Traits in Lepidoptera assemblages are differently influenced by local and landscape scale factors in farmland habitat islands

Semi-natural grassland islands have a key role in slowing down biodiversity decline in intensively cultivated agricultural landscapes. Assemblages in such habitat patches are not only limited by local habitat quality, but are also influenced by the suitability and distribution of different habitat types in the surrounding landscape. If we want to preserve a functionally diverse Lepidoptera fauna, both local and landscape scale environmental effects, including land use and management, should be considered. In the present study, we describe trait-based characteristics of noctuid dominated macro-moth assemblages (MMAs) in grassland remnants of an intensively cultivated agricultural area. By gathering environmental data from local to landscape scales, we aimed to identify the most influential scales, possible interactions between scales and the role of integrated arable fields in shaping MMAs. We conducted abundance weighted trait-based multivariate analysis of the assemblages based on six trait groups. Both local and landscape scale variables had important influence, acting on different traits of the assemblages. By variance partitioning, we could identify variables that exerted maximal effect at 50 m and 250 m radii circles. Variables describing local vegetation and identity of neighbouring crop were responsible for species richness and rarity status, while the area of arable and wooded habitats within 250 m were responsible for total catch and pest status related traits. There was significant interaction between principal components axes representing local and landscape variables. Rarity, more than other traits, was influenced by the interaction. Integrated fields had no effect on MMAs. The present study highlights the contributions of both local and landscape scales to the shaping of MMAs and suggests that the preservation of both local habitat quality and landscape heterogeneity are important if we would like to maintain species rich and functionally diverse Lepidoptera fauna

Validation and Optimization of Barrow Neurological Institute Score in Prediction of Adverse Events and Functional Outcome After Subarachnoid Hemorrhage-Creation of the HATCH (Hemorrhage, Age, Treatment, Clinical State, Hydrocephalus) Score.

BACKGROUND: The Barrow Neurological Institute (BNI) score, measuring maximal thickness of aneurysmal subarachnoid hemorrhage (aSAH), has previously shown to predict symptomatic cerebral vasospasms (CVSs), delayed cerebral ischemia (DCI), and functional outcome. OBJECTIVE: To validate the BNI score for prediction of above-mentioned variables and cerebral infarct and evaluate its improvement by integrating further variables which are available within the first 24 h after hemorrhage. METHODS: We included patients from a single center. The BNI score for prediction of CVS, DCI, infarct, and functional outcome was validated in our cohort using measurements of calibration and discrimination (area under the curve [AUC]). We improved it by adding additional variables, creating a novel risk score (measure by the dichotomized Glasgow Outcome Scale) and validated it in a small independent cohort. RESULTS: Of 646 patients, 41.5% developed symptomatic CVS, 22.9% DCI, 23.5% cerebral infarct, and 29% had an unfavorable outcome. The BNI score was associated with all outcome measurements. We improved functional outcome prediction accuracy by including age, BNI score, World Federation of Neurologic Surgeons, rebleeding, clipping, and hydrocephalus (AUC 0.84, 95% CI 0.8-0.87). Based on this model we created a risk score (HATCH-Hemorrhage, Age, Treatment, Clinical State, Hydrocephalus), ranging 0 to 13 points. We validated it in a small independent cohort. The validated score demonstrated very good discriminative ability (AUC 0.84 [95% CI 0.72-0.96]). CONCLUSION: We developed the HATCH score, which is a moderate predictor of DCI, but excellent predictor of functional outcome at 1 yr after aSAH

The association of patient age with postoperative morbidity and mortality following resection of intracranial tumors

INTRODUCTION The postoperative functional status of patients with intracranial tumors is influenced by patient-specific factors, including age. RESEARCH QUESTION This study aimed to elucidate the association between age and postoperative morbidity or mortality following the resection of brain tumors. MATERIAL AND METHODS A multicenter database was retrospectively reviewed. Functional status was assessed before and 3-6 months after tumor resection by the Karnofsky Performance Scale (KPS). Uni- and multivariable linear regression were used to estimate the association of age with postoperative change in KPS. Logistic regression models for a ≥10-point decline in KPS or mortality were built for patients ≥75 years. RESULTS The total sample of 4864 patients had a mean age of 56.4 ​± ​14.4 years. The mean change in pre-to postoperative KPS was -1.43. For each 1-year increase in patient age, the adjusted change in postoperative KPS was -0.11 (95% CI -0.14 - - 0.07). In multivariable analysis, patients ≥75 years had an odds ratio of 1.51 to experience postoperative functional decline (95%CI 1.21-1.88) and an odds ratio of 2.04 to die (95%CI 1.33-3.13), compared to younger patients. DISCUSSION Patients with intracranial tumors treated surgically showed a minor decline in their postoperative functional status. Age was associated with this decline in function, but only to a small extent. CONCLUSION Patients ≥75 years were more likely to experience a clinically meaningful decline in function and about two times as likely to die within the first 6 months after surgery, compared to younger patients

Photo-elastic properties of the wing imaginal disc of Drosophila

In the study of developmental biology, the physical properties and constraints of the developing tissues are of great importance. In spite of this, not much is known about the elastic properties of biologically relevant tissues that are studied in biology labs. Here, we characterize properties of the wing imaginal disc of Drosophila, which is a precursor organ intensely studied in the framework of growth control and cell polarity. In order to determine the possibility of measuring mechanical stresses inside the tissue during development, we quantify the photo-elastic properties of the tissue by direct mechanical manipulation. We obtain a photo-elastic constant of [Formula: see text]

Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

BACKGROUND:Comparative studies using hundreds of sequences can give a detailed picture of the evolution of a given gene family. Nevertheless, retrieving only the sequences of interest from public databases can be difficult, in particular, when working with highly divergent sequences. The difficulty increases substantially when one wants to include in the study sequences from many (or less well studied) species whose genomes are non-annotated or incompletely annotated. METHODOLOGY/PRINCIPAL FINDINGS:In this work we evaluate the usefulness of different approaches of gene retrieval and classification, using the distal-less (DLX) gene family as a test case. Furthermore, we evaluate whether the use of a large number of gene sequences from a wide range of animal species, the use of multiple alternative alignments, and the use of amino acids aligned with high confidence only, is enough to recover the accepted DLX evolutionary history. CONCLUSIONS/SIGNIFICANCE:The canonical DLX homeobox gene sequence here derived, together with the characteristic amino acid variants here identified in the DLX homeodomain region, can be used to retrieve and classify DLX genes in a simple and efficient way. A program is made available that allows the easy retrieval of synteny information that can be used to classify gene sequences. Maximum likelihood trees using hundreds of sequences can be used for gene identification. Nevertheless, for the DLX case, the proposed DLX evolutionary is not recovered even when multiple alignment algorithms are used

Integrated Molecular-Morphologic Meningioma Classification: A Multicenter Retrospective Analysis, Retrospectively and Prospectively Validated

PURPOSE: Meningiomas are the most frequent primary intracranial tumors. Patient outcome varies widely from benign to highly aggressive, ultimately fatal courses. Reliable identification of risk of progression for individual patients is of pivotal importance. However, only biomarkers for highly aggressive tumors are established (CDKN2A/B and TERT), whereas no molecularly based stratification exists for the broad spectrum of patients with low- and intermediate-risk meningioma. METHODS: DNA methylation data and copy-number information were generated for 3,031 meningiomas (2,868 patients), and mutation data for 858 samples. DNA methylation subgroups, copy-number variations (CNVs), mutations, and WHO grading were analyzed. Prediction power for outcome was assessed in a retrospective cohort of 514 patients, validated on a retrospective cohort of 184, and on a prospective cohort of 287 multicenter cases. RESULTS: Both CNV- and methylation family-based subgrouping independently resulted in increased prediction accuracy of risk of recurrence compared with the WHO classification (c-indexes WHO 2016, CNV, and methylation family 0.699, 0.706, and 0.721, respectively). Merging all risk stratification approaches into an integrated molecular-morphologic score resulted in further substantial increase in accuracy (c-index 0.744). This integrated score consistently provided superior accuracy in all three cohorts, significantly outperforming WHO grading (c-index difference P = .005). Besides the overall stratification advantage, the integrated score separates more precisely for risk of progression at the diagnostically challenging interface of WHO grade 1 and grade 2 tumors (hazard ratio 4.34 [2.48-7.57] and 3.34 [1.28-8.72] retrospective and prospective validation cohorts, respectively). CONCLUSION: Merging these layers of histologic and molecular data into an integrated, three-tiered score significantly improves the precision in meningioma stratification. Implementation into diagnostic routine informs clinical decision making for patients with meningioma on the basis of robust outcome prediction

Quantification of the Temporal Evolution of Collagen Orientation in Mechanically Conditioned Engineered Cardiovascular Tissues

Load-bearing soft tissues predominantly consist of collagen and exhibit anisotropic, non-linear visco-elastic behavior, coupled to the organization of the collagen fibers. Mimicking native mechanical behavior forms a major goal in cardiovascular tissue engineering. Engineered tissues often lack properly organized collagen and consequently do not meet in vivo mechanical demands. To improve collagen architecture and mechanical properties, mechanical stimulation of the tissue during in vitro tissue growth is crucial. This study describes the evolution of collagen fiber orientation with culture time in engineered tissue constructs in response to mechanical loading. To achieve this, a novel technique for the quantification of collagen fiber orientation is used, based on 3D vital imaging using multiphoton microscopy combined with image analysis. The engineered tissue constructs consisted of cell-seeded biodegradable rectangular scaffolds, which were either constrained or intermittently strained in longitudinal direction. Collagen fiber orientation analyses revealed that mechanical loading induced collagen alignment. The alignment shifted from oblique at the surface of the construct towards parallel to the straining direction in deeper tissue layers. Most importantly, intermittent straining improved and accelerated the alignment of the collagen fibers, as compared to constraining the constructs. Both the method and the results are relevant to create and monitor load-bearing tissues with an organized anisotropic collagen network

A T-cell antigen atlas for meningioma: novel options for immunotherapy

Meningiomas are the most common primary intracranial tumors. Although most symptomatic cases can be managed by surgery and/or radiotherapy, a relevant number of patients experience an unfavorable clinical course and additional treatment options are needed. As meningiomas are often perfused by dural branches of the external carotid artery, which is located outside the blood-brain barrier, they might be an accessible target for immunotherapy. However, the landscape of naturally presented tumor antigens in meningioma is unknown. We here provide a T-cell antigen atlas for meningioma by in-depth profiling of the naturally presented immunopeptidome using LC-MS/MS. Candidate target antigens were selected based on a comparative approach using an extensive immunopeptidome data set of normal tissues. Meningioma-exclusive antigens for HLA class I and II are described here for the first time. Top-ranking targets were further functionally characterized by showing their immunogenicity through in vitro T-cell priming assays. Thus, we provide an atlas of meningioma T-cell antigens which will be publicly available for further research. In addition, we have identified novel actionable targets that warrant further investigation as an immunotherapy option for meningioma

Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

Background:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.Results:Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.Conclusions:Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution

Multiple Chromosomal Rearrangements Structured the Ancestral Vertebrate Hox-Bearing Protochromosomes

While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion—such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these—is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model) occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox “paralogon”) and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates