An instance segmentation dataset of cabbages over the whole growing season for UAV imagery.

Crop growth monitoring is essential for both crop and supply chain management. Conventional manual sampling is not feasible for assessing the spatial variability of crop growth within an entire field or across all fields. Meanwhile, UAV-based remote sensing enables the efficient and nondestructive investigation of crop growth. A variety of crop-specific training image datasets are needed to detect crops from UAV imagery using a deep learning model. Specifically, the training dataset of cabbage is limited. This data article includes annotated cabbage images in the fields to recognize cabbages using machine learning models. This dataset contains 458 images with 17,621 annotated cabbages. Image sizes are approximately 500 to 1000 pixel squares. Since these cabbage images were collected from different cultivars during the whole growing season over the years, deep learning models trained with this dataset will be able to recognize a wide variety of cabbage shapes. In the future, this dataset can be used not only in UAVs but also in land-based robot applications for crop sensing or associated plant-specific management.

Damage to tropical forests caused by cyclones is driven by wind speed but mediated by topographical exposure and tree characteristics.

Each year, an average of 45 tropical cyclones affect coastal areas and potentially impact forests. The proportion of the most intense cyclones has increased over the past four decades and is predicted to continue to do so. Yet, it remains uncertain how topographical exposure and tree characteristics can mediate the damage caused by increasing wind speed. Here, we compiled empirical data on the damage caused by 11 cyclones occurring over the past 40 years, from 74 forest plots representing tropical regions worldwide, encompassing field data for 22,176 trees and 815 species. We reconstructed the wind structure of those tropical cyclones to estimate the maximum sustained wind speed (MSW) and wind direction at the studied plots. Then, we used a causal inference framework combined with Bayesian generalised linear mixed models to understand and quantify the causal effects of MSW, topographical exposure to wind (EXP), tree size (DBH) and species wood density (ρ) on the proportion of damaged trees at the community level, and on the probability of snapping or uprooting at the tree level. The probability of snapping or uprooting at the tree level and, hence, the proportion of damaged trees at the community level, increased with increasing MSW, and with increasing EXP accentuating the damaging effects of cyclones, in particular at higher wind speeds. Higher ρ decreased the probability of snapping and to a lesser extent of uprooting. Larger trees tended to have lower probabilities of snapping but increased probabilities of uprooting. Importantly, the effect of ρ decreasing the probabilities of snapping was more marked for smaller than larger trees and was further accentuated at higher MSW. Our work emphasises how local topography, tree size and species wood density together mediate cyclone damage to tropical forests, facilitating better predictions of the impacts of such disturbances in an increasingly windier world.

Toward a high-resolution mechanism of intrinsically disordered protein self-assembly.

Membraneless organelles formed via the self-assembly of intrinsically disordered proteins (IDPs) play a crucial role in regulating various physiological functions. Elucidating the mechanisms behind IDP self-assembly is of great interest not only from a biological perspective but also for understanding how amino acid mutations in IDPs contribute to the development of neurodegenerative diseases and other disorders. Currently, two proposed mechanisms explain IDP self-assembly: (1) the sticker-and-spacer framework, which considers amino acid residues as beads to simulate the intermolecular interactions, and (2) the cross-ß hypothesis, which focuses on the ß-sheet interactions between the molecular surfaces constructed by multiple residues. This review explores the advancement of new models that provide higher resolution insights into the IDP self-assembly mechanism based on new findings obtained from structural studies of IDPs.

A germline-targeted genetic screen for xrn-2 suppressors identifies a novel gene C34C12.2 in Caenorhabditis elegans.

XRN2 is an evolutionarily conserved 5'-to-3' exoribonuclease, which degrades or trims various types of RNA in the nucleus. Although XRN-2 is essential for embryogenesis, larval development and reproduction in Caenorhabditis elegans, relevant molecular pathways remain unidentified. Here we create a germline-specific xrn-2 conditional mutant and perform a mutagenesis screen for suppressors of sterility. Loss-of-function alleles of dpy-10, osr-1, ptr-6 and C34C12.2 genes are identified. Depletion of DPY-10, OSR-1 or PTR-6 increases expression of gpdh-1 that encodes a glycerol-3-phosphate dehydrogenase, thereby elevates glycerol accumulation to suppress sterility of the mutant. The C34C12.2 protein is predominantly localized in the nucleolus of germ cells and shows a similarity to Saccharomyces cerevisiae Net1, which is involved in rDNA silencing. Depletion of NRDE-2, a putative interacting partner of C34C12.2 and a component of the nuclear RNAi machinery, restores fertility to the xrn-2 conditional mutant. These results may help to identify an essential role of XRN-2 in germline development.

Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia.

Despite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha-1), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha-1 yr-1). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.

Importin alpha family NAAT/IBB domain: Functions of a pleiotropic long chameleon sequence.

Nuclear transport is essential for eukaryotic cell survival and regulates the movement of functional molecules in and out of the nucleus via the nuclear pore. Transport is facilitated by protein-protein interactions between cargo and transport receptors, which contribute to the expression and regulation of downstream genetic information. This chapter focuses on the molecular basis of the multifunctional nature of the importin α family, the representative transport receptors that bring proteins into the nucleus. Importin α performs multiple functions during the nuclear transport cycle through interactions with multiple molecules by a single domain called the IBB domain. This domain is a long chameleon sequence, which can change its conformation and binding mode depending on the interaction partners. By considering the evolutionarily conserved biochemical/physicochemical propensities of the amino acids constituting the functional complex interfaces, together with their structural properties, the mechanisms of switching between multiple complexes formed via IBB and the regulation of downstream functions are examined in detail. The mechanism of regulation by IBB indicates that the time has come for a paradigm shift in the way we view the molecular mechanisms by which proteins regulate downstream functions through their interactions with other molecules.

Magnetic resonance brain volumetry biomarkers of CLN2 Batten disease identified with miniswine model.

Late-infantile neuronal ceroid lipofuscinosis type 2 (CLN2) disease (Batten disease) is a rare pediatric disease, with symptom development leading to clinical diagnosis. Early diagnosis and effective tracking of disease progression are required for treatment. We hypothesize that brain volumetry is valuable in identifying CLN2 disease at an early stage and tracking disease progression in a genetically modified miniswine model. CLN2R208X/R208X miniswine and wild type controls were evaluated at 12- and 17-months of age, correlating to early and late stages of disease progression. Magnetic resonance imaging (MRI) T1- and T2-weighted data were acquired. Total intercranial, gray matter, cerebrospinal fluid, white matter, caudate, putamen, and ventricle volumes were calculated and expressed as proportions of the intracranial volume. The brain regions were compared between timepoints and cohorts using Gardner-Altman plots, mean differences, and confidence intervals. At an early stage of disease, the total intracranial volume (- 9.06 cm3), gray matter (- 4.37% 95 CI - 7.41; - 1.83), caudate (- 0.16%, 95 CI - 0.24; - 0.08) and putamen (- 0.11% 95 CI - 0.23; - 0.02) were all notably smaller in CLN2R208X/R208X miniswines versus WT, while cerebrospinal fluid was larger (+ 3.42%, 95 CI 2.54; 6.18). As the disease progressed to a later stage, the difference between the gray matter (- 8.27%, 95 CI - 10.1; - 5.56) and cerebrospinal fluid (+ 6.88%, 95 CI 4.31; 8.51) continued to become more pronounced, while others remained stable. MRI brain volumetry in this miniswine model of CLN2 disease is sensitive to early disease detection and longitudinal change monitoring, providing a valuable tool for pre-clinical treatment development and evaluation.

Association between an Increased Serum CCL5 Level and Pathophysiology of Degenerative Joint Disease in the Temporomandibular Joint in Females.

Degenerative joint disease of the temporomandibular joints (DJD-TMJ) clinically manifests with symptoms such as orofacial pain, joint sounds and limited jaw movements. Our research group previously reported the functional necessity of a chemokine-chemokine receptor axis of CCL5-CCR5 in osteoclasts. Accumulated studies reported that this axis was involved in the pathogenesis of bone and joint destructive diseases, suggesting CCL5 as a potent biomarker. This study investigated whether or not the serum level of CCL5 can be a biomarker of DJD-TMJ and concomitantly analyzed changes in the serum and urine levels of bone markers to see whether or not changes in the rate of bone metabolism were predisposing. We enrolled 17 female subjects with diagnosed DJD-TMJ and sexually and age-matched 17 controls. The serum CCL5 level in DJD-TMJ subjects was significantly higher than that in the control subjects. Multivariate analyses indicated an association between an augmented CCL5 level and the rate of bone metabolism, especially in relatively young DJD-TMJ subjects without other systemic symptoms. A principal component analysis of serum markers and our pharmacological experiment using a postmenopausal model of ovariectomized rats suggested that an augmented serum CCL5 level specifically reflected DJD-TMJ and that covert changes in the rate of bone metabolism predisposed individuals to DJD-TMJ.

ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.

