White paper – On the use of LiDAR data at AmeriFlux sites

Our aim is to inform the AmeriFlux community on existing and upcoming LiDAR technologies (atmospheric Doppler or Raman LiDAR often deployed at flux sites are not considered here), how it is currently used at flux sites, and how we believe it could, in the future, further contribute to the AmeriFlux vision. Heterogeneity in vegetation and ground properties at various spatial scales is omnipresent at flux sites, and 3D mapping of canopy, understory, and ground surface can help move the science forward

Functional genetic variation of human miRNAs and phenotypic consequences

A large number of human protein-coding genes are finely regulated by one or more microRNAs. Members of this small noncoding RNA family have emerged as important post-transcriptional regulators of gene expression and are involved in a number of disease phenotypes. Variability in the human genome is extensive and includes the common and rare single nucleotide polymorphisms (SNPs) and copy number variations (CNVs). The functional significance of the genome's variability is under intense investigation. In this article we review the emerging literature on how human genomic variation influences the outcome of microRNA targeting and the associated phenotypic effects. Illustrative examples are discussed that demonstrate the biological importance of functional polymorphisms affecting miRNA-mediated gene regulatio

Predictive value of masseter muscle thickness and bite force on Class II functional appliance treatment: a prospective controlled study

SummaryAim: To prospectively evaluate the functional capacity of the masticatory musculature as a predictive variable in determining functional appliance treatment outcomes in Class II/1 malocclusion children. Methods: Twenty Class II/1 malocclusion children (11.4±1.7 years) were treated with functional appliances during 1 year. Masseter muscle thickness and maximal molar bite force measurements, lateral cephalograms, and study casts were taken before and after treatment. Twenty age- and gender-matched untreated children were included as a control group. Regression analyses were used to identify correlations between pre-treatment muscle characteristics and treatment outcomes. Results: All treated patients showed dentoalveolar sagittal improvement. Maximal molar bite force and masseter muscle thickness decreased during the treatment period in the experimental group but increased in the control group. Children with lower pre-treatment maximal molar bite force showed more mesial movement of mandibular first molars, distal movement of maxillary first molars, and larger change in molar class during treatment. Children with thinner pre-treatment masseter muscles demonstrated more mandibular first molar mesialisation, mandibular incisor proclination, and opening of the gonial angle during treatment. Conclusions: The initial condition of the masticatory muscles may partly determine treatment outcomes. Children with thinner pre‐treatment masseter muscles or weaker bite force show greater dentoalveolar change

Regional carbon predictions in a temperate forest using satellite lidar

Large uncertainties in terrestrial carbon stocks and sequestration predictions result from insufficient regional data characterizing forest structure. This study uses satellite waveform lidar from ICESat to estimate regional forest structure in central New England, where each lidar waveform estimates fine-scale forest heterogeneity. ICESat is a global sampling satellite, but does not provide wall-to-wall coverage. Comprehensive, wall-to-wall ecosystem state characterization is achieved through spatial extrapolation using the random forest machine-learning algorithm. This forest description allows for effective initialization of individual-based terrestrial biosphere models making regional carbon flux predictions. Within 42/43.5 N and 73/71.5 W, aboveground carbon was estimated at 92.47 TgC or 45.66 MgC ha−1, and net carbon fluxes were estimated at 4.27 TgC yr−1 or 2.11 MgC ha−1 yr−1. This carbon sequestration potential was valued at 47% of fossil fuel emissions in eight central New England counties. In preparation for new lidar and hyperspectral satellites, linking satellite data and terrestrial biosphere models are crucial in improving estimates of carbon sequestration potential counteracting anthropogenic sources of carbon

Mesiodistal tooth size in non-syndromic unilateral cleft lip and palate patients: a meta-analysis

Objectives: To evaluate, using meta-analysis methodology, mesiodistal tooth dimensions in non-syndromic unilateral cleft lip and palate (CLP) patients. Materials and methods: A literature search was conducted using PubMed, Medline, Google Scholar Beta, EMBASE Excerpta Medica, CINAHL, Web of Science, and the Cochrane Collaboration, identifying English and non-English articles reporting on mesiodistal tooth dimensions on the cleft and non-cleft side of non-syndromic unilateral CLP patients. Additional studies were identified by searching reference lists of articles consulted. Only studies with a suitable control group were included. Two examiners independently performed the literature search and data extraction. Using meta-analysis software, data extracted from each selected study were statistically combined using the fixed-effects model. Weighted mean differences, 95% confidence intervals, and heterogeneity were calculated for each measurement. Results: Four articles fulfilling the inclusion criteria were located and included in the meta-analysis. Maxillary incisors and first molars were found to be significantly larger on the non-cleft side while mandibular incisors and premolars were larger on the cleft side, in non-syndromic unilateral CLP patients. On the cleft side, maxillary premolars and second molars were larger in cleft than control patients while incisors were smaller, whereas all mandibular teeth were larger in cleft patients. On the non-cleft side, all maxillary teeth except for the central incisors were larger in the cleft than control patients, while all mandibular teeth were larger in the cleft patients except for lateral incisors. Conclusions: Non-syndromic unilateral CLP patients tend to have larger posterior but smaller anterior teeth compared with the general population. Comparing sides, unilateral CLP patients tend to have smaller maxillary but larger mandibular teeth on the cleft than on the non-cleft side. Clinical relevance: Given that obtaining a stable, functional, and esthetic occlusion requires a thorough evaluation of tooth size, knowledge about trends in tooth size variations in CLP patients can help with dental and orthodontic treatment plannin

