BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

Vaa3D-x for cross-platform teravoxel-scale immersive exploration of multidimensional image data

SUMMARY

Vaa3D is a software package that has been widely used to visualize and analyze multidimensional microscopic images in a number of cutting edge bioimage informatics applications. However, due to many recent updates of both software development environments and operating systems, it was highly requested to maintain Vaa3D and disseminate it on latest operating systems. In addition, there has never been a showcase about how to use Vaa3D's cross-platform visualization and immersive exploration functions for multidimensional and teravoxel-scale images. Here, we introduce a newly developed version of the software, called Vaa3D-x, to address all the above issues.

AVAILABILITY AND IMPLEMENTATION

Vaa3D-x is released in both binary and Open-Source available at vaa3d.org and GitHub (https://github.com/Vaa3D).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Functional Dissection of Protein Kinases in Sexual Development and Female Receptivity of Drosophila

Protein phosphorylation is crucial for a variety of biological functions, but how it is involved in sexual development and behavior is rarely known. In this study, we performed a screen of RNA interference targeting 177 protein kinases in Drosophila and identified 13 kinases involved in sexual development in one or both sexes. We further identified that PKA and CASK promote female sexual behavior while not affecting female differentiation. Knocking down PKA or CASK in about five pairs of pC1 neurons in the central brain affects the fine projection but not cell number of these pC1 neurons and reduces virgin female receptivity. We also found that PKA and CASK signaling is required acutely during adulthood to promote female sexual behavior. These results reveal candidate kinases required for sexual development and behaviors and provide insights into how kinases would regulate neuronal development and physiology to fine tune the robustness of sexual behaviors.

Morphological diversity of single neurons in molecularly defined cell types

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.

A multimodal cell census and atlas of the mammalian primary motor cortex

Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

ILC3 cells promote the proliferation and invasion of pancreatic cancer cells through IL-22/AKT signaling

PURPOSE

Type 3 innate lymphocytes (ILC3s) are reported to be involved in lung cancer, possibly by producing interleukin-22 (IL-22). However, whether ILC3s and their secreted IL-22 molecules contribute to the pathogenesis of pancreatic cancer (PC) remains unclear. To this end, in this study, we investigated the effects and possible mechanisms of ILC3s on PC pathogenesis.

METHOD

The IL-22 and IL-2i2R levels and the ILC3s' frequency in cancer tissues from PC patients and in peripheral blood from PC patients and healthy controls were analyzed by flow cytometry, immunochemistry, or immunofluorescence. The effects of IL-22-induced AKT signaling on the proliferation, invasion, and migration of PC cells were examined by co-culturing PC cell lines with ILC3s isolated from PC tissues, with or without the addition of neutralizing IL-22 antibody, IL-22R antibody or AKT inhibitor.

RESULTS

Our results showed that IL-22 and ILC3s were significantly upregulated in the PBMCs and cancer tissues of PC patients, and the IL-22R level was increased in PC cells. The increased frequency of ILC3s was positively correlated with the clinical features of PC patients. Co-culture experiments indicated that ILC3s promoted the proliferation, invasion, and migration of PC cell lines by secreting IL-22 to activate AKT signaling because IL-22/IL-22R or AKT blockage markedly counteracted such effects on PC cells.

CONCLUSION

Our data demonstrated that ILC3s may promote PC pathogenesis through IL-22/IL-22R-AKT signaling, suggesting a potential intervention target for PC treatment in the future.

TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain

Neuron morphology is recognized as a key determinant of cell type, yet the quantitative profiling of a mammalian neuron's complete three-dimensional (3-D) morphology remains arduous when the neuron has complex arborization and long projection. Whole-brain reconstruction of neuron morphology is even more challenging as it involves processing tens of teravoxels of imaging data. Validating such reconstructions is extremely laborious. We develop TeraVR, an open-source virtual reality annotation system, to address these challenges. TeraVR integrates immersive and collaborative 3-D visualization, interaction, and hierarchical streaming of teravoxel-scale images. Using TeraVR, we have produced precise 3-D full morphology of long-projecting neurons in whole mouse brains and developed a collaborative workflow for highly accurate neuronal reconstruction.

Association between rs12742784 polymorphism and hip fracture, bone mineral density, and EPHB2 mRNA expression levels in elderly Chinese women

Objective: This study aimed to determine the association between rs12742784 polymorphism in the non-coding area and hip fracture, bone mineral density (BMD), and EPHB2 mRNA expression levels in elderly Chinese women.Methods: We investigated 250 Chinese women (mean age: 63.5 ± 8.3 years) including 123 hip fracture patients and 127 non-fracture controls. All participants underwent clinical examination to meet the inclusion criteria. Lumbar and hip BMD were detected by dual-energy X-ray absorptiometry. rs12742784 polymorphism was determined by restriction fragment length polymorphism and EPHB2 mRNA expression levels were measured by real-time polymerase chain reaction.Results: Distribution of rs12742784 genotypes agreed with Hardy-Weinberg equilibrium. The frequency of the CT + TT genotype was significantly associated with decreased risk of hip fracture (adjusted odds ratio = 0.57, p < 0.01) after adjusting for age and body mass index, and with increased BMD and EPHB2 mRNA expression levels. The T allele of the rs12742784 single nucleotide polymorphism (SNP) was a protective factor for hip fracture (adjusted odds ratio = 0.56, p < 0.01).Conclusion: rs12742784 polymorphism was associated with EPHB2 mRNA expression levels, BMD, and hip fracture in Chinese women. The T allele of the rs12742784 SNP was a protective factor for osteoporosis and hip fracture.

Tetramethylpyrazine (TMPZ) triggers S-phase arrest and mitochondria-dependent apoptosis in lung cancer cells

Tetramethylpyrazine (TMPZ) is one of the active compounds extracted from the traditional Chinese herb Chuanxiong. Several studies have shown its anti-cancer properties. However, its functions in lung cancer and the underlying cellular mechanisms are relatively unknown. Our present study aimed to investigate the effects of TMPZ on A549 and 95D cells. The MTT assay showed that TMPZ decreased cell viability in a dose- and time-dependent manner. The results of the colony formation assay indicated that TMPZ strongly suppressed colony formation ability in A549 and 95D cells. Flow cytometric analysis revealed that TMPZ induced S phase arrest in lung cancer cells. In addition, TMPZ induced apoptosis, as shown by the results of propidium iodide/Annexin V double-staining. Furthermore, TMPZ decreased mitochondrial membrane potential (∆Ψm) in a dose-dependent manner. Finally, western blot analysis of TMPZ-treated cells revealed the activation of Caspase-3 and the increase of the ratio of Bax/Bcl-2. These results demonstrated that TMPZ could suppress carcinogenesis of lung cancer cells through blocking cell cycle and inducing mitochondria-dependent apoptosis by regulating Caspase-3 and Bax/Bcl-2, suggesting that TMPZ may be a promising drug to treat lung cancer.

[Rapid determination of volatile organic compounds in workplace air by protable gas chromatography-mass spectrometer]

Objective: To establish a method for rapid determination of 47 volatile organic compounds in the air of workplace using portable gas chromatography-mass spectrometer(GC-MS). Methods: The mixed standard gas with different concentration levels was made by using the static gas distribution method with the high purity nitrogen as dilution gas. The samples were injected into the GC-MS by a hand-held probe. Retention time and characteristic ion were used for qualitative analysis,and the internal standard method was usd for quantitation. Results: The 47 poisonous substances were separated and determined well. The linear range of this method was 0.2-16.0 mg/m(3),and the relative standard deviation of 45 volatile ovganic compounds was 3.8%-15.8%. The average recovery was 79.3%-119.0%. Conclusion: The method is simple,accurate,sensitive,has good separation effect,short analysis period, can be used for qualitative and quantitative analysis of volatile organic compounds in the workplace, and also supports the rapid identification and detection of occupational hazards.