T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) or Welander distal myopathy (WDM), have been identified. However, how these mutations affect PLD self-assembly properties has remained elusive. In this study, we uncovered the implicit pathogenic structures caused by the mutations. NMR analysis indicated that the dynamic structures of the PLD are synergistically determined by the physicochemical properties of amino acids in units of five residues. Molecular dynamics simulations and three-dimensional electron crystallography, together with biochemical assays, revealed that the WDM mutation E384K attenuated the sticky properties, whereas the ALS mutations P362L and A381T enhanced the self-assembly by inducing ß-sheet interactions and highly condensed assembly, respectively. These results suggest that the P362L and A381T mutations increase the likelihood of irreversible amyloid fibrillization after phase-separated droplet formation, and this process may lead to pathogenicity.

Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain.

Importin α has been described as a nuclear protein transport receptor that enables proteins synthesized in the cytoplasm to translocate into the nucleus. Besides its function in nuclear transport, an increasing number of studies have examined its non-nuclear transport functions. In both nuclear transport and non-nuclear transport, a functional domain called the IBB domain (importin ß binding domain) plays a key role in regulating importin α behavior, and is a common interacting domain for multiple binding partners. However, it is not yet fully understood how the IBB domain interacts with multiple binding partners, which leads to the switching of importin α function. In this study, we have distinguished the location and propensities of amino acids important for each function of the importin α IBB domain by mapping the biochemical/physicochemical propensities of evolutionarily conserved amino acids of the IBB domain onto the structure associated with each function. We found important residues that are universally conserved for IBB functions across species and family members, in addition to those previously known, as well as residues that are presumed to be responsible for the differences in complex-forming ability among family members and for functional switching.

Nuclear RNA Regulation by XRN2 and XTBD Family Proteins.

XRN2 is a 5'-to-3' exoribonuclease that is predominantly localized in the nucleus. By degrading or trimming various classes of RNA, XRN2 contributes to essential processes in gene expression such as transcription termination and ribosome biogenesis. Despite limited substrate specificity in vitro, XRN2 targets a specific subset of RNA by interacting with other proteins in cells. Here we review the functions of proteins that have an evolutionarily conserved XRN2-binding domain, XTBD. These proteins modulate activity of XRN2 by stabilizing it, controlling its subcellular localization or recruiting it to specific RNA targets, and thereby impact on various cellular processes.Key words: RNA regulation, XRN2, XTBD, ribosome biogenesis, subcellular localization.

Importin α2 association with chromatin: Direct DNA binding via a novel DNA-binding domain.

The nuclear transport of proteins is important for facilitating appropriate nuclear functions. The importin α family proteins play key roles in nuclear transport as transport receptors for copious nuclear proteins. Additionally, these proteins possess other functions, including chromatin association and gene regulation. However, these nontransport functions of importin α are not yet fully understood, especially their molecular-level mechanisms and consequences for functioning with chromatin. Here, we report the novel molecular characteristics of importin α binding to diverse DNA sequences in chromatin. We newly identified and characterized a DNA-binding domain-the Nucleic Acid Associating Trolley pole domain (NAAT domain)-in the N-terminal region of importin α within the conventional importin ß binding (IBB) domain that is necessary for nuclear transport of cargo proteins. Furthermore, we found that the DNA binding of importin α synergistically coupled the recruitment of its cargo protein to DNA. This is the first study to delineate the interaction between importin α and chromatin DNA via the NAAT domain, indicating the bifunctionality of the importin α N-terminal region for nuclear transport and chromatin association.

Kidney Imaging Surveillance in Commercially Insured Patients With Tuberous Sclerosis Complex.

BACKGROUND: Kidney disease has historically been the primary source of early mortality in adults with tuberous sclerosis complex (TSC). Kidney imaging surveillance promotes early detection of lesions requiring intervention. We describe kidney imaging frequency in relationship to patient-level characteristics for commercially insured patients with TSC in the United States. METHODS: This retrospective observational study used 2003 to 2016 enrollment and claims data from a de-identified fully insured commercial health insurer. Patients with TSC less than 65 years were included. The patient-level kidney imaging rate was calculated as the number of kidney imaging procedures divided by length of continuous enrollment. A multiple linear regression model was used to determine the relationship between imaging rate and progression of TSC-associated kidney disease, number of specialists seen, and nephrologist care. RESULTS: At least half of the 70 patients with TSC included in the study were aged 16 years or younger. Over a follow-up period of up to 14 years, the median kidney imaging rate was 0.13 procedures per year with 43% (N = 30) of patients lacking evidence of kidney imaging during the observation period. Imaging frequency increased with progression of TSC-associated kidney disease, more specialists, and nephrologist care (P < 0.05 for all three in regression model). CONCLUSIONS: A substantial percentage of patients with TSC in the United States are at risk for delayed detection of kidney manifestations due to infrequent kidney imaging surveillance. Multispecialty care, including neurologists, may positively affect kidney surveillance rates.

