Reprint of: Prelude to molecularization: The double gradient model of Sulo Toivonen and Lauri Saxén

The present molecular investigations of Organizer phenomena show a remarkable connection to the earlier classical embryological studies that used transplantation as a method for making mechanistic models of induction. One of the most prominent of these connections is the dual gradient model for anterior-posterior and dorsal-ventral polarity. This paper will discuss some of the history of how transplantation experiments provided data that could be interpreted in terms of two gradients of biologically active materials. It will highlight how the attempts to discover the elusive Induktionsstoffen gave rise to the double gradient model of Sulo Toivonen and Lauri Saxén in the 1950s and 1960s. This paper will also document how this research into the identity of these molecules gave rise to the developmental genetics that eventually would find the molecules responsible for primary embryonic induction.

Graded and sharp transitions in semantic function in left temporal lobe

Recent work has focussed on how patterns of functional change within the temporal lobe relate to whole-brain dimensions of intrinsic connectivity variation (Margulies et al., 2016). We examined two such 'connectivity gradients' reflecting the separation of (i) unimodal versus heteromodal and (ii) visual versus auditory-motor cortex, examining visually presented verbal associative and feature judgments, plus picture-based context and emotion generation. Functional responses along the first dimension sometimes showed graded change between modality-tuned and heteromodal cortex (in the verbal matching task), and other times showed sharp functional transitions, with deactivation at the extremes and activation in the middle of this gradient (internal generation). The second gradient revealed more visual than auditory-motor activation, regardless of content (associative, feature, context, emotion) or task process (matching/generation). We also uncovered subtle differences across each gradient for content type, which predominantly manifested as differences in relative magnitude of activation or deactivation.

Prelude to molecularization: The double gradient model of Sulo Toivonen and Lauri Saxén

The present molecular investigations of Organizer phenomena show a remarkable connection to the earlier classical embryological studies that used transplantation as a method for making mechanistic models of induction. One of the most prominent of these connections is the dual gradient model for anterior-posterior and dorsal-ventral polarity. This paper will discuss some of the history of how transplantation experiments provided data that could be interpreted in terms of two gradients of biologically active materials. It will highlight how the attempts to discover the elusive Induktionsstoffen gave rise to the double gradient model of Sulo Toivonen and Lauri Saxén in the 1950s and 1960s. This paper will also document how this research into the identity of these molecules gave rise to the developmental genetics that eventually would find the molecules responsible for primary embryonic induction.

Gradient Organization of Space, Time, and Numbers in the Brain: A Meta-analysis of Neuroimaging Studies

In this study, we ran a meta-analysis of neuroimaging studies to pinpoint the neural regions that are commonly activated across space, time, and numerosity, and we tested the existence of gradient transitions among these magnitude representations in the brain. Following PRISMA guidelines, we included in the meta-analysis 112 experiments (for space domain), 114 experiments (time domain), and 115 experiments (numerosity domain), and we used the activation likelihood estimation method. We found a system of brain regions that was commonly recruited in all the three magnitudes, which included bilateral insula, the supplementary motor area (SMA), the right inferior frontal gyrus, and bilateral intraparietal sulci. Gradiental transitions between different magnitudes were found along all these regions but insulae, with space and numbers leading to gradients mainly over parietal regions (and SMA) whereas time and numbers mainly over frontal regions. These findings provide evidence for the GradiATOM theory (Gradient Theory of Magnitude), suggesting that spatial proximity given by overlapping activations and gradients is a key aspect for efficient interactions and integrations among magnitudes.

Cortical gradients during naturalistic processing are hierarchical and modality-specific

Understanding cortical topographic organization and how it supports complex perceptual and cognitive processes is a fundamental question in neuroscience. Previous work has characterized functional gradients that demonstrate large-scale principles of cortical organization. How these gradients are modulated by rich ecological stimuli remains unknown. Here, we utilize naturalistic stimuli via movie-fMRI to assess macroscale functional organization. We identify principal movie gradients that delineate separate hierarchies anchored in sensorimotor, visual, and auditory/language areas. At the opposite/heteromodal end of these perception-to-cognition axes, we find a more central role for the frontoparietal network along with the default network. Even across different movie stimuli, movie gradients demonstrated good reliability, suggesting that these hierarchies reflect a brain state common across different naturalistic conditions. The relative position of brain areas within movie gradients showed stronger and more numerous correlations with cognitive behavioral scores compared to resting state gradients. Together, these findings provide an ecologically valid representation of the principles underlying cortical organization while the brain is active and engaged in multimodal, dynamic perceptual and cognitive processing.

