Learning-based Single-step Quantitative Susceptibility Mapping Reconstruction Without Brain Extraction

Quantitative susceptibility mapping (QSM) estimates the underlying tissue magnetic susceptibility from MRI gradient-echo phase signal and typically requires several processing steps. These steps involve phase unwrapping, brain volume extraction, background phase removal and solving an ill-posed inverse problem. The resulting susceptibility map is known to suffer from inaccuracy near the edges of the brain tissues, in part due to imperfect brain extraction, edge erosion of the brain tissue and the lack of phase measurement outside the brain. This inaccuracy has thus hindered the application of QSM for measuring the susceptibility of tissues near the brain edges, e.g., quantifying cortical layers and generating superficial venography. To address these challenges, we propose a learning-based QSM reconstruction method that directly estimates the magnetic susceptibility from total phase images without the need for brain extraction and background phase removal, referred to as autoQSM. The neural network has a modified U-net structure and is trained using QSM maps computed by a two-step QSM method. 209 healthy subjects with ages ranging from 11 to 82 years were employed for patch-wise network training. The network was validated on data dissimilar to the training data, e.g. in vivo mouse brain data and brains with lesions, which suggests that the network has generalized and learned the underlying mathematical relationship between magnetic field perturbation and magnetic susceptibility. AutoQSM was able to recover magnetic susceptibility of anatomical structures near the edges of the brain including the veins covering the cortical surface, spinal cord and nerve tracts near the mouse brain boundaries. The advantages of high-quality maps, no need for brain volume extraction and high reconstruction speed demonstrate its potential for future applications.Comment: 26 page

Global metabolic responses of the lenok (Brachymystax lenok) to thermal stress

High temperature is a powerful stressor for fish living in natural and artificial environments, especially for cold water species. Understanding the impact of thermal stress on physiological processes of fish is crucial for better cultivation and fisheries management. However, the metabolic mechanism of cold water fish to thermal stress is still not completely clear. In this study, a NMR-based metabonomic strategy in combination with high throughput RNA-Seq was employed to investigate global metabolic changes of plasma and liver in a typical cold water fish species lenok (Brachymystax lenok) subjected to a sub-lethal high temperature. Our results showed that thermal stress caused multiple dynamic metabolic alterations of the lenok with prolonged stress, including repression of energy metabolism, shifts in lipid metabolism, alterations in amino acid metabolism, changes in choline and nucleotide metabolisms. Specifically, thermal stress induced an activation of glutamate metabolism, indicating that glutamate could be an important biomarker associated with thermal stress. Evidence from Hsp 70 gene expression, blood biochemistry and histology confirmed that high temperature exposure had negative effects on health of the lenok. These findings imply that thermal stress has a severe adverse effect on fish health and demonstrate that the integrated analyses combining NMR-based metabonomics and transcriptome strategy is a powerful approach to enhance our understanding of metabolic mechanisms of fish to thermal stress.</p

Genome-Wide Identification and Expression Profiles of Myosin Genes in the Pacific White Shrimp, Litopenaeus vannamei

As the main structural protein of muscle fiber, myosin is essential for multiple cellular processes or functions, especially for muscle composition and development. Although the shrimp possess a well-developed muscular system, the knowledge about the myosin family in shrimp is far from understood. In this study, we performed comprehensive analysis on the myosin genes in the genome of the Pacific white shrimp, Litopenaeus vannamei. A total of 29 myosin genes were identified, which were classified into 14 subfamilies. Among them, Myo2 subfamily was significantly expanded in the penaeid shrimp genome. Most of the Myo2 subfamily genes were primarily expressed in abdominal muscle, which suggested that Myo2 subfamily genes might be responsible for the well-developed muscular system of the penaeid shrimp. In situ hybridization detection showed that the slow-type muscle myosin gene was mainly localized in pleopod muscle and superficial ventral muscle of the shrimp. This study provides valuable insights into the evolutionary and functional characterization of myosin genes in shrimps, which provides clues for us to understand the well-developed muscular system of shrimp

Chinese Medicinal Herbs for Childhood Pneumonia: A Systematic Review of Effectiveness and Safety