All tubers are not created equal: Cerebellar tubers in a pediatric patient with tuberous sclerosis.

Tuberous sclerosis complex (TSC) is a rare autosomal dominant disease characterized by multiple tumors throughout the body. Supratentorial hamartomas (or tubers), are a very common CNS feature of TSC. Cerebellar tubers are much less common in TSC. We present an interesting case of cerebellar tuber in a 14-year-old patient with TSC, highlighting clinical and diagnostic criteria for TSC and review the unique features of cerebellar tubers, differentiating these lesions from their more common supratentorial counterparts. This case serves as an educational tool to improve awareness of cerebellar tubers in patients with tuberous sclerosis.

Longitudinal phenotype development in a minipig model of neurofibromatosis type 1.

Neurofibromatosis type 1 (NF1) is a rare, autosomal dominant disease with variable clinical presentations. Large animal models are useful to help dissect molecular mechanisms, determine relevant biomarkers, and develop effective therapeutics. Here, we studied a NF1 minipig model (NF1+/ex42del) for the first 12 months of life to evaluate phenotype development, track disease progression, and provide a comparison to human subjects. Through systematic evaluation, we have shown that compared to littermate controls, the NF1 model develops phenotypic characteristics of human NF1: [1] café-au-lait macules, [2] axillary/inguinal freckling, [3] shortened stature, [4] tibial bone curvature, and [5] neurofibroma. At 4 months, full body computed tomography imaging detected significantly smaller long bones in NF1+/ex42del minipigs compared to controls, indicative of shorter stature. We found quantitative evidence of tibial bowing in a subpopulation of NF1 minipigs. By 8 months, an NF1+/ex42del boar developed a large diffuse shoulder neurofibroma, visualized on magnetic resonance imaging, which subsequently grew in size and depth as the animal aged up to 20 months. The NF1+/ex42del minipig model progressively demonstrates signature attributes that parallel clinical manifestations seen in humans and provides a viable tool for future translational NF1 research.

Fruit development of Lithocarpus (Fagaceae) and the role of heterochrony in their evolution.

Stone oaks, or Lithocarpus species of Fagaceae are ecologically important canopy trees in the tropical and subtropical forests over East Asia, and the fruits of which are important food sources for insects and vertebrates there. The great fruit morphological variation of this genus represents two fruit types, acorn and enclosed receptacle fruit types. However, the evolutionary mechanisms of differentiation into these two fruit types with contrasting morphology remain a puzzle. To reveal the morphogenetic properties of two fruit types, we observed tissue differentiation and development among 20 Lithocarpus species from fruit set to maturity. Unlike in fruits of Quercus, the endocarp differentiation in Lithocarpus fruits occurred later than exocarp and mesocarp. Cupules provided further protection of developing seeds, particularly of acorn-type fruits. Fruits of Lithocarpus and Quercus acorns share similar insect predators. At fruit set, both acorn and enclosed receptacle types were largely identical, with similar tissue morphology and the sequence of differentiation. The distinct difference between two fruit types at maturity came from varied rates and degrees of development between the pericarp and receptacle tissues. We found that heterochrony between two tissues could create substantially divergent ecological strategies for protection and dispersal of their seeds, which is essential for the evolution of two fruit types.

Whole-exome sequencing in a Japanese pedigree implicates a rare non-synonymous single-nucleotide variant in BEST3 as a candidate for mandibular prognathism.

Mandibular prognathism is a phenotype of facial deformity seen in populations around the world, but with higher incidence among East Asian populations. Five genome-wide nonparametric linkage analyses and a genome-wide association study to identify susceptibility loci of the phenotype have shown inconsistent results. To explore variants related to mandibular prognathism, we undertook whole-exome sequencing in a Japanese pedigree. The pedigree was ascertained as mandibular prognathism. The pedigree comprised 15 individuals from 4 generations. Four affected individuals across 2 generations and 5 unaffected individuals were chosen for whole-exome sequencing. Five non-synonymous single-nucleotide variants (SNVs) of UBASH3B, OR6M1, OR8D4, OR8B4, and BEST3 genes were detected in all 4 affected individuals, but in none of the 5 unaffected individuals. A non-synonymous SNV of the BEST3 gene, Chr12(GRCh37):g.70048878G>T, NM_032735.2:c.1816C>A, p.(L606I), was identified as rare missense variant. BEST3 is located on chromosome 12q15 and encodes bestrophin 3 from the bestrophin family of anion channels. The 4 other non-synonymous SNVs of UBASH3B, OR6M1, OR8D4, and OR8B4 were not considered plausible candidates for mandibular prognathism. Our whole-exome sequencing implicates a rare non-synonymous SNV of BEST3 as a candidate for mandibular prognathism in the Japanese pedigree.