Joint-embeddings reveal functional differences in default-mode network architecture between marmosets and humans

The default-mode network (DMN) is a distributed functional brain system integral for social and higher-order cognition in humans with implications in a myriad of neuropsychological disorders. In this study, we compared the functional architecture of the DMN between humans and marmosets to assess their similarities and differences using joint gradients. This approach permits simultaneous large-scale mapping of functional systems across the cortex of humans and marmosets, revealing evidence of putative homologies between them. In doing so, we find that the DMN architecture of the marmoset exhibits differences along its anterolateral-posterior axis. Specifically, the anterolateral node of the DMN (dorsolateral prefrontal cortex) displayed weak connections and inconsistent connection topographies as compared to its posterior DMN-nodes (posterior cingulate and posterior parietal cortices). We also present evidence that the marmoset medial prefrontal cortex and temporal lobe areas correspond to other macroscopical distributed functional systems that are not part of the DMN. Given the importance of the marmoset as a pre-clinical primate model for higher-order cognitive functioning and the DMN's relevance to cognition, our results suggest that the marmoset may lack the capacity to integrate neural information to subserve cortical dynamics that is necessary for supporting diverse cognitive demands.

Functional Gradients of the Cerebellum: a Review of Practical Applications

Gradient-based analyses have contributed to the description of cerebellar functional neuroanatomy. More recently, functional gradients of the cerebellum have been used as a multi-purpose tool for neuroimaging research. Here, we provide an overview of the many practical applications of cerebellar functional gradient analyses. These practical applications include examination of intra-cerebellar and cerebellar-extracerebellar organization; transformation of functional gradients into parcellations with discrete borders; projection of functional gradients calculated within cerebellar structures to other extracerebellar structures; interpretation of cerebellar neuroimaging findings using qualitative and quantitative methods; detection of differences in patient populations; and other more complex practical applications of cerebellar gradient-based analyses. This review may serve as an introduction and catalog of options for neuroscientists who wish to design and analyze imaging studies using functional gradients of the cerebellum.

Heritability of hippocampal functional and microstructural organisation

The hippocampus is a uniquely infolded allocortical structure in the medial temporal lobe that consists of the microstructurally and functionally distinct subregions: subiculum, cornu ammonis, and dentate gyrus. The hippocampus is a remarkably plastic region that is implicated in learning and memory. At the same time it has been shown that hippocampal subregion volumes are heritable, and that genetic expression varies along a posterior to anterior axis. Here, we studied how a heritable, stable, hippocampal organisation may support its flexible function in healthy adults. Leveraging the twin set-up of the Human Connectome Project with multimodal neuroimaging, we observed that the functional connectivity between hippocampus and cortex was heritable and that microstructure of the hippocampus genetically correlated with cortical microstructure. Moreover, both functional and microstructural organisation could be consistently captured by anterior-to-posterior and medial-to-lateral axes across individuals. However, heritability of functional, relative to microstructural, organisation was found reduced, suggesting individual variation in functional organisation may be explained by experience-driven factors. Last, we demonstrate that structure and function couple along an inherited macroscale organisation, suggesting an interplay of stability and plasticity within the hippocampus. Our study provides new insights on the heritability of the hippocampal of the structure and function within the hippocampal organisation.

A dynamic gradient architecture generates brain activity states

The human brain exhibits a diverse yet constrained range of activity states. While these states can be faithfully represented in a low-dimensional latent space, our understanding of the constitutive functional anatomy is still evolving. Here we applied dimensionality reduction to task-free and task fMRI data to address whether latent dimensions reflect intrinsic systems and if so, how these systems may interact to generate different activity states. We find that each dimension represents a dynamic activity gradient, including a primary unipolar sensory-association gradient underlying the global signal. The gradients appear stable across individuals and cognitive states, while recapitulating key functional connectivity properties including anticorrelation, modularity, and regional hubness. We then use dynamical systems modeling to show that gradients causally interact via state-specific coupling parameters to create distinct brain activity patterns. Together, these findings indicate that a set of dynamic, intrinsic spatial gradients interact to determine the repertoire of possible brain activity states.

Progress in Osteochondral Regeneration with Engineering Strategies

Osteoarthritis, the main cause of disability worldwide, involves not only cartilage injury but also subchondral bone injury, which brings challenges to clinical repair. Tissue engineering strategies provide a promising solution to this degenerative disease. Articular cartilage connects to subchondral bone through the osteochondral interfacial tissue, which has a complex anatomical architecture, distinct cell distribution and unique biomechanical properties. Forming a continuous and stable osteochondral interface between cartilage tissue and subchondral bone is challenging. Thus, successful osteochondral regeneration with engineering strategies requires intricately coordinated interplay between cells, materials, biological factors, and physical/chemical factors. This review provides an overview of the anatomical composition, microstructure, and biomechanical properties of the osteochondral interface. Additionally, the latest research on the progