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Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria were found, belonging to Enterobacteriaceae Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), Comamonadaceae (4.25%). The major viruse families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae and Herpesviridae, showing in 34.96%, 47.37%, 30.89%, 5.69%, 3.25% and 1,63% patients, respectively. Using Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold > 10, p = 0.021); Tetra-PGDM (fold = 5.29, p = 0.037) and 20-HETE (fold > 10, p = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.

Human brucellosis is one of the most prevalent zoonoses. There are many similarities between the pathogenesis of Mycobacterium tuberculosis (MTB) infection and that of brucellosis. Immune reconstitution inflammatory syndrome (IRIS) may occur during the treatment of MTB infection, but it has not been reported in brucellosis cases thus far. We report the case of a 40-year-old male whose condition initially improved after adequate anti-Brucella therapy. However, 3 weeks later, the patient presented with exacerbation of symptoms and development of a paravertebral abscess. After exclusion of other possible causes of clinical deterioration, immune reconstitution inflammatory syndrome (IRIS) with brucellosis was presumed. After supplementation with anti-Brucella treatment with corticosteroids, the abscess disappeared, and the symptoms completely resolved. Our case suggests that it is necessary to be aware of the possible occurrence of IRIS in patients with brucellosis in clinical practice.

This paper reports part of the findings of a project conducted to investigate the current research landscape of archival studies in China and internationally. Study results show that there are similarities and differences between the most popularly studied research areas in Chinese and international archival fields and between the key research topics recommended for the next 5 years by Chinese and international scholars. Three research orientations of archival studies—management, technology, and humanities as well as the areas that need to be delved into in the next 5 years for global and Chinese archival community—were identified. The findings of this article contribute more broadly to our understanding of the status quo and trends of archival research, and can provide a reference for archival scholars to set research agendas at the individual, institutional, local, and national level. The research priorities identified for the next 5 years may be potential areas where international and transdisciplinary cooperation can occur.

China is one of the world’s earliest civilisations with a written history extending back nearly five thousand years and an accompanying history of over three thousand six hundred years of archival work. The Three-Character Classic of Archival Work, a poem written in a traditional Chinese style, outlines this long history of the development of archival work in China. Through the presentation and analysis of an English translation of the newly revised version of this poem, the authors examine the archival history and practice of China from ancient times to the present day. In explanatory notes and a reflection examining the historical overview the poem provides, the authors consider the formation, change, transition, and development of Chinese archival traditions to demonstrate the multi-faceted impact on archival work today. The article establishes how, over time, some of these traditions have been incorporated into current practice, whereas others have been updated or rejected. Alongside this, the development of Chinese archival education over the past century is also detailed, to illustrate how this has been key to the professionalisation of archival work. The article concludes by arguing that, in the context of rapidly changing society and technology, the experience and tradition of the past will continue to provide a valuable reference point for the future development of archival work in China.

Background This study aims to evaluate the efficacy of the standard agglutination test (SAT), the Brucellacapt test and enzyme-linked immunosorbent assay (ELISA) in clinical specimens collected from patients with suspected brucellosis. Methods A prospective study was conducted from December 2020 to December 2021. Brucellosis was diagnosed on the basis of clinical evidence, and confirmed by isolation of Brucella or a four-fold rise in SAT titer. All samples were tested by the SAT, ELISA and the Brucellacapt test. Titers ≥1:100 were considered as SAT positive; ELISA was considered positive when an index greater than 11 was detected, while titers ≥1/160 indicated positivity on the Brucellacapt test. The specificity, sensitivity, and positive (PPVs) and negative predictive values (NPVs) of the three different methods were calculated. Results A total of 149 samples were collected from patients with suspected brucellosis. The sensitivities for the SAT, IgG, and IgM detection were 74.42%, 88.37% and 74.42%, respectively. The specificities were 95.24%, 93.65%, and 88.89%, respectively. The simultaneous measurement of IgG and IgM improved the sensitivity (98.84%) but reduced the specificity (84.13%) compared to each antibody test separately. The Brucellacapt test had excellent specificity (100%) and a high PPV (100%); however, the sensitivity and NPV were 88.37% and 86.30%, respectively. The combination of IgG detection by ELISA and the Brucellacapt test had excellent diagnostic performance, with 98.84% sensitivity and 93.65% specificity. Conclusion This study showed that the simultaneous performance of IgG detection by ELISA and the Brucellacapt test has the potential to overcome the current limitations of detection.

With the development of next generation sequencing technologies, transcriptome level sequence collections are emerging as prominent resources for the discovery of gene-based molecular markers. In this study, we described the isolation and characterization of 46 novel polymorphic microsatellite loci for Siniperca chuatsi and Siniperca scherzeri from the transcriptome of their F1 interspecies hybrids. Forty-three of these loci were polymorphic in S. chuatsi, and 20 were polymorphic in S. scherzeri. In S. chuatsi, the number of alleles per locus ranged from 2 to 8, and the observed and expected heterozygosities varied from 0.13 to 1.00 and from 0.33 to 0.85, respectively. In S. scherzeri, the number of alleles per locus ranged from 3 to 9, and the observed and expected heterozygosities varied from 0.19 to 1.00 and from 0.28 to 0.88, respectively. We also evaluated the cross-amplification of 46 polymorphic loci in four species of sinipercine fishes: Siniperca kneri, Siniperca undulata, Siniperca obscura, and Coreoperca whiteheadi. The interspecies cross-amplification rate was very high, totaling 94% of the 184 locus/taxon combinations tested. These markers will be a valuable resource for population genetic studies in sinipercine fishes.

Chantier qualité GA; International audience; Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.

Aim The euglycemic-hyperinsulinemic clamp (EHC) is not available in most clinical settings and is costly, time consuming and invasive, and requires trained staff. Therefore, an accessible and inexpensive test to identify insulin resistance (IR) is needed. The aim of this study is to assess whether zinc-α2-glycoprotein (ZAG) index [Ln ZAG/homeostasis model assessment of IR (HOMA-IR)] is a better surrogate index for estimating IR or metabolic syndrome (MetS) compared with other surrogate indices. Methods We performed a population-based cross-sectional study. Two hundred healthy subjects, 102 polycystic ovary syndrome (PCOS) patients, 97 newly diagnosed type 2 diabetes mellitus (nT2DM) and 84 impaired glucose tolerance (IGT) subjects were enrolled. The EHC was performed to identify IR. Circulating ZAG and adiponectin levels were determined by ELISA. Results The ZAG index was significantly lower in participants with IR including IGT, nT2DM and PCOS than in those without IR. In addition, subjects with MetS had lower ZAG indices and higher the product of fasting triglycerides and glucose (TyG) indices than those without MetS. The ZAG index showed a significantly stronger association with M values than the other surrogate indices, whereas the TyG index showed a stronger association with MetS. The optimal cutoff value of the ZAG index for detection of IR was 2.97 with a sensitivity of 88% and a specificity of 91%, whereas the optimal cutoff value of TyG index for detection of MetS was 4.90 with a sensitivity of 82% and a specificity of 86%. Conclusion The ZAG index is a better marker than the other surrogate indices for identifying IR, whereas the TyG index has high sensitivity and specificity for identifying MetS.

The aim of this study was to determine the effects of combinations of fosfomycin, minocycline and polymyxin B in the treatment of pan-drug-resistant Acinetobacter baumannii (PDR-Ab). The in vitro antibacterial activities of the drugs were evaluated by determination of the minimum inhibitory concentration (MIC) and the fractional inhibitory concentration index (FICI). A total of 25 strains of PDR-Ab were selected using the VITEK32 microbial analysis instrument and the Kirby-Bauer (K-B) method. A broth microdilution method was used to determine the MIC for each of the three drugs, and the checkerboard method was simultaneously used to determine the MICs for combinations of the drugs. FICI values were also calculated. While fosfomycin alone was ineffective for the treatment of PDR-Ab, its MIC value was significantly reduced when used in combination with minocycline or polymyxin B. The combined use of minocycline and polymyxin B also significantly reduced the MIC value of each drug. The FICI values revealed that the drugs had synergistic or additive effects when used in combination. The determination of the MIC and FICI values for the combinations of drugs demonstrated that there is synergistic or additive effect upon the combined use of fosfomycin with minocycline or polymyxin B. The combined use of minocycline and polymyxin B also results in a significant reduction in the MIC values of the two drugs. These experimental results may provide a basis for the future clinical treatment of Acinetobacter baumannii.

Acute gastroenteritis caused by human noroviruses (NoVs) has become an important public health problem worldwide. This study was carried out to investigate the rates of NoV infections and the genetic characteristics of NoVs in adult outpatients with acute gastroenteritis in Ji’nan, a large eastern city in China. A total of 480 fecal samples were collected from outpatients at the Shandong University Qilu Hospital between June 2010 and May 2011. Of the collected samples, 42 (42/480, 8.75 %) were positive for NoVs by RT-PCR, and seven different genotypes were identified: GI-1, GI-4, GII-1, GII-3, GII-4, GII-6 and GII-13, of which GII-4 was the most prevalent (29/42, 69.0 %). Phylogenetic and Simplot analyses showed that three recombinant strains were detected: two GII-4 polymerase/GII-3 capsid recombinants and one GII-6 polymerase/GII-4 capsid recombinant. This study indicated that NoV was a common causative agent of sporadic acute gastroenteritis in adults in Ji’nan, China, and that NoV GII-4 was the predominant strain during this period. Three recombinant strains were identified in which GII-6 polymerase/GII-4 capsid was detected for the first time in China.

Vegetation cover is an important parameter used in monitoring ecological changes of the source region of Yangtze, Yellow and Lantsang Rivers and understanding human activities. Thus, how to extract the large area's vegetation fraction quickly effectively is an open question. The traditional linear spectral mixture analysis (LSMA) assumes that the spectral reflectance is a mixture of several fixed endmember spectral values, which ignores considerable within-class variability. However, multiple endmember spectral mixture analysis (MESMA) overcomes the disadvantage by allowing the number and types to vary on a per-pixel basis. This paper proposes a stepwise spectral mixture analysis (SSMA) containing two steps of MESMA and adding the endmember fraction rationality rule in each step. The aim of the first step is to detect the pixels that didn't contain vegetation information at all and these pixels would be masked out. In the second step, MESMA is used to unmix the pixels only reserved in previous process. The results show that SSMA is more accurate than LSMA in extracting the vegetation fraction for the Three-Rivers. This means that SSMA is a good substitute for LSMA in studies on ecological changes. The concept of SSMA also can be applied for other large study areas.

With the introduction of massively parallel, microminiature-based instrumentation for DNA sequencing, robust, reproducible, optimized methods are needed to prepare the target DNA for analysis using these high-throughput approaches because the cost per instrument run is orders of magnitude more than for typical Sanger dideoxynucleotide sequencing on fluorescence-based capillary systems. The methods provided by the manufacturer for genome sequencing using the 454/Roche GS-20 and GS-FLX instruments are robust. However, in an effort to streamline them for automation, we have incorporated several novel changes and deleted several extraneous steps. As a result of modifying these sample preparation protocols, the number of manual manipulations has also been minimized, and the overall yields have been improved for both shotgun and mixed shotgun/paired-end libraries.

A metagenomic library was constructed from the anaerobic sediments of a mesophilic sulfur spring. Thirty-five bacterial 16S rRNA gene-containing clones were identified in this library. Analysis of a genomic fragment belonging to candidate division OD1 provided useful insights into the physiology and biochemistry of this novel, yet-uncultured candidate division.

Background The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. Methodology/Principal Findings We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. Conclusions/Significance We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.