Predictive value of molar bite force on Class II functional appliance treatment outcomes

Sagittal intermaxillary changes brought about by functional appliances show large inter-individual variation. One factor that may in part explain these differences is the masticatory musculature and its functional capacity. The aims of this study were to investigate changes in maximal molar bite force during functional appliance treatment and to assess the influence of pre-treatment maximal molar bite force on treatment outcomes with functional appliances used in Class II malocclusion children. Twenty-five children (17 males and 8 females), aged 9-13 years, with a Class II malocclusion and increased overjet were treated with functional appliances for 1-2 years. Dental casts, lateral cephalograms, maximal molar bite force, and finger force measurements were performed before (T1) and after (T2) treatment. These same measurements were also performed 1-2 years before treatment (T0); the intermediate period before starting treatment served as the control. Multiple regression analyses were used to determine possible correlations between initial maximal molar bite force and dental or cephalometric changes during treatment. Maximal molar bite force, which increased pre-treatment (T0-T1), decreased during functional appliance treatment (T1-T2). Children with a weaker T1 maximal molar bite force showed a larger overjet reduction, greater improvement in molar relationship, greater reduction in ANB angle, and greater augmentation in SNB angle from T1 to T2. Treatment of children with Class II malocclusions with functional appliances seems to lead to more favourable treatment outcomes in those with a weaker maximal molar bite force. This was observed both as regards improvements in dental sagittal relationships, namely overjet and molar Class, as well as skeletal changes due to a decrease in ANB and an increase in SNB angle

Uncertainty in parameterizing floodplain forest friction for natural flood management, using remote sensing

One potential Natural Flood Management (NFM) option is floodplain reforestation or manage existing riparian forests, with a view to increasing flow resistance and attenuate flood hydrographs. However, the effectiveness of floodplain forests as resistance agents, during different magnitude overbank floods, has yet to be appropriately parameterized for hydraulic models. Remote sensing offers high-resolution datasets capable of characterizing vegetation structure from a variety of platforms, but they contain uncertainty. For the first time, we demonstrate uncertainty propagation in remote sensing derivations of complex vegetation structure through roughness prediction and floodplain flow for extreme flows and different forest types (young and old Poplar plantations, young and old Pine plantations, and an unmanaged riparian forest). The lowest uncertainties resulted from terrestrial and airborne lidar, where airborne lidar is currently best at defining canopy leaf area, but more research is needed to determine wood area. Mean literature uncertainties in stem density, trunk diameter, wood, and leaf area indices (20, 10, 30, 20%, respectively) resulted in a combined Manning’s n uncertainty from 11–13% to 11–17% at 2 m to 8 m flow depths. This equates to 7–8% roughness uncertainty per 10% combined forest structure uncertainty. Individually, stem density and trunk diameter uncertainties resulted in the largest Manning’s n uncertainty at all flow depths, especially for flow though Pine plantations. For deeper flows, leaf and woody areas become much more important, especially for unmanaged riparian forests with low canopy morphology. Forest structure errors propagated to flow depth demonstrate that even small flows can change by a decimeter, while deeper flows can change by 40 cm or more. For flow depth, errors in canopy structure are deemed more severe in flows depths beyond 4–6 m. This study highlights the need for lower uncertainty in all forest structure components using remote sensing, to improve roughness parameterization and flood modeling for NFM

Welcome to PathoGenetics

Disease gene identification has made enormous strides in the past twenty years through functional, positional and candidate gene approaches, and more recently by the exploitation of genome-wide strategies. However, although pathogenic mutations in over 2000 genes have been identified as causative of human diseases, much less is known about the relationship between the molecular defects and mechanisms that lead to disease pathology and symptoms. Recent advances in diverse fields such as genomics, proteomics, cell biology, as well as studies on transgenic animals have greatly accelerated our understanding of the biochemical and cellular basis of many diseases but much still remains to be discovered. The current challenge is to understand the molecular and metabolic pathways by which a particular pathogenic variation leads to a specific phenotype. The study of abnormal conditions is of crucial importance for the understanding of normal physiology and often provides us with the rationale for the development of novel therapeutic strategies

Peutz-Jeghers LKB1 mutants fail to activate GSK-3β, preventing it from inhibiting Wnt signaling

Peutz-Jeghers syndrome (PJS) is caused by germline mutations in the LKB1 gene, which encodes a serine-threonine kinase that regulates cell proliferation and polarity. This autosomal dominant disorder is characterized by mucocutaneous melanin pigmentation, multiple gastrointestinal hamartomatous polyposis and an increased risk of developing various neoplasms. To understand the molecular pathogenesis of PJS phenotypes, we used microarrays to analyze gene expression profiles in proliferating HeLa cells transduced with lentiviral vectors expressing wild type or mutant LKB1 proteins. We show that gene expression is differentially affected by mutations that impair the kinase activity (K78I) or alter the cellular localization of the LKB1 protein. However, both mutations abrogate the ability of LKB1 to up-regulate the transcription of several genes involved in Wnt signaling, including DKK3, WNT5B and FZD2. In addition—and in contrast to the wild type protein—these LKB1 mutants fail to activate the GSK-3β kinase, which otherwise phosphorylates β-catenin. The increase in β-catenin phosphorylation that occurs upon expression of wild-type LKB1 results in transcriptional inhibition of a canonical Wnt reporter gene. This suggests that pathogenic LKB1 mutations that lead to activation of the Wnt/β-catenin pathway could contribute to the cancer predisposition of PJS patient