DNA methylation and expression of imprinted genes are associated with the viability of different sexual cloned buffaloes

The DNA methylation of imprinted genes is an important way to regulate epigenetic reprogramming of donor cells in somatic cell nuclear transfer (SCNT). However, the effects of sexual distinction on the DNA methylation of imprinted genes in cloned animals have seldom been reported. In this study, we analysed the DNA methylation status of three imprinted genes (Xist, IGF2 and H19) from liveborn cloned buffaloes (L group, three female and three male), stillborn cloned buffaloes (S group, three female and three male) and natural reproduction buffaloes (N group, three female and three male), using bisulphite sequencing polymerase chain reaction (BS-PCR). The expression levels of these imprinted genes were also investigated by quantitative real-time PCR (QRT-PCR). The DNA methylation levels of H19 were not significantly different among the groups. However, the Xist in female and IGF2 in male of the S group were found to be significantly hypomethylated in comparison with the same sexual buffaloes in L group and N group (p < .05). Furthermore, the expression levels of Xist, IGF2 and H19 in the stillborn female cloned buffaloes of S group were significantly higher than that of the female buffaloes in the L group and N group (p < .05). The expression levels of IGF2 and H19 in the stillborn male cloned buffaloes in the S group were significantly higher than that of the male buffaloes in the L group and N group (p < .05). These results indicate that Xist may be associated with the viability of female cloned buffaloes, and IGF2 may also be related to the viability of male cloned buffaloes.

Dose Proportionality and Pharmacokinetics of Eplerenone in Healthy Chinese Subjects

BACKGROUND

Eplerenone (CAS 107724-20-9) is the first highly selective aldosterone receptor blocker and is used worldwide for treatment of hypertension and heart failure.

OBJECTIVE

The objective of this study was to investigate the eplerenone pharmacokinetics in healthy Chinese subjects and assess the dose proportionality over the therapeutic dose range.

METHODS

A single-dose, randomized, 6-sequence, 3-treatment, 3-period crossover, open label study was conducted in 12 healthy Chinese subjects, who received 3 doses of eplerenone in random order (25, 50, 100 mg). The power model was used to evaluate the dose proportionality of eplerenone. The pharmacokinetic study of multiple-dose of eplerenone was also conducted.

RESULTS

After single-dose oral administration, the mean C max value increased from 489 to 1 641 ng/mL, and the mean AUC 0-t value increased from 3 030 to 10 893 ng/mL·h with an increase in dose from 25 to 100 mg, respectively. The mean value for terminal T 1/2 was approximate 3 h with no significant differences among different dose groups. Though dose proportionality of eplerenone was inconclusive in Chinese subjects over the dose range of 25-100 mg, the maximal proportionality dose range (ρ1) was 2.06 based on power model. Steady state could achieve within at least 4 days and no accumulation was observed after multiple-dose of eplerenone.

CONCLUSION

Dose proportionality was inconclusive in over the dose range of 25-100 mg; however, linear pharmacokinetics could be considered when dose ratio is no more than 2.06.

Quantum-trajectory Monte Carlo method for study of electron–crystal interaction in STEM

A quantum trajectory Monte Carlo method is developed to simulate electron scattering and secondary electron cascade process in crystalline specimen.

