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Purpose Meningiomas are the most common primary brain tumor in adults. Traditionally they have been understudied compared to other central nervous system (CNS) tumors. However over the last decade, there has been renewed interest in uncovering the molecular topography of these tumors, with landmark studies identifying key driver alterations contributing to meningioma development and progression. Recent work from several independent research groups have integrated different genomic and epigenomic platforms to develop a molecular-based classification scheme for meningiomas that could supersede histopathological grading in terms of diagnostic accuracy, biological relevance, and outcome prediction, keeping pace with contemporary grading schemes for other CNS tumors including gliomas and medulloblastomas. Methods Here we summarize the studies that have uncovered key alterations in meningiomas which builds towards the discovery of consensus molecular groups in meningiomas by integrating these findings. These groups supersede WHO grade and other clinical factors in being able to accurately predict tumor biology and clinical outcomes following surgery. Results Despite differences in the nomenclature of recently uncovered molecular groups across different studies, the biological similarities between these groups enables us to likely reconciliate these groups into four consensus molecular groups: two benign groups largely dichotomized by NF2-status, and two clinically aggressive groups defined by their hypermetabolic transcriptome, and by their preponderance of proliferative, cell-cycling pathways respectively. Conclusion Future work, including by our group and others are underway to validate these molecular groups and harmonize the nomenclature for routine clinical use.

Immune-mediated anti-tumoral responses, elicited by oncolytic viruses and augmented with checkpoint inhibition, may be an effective treatment approach for glioblastoma. Here in this multicenter phase 1/2 study we evaluated the combination of intratumoral delivery of oncolytic virus DNX-2401 followed by intravenous anti-PD-1 antibody pembrolizumab in recurrent glioblastoma, first in a dose-escalation and then in a dose-expansion phase, in 49 patients. The primary endpoints were overall safety and objective response rate. The primary safety endpoint was met, whereas the primary efficacy endpoint was not met. There were no dose-limiting toxicities, and full dose combined treatment was well tolerated. The objective response rate was 10.4% (90% confidence interval (CI) 4.2–20.7%), which was not statistically greater than the prespecified control rate of 5%. The secondary endpoint of overall survival at 12 months was 52.7% (95% CI 40.1–69.2%), which was statistically greater than the prespecified control rate of 20%. Median overall survival was 12.5 months (10.7–13.5 months). Objective responses led to longer survival (hazard ratio 0.20, 95% CI 0.05–0.87). A total of 56.2% (95% CI 41.1–70.5%) of patients had a clinical benefit defined as stable disease or better. Three patients completed treatment with durable responses and remain alive at 45, 48 and 60 months. Exploratory mutational, gene-expression and immunophenotypic analyses revealed that the balance between immune cell infiltration and expression of checkpoint inhibitors may potentially inform on response to treatment and mechanisms of resistance. Overall, the combination of intratumoral DNX-2401 followed by pembrolizumab was safe with notable survival benefit in select patients (ClinicalTrials.gov registration: NCT02798406).

BackgroundHomozygous loss of CDKN2A/B is a genetic alteration found in many cancer types including meningiomas, where it is associated with poor clinical outcome. It is now also a diagnostic criterion for grade 3 meningiomas in the 2021 WHO classification for central nervous system tumors. However, as in other cancers, the relationship between copy number loss of CDKN2A/B and expression of its gene product is unclear and may be either commensurate or paradoxical in nature. Therefore, we aimed to investigate the association of CDKN2A mRNA expression with clinical prognosis, WHO grade, and other molecular biomarkers in meningiomas such as DNA methylation, molecular group, and proteomics.MethodsWe used multidimensional molecular data of 490 meningioma samples from 4 independent cohorts to examine the relationship between mRNA expression of CDKN2A and copy number status, its correlation to clinical outcome, the transcriptomic pathways altered in differential CDKN2A expression, and its relationship with DNA methylation, and proteomics using an integrated molecular approach.ResultsMeningiomas without any copy number loss were dichotomized into high (CDKN2Ahigh) and low (CDKN2Alow) CDKN2A mRNA expression groups. Patients with CDKN2Ahighmeningiomas had poorer progression free survival (PFS) compared to those with CDKN2Alowmeningiomas. CDKN2A mRNA expression was increased in more aggressive molecular groups, and in higher WHO grade meningiomas across all cohorts. CDKN2Ahighmeningiomas and meningiomas with CDKN2A copy number loss shared common up-regulated cell cycling pathways. CDK4 mRNA expression was increased in CDKN2Ahighmeningiomas and both p16 and CDK4 protein were more abundant in CDKN2Ahighmeningiomas. CDKN2Ahighmeningiomas were frequently hypermethylated at the gene body and UTR compared to CDKN2Alowmeningiomas and found be more commonly Rb-deficient.ConclusionsAn intermediate level of CDKN2A mRNA expression appears to be optimal as significantly low (CDKN2A deleted) or high expression (CDKN2Ahigh) are associated with poorer outcomes clinically. Though CDK4 is elevated in CDKN2Ahighmeningiomas, Rb-deficiency may be more common in this group, leading to lack of response to CDK inhibitors.

Dobzhansky–Muller incompatibilities represent a major driver of reproductive isolation between species. They are caused when interacting components encoded by alleles from different species cannot function properly when mixed. At incipient stages of speciation, complex incompatibilities involving multiple genetic loci with weak effects are frequently observed, but the underlying mechanisms remain elusive. Here we show perturbed proteostasis leading to compromised mitosis and meiosis in Saccharomyces cerevisiae hybrid lines carrying one or two chromosomes from Saccharomyces bayanus var. uvarum. Levels of proteotoxicity are correlated with the number of protein complexes on replaced chromosomes. Proteomic approaches reveal that multi-protein complexes with subunits encoded by replaced chromosomes tend to be unstable. Furthermore, hybrid defects can be alleviated or aggravated, respectively, by up- or down-regulating the ubiquitin-proteasomal degradation machinery, suggesting that destabilized complex subunits overburden the proteostasis machinery and compromise hybrid fitness. Our findings reveal the general role of impaired protein complex assembly in complex incompatibilities.

Description, Gene expression profiling of medulloblastoma cells undergoing therapy identifies BPIFB4 as a novel target for recurrent disease., Medulloblastoma (MB) remains a leading cause of cancer-related mortality among children. The paucity of MB samples collected at relapse has hindered the functional understanding of molecular mechanisms driving therapy failure. New models capable of accurately recapitulating tumor progression in response to conventional therapeutic interventions are urgently needed. In this study, we developed a therapy-adapted PDX MB model that has a distinct advantage of generating human MB recurrence. The comparative gene expression analysis of MB cells collected throughout therapy led to identification of genes specifically up-regulated after therapy, including one previously undescribed in the setting of brain tumors, bactericidal/permeability-increasing fold-containing family B member 4 (BPIFB4). Subsequent functional validation resulted in a markedly diminished in vitro proliferation, self-renewal, and longevity of MB cells, translating into extended survival and reduced tumor burden in vivo. Targeting endothelial nitric oxide synthase, a downstream substrate of BPIFB4, impeded growth of several patient-derived MB lines at low nanomolar concentrations.

BACKGROUND Aside from surgery, radiotherapy (RT) remains the only standard of care treatment for meningiomas. However, few studies have identified clinical/molecular biomarkers associated with responsiveness to RT and the optimal timing of RT after surgery remains controversial. We aimed to assess outcomes in a large multi-institutional cohort of RT-treated meningiomas to identify clinical factors and DNA methylation and RNA expression markers associated with progression-free survival (PFS) post-RT. METHODS Patients with intracranial meningiomas who underwent treatment with fractionated RT between 1997-2018 were included. DNA-methylation using the Illumina 850K EPICArray and RNA-sequencing were performed on tumours with sufficient tissue. Primary endpoints were radiographic recurrence of progression and time to progression from the time of RT completion. RESULTS 404 meningiomas were included for analysis. Of these, 167 (41.3%) recurred post-RT, usually within 5-years of RT. Previous RT to the meningioma, having a WHO grade 3 meningioma, and older age at diagnosis were independently associated with poorer PFS post-RT. Following propensity score matching, patients that received adjuvant RT had significantly better PFS post-RT compared to those that received salvage RT after recurrence (p=0.04). DNA methylation on 220 of these meningiomas segregated tumours into two distinct methylation groups (RT-resistant and RT-sensitive) based on unsupervised consensus clustering. DNA methylation were able to independently predict PFS post-RT better than all clinical factors. Differential RNA-expression analysis of these groups showed up-regulation of pathways involved in chromosome segregation and mitotic cell cycle and down-regulation of fatty acid metabolism pathways in RT-resistant meningiomas. CONCLUSION While there are a paucity of clinical factors that can reliably predict a meningioma’s response to RT, DNA methylation and RNA expression biomarkers may aid in differentiating RT-resistant meningiomas from RT-sensitive tumours. Patients that receive adjuvant RT may have prolonged PFS post-RT compared to those that receive salvage RT only after recurrence has already occurred.

Meningiomas are the most common primary intracranial tumour in adults

BackgroundCiliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains ofParamecium bursaria, a highly divergent species of the genusParameciumwhich can stably establish endosymbioses with green algae.ResultsWe assembled a high-quality macronuclear genome ofP.bursariaand further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways.ConclusionsWe report programmed DNA rearrangements in theP.bursariamacronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.

The disability, mortality and costs caused by non-vertebral osteoporotic fractures are enormous. Existing osteoporosis therapies are highly effective at reducing vertebral but not non-vertebral fractures. Cortical bone is a major determinant of non-vertebral bone strength. To identify novel osteoporosis drug targets, we phenotyped cortical bone of 3 366 viable mouse strains with global knockouts of druggable genes. Cortical bone thickness was substantially elevated in Notum−/− mice. NOTUM is a secreted WNT lipase and we observed high NOTUM expression in cortical bone and osteoblasts but not osteoclasts. Three orally active small molecules and a neutralizing antibody inhibiting NOTUM lipase activity were developed. They increased cortical bone thickness and strength at multiple skeletal sites in both gonadal intact and ovariectomized rodents by stimulating endocortical bone formation. Thus, inhibition of NOTUM activity is a potential novel anabolic therapy for strengthening cortical bone and preventing non-vertebral fractures., Bone Development: NOTUM inhibition stimulates bone formation NOTUM is an enzyme that inactivates WNT proteins (which play a key role in early tissue development), and inhibiting NOTUM has been found to increase the formation of endocortical bone (within the cortex, the hard exterior of bone) and enhance bone strength. Existing therapies for osteoporosis (condition causing bone to become weak and brittle) are effective in reducing vertebral, but not non-vertebral, fractures. A team headed by Robert Brommage at Lexicon Pharmaceuticals, Texas aimed to identify novel osteoporosis drug targets in mice. Following inhibition of NOTUM activity, the authors observed increased cortical bone thickness and strength at multiple skeletal sites through stimulation of endocortical bone formation. The team concluded that inhibiting NOTUM activity has good potential as a new therapeutic strategy and could be beneficial in preventing non-vertebral osteoporotic fractures.

Xerostomia, or dry mouth syndrome, is one of the radiation therapy (RT)-induced side effects experienced by head and neck cancer patients. Measuring the severity of xerostomia can be performed by several techniques such as measuring the differential weight of dental rolls placed in the mouth for a fixed time period, measuring the electromyographic activity of musculus digastricus, using parotid cup, and electrophysiological measurements by electrical impedance. The present study focuses on detecting the change in bioimpedance around the oral cavity when salivation is induced using lime juice on healthy human subjects. In this study, impedance changes between stimulated and resting states of the salivary glands for 31 healthy volunteers were measured and analyzed. Pre- and post-stimulation impedance measurement was performed on healthy volunteer subjects using impedance spectroscopy over 50 frequencies ranging from 10 kHz to 1 MHz. The electrical properties of salivary glands were extracted by fitting the measured admittance data to the well-known Cole model. Comparison of measured electrical properties of gland at the resting and stimulated states reveals the changes in the intra- and extra-cellular spaces of salivary gland as a result of saliva secretion. Statistical analysis of the spectroscopy data collected shows that there is a significant difference in electrical properties of tissue between resting and stimulated states of the salivary activity. These electrical impedance spectroscopy measurements will be used to benchmark changes of impedance due to salivary gland stimulation.

Additional file 1: Figure S1. De novo assembly of the P. bursaria MAC genome. Figure S2. P. bursaria introns have very conserved 5′ and 3′ splice sites. Figure S3. PFG Southern blot analysis of the genomic DNA of different P. bursaria strains. Figure S4. The extensive chromosome breakage pattern in the MAC. Figure S5. A model showing how highly variable breaking sites lead to non-uniform gene dosage. Figure S6. Contig copy number is uniform in T. thermophila. Different P. bursaria strains show similar patterns of copy number distribution. Figure S7. Conserved GA-rich motifs are found near chromosome breakage sites. Figure S8. DK1 and DK2 strains are the real F1 progeny of Dd1 and KM2.

Additional file 2: Table S1. Basic statistics for the coding regions of the two haplotypes of the Dd1 reference genome. Table S2. Statistics of sequence diversity for different P. bursaria strains compared to the H1 haplotype of Dd1. Table S3. Basic statistics for the intergenic and intron regions on two haplotypes of the reference genome. Table S5. Enriched GO terms for P. bursaria specific genes (p-value ≤0.05 after the Benjamini-Hochberg correction). Table S7. The correlation matrix (Spearman’s correlation coefficient ρ) of the gene copy number between genetically divergent strains. Table S8. Enriched GO terms for the conserved and non-conserved groups of genes (p-value ≤0.05 after the Benjamini-Hochberg correction). Table S9. DNA and RNA sequencing library list and data accession numbers. Table S10. Primer list used in qPCR and Southern blot and F1 progeny validation.

Hip fractures at the femoral neck are a major cause of morbidity and mortality, but aside from biomechanical strength testing, little is known about femoral neck architecture in mice. Procedures were optimized to analyze high-resolution (6 μm voxel size) microCT scans of the mouse femoral neck to provide bone mass and architectural information. Similar to histomorphometric observations in rats, the boundary between cortical and trabecular bone is difficult to identify in the mouse femoral mid-neck and these compartments were not analyzed separately. Analyses included total area, mineralized bone area, and bone volume fraction (BV/TV). Femoral neck architecture varies in C57BL6/J, 129SvEv and BALB/c mouse strains. Bone cross sectional area and BV/TV were low in Lrp5 but elevated in Sost gene knockout mice. Sfrp4 gene knockout resulted in high total area, normal bone area, low BV/TV and, as indicated by BS/BV values, greater trabecularization. Femoral neck BV/TV declined with age and ovariectomy, but increased with teriparatide treatment. These findings demonstrate that the architecture of the mouse femoral neck mimics phenotypes and treatment effects observed at other skeletal sites and is a relevant bone site for translational studies examining osteoporosis therapies.

This article discusses the design, operation, and performance evaluation of a unique cable-operated 6.24 kWp commercial-size solar tracking system called iPV dual-axis tracker or iPV DAT with a position detector to gain the maximum power from the sunlight. Compared with other solar tracking systems, low cost, simplified hardware structure, and controlling algorithm are the advantages of this system. The operating method of the 6.24 kWp iPV DAT follow a simple pull and release of the steel cables connecting the corners of the PV module frame to the electric motors and directed by an electronic control system. The steel cables attached to the corners of the module frame also provide an extra stability in the event of high wind of up to 220 km/h. The accuracy of the tracking effect is managed by an astronomical algorithm that enables a full 360° azimuth rotation and altitude tilt of −40° to 40° (0 = horizontal). The controller algorithm also includes backtracking capability that allows optimization of ground cover ratio. Performance evaluation of the iPV DAT installed and operated in Taiwan for 12 months is compared with a fixed-tilt PV system. An average electricity gain of 30.1% and performance ratio of 93% are realized using iPV DAT.

This paper analyzes a capacity management problem in which two service providers utilize a common facility to serve two separate markets with time-sensitive demands. The facility provider has a fixed capacity and all parties maximize demand rates. When the service providers share the facility, they play a frequency competition game with a unique Nash equilibrium. When the service providers have dedicated facilities, the facility provider leads two separate Stackelberg games. A centralized system with the first-best outcome is also examined. Based on closed-form solutions under all three scenarios, we find that facility capacity competition is a prerequisite condition for not pooling the service providers. Moreover, we establish the rankings of preferred strategies for all parties with respect to the ratio of the service providers’ demand loss rates, which are proportional to the time sensitivity of demand and the potential market size. Interestingly a triple-agreement situation for the pooling strategy exists if the rates are close, and the facility provider permits a request for dedicated facilities only if the service provider has an overwhelming dominance at the demand loss rate. We connect these managerial insights with strategic seaport capacity management.