Clinical Investigation of Congenital Factor Affecting Craniofacial Morphology of Unilateral Cleft Lip and Palate in Japanese Patients

Objective: To evaluate the craniofacial morphology of Japanese patients with unilateral cleft lip and palate and to evaluate the multiple congenital factors that affects craniofacial morphology in unilateral cleft lip and palate patients. Material and Methods: Lateral cephalograms of 140 subjects with unilateral cleft lip and palate were taken before any orthodontic treatment and alveolar bone graft. Subjects mean age was 6.85 ±1.56 years. Primary surgeries performed by surgeons from Hokkaido University Hospital. The craniofacial morphology of the 140 subjects was assessed by angular and linear cephalometric measurements. Gender, side of cleft, complete/incomplete type of cleft, presence/absence of lateral incisor in the affected side, family history of cleft and family history of skeletal Class III was chosen as congenital factors. To compare the assessments using congenital factors affecting craniofacial morphology in the unilateral cleft lip and palate subjects, angular and linear cephalometric measured values from each individual subject (control group) were converted into Z scores in relation to the means and standard deviation of the two parameters. Results: Twelve out of 13 craniofacial morphology outcomes were insignificant in 5 out of 6 dependent variables. Only 1 dependent variable showed 3/13 significant differences. Conclusion: Current study revealed the evidence that there were almost no significant differences in the craniofacial morphology outcome among various congenital factors. This will provide base line information and help determine the effectiveness of such factors.

Treatment Outcome Based on GOSLON Score of Multiple Factors in Unilateral Cleft Lip and Palate Children of Four Different Ethnic

Objective: To evaluate and compare the effect of each congenital and postnatal treatment factors in treatment outcome based on dental arch relationship (DAR) of four different populations at a time using GOSLON yardstick. Material and Methods: 432 unilateral cleft lip and palate subjects (Japanese, Malay ethnic group, Bangladeshi and Pakistani populations) age 5 to 12 years were taken before orthodontic treatment and alveolar bone grafting. The DAR was assessed by GOSLON Yardstick. Independent t-test was performed to compare the GOSLON score for each factors. A multiple comparison (Anova) was also conducted between the GOSLON score of four different populations. The significance level was set at p<0.05. Results: Statistically no significant different was found among the congenital factors. However, the family history of Class III malocclusion showed most likely to associate with, though there was no significant difference (p=0.069). Significant difference revealed between two techniques of cheiloplasty in both Malay ethnic group and Pakistani population (p=0.038 and p=0.000, respectively). Gender and Techniques of palatoplasty also showed significant difference in Pakistani population (p=0.026 and p=0.000, respectively). Japanese and Bangladeshi population showed no significant differences. Also no significant differences found between the GOSLON score and different countries. Conclusion: The treatment outcome based on DAR significantly varies in individual population [Malay ethnic group (cheiloplasty); Pakistan (gender, cheiloplasty and palatoplasty)].

Maxillofacial morphological factors related to acceleration of maxillary growth attributed to facial mask treatment: a structural superimposition study.

BACKGROUND: Anatomical textbooks mention that the contact between the pterygoid process and the palatine's pyramidal process is not a "suture" but "conjugation.".The aim was to evaluate the maxillofacial morphological factor responding most to the orthopedic force of facial mask treatment, using the structural superimposition analysis. METHODS: Thirty-one girls with Angle Class III malocclusion treated using a facial mask (FM group) and 11 girls with pseudo-Class III malocclusion (pseudo-III group) were examined. Lateral cephalograms at pre- and posttreatment were analyzed to evaluate maxillofacial changes. Cephalometric structural superimposition analysis originating with Björk and Skieller was also performed. RESULTS: In the FM group, a multiple linear regression model showed that maxillary sutural growth was significantly associated with counter-clockwise rotation of the maxilla and treatment changes in the anteroposterior distance from the pterygomaxillary fissure to the maxillary anterior alveolus, not changes in the distance from the nasion to the maxillary anterior alveolus. CONCLUSIONS: Structural superimposition analysis showed that counter-clockwise rotation of the maxilla and changes in the distance from the pterygomaxillary fissure to the maxillary anterior alveolus responded most to the orthopedic force of facial mask treatment. The analysis implicated that the pterygoid fissure-palatine's pyramidal process conjugation responds most to facial mask treatment among maxillofacial sutures and conjugation, and that the difference in the response induces maxillary counter-clockwise rotation.