123 EFFECTS OF TAURO URSODEOXYCHOLIC ACID ON DEVELOPMENT OF BOVINE EMBRYOS FROM IN VITRO FERTILIZATION

Endoplasmic reticulum stress (ERS) is a novel apoptotic pathway and plays an important role for embryonic development. Tauro ursodeoxycholic acid (TUDCA) is a specific chemical chaperone that can inhibit ERS. In this study, we investigated the effects of TUDCA on the development and mRNA expression of ERS-related genes in bovine embryos from IVF in order to improve the efficiency of embryo in vitro culture. Bovine oocytes collected from ovaries at slaughter were cultured in the maturation medium (TCM-199 + 26.2 mmol L–1 NaHCO3 + 5 mmol L–1 HEPES + 5% fetal bovine serum) for 24 h and fertilized in vitro with bovine sperm. After fertilization, the embryos were respectively placed into the medium (TCM-199 + 3% fetal bovine serum) containing different concentrations of TUDCA (0, 100, 250, 500, 1000 μmol L–1) and cultured in the 5% CO2 at 38.5°C. Blastocyst development was evaluated after 7 days of culture, and then the total cell number and apoptosis index of blastocysts were detected with TUNEL. In addition, X-box binding protein 1 (XBP-1) of embryos at 2-cell, 4-cell, morula, and blastocyst stages was detected with RT-PCR, and the change of the mRNA expression of ERS-related (Grp78, Ire1, Chop) and apoptosis-related (Bax, Bcl-2) genes in blastocyst collected at 7 days of culture were analysed by QRT-PCR. A total of 1336 oocytes were used in this study, and each experimental group comprised 6 replicates. The results revealed that the splicing of XBP-1 was present during the development of bovine embryos, and especially obvious at the 4-cell, morula, and blastocyst stages. When embryos were cultured in medium with different concentrations of TUDCA, compared with the control group (0 μmol L–1), more embryos developed to blastocyst stage with 500 μmol L–1 TUDCA (31.86 ± 7.32% v. 21.11 ± 8.05%; P < 0.05), but the cleavage rate was not significantly different among groups (P > 0.05). The result for TUNEL found that when adding 500 μmol L–1 TUDCA to culture, the bovine embryos significantly improved the total cell number of blastocysts (110. ± 15.21 v. 102.3 ± 8.62; P < 0.05), and the apoptosis index of blastocysts was markedly decreased (3.71 ± 0.91 v. 5.36 ± 1.92; P < 0.05) relative to the control group. Moreover, the result of QRT-PCR analysis showed that treating embryos with 500 μmol L–1 TUDCA significantly reduced the mRNA expression level of Ire1 and Chop genes (P < 0.05) and up-regulated the expression of anti-apoptotic Bcl-2 gene (P < 0.05), while down-regulated the expression of pro-apoptotic Bax gene (P < 0.05). Furthermore, XBP-1 splicing in blastocysts also abated after embryos were treated with 500 μmol L–1 TUDCA. In conclusion, ERS occurs in bovine embryos during in vitro culture, but treating embryos with 500 μmol L–1 TUDCA may reduce ERS to facilitate embryonic development. This work was funded by the China High Technology Development Program (2011AA100607), China Natural Science Foundation (31072033), and Guangxi Science Foundation (2011GXNSFA018084, 2012GXNSFFA060004).

Prevalence of carbapenem-hydrolyzing class D β-lactamase genes in Acinetobacter spp. isolates in China

In order to assess the prevalence of carbapenem-hydrolyzing class D β-lactamase genes in Acinetobacter spp. isolates in China, we conducted a polymerase chain reaction (PCR)-based surveillance of OXA-type β-lactamase gene clusters for a total of 2,880 Acinetobacter spp. isolates collected from 23 Chinese provinces. All isolates were tested for susceptibility to 12 antimicrobial agents and showed high rates of resistance to all these agents except minocycline. We also found that the vast majority of carbapenem-resistant Acinetobacter spp. were OXA-23-like-producing isolates, predominantly Acinetobacter baumannii isolates. Besides, bla OXA-58-like and bla OXA-24-like genes were detected in 32 and 11 isolates, respectively, involving many provinces throughout China. Furthermore, these two carbapenem-resistance determinants were located on transferable plasmids in most cases, indicating an emerging threat for both OXA-58-like- and OXA-24-like-producing Acinetobacter spp. isolates in China. Interestingly, a novel homologue of the bla OXA-143 gene was identified in a susceptible Acinetobacter pittii isolate. Overall, these observations suggest that the bla OXA-23-harboring A. baumannii isolates are the most frequent carbapenem-resistant Acinetobacter spp. in China, and the bla OXA-24-like and bla OXA-58-like genes have emerged as potential threats of hospital outbreaks of multidrug-resistant Acinetobacter spp.