One of the challenges to describing the human liver on a single cell level is the process of cell dissociation. Cell dissociation methods can be quite damaging to the cells and can lead to a biasing of the transcriptome. We have developed gentle surgical and perfusion techniques to isolate and transcriptionally profile viable resident cells from liver samples taken from deceased donor liver grafts prior to organ transplantation.

Phantoms are widely used in medical imaging to predict image quality prior to clinical imaging. This paper discusses the possible use of bolus material, as a conductivity phantom, for validation and interpretation of electrical impedance tomography (EIT) images. Bolus is commonly used in radiation therapy to mimic tissue. When irradiated, it has radiological characteristics similar to tissue. With increased research interest in CT/EIT fusion imaging there is a need to find a material which has both the absorption coefficient and electrical conductivity similar to biological tissues. In the present study the electrical properties, specifically resistivity, of various commercially available bolus materials were characterized by comparing their frequency response with that of in-vivo connective adipose tissue. It was determined that the resistivity of Gelatin Bolus is similar to in-vivo tissue in the frequency range 10 kHz to 1MHz and therefore has potential to be used in EIT/CT fusion imaging studies.

To assess the roles of Lrrk1 and Lrrk2, we examined skeletal phenotypes in Lrrk1 and Lrrk2 knockout (KO) mice. Lrrk1 KO mice exhibit severe osteopetrosis caused by dysfunction of multinucleated osteoclasts, reduced bone resorption in endocortical and trabecular regions, and increased bone mineralization. Lrrk1 KO mice have lifelong accumulation of bone and respond normally to the anabolic actions of teriparatide treatment, but are resistant to ovariectomy-induced bone boss. Precursors derived from Lrrk1 KO mice differentiate into multinucleated cells in response to macrophage colony-stimulating factor (M-CSF)/receptor activator of NF-κB ligand (RANKL) treatment, but these cells fail to form peripheral sealing zones and ruffled borders, and fail to resorb bone. The phosphorylation of cellular Rous sarcoma oncogene (c-Src) at Tyr-527 is significantly elevated whereas at Tyr-416 is decreased in Lrrk1-deficient osteoclasts. The defective osteoclast function is partially rescued by overexpression of the constitutively active form of Y527F c-Src. Immunoprecipitation assays in osteoclasts detected a physical interaction of Lrrk1 with C-terminal Src kinase (Csk). Lrrk2 KO mice do not show obvious bone phenotypes. Precursors derived from Lrrk2 KO mice differentiate into functional multinucleated osteoclasts. Our finding of osteopetrosis in Lrrk1 KO mice provides convincing evidence that Lrrk1 plays a critical role in negative regulation of bone mass in part through modulating the c-Src signaling pathway in mice.

WNT16 is associated with bone mineral density, osteoporotic fracture and bone strength : a large-scale meta-analysis of genomewide association studies

Using mouse gene knock-out models, we identify aldehyde reductase (EC 1.1.1.2, Akr1a4 (GR)) and aldose reductase (EC 1.1.1.21, Akr1b3 (AR)) as the enzymes responsible for conversion of D-glucuronate to L-gulonate, a key step in the ascorbate (ASC) synthesis pathway in mice. The gene knock-out (KO) mice show that the two enzymes, GR and AR, provide approximately 85 and approximately 15% of L-gulonate, respectively. GRKO/ARKO double knock-out mice are unable to synthesize ASC (>95% ASC deficit) and develop scurvy. The GRKO mice ( approximately 85% ASC deficit) develop and grow normally when fed regular mouse chow (ASC content = 0) but suffer severe osteopenia and spontaneous fractures with stresses that increase ASC requirements, such as pregnancy or castration. Castration greatly increases osteoclast numbers and activity in GRKO mice and promotes increased bone loss as compared with wild-type controls and additionally induces proliferation of immature dysplastic osteoblasts likely because of an ASC-sensitive block(s) in early differentiation. ASC and the antioxidants pycnogenol and resveratrol block osteoclast proliferation and bone loss, but only ASC feeding restores osteoblast differentiation and prevents their dysplastic proliferation. This is the first in vivo demonstration of two independent roles for ASC as an antioxidant suppressing osteoclast activity and number as well as a cofactor promoting osteoblast differentiation. Although humans have lost the ability to synthesize ASC, our mouse models suggest the mechanisms by which suboptimal ASC availability facilitates the development of osteoporosis, which has important implications for human osteoporosis.

BACKGROUND\ud Cortical-bone fragility is a common feature in osteoporosis that is linked to non\ud -\ud vertebral fractures. Regulation of cortical-bone homeostasis has proved elusive. The \ud study of genetic disorders of the skeleton can yield insights that fuel experimental \ud therapeutic approaches to the treatment of rare disorders and common skeletal \ud ailments.\ud METHODS\ud We evaluated four patients with Pyle’s disease, a genetic disorder that is characterized \ud by cortical-bone thinning, limb deformity, and fractures; two patients were examined \ud by means of exome sequencing, and two were examined by means of Sanger se\ud -\ud quencing. After a candidate gene was identified, we generated a knockout mouse \ud model that manifested the phenotype and studied the mechanisms responsible for \ud altered bone architecture.\ud RESULTS\ud In all affected patients, we found biallelic truncating mutations in \ud SFR P4\ud , the gene \ud encoding secreted frizzled-related protein 4, a soluble Wnt inhibitor. Mice deficient \ud in \ud Sfrp4\ud , like persons with Pyle’s disease, have increased amounts of trabecular bone \ud and unusually thin cortical bone, as a result of differential regulation of Wnt and \ud bone morphogenetic protein (BMP) signaling in these two bone compartments. Treat\ud -\ud ment of \ud Sfrp4-\ud deficient mice with a soluble Bmp2 receptor (RAP-661) or with anti\ud -\ud bodies to sclerostin corrected the cortical-bone defect.\ud CONCLUSIONS\ud Our study showed that Pyle’s disease was caused by a deficiency of sFRP4, that cortical-\ud bone and trabecular-bone homeostasis were governed by different mechanisms, and \ud that sFRP4-mediated cross-regulation between Wnt and BMP signaling was critical \ud for achieving proper cortical-bone thickness and stability. (Funded by the Swiss Na\ud -\ud tional Foundation and the National Institutes of Health.)

MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs in human have been discovered and registered, but still lack of information or algorithms to reveal the relations among miRNAs, environmental chemicals and human health. Chemicals in environment affect our health and daily life, and some of them can lead to diseases by inferring biological pathways. We develop a creditable online web server, ChemiRs, for predicting interactions and relations among miRNAs, chemicals and pathways. The database not only compares gene lists affected by chemicals and miRNAs, but also incorporates curated pathways to identify possible interactions. Here, we manually retrieved associations of miRNAs and chemicals from biomedical literature. We developed an online system, ChemiRs, which contains miRNAs, diseases, Medical Subject Heading (MeSH) terms, chemicals, genes, pathways and PubMed IDs. We connected each miRNA to miRBase, and every current gene symbol to HUGO Gene Nomenclature Committee (HGNC) for genome annotation. Human pathway information is also provided from KEGG and REACTOME databases. Information about Gene Ontology (GO) is queried from GO Online SQL Environment (GOOSE). With a user-friendly interface, the web application is easy to use. Multiple query results can be easily integrated and exported as report documents in PDF format. Association analysis of miRNAs and chemicals can help us understand the pathogenesis of chemical components. ChemiRs is freely available for public use at http://omics.biol.ntnu.edu.tw/ChemiRs .

Disruption of serotonin synthesis in neurons and the periphery by knockout (KO) of mouse genes for tryptophan hydroxylases (peripheral Tph1 and neuronal Tph2) has been claimed to decrease (Tph2 KO) and increase (Tph1 KO) bone mass. In this report, adult male and female Tph2 KO mice were observed to have elevated spine trabecular bone. Female Tph2 KO mice have reduced midshaft femur cortical bone thickness. Bone mass was normal in male and female Tph1 KO mice examined as part of a Tph1/Tph2 double knockout (DKO) mouse cohort.

Lrp5 deficiency decreases bone formation and results in low bone mass. This study evaluated the bone anabolic response to intermittent PTH treatment in Lrp5-deficient mice. Our results indicate that Lrp5 is not essential for the stimulatory effect of PTH on cancellous and cortical bone formation. Introduction: Low-density lipoprotein receptor–related protein 5 (Lrp5), a co-receptor in canonical Wnt signaling, increases osteoblast proliferation, differentiation, and function. The purpose of this study was to use Lrp5-deficient mice to evaluate the potential role of this gene in mediating the bone anabolic effects of PTH. Materials and Methods: Adult wildtype (WT, 23 male and 25 female) and Lrp5 knockout (KO, 27 male and 26 female) mice were treated subcutaneously with either vehicle or 80 μg/kg human PTH(1-34) on alternate days for 6 weeks. Femoral BMC and BMD were determined using DXA. Lumbar vertebrae were processed for quantitative bone histomorphometry. Bone architecture was evaluated by μCT. Data were analyzed using a multiway ANOVA. Results: Cancellous and cortical bone mass were decreased with Lrp5 deficiency. Compared with WT mice, cancellous bone volume in the distal femur and the lumbar vertebra in Lrp5 KO mice was 54% and 38% lower, respectively (p < 0.0001), whereas femoral cortical thickness was 11% lower in the KO mice (p < 0.0001). The decrease in cancellous bone volume in the lumbar vertebrae was associated with a 45% decrease in osteoblast surface (p < 0.0001) and a comparable decrease in bone formation rate (p < 0.0001). Osteoclast surface, an index of bone resorption, was 24% lower in Lrp5 KO compared with WT mice (p < 0.007). Treatment of mice with PTH for 6 weeks resulted in a 59% increase in osteoblast surface (p < 0.0001) and a 19% increase in osteoclast surface (p = 0.053) in both genotypes, but did not augment cancellous bone volume in either genotype. Femur cortical thickness was 11% higher in PTH-treated mice in comparison with vehicle-treated mice (p < 0.0001), regardless of genotype. Conclusions: Whereas disruption of Lrp5 results in decreased bone mass because of decreased bone formation, Lrp5 does not seem to be essential for the stimulatory effects of PTH on cancellous and cortical bone formation.

