct showed a good performance in urethral reconstruction when applied in vivo. The study provided a novel strategy for tissue engineering of pre‐vascularized urethral construct for the defective urethra, representing a further advancement in urethral reconstruction.     

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011

The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.     

High resolution electron tomography and segmentation‐by‐modeling interpretation in Bsoft

Bsoft offers many tools for the processing of tomographic tilt series and the interpretation of tomograms. Since I introduced tomography into Bsoft almost two decades ago, the field has advanced significantly, requiring refinement of old algorithms and development of new ones. The current direct detectors allow us to collect data more efficiently and with better quality, progressing towards automation. The goal is then to also automate alignment of tilt series and reconstruction. I added an estimation of the specimen thickness as well as fiducialless alignment, to augment the existing fiducial‐based alignment. High‐resolution work requires correction for the contrast transfer function, in tomography complicated by the tilted specimen. For this, I developed a method to generate a power spectrum using the whole micrograph, compensating for tilting. This is followed by routine determination of the contrast transfer function, and correction for it during reconstruction. The next steps involve interpretation of the tomogram, either by subtomogram averaging where possible, or by segmentation and modeling otherwise. Such interpretation actually constitutes the main time‐consuming part of tomography and is less amenable to automation compared to the initial reconstruction.     

The influence of sampling design on tree‐ring‐based quantification of forest growth

Tree‐rings offer one of the few possibilities to empirically quantify and reconstruct forest growth dynamics over years to millennia. Contemporaneously with the growing scientific community employing tree‐ring parameters, recent research has suggested that commonly applied sampling designs (i.e. how and which trees are selected for dendrochronological sampling) may introduce considerable biases in quantifications of forest responses to environmental change. To date, a systematic assessment of the consequences of sampling design on dendroecological and‐climatological conclusions has not yet been performed. Here, we investigate potential biases by sampling a large population of trees and replicating diverse sampling designs. This is achieved by retroactively subsetting the population and specifically testing for biases emerging for climate reconstruction, growth response to climate variability, long‐term growth trends, and quantification of forest productivity. We find that commonly applied sampling designs can impart systematic biases of varying magnitude to any type of tree‐ring‐based investigations, independent of the total number of samples considered. Quantifications of forest growth and productivity are particularly susceptible to biases, whereas growth responses to short‐term climate variability are less affected by the choice of sampling design. The world's most frequently applied sampling design, focusing on dominant trees only, can bias absolute growth rates by up to 459% and trends in excess of 200%. Our findings challenge paradigms, where a subset of samples is typically considered to be representative for the entire population. The only two sampling strategies meeting the requirements for all types of investigations are the (i) sampling of all individuals within a fixed area; and (ii) fully randomized selection of trees. This result advertises the consistent implementation of a widely applicable sampling design to simultaneously reduce uncertainties in tree‐ring‐based quantifications of forest growth and increase the comparability of datasets beyond individual studies, investigators, laboratories, and geographical boundaries.     

PRIMO/PRIMONA: A coarse‐grained model for proteins and nucleic acids that preserves near‐atomistic accuracy

The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse‐grained sites that are chosen to allow an analytical, high‐resolution reconstruction of all‐atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets. Proteins 2010. © 2009 Wiley‐Liss, Inc.