Development of a multilocus sequence typing scheme for Ureaplasma

Ureaplasma is a commensal of the human urogenital tract but is always associated with invasive diseases such as non-gonococcal urethritis and infertility adverse pregnancy outcomes. To better understand the molecular epidemiology and population structure of Ureaplasma, a multilocus sequence typing (MLST) scheme based on four housekeeping genes (ftsH, rpL22, valS, thrS) was developed and validated using 283 isolates, including 14 serovars of reference strains and 269 strains obtained from clinical patients. A total of 99 sequence types (STs) were revealed: the 14 type strains of the Ureaplasma serovars were assigned to 12 STs, and 87 novel and special STs appeared among the clinical isolates. ST1 and ST22 were the predominant STs, which contained 68 and 70 isolates, respectively. Two clonal lineages (CC1 and CC2) were shown by eBURST analysis, and linkage disequilibrium was revealed through a standardized index of association (I A (S)). The neighbor-joining tree results of 14 Ureaplasma serovars showed two genetically significantly distant clusters, which was highly congruent with the species taxonomy of ureaplasmas [Ureaplasma parvum (UPA) and Ureaplasma urealyticum (UUR)]. Analysis of the biotypes of 269 clinical isolates revealed that all the isolates of CC1 were UPA and those of CC2 were UUR. Additionally, CC2 was found more often in symptomatic patients with vaginitis, tubal obstruction, and cervicitis. In conclusion, this MLST scheme is adequate for investigations of molecular epidemiology and population structure with highly discriminating capacity.

The clinical application of absorbable intramedullary nail and claw plate on treating multiple rib fractures

AIM

The absorption intramedullary nail and claw plate indications and efficacy were investigated in the treatment of a life-threatening multiple rib fractures.

METHODS

A retrospective analysis of 248 surgically treated rib fracture patients was performed who admitted to our hospital from March 2007 to December 2012. Intramedullary nailing was performed in 28 cases, a claw-type bone plate was fixed in 141 cases, and a combination of both was fixed in 79 cases.

RESULTS

All internal fixation patients were clinically cured except 1 patient died 14 days after a massive pulmonary embolism. The patients with flail chest and floating chest wall causing respiratory and circulatory disorders were promptly corrected. Routine follow-up was from 1 to 2 years, displaced fractures were in 2 cases, and there were 11 cases of internal fixation and extraction.

CONCLUSION

Internal fixation is a simple and reliable method for the treatment of multiple rib fractures. Both internal fixation materials have their pros and cons but the claw bone plate is more robust. The actual selection of appropriate treatment options helps to improve the treatment efficacy.

Reveals new lung adenocarcinoma cancer genes based on gene expression

BACKGROUND

Lung adenocarcinoma (LAC) is the most common type of lung cancer, accounting for 30-35% of all cases.

AIM

In this study we aim to predict potential genes and confirm pathways which are associated with LAC.

MATERIALS AND METHODS

By using the meta-analysis method, GSE10072 and GSE 2514 datasets were merged to find potential genes and pathways which are associated with LAC.

RESULTS

Our analysis indicated identified differentially expressed genes enriched in multicellular organismal metabolic process, gland development, and urogenital system development. Further, we predicted genes including EGF-like domain might be the potential target genes for further study, such as NGX6, MUC17, and Nel. In addition, a number of genes that associated with axon guidance, focal adhesion, and complement and coagulation cascades pathway might be also involved in LAC in a direct or indirectly manner.

CONCLUSIONS

Our analysis indicated identified differentially expressed genes enriched in multicellular organismal metabolic process, gland development, and urogenital system development We anticipate numerous advances in LAC research in the coming years based on our meta-analysis.

Bioequivalence evaluation of cefdinir in healthy fasting subjects

A simple and sensitive HPLC method was developed to determine cefdinir (CAS 91832-40-5) in human plasma. The method was validated by investigating the accuracy and precision for intra- and inter-day runs in a linear concentration from 0.05-2.0 µg/ml. The object of this study was to compare the bioavailability of cefdinir capsule (reference) and cefdinir granule (test) containing 100 mg of cefdinir. A randomized, open-label, single-dose, 2-way crossover bioequivalence study in 20 healthy, Chinese, male subjects was conducted. A 1-week wash-out period was applied. Blood samples were collected before and with 10 h after drug administration. The formulations were compared using the following pharmacokinetic parameters: AUC0-t, AUC0-∞ and C max. The 90% confidence interval (CI) of the ratios of log-transformed AUC0-t and AUC0-∞ were used to assess bioequivalence between the 2 formulations using the equivalence interval of 80 and 125%. The results showed that the 90% CI of the ratios of AUC0-t, AUC0-∞ and C max were 102.5% (94.7-111.0%), 103.4% (94.8-112.7%) and 106.4% (97.0-116.7%), respectively, which indicated 2 formulations of cefidinir are bioequivalent. Both treatments showed similar tolerability and safety.