Objective. To assess the efficacy and safety of Chinese medicinal herbs for Childhood Pneumonia. Methods. We included randomized controlled trials (RCTs). The searched electronic databases included PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, CBM, CNKI, and VIP. All studies included were assessed for quality and risk bias. Review Manager 5.1.6 software was used for data analyses, and the GRADEprofiler software was applied to classify the systematic review results. Results. Fourteen studies were identified (n=1.824). Chinese herbs may increase total effective rate (risk ratio (RR) 1.18; 95% confidence interval (CI), 1.11–1.26) and improve cough (total mean difference (MD), −2.18; 95% CI, (−2.66)–(−1.71)), fever (total MD, −1.85; 95% CI, (−2.29)–(−1.40)), rales (total MD, −1.53; 95% CI, (−1.84)–(−1.23)), and chest films (total MD, −3.10; 95% CI, (−4.11)–(−2.08)) in Childhood Pneumonia. Chinese herbs may shorten the length of hospital stay (total MD, −3.00; 95% CI, (−3.52)–(−2.48)), but no significant difference for adverse effects (RR, 0.39; 95% CI, 0.09–1.72) was identified. Conclusion. Chinese herbs may increase total effective rate and improve symptoms and signs. However, large, properly randomized, placebo-controlled, double-blind studies are required

Granulocyte colony-stimulating factor affects the distribution and clonality of TRGV and TRDV repertoire of T cells and graft-versus-host disease

<p>Abstract</p> <p>Background</p> <p>The immune modulatory effect of granulocyte colony-stimulating factor (G-CSF) on T cells resulted in an unexpected low incidence of graft-versus-host disease (GVHD) in allogeneic peripheral blood stem cell transplantation (allo-PBSCT). Recent data indicated that gamma delta⁺T cells might participate in mediating graft-versus-host disease (GVHD) and graft-versus-leukemia (GVL) effect after allogeneic hematopoietic stem cell transplantation. However, whether G-CSF could influence the T cell receptors (TCR) of gamma delta⁺T cells (<it>TRGV </it>and <it>TRDV </it>repertoire) remains unclear. To further characterize this feature, we compared the distribution and clonality of <it>TRGV </it>and <it>TRDV </it>repertoire of T cells before and after G-CSF mobilization and investigated the association between the changes of TCR repertoire and GVHD in patients undergoing G-CSF mobilized allo-PBSCT.</p> <p>Methods</p> <p>The complementarity-determining region 3 (CDR3) sizes of three <it>TRGV </it>and eight <it>TRDV </it>subfamily genes were analyzed in peripheral blood mononuclear cells (PBMCs) from 20 donors before and after G-CSF mobilization, using RT-PCR and genescan technique. To determine the expression levels of <it>TRGV </it>subfamily genes, we performed quantitative analysis of <it>TRGV</it>I~III subfamilies by real-time PCR.</p> <p>Results</p> <p>The expression levels of three <it>TRGV </it>subfamilies were significantly decreased after G-CSF mobilization (<it>P </it>= 0.015, 0.009 and 0.006, respectively). The pattern of <it>TRGV </it>subfamily expression levels was <it>TRGV</it>II ><it>TRGV </it>I ><it>TRGV </it>III before mobilization, and changed to <it>TRGV </it>I ><it>TRGV </it>II ><it>TRGV </it>III after G-CSF mobilization. The expression frequencies of <it>TRGV </it>and <it>TRDV </it>subfamilies changed at different levels after G-CSF mobilization. Most <it>TRGV </it>and <it>TRDV </it>subfamilies revealed polyclonality from pre-G-CSF-mobilized and G-CSF-mobilized samples. Oligoclonality was detected in <it>TRGV </it>and <it>TRDV </it>subfamilies in 3 donors before mobilization and in another 4 donors after G-CSF mobilization, distributed in <it>TRGV</it>II, <it>TRDV</it>1, <it>TRDV</it>3 and <it>TRDV</it>6, respectively. Significant positive association was observed between the invariable clonality of <it>TRDV</it>1 gene repertoire after G-CSF mobilization and low incidence of GVHD in recipients (<it>P </it>= 0.015, <it>OR </it>= 0.047).</p> <p>Conclusions</p> <p>G-CSF mobilization not only influences the distribution and expression levels of <it>TRGV </it>and <it>TRDV </it>repertoire, but also changes the clonality of gamma delta⁺T cells. This alteration of <it>TRGV </it>and <it>TRDV </it>repertoire might play a role in mediating GVHD in G-CSF mobilized allo-PBSCT.</p