In this investigation, a three dimensional gradient deficient beam element (BEAM9) using the absolute nodal coordinate formulation (ANCF) is introduced. This element has nine coordinates per node, this includes the position vector and the two gradient vectors rx and ry. Like most of the ANCF elements, this element has constant mass matrix and zero centrifugal and Coriolis inertia forces. The plane strain elastic force model and the elastic line approach are two elastic force models presented in this paper in order to simulate the element internal resistance. Both models support resistance to the general bending and twist moments. The possibilities of employing nonlinear material models will be discussed in future work. Furthermore, the proposed element has the advantage of easy integration over general cross section area that is not easy to perform using the fully parameterized ANCF beam element (BEAM12). Comparing to the ANCF cable element (BEAM6), the proposed element can resist general bending and twist loads. Moreover, shear deformations in the xy plane due to shear force and in the yz plane due to twist moment are considered with the gradient deficient beam element proposed in this work. However, no shear deformations are considered with the ANCF cable element. Comparing to the fully parameterized ANCF beam element, the gradient deficient beam element (BEAM9) avoids some locking issues, shows better computational efficiency and offers better convergency characteristics. Numerical examples are presented in order to validate the proposed gradient deficient beam element and to compare with other ANCF beam elements.Copyright © 2014 by ASME

Screening gene function in vivo is a powerful approach to discover novel drug targets. We present high-throughput screening (HTS) data for 3 762 distinct global gene knockout (KO) mouse lines with viable adult homozygous mice generated using either gene-trap or homologous recombination technologies. Bone mass was determined from DEXA scans of male and female mice at 14 weeks of age and by microCT analyses of bones from male mice at 16 weeks of age. Wild-type (WT) cagemates/littermates were examined for each gene KO. Lethality was observed in an additional 850 KO lines. Since primary HTS are susceptible to false positive findings, additional cohorts of mice from KO lines with intriguing HTS bone data were examined. Aging, ovariectomy, histomorphometry and bone strength studies were performed and possible non-skeletal phenotypes were explored. Together, these screens identified multiple genes affecting bone mass: 23 previously reported genes (Calcr, Cebpb, Crtap, Dcstamp, Dkk1, Duoxa2, Enpp1, Fgf23, Kiss1/Kiss1r, Kl (Klotho), Lrp5, Mstn, Neo1, Npr2, Ostm1, Postn, Sfrp4, Slc30a5, Slc39a13, Sost, Sumf1, Src, Wnt10b), five novel genes extensively characterized (Cldn18, Fam20c, Lrrk1, Sgpl1, Wnt16), five novel genes with preliminary characterization (Agpat2, Rassf5, Slc10a7, Slc26a7, Slc30a10) and three novel undisclosed genes coding for potential osteoporosis drug targets.

Fusion of electrical impedance tomography (EIT) with computed tomography (CT) can be useful as a clinical tool for providing additional physiological information about tissues, but requires suitable fusion algorithms and validation procedures. This work explores the feasibility of fusing EIT and CT images using an algorithm for coregistration. The imaging performance is validated through feature space assessment on phantom contrast targets.EIT data were acquired by scanning a phantom using a circuit, configured for injecting current through 16 electrodes, placed around the phantom. A conductivity image of the phantom was obtained from the data using electrical impedance and diffuse optical tomography reconstruction software (EIDORS). A CT image of the phantom was also acquired. The EIT and CT images were fused using a region of interest (ROI) coregistration fusion algorithm. Phantom imaging experiments were carried out on objects of different contrasts, sizes, and positions. The conductive medium of the phantoms was made of a tissue-mimicking bolus material that is routinely used in clinical radiation therapy settings. To validate the imaging performance in detecting different contrasts, the ROI of the phantom was filled with distilled water and normal saline. Spatially separated cylindrical objects of different sizes were used for validating the imaging performance in multiple target detection. Analyses of the CT, EIT and the EIT/CT phantom images were carried out based on the variations of contrast, correlation, energy, and homogeneity, using a gray level co-occurrence matrix (GLCM). A reference image of the phantom was simulated using EIDORS, and the performances of the CT and EIT imaging systems were evaluated and compared against the performance of the EIT/CT system using various feature metrics, detectability, and structural similarity index measures.In detecting distilled and normal saline water in bolus medium, EIT as a stand-alone imaging system showed contrast discrimination of 47%, while the CT imaging system showed a discrimination of only 1.5%. The structural similarity index measure showed a drop of 24% with EIT imaging compared to CT imaging. The average detectability measure for CT imaging was found to be 2.375 ± 0.19 before fusion. After complementing with EIT information, the detectability measure increased to 11.06 ± 2.04. Based on the feature metrics, the functional imaging quality of CT and EIT were found to be 2.29% and 86%, respectively, before fusion. Structural imaging quality was found to be 66% for CT and 16% for EIT. After fusion, functional imaging quality improved in CT imaging from 2.29% to 42% and the structural imaging quality of EIT imaging changed from 16% to 66%. The improvement in image quality was also observed in detecting objects of different sizes.The authors found a significant improvement in the contrast detectability performance of CT imaging when complemented with functional imaging information from EIT. Along with the feature assessment metrics, the concept of complementing CT with EIT imaging can lead to an EIT/CT imaging modality which might fully utilize the functional imaging abilities of EIT imaging, thereby enhancing the quality of care in the areas of cancer diagnosis and radiotherapy treatment planning.

GREMLIN 2 ( GREM2)—formerly, protein related to Dan and cerberus ( PRDC)—is a potent antagonist of the bone morphogenetic proteins 2 and 4, but little else in known about its functions. We found that Grem2-/- mice developed small deformed mandibular and maxillary incisors, indicating that GREMLIN2 is required for normal tooth morphogenesis. Although DEXA scans suggested that bone mineral density might be increased in Grem2-/- mice, histology did not reveal any evident bone phenotype. Grem2-/- mice did not display any other notable phenotypes evaluated in a high-throughput screening process that encompassed a range of immunologic, metabolic, ophthalmic, and behavioral parameters. Our findings indicate that Grem2 can be added to the growing list of genes that affect tooth development in mice.