Detecting abnormalities of corpus callosum connectivity in autism using magnetic resonance imaging and diffusion tensor tractography

The corpus callosum (CC) has emerged as one of the primary targets of autism research. To detect aberrant CC interhemispheric connectivity in autism, we performed T1-weighted magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI)-based tractography in 18 children with high functioning autism (HFA) and 16 well-matched typically developing (TD) children. We compared global and regional T1 measures (CC volume, and CC density), and the DTI measures [fractional anisotropy (FA), apparent diffusion coefficient (ADC), average fiber length (AFL), and fiber number (FN)] of transcallosal fibers, between the two groups. We also evaluated the relationships between scores on the Childhood Autism Rating Scale (CARS) and CC T1 or DTI measurements. Significantly less white matter density in the anterior third of the CC, and higher ADC and lower FN values of the anterior third transcallosal fiber tracts were found in HFA patients compared to TD children. These results suggested that the anterior third CC density and transcallosal fiber connectivity were affected in HFA children.

Microbial strategies to control aflatoxins in food and feed

Aflatoxins are a group of toxic and carcinogenic fungal metabolites. They are commonly found in cereals, nuts and animal feeds and create a significant threat to the food industry and animal production. Several strategies have been developed to avoid or reduce harmful effects of aflatoxins since the 1960s. However, prevention of aflatoxin contamination pre/post harvest or during storage has not been satisfactory and control strategies such as physical removing and chemical inactivating used in food commodities have their deficiencies, which limit their large scale application. It is expected that progress in the control of aflatoxin contamination will depend on the introduction of technologies for specific, efficient and environmentally sound detoxification. The utilisation of biological detoxification agents, such as microorganisms and/or their enzymatic products to detoxify aflatoxins in contaminated food and feed can be a choice of such technology. To date, many of the microbial strategies have only showed reduced concentration of aflatoxins and the structure and toxicity of the detoxified products are unclear. More attention should be paid to the detoxification reactions, the structure of biotransformed products and the enzymes responsible for the detoxification. In this article, microbial strategies for aflatoxin control such as microbial binding and microbial biotransformation are reviewed.

A rare case of circumferential intramural dissection of the thoracic esophagus

Esophageal intramural dissection is a rare disease, and whole thoracic esophageal intramural dissection is extremely rare. We report a case of circumferential intramural dissection of the thoracic esophagus, which occurred between the submucosal layer and the muscularis propria layer, with inflammation in the false lumen mimicking esophageal mediastinal fistula in the endoscopic view. The diagnosis was finally confirmed at operation and cured by thoracic esophagectomy.

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model

Motivation: Digital reconstruction of 3D neuron structures is an important step toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns.

Results: We developed a graph-augmented deformable model (GD) to reconstruct (trace) the 3D structure of a neuron when it has a broken structure and/or fuzzy boundary. We formulated a variational problem using the geodesic shortest path, which is defined as a combination of Euclidean distance, exponent of inverse intensity of pixels along the path and closeness to local centers of image intensity distribution. We solved it in two steps. We first used a shortest path graph algorithm to guarantee that we find the global optimal solution of this step. Then we optimized a discrete deformable curve model to achieve visually more satisfactory reconstructions. Within our framework, it is also easy to define an optional prior curve that reflects the domain knowledge of a user. We investigated the performance of our method using a number of challenging 3D neuronal image datasets of different model organisms including fruit fly, Caenorhabditis elegans, and mouse. In our experiments, the GD method outperformed several comparison methods in reconstruction accuracy, consistency, robustness and speed. We further used GD in two real applications, namely cataloging neurite morphology of fruit fly to build a 3D ‘standard’ digital neurite atlas, and estimating the synaptic bouton density along the axons for a mouse brain.