CRISPR/Cas9-mediated gene mutation of EcIAG leads to sex reversal in the male ridgetail white prawn Exopalaemon carinicauda

In the culture of crustaceans, most species show sexual dimorphism. Monosex culture is an effective approach to achieve high yield and economic value, especially for decapods of high value. Previous studies have developed some sex control strategies such as manual segregation, manipulation of male androgenic gland and knockdown of the male sexual differentiation switch gene encoding insulin-like androgenic gland hormone (IAG) in decapods. However, these methods could not generate hereditable changes. Genetic manipulation to achieve sex reversal individuals is absent up to now. In the present study, the gene encoding IAG (EcIAG) was identified in the ridgetail white prawn Exopalaemon carinicauda. Sequence analysis showed that EcIAG encoded conserved amino acid structure like IAGs in other decapod species. CRISPR/Cas9-mediated genome editing technology was used to knock out EcIAG. Two sgRNAs targeting the second exon of EcIAG were designed and microinjected into the prawn zygotes or the embryos at the first cleavage with commercial Cas9 protein. EcIAG in three genetic males was knocked out in both chromosome sets, which successfully generated sex reversal and phenotypic female characters. The results suggest that CRISPR/Cas9-mediated genome editing technology is an effective way to develop sex manipulation technology and contribute to monosex aquaculture in crustaceans

Ultrathin Few-Layer GeP Nanosheets via Lithiation-Assisted Chemical Exfoliation and Their Application in Sodium Storage

2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Ultrathin few-layer materials have attracted intensive research attention because of their distinctive and unique properties. Few-layer GeP (FL-GP) is potentially interesting for application in electronics and optoelectronics because of its appropriate band gap and good stability under ambient conditions. Nevertheless, it is a challenge to achieve ultrathin few-layer or single layer GeP from exfoliation of bulk crystals. Here, a lithiation-assisted chemical exfoliation technique is employed to achieve FL-GP, in which the interlayer spacing can be efficiently enlarged after a preliminary lithium ion intercalation, allowing the bulk crystal to be readily exfoliated in a following ultrasonication. As a result, ultrathin FL-GP is obtained. In a demonstration, the FL-GP/reduced graphene oxide (rGO) demonstrates remarkable sodium storage performance. The FL-GP with a two-dimensional structure shortens the ion transport pathways and alleviates the volume variation during sodiation. Meanwhile, the rGO in the composite improves the conductivity of the whole electrode. The as-prepared FL-GP/rGO electrode exhibits a high capacity of 504.2 mAh g−1 at 100 mA g−1, remarkable rate performance, and superior cycling stability in the half cells. FL-GP/rGO//Na3V2(PO4)3 full cells are also assembled and demonstrated satisfactory electrochemical performance, indicating potential application of the as-prepared anode materials

Failure of early mycological clearance in HIV-negative cryptococcal meningitis

BACKGROUND: Negative cerebrospinal fluid (CSF) cultures at 2 weeks after antifungal treatment (early mycological clearance [EMC]) should be a treatment goal of cryptococcal meningitis (CM). However, EMC in human immunodeficiency virus (HIV)-negative patients with CM is poorly understood. METHODS: We conducted a retrospective review of medical records and 1-year follow-up of 141 HIV-negative patients with CM with an initial positive CSF culture for RESULTS: Of 141 patients, 28 (19.9%) had EMC failure. The 1-year mortality rate was 5.7% (8/141). Multivariate analysis showed that non-amphotericin B (AmB)-based regimens, baseline log CONCLUSIONS: EMC failure in HIV-negative CM is attributed to non-AmB-based therapy and is associated with lo