In addition to the load transmission, the rubber bushings play an important role in the noise and vibration reduction. This paper presents a new three dimensional bushing element based on the absolute nodal coordinate formulation (ANCF). This element is used to simulate the torsional and axial bushing stiffness between two fully parameterized ANCF nodes. Tangent frame of reference is used to define local coordinates at each node. Rodrigues’ formula is used to define the angle and the axis of rotation between the two coordinates. Linear relationship, between the bushing forces and the relative deflections between the coordinates attached to the two ANCF nodes, is assumed. The numerical implementation of the proposed ANCF bushing element is validated by comparing with the expected results.Copyright © 2013 by ASME

To assess the roles of Lrrk1 and Lrrk2, we examined skeletal phenotypes in Lrrk1 and Lrrk2 knockout (KO) mice. Lrrk1 KO mice exhibit severe osteopetrosis caused by dysfunction of multinucleated osteoclasts, reduced bone resorption in endocortical and trabecular regions, and increased bone mineralization. Lrrk1 KO mice have lifelong accumulation of bone and respond normally to the anabolic actions of teriparatide treatment, but are resistant to ovariectomy-induced bone boss. Precursors derived from Lrrk1 KO mice differentiate into multinucleated cells in response to macrophage colony-stimulating factor (M-CSF)/receptor activator of NF-κB ligand (RANKL) treatment, but these cells fail to form peripheral sealing zones and ruffled borders, and fail to resorb bone. The phosphorylation of cellular Rous sarcoma oncogene (c-Src) at Tyr-527 is significantly elevated whereas at Tyr-416 is decreased in Lrrk1-deficient osteoclasts. The defective osteoclast function is partially rescued by overexpression of the constitutively active form of Y527F c-Src. Immunoprecipitation assays in osteoclasts detected a physical interaction of Lrrk1 with C-terminal Src kinase (Csk). Lrrk2 KO mice do not show obvious bone phenotypes. Precursors derived from Lrrk2 KO mice differentiate into functional multinucleated osteoclasts. Our finding of osteopetrosis in Lrrk1 KO mice provides convincing evidence that Lrrk1 plays a critical role in negative regulation of bone mass in part through modulating the c-Src signaling pathway in mice.

A couple of issues are identified in the process to embed absolute nodal coordinate formulation (ANCF) flexible bodies in an existing multibody dynamics code. (1) The generalized coordinates of ANCF must be solved together with those of the rest of the mechanism in a combined system of the equations of motion. (2) The various constraints, joints, and forces elements supported in the multibody dynamics code must be extended to the ANCF flexible bodies without major code restructuring. This paper describes two novel techniques that were devised to solve these issues. The first is the idea of interface triad. We will demonstrate how to construct the interface triad such that all exiting constraints, joints, and forces elements are automatically supported. The second idea is to represent the equations of motion of the ANCF body as a user-defined subroutine element representing a set of implicit general state equations subroutine (GSESUB). By treating each ANCF body modularly as a user-defined subroutine, not only all existing integration options of its host solver, e.g., HHT or DAE index-1, 2, and 3, etc., are automatically supported, but also the existing features such as parallel computing and sparse matrix solution of the existing multibody dynamics software are supported with minimum programming. Numerical examples are presented to demonstrate the efficiency and the success of these two techniques.Copyright © 2012 by ASME

We aimed to identify genetic variants associated with cortical bone thickness (CBT) and bone mineral density (BMD) by performing two separate genome-wide association study (GWAS) meta-analyses for CBT in 3 cohorts comprising 5,878 European subjects and for BMD in 5 cohorts comprising 5,672 individuals. We then assessed selected single-nucleotide polymorphisms (SNPs) for osteoporotic fracture in 2,023 cases and 3,740 controls. Association with CBT and forearm BMD was tested for ∼2.5 million SNPs in each cohort separately, and results were meta-analyzed using fixed effect meta-analysis. We identified a missense SNP (Thr>Ile; rs2707466) located in the WNT16 gene (7q31), associated with CBT (effect size of −0.11 standard deviations [SD] per C allele, P = 6.2×10−9). This SNP, as well as another nonsynonymous SNP rs2908004 (Gly>Arg), also had genome-wide significant association with forearm BMD (−0.14 SD per C allele, P = 2.3×10−12, and −0.16 SD per G allele, P = 1.2×10−15, respectively). Four genome-wide significant SNPs arising from BMD meta-analysis were tested for association with forearm fracture. SNP rs7776725 in FAM3C, a gene adjacent to WNT16, was associated with a genome-wide significant increased risk of forearm fracture (OR = 1.33, P = 7.3×10−9), with genome-wide suggestive signals from the two missense variants in WNT16 (rs2908004: OR = 1.22, P = 4.9×10−6 and rs2707466: OR = 1.22, P = 7.2×10−6). We next generated a homozygous mouse with targeted disruption of Wnt16. Female Wnt16−/− mice had 27% (P, Author Summary Bone traits are highly dependent on genetic factors. To date, numerous genetic loci for bone mineral density (BMD) and only one locus for osteoporotic fracture have been previously identified to be genome-wide significant. Cortical bone has been reported to be an important determinant of bone strength; so far, no genome-wide association studies (GWAS) have been performed for cortical bone thickness (CBT) of the tibial and radial diaphysis or BMD at forearm, a skeletal site rich in cortical bone. Therefore, we performed two separated meta-analyses of GWAS for cortical thickness of the tibia in 3 independent cohorts of 5,878 men and women, and for forearm BMD in 5 cohorts of 5,672 individuals. We identified the 7q31 locus, which contains WNT16, to be associated with CBT and BMD. Four SNPs from this locus were then tested in 2,023 osteoporotic fracture cases and 3,740 controls. One of these SNPs was genome-wide significant, and two were genome-wide suggestive, for forearm fracture. Generating a mouse with targeted disruption of Wnt16, we also demonstrated that mice lacking this protein had substantially thinner bone cortices and reduced bone strength than their wild-type littermates. These findings highlight WNT16 as a clinically relevant member of the Wnt signaling pathway and increase our understanding of the etiology of osteoporosis-related phenotypes and fracture.