Availability: The software is provided as part of the V3D-Neuron 1.0 package freely available at http://penglab.janelia.org/proj/v3d

Contact:pengh@janelia.hhmi.org

Pulmonary sequestration: angioarchitecture evaluated by three-dimensional computed tomography angiography

Pulmonary sequestration represents an anomaly of nonfunctioning tracheobronchial branching with retention of the embryonic systemic arterial supply. We report a case of intralobar pulmonary sequestration, in which the abnormal supplying artery and especially the abnormal draining vein were demonstrated by three-dimensional computed tomography angiography and were confirmed and treated using a video-assisted thoracoscopic procedure.

Central role of nitric oxide synthase in AICAR and caffeine-induced mitochondrial biogenesis in L6 myocytes

5-Aminoimidazole-4-carboxamide-ribonucleoside (AICAR) and caffeine, which activate AMP-activated protein kinase (AMPK) and cause sarcoplasmic reticulum calcium release, respectively, have been shown to increase mitochondrial biogenesis in L6 myotubes. Nitric oxide (NO) donors also increase mitochondrial biogenesis. Since neuronal and endothelial NO synthase (NOS) are calcium dependent and are also phosphorylated by AMPK, we hypothesized that NOS inhibition would attenuate the activation of mitochondrial biogenesis in response to AICAR and caffeine. L6 myotubes either were not treated (control) or were exposed acutely or for 5 h/day over 5 days to 100 microM of N(G)-nitro-L-arginine methyl ester (L-NAME, NOS inhibitor), 100 microM S-nitroso-N-acetyl-penicillamine (SNAP) (NO donor) +/- 100 microM L-NAME, 2 mM AICAR +/- 100 microM L-NAME, or 5 mM caffeine +/- 100 microM L-NAME (n = 12/treatment). Acute AICAR administration increased (P < 0.05) phospho- (P-)AMPK, but also increased P-CaMK, with resultant chronic increases in peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1 alpha), cytochrome-c oxidase (COX)-1, and COX-4 protein expression compared with control cells. NOS inhibition, which had no effect on AICAR-stimulated P-AMPK, surprisingly increased P-CaMK and attenuated the AICAR-induced increases in COX-1 and COX-4 protein. Caffeine administration, which increased P-CaMK without affecting P-AMPK, increased COX-1, COX-4, PGC-1 alpha, and citrate synthase activity. NOS inhibition, surprisingly, greatly attenuated the effect of caffeine on P-CaMK and attenuated the increases in COX-1 and COX-4 protein. SNAP increased all markers of mitochondrial biogenesis, and it also increased P-AMPK and P-CaMK. In conclusion, AICAR and caffeine increase mitochondrial biogenesis in L6 myotubes, at least in part, via interactions with NOS.

Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains

Automatic alignment (registration) of 3D images of adult fruit fly brains is often influenced by the significant displacement of the relative locations of the two optic lobes (OLs) and the center brain (CB). In one of our ongoing efforts to produce a better image alignment pipeline of adult fruit fly brains, we consider separating CB and OLs and align them independently. This paper reports our automatic method to segregate CB and OLs, in particular under conditions where the signal to noise ratio (SNR) is low, the variation of the image intensity is big, and the relative displacement of OLs and CB is substantial. We design an algorithm to find a minimum-cost 3D surface in a 3D image stack to best separate an OL (of one side, either left or right) from CB. This surface is defined as an aggregation of the respective minimum-cost curves detected in each individual 2D image slice. Each curve is defined by a list of control points that best segregate OL and CB. To obtain the locations of these control points, we derive an energy function that includes an image energy term defined by local pixel intensities and two internal energy terms that constrain the curve's smoothness and length. Gradient descent method is used to optimize this energy function. To improve both the speed and robustness of the method, for each stack, the locations of optimized control points in a slice are taken as the initialization prior for the next slice. We have tested this approach on simulated and real 3D fly brain image stacks and demonstrated that this method can reasonably segregate OLs from CBs despite the aforementioned difficulties.

