A tensor approach to the estimation of hydraulic conductivities in Table Mountain Group aquifers of South Africa

Based on the field measurements of the physical properties of fractured rocks, the anisotropic properties of hydraulic conductivity (HC) of the fractured rock aquifer can be assessed and presented using a tensor approach called hydraulic conductivity tensor. Three types of HC values, namely point value, axial value and flow direction one, are derived for their possible applications. The HC values computed from the data measured on the weathered or disturbed zones of rock outcrops tend to give the upper limit values. To simulate realistic variations of the hydraulic property in a fractured rock aquifer, two correction coefficients, i.e. the fracture roughness and combined stress conditions, are adapted to calibrate the tensor model application. The application results in the Table Mountain Group (TMG) aquifers show that the relationship between the HC value and fracture burial depths follows an exponential form with the power hyperbola.Web of Scienc

Specific primers for the detection of freshwater alphaproteobacterial magnetotactic cocci

Freshwater magnetotactic cocci within Alphaproteobacteria are of ecological interest due to their ubiquitous distribution in aquatic environments as well as their potential roles in iron cycling and the bulk magnetism of sediment. To effectively investigate the diversity and distribution of these cocci, specific primers (FMTCf and FMTCr) were developed. Their specificity, applicability, and effectiveness were then evaluated theoretically and empirically. [Int Microbiol 2009; 12(4):237-242

MR image reconstruction from under-sampled measurements using local and global sparse representations

This work presented a new model by enforcing both local and global sparsity, which captures both the patch-level and global sparse structures of the anatomical images. Using a model split approach, the image reconstruction quality can be iteratively further improved. Our simulation results demonstrate that, the proposed method outperform those existing methods using only the patch-level or global sparse structure

Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria. The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria

Exploring OCR Capabilities of GPT-4V(ision) : A Quantitative and In-depth Evaluation

This paper presents a comprehensive evaluation of the Optical Character Recognition (OCR) capabilities of the recently released GPT-4V(ision), a Large Multimodal Model (LMM). We assess the model's performance across a range of OCR tasks, including scene text recognition, handwritten text recognition, handwritten mathematical expression recognition, table structure recognition, and information extraction from visually-rich document. The evaluation reveals that GPT-4V performs well in recognizing and understanding Latin contents, but struggles with multilingual scenarios and complex tasks. Specifically, it showed limitations when dealing with non-Latin languages and complex tasks such as handwriting mathematical expression recognition, table structure recognition, and end-to-end semantic entity recognition and pair extraction from document image. Based on these observations, we affirm the necessity and continued research value of specialized OCR models. In general, despite its versatility in handling diverse OCR tasks, GPT-4V does not outperform existing state-of-the-art OCR models. How to fully utilize pre-trained general-purpose LMMs such as GPT-4V for OCR downstream tasks remains an open problem. The study offers a critical reference for future research in OCR with LMMs. Evaluation pipeline and results are available at https://github.com/SCUT-DLVCLab/GPT-4V_OCR

Clinical Features and Visual Acuity Outcomes in Culture-Positive Endogenous Fungal Endophthalmitis in Southern China

Purpose. To report the causative organisms, management strategies, and visual outcomes of culture-proven endogenous fungal endophthalmitis in a case series from southern China. Methods. We reviewed the microbiological and medical records of patients with culture-positive endogenous fungal endophthalmitis visiting the Zhongshan Ophthalmic Center, Guangzhou, China, between January 1, 2006, and March 31, 2016. Results. The inclusion criteria were met in 32 eyes of 29 patients. Molds were a common causative organism in 15 patients (51.7%), while yeasts appeared in 14 patients (48.3%). Initial visual acuity (VA) at the level of finger counting or better was significantly related to a good visual outcome (P=0.002). Molds as a causative agent were significantly associated with worse visual outcome than yeasts (P=0.020). Conclusion. Molds were a common cause of culture-proven fungal endophthalmitis. Endogenous fungal endophthalmitis is generally associated with poor VA outcomes, especially if caused by molds and if the patient’s initial VA is too low to permit finger counting

Genomic Expansion of Magnetotactic Bacteria Reveals an Early Common Origin of Magnetotaxis with Lineage-specific Evolution

The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth’s magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and “Candidatus Lambdaproteobacteria” classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB

Origin of microbial biomineralization and magnetotaxis during the Archean

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time