To identify genetic loci influencing bone accrual, we performed a genome-wide association scan for total-body bone mineral density (TB-BMD) variation in 2,660 children of different ethnicities. We discovered variants in 7q31.31 associated with BMD measurements, with the lowest P = 4.1×10−11 observed for rs917727 with minor allele frequency of 0.37. We sought replication for all SNPs located ±500 kb from rs917727 in 11,052 additional individuals from five independent studies including children and adults, together with de novo genotyping of rs3801387 (in perfect linkage disequilibrium (LD) with rs917727) in 1,014 mothers of children from the discovery cohort. The top signal mapping in the surroundings of WNT16 was replicated across studies with a meta-analysis P = 2.6×10−31 and an effect size explaining between 0.6%–1.8% of TB-BMD variance. Conditional analyses on this signal revealed a secondary signal for total body BMD (P = 1.42×10−10) for rs4609139 and mapping to C7orf58. We also examined the genomic region for association with skull BMD to test if the associations were independent of skeletal loading. We identified two signals influencing skull BMD variation, including rs917727 (P = 1.9×10−16) and rs7801723 (P = 8.9×10−28), also mapping to C7orf58 (r2 = 0.50 with rs4609139). Wnt16 knockout (KO) mice with reduced total body BMD and gene expression profiles in human bone biopsies support a role of C7orf58 and WNT16 on the BMD phenotypes observed at the human population level. In summary, we detected two independent signals influencing total body and skull BMD variation in children and adults, thus demonstrating the presence of allelic heterogeneity at the WNT16 locus. One of the skull BMD signals mapping to C7orf58 is mostly driven by children, suggesting temporal determination on peak bone mass acquisition. Our life-course approach postulates that these genetic effects influencing peak bone mass accrual may impact the risk of osteoporosis later in life., Author Summary Genetic investigations on bone mineral density (BMD) variation in children allow the identification of factors determining peak bone mass and their influence on developing osteoporosis later in life. We ran a genome-wide association study (GWAS) for total body BMD based on 2,660 children of different ethnic backgrounds, followed by replication in an additional 12,066 individuals comprising children, young adults, and elderly populations. Our GWAS meta-analysis identified two independent signals in the 7q31.31 locus, arising from SNPs in the vicinity of WNT16, FAM3C, and C7orf58. These variants were also associated with skull BMD, a skeletal trait with much less environmental influence for which one of the signals displayed age-specific effects. Integration of functional studies in a Wnt16 knockout mouse model and gene expression profiles in human bone tissue provided additional evidence that WNT16 and C7orf58 underlie the described associations. All together our findings demonstrate the relevance of these factors for bone biology, the attainment of peak bone mass, and their likely impact on bone fragility later in life.

Magnetoencephalography (MEG) has gained its importance in the real-time detection of brain neuronal activities, based on the magnetic flux generated by ion exchange in brain neurons [1]. However, mapping of the actual magnetic dipole locations from the magnetic fields detected by MEG still remains a challenge [2], [3]. This study presents the method of developing a device which physically simulates human brainwave due to neuronal activities. Instead of using a human test subject, in which the information of the exact locations of dipoles is difficult to obtain, a brain phantom, which consists of coils controlled by waveform-generating circuits and mounted on different locations of a head-shaped object, is constructed. The magnetic flux density, which is proportional to the current in a coil, is controlled by the electronic unit attached to it. This study has also developed a technique using inverse analysis to localize the corresponding dipoles from the data collected by an MEG machine [4]. We have conducted experiments to verify the proposed brain phantom. The accuracy of the dipole localization technique is also verified using the brain phantom device developed, as the magnitudes and locations of the dipoles created by these coils are carefully controlled. The proposed localization technique has demonstrated close estimation of the dipoles from the raw MEG data [5]. Future research of the brain mapping project includes up-scaling the number of individually controlled coils and generating magnetic field pattern more closely resembling the actual human brainwave.

Photogate APS pixels use a MOS capacitor created potential well to capture photocarriers. However, optical absorption of the poly-silicon gate reduces photon transmission. We investigate multi-fingered photogates with openings in the gate to increase photon collection. 0.18 μm CMOS standard and multi-fingered photogates were implemented where the enclosed detection area is divided by 1, 3 and 5 poly fingers. Preliminary response comparison with standard photogates suggested the sensitivity of 1-finger pixels dropped ~22% implying open areas collected 62% of the photocarriers. The sensitivity of 3 and 5 finger pixels increased ~33 - 49% over standard, with open area collection ~170 - 290% more photocarriers due to fringing field created potential wells. These results indicated at least 66% of the incident light is absorbed by the poly-silicon gate. In spectral response multi-fingered pixels showed an increase in sensitivity in the red (631 nm) - yellow (587 nm) - green (571 nm) wavelengths but a relative decline in the blue (470 nm) possibly due to more absorption in the Silicon Nitride insulator layers. Some Silicon Nitride (SixNy) compositions have higher absorption coefficients in the Blue than poly-silicon and thus may dominate the absorption in these photogates structures. Extended analysis on the potential well formation in the multi-fingered photogates was perform using 2-D device simulation. Simulated multi-fingered photogates showed the strength of the fringing field increased as the open area spacing between poly-fingered decreases; with the 5-finger having a nearly uniform depleted region over the entire photogate area.