Multicontext wavelet-based thresholding segmentation of brain tissues in magnetic resonance images

A novel segmentation method based on wavelet transform is presented for gray matter, white matter and cerebrospinal fluid in thin-sliced single-channel brain magnetic resonance (MR) scans. On the basis of the local image model, multicontext wavelet-based thresholding segmentation (MCWT) is proposed to classify 2D MR data into tissues automatically. In MCWT, the wavelet multiscale transform of local image gray histogram is done, and the gray threshold is gradually revealed from large-scale to small-scale coefficients. Image segmentation is independently performed in each local image to calculate the degree of membership of a pixel to each tissue class. Finally, a strategy is adopted to integrate the intersected outcomes from different local images. The result of the experiment indicates that MCWT outperforms other traditional segmentation methods in classifying brain MR images.

Gender difference in hemodynamic responses of prefrontal area to emotional stress by near-infrared spectroscopy

Presentation of negative pictures was used as emotional stress to assess gender differences in prefrontal area activation in a functional near-infrared spectroscopy (NIRS) study. Compared with neutral condition, the response of oxy-HB for men yielded no significant difference during stress period, but the response induced by stress pictures for women showed significant enhancement. It was indicated that it is crucial to take gender difference into account when negative stimuli are used in functional brain imaging.

RP-HPLC analysis of flucloxacillin in human plasma: validation and application to a bioequivalence study

A RP-HPLC method with rapid sample processing was developed for quantitation of flucloxacillin in human plasma using dicloxacillin as the internal standard. The plasma sample (100 microL) was acidified with glacial acetic acid, and deproteinized by precipitation with acetonitrile. The supernatant was directly injected into the HPLC system. Separation was achieved on an Alltima C18 column (250 mmx4.6 mm I.D., 5 microm), with a mixture of 10 mmol x L(-1) KH2PO4-acetonitrile (64.5:35.5, v/v) as mobile phase. The assay was successfully applied to a randomized, two-period cross-over bioequivalence study in 20 healthy Chinese volunteers following a single oral dose of 250 mg flucloxacillin capsules. A non-compartmental method was used for pharmacokinetic analysis. Compared with data in the literature, flucloxacillin was eliminated more slowly in Chinese than in Caucasians. Cmax, AUC(0-t) and AUC(0-infinity) were tested for bioequivalence after log-transformation of data. No significant difference was found. Tmax was analyzed by Wilcoxon's test and no significant difference was obtained (P > 0.05). Based on these statistical inferences, the two formulations were judged to be bioequivalent and, thus, can be prescribed interchangeably.

Expression of the novel co-stimulatory molecule B7-H4 by renal tubular epithelial cells

Crosstalk between T cells and renal tubular epithelial cells (TECs) in the pathogenesis of tubular lesions, the most important sign of progressive renal diseases, has not been clarified. Previous work has shown that TECs harbor co-stimulatory signals that promote T-cell activation, which induces tubular lesions. Nevertheless, the expression and functional role of B7-H4, a recently identified co-stimulatory ligand of the B7 superfamily, in pathologic human kidneys is unclear. We investigated the expression of B7-H4 on cryostat renal biopsies from patients with idiopathic membranous nephropathy (n=20), immunoglobulin A nephropathy (n=19), lupus nephritis (n=16), and acute renal allograft rejection (n=15) using immunohistochemistry. In addition, we also analyzed TEC-associated B7-H4 in the regulation of T-cell activation. Immunohistological staining revealed that B7-H4 antigen is restricted to tubular epithelium and that the protein is prominent in sections with severe tubular lesions, although no correlation was observed between tubular B7-H4 expression and levels of serum creatinine, serum urea nitrogen concentration, and 24-h proteinuria in each type of nephropathy. In vitro, mixed lymphocyte reactions revealed that TEC-related B7-H4 promotes cytokine (interleukin-2 and interferon-gamma) production and proliferation of co-cultured T cells. Interestingly, the secretion of interleukin-2 by C10 T cell hybridomas also increased when C10 cells were co-cultured with the B7-H4-transgenic murine TEC line, 3M-1-secreting tubular epithelial cells (MCT) in the presence of the antigen hen egg lysozyme. Our results clearly show that TEC-associated B7-H4 induces T-cell activation and we propose that B7-H4 is a potential activator that promotes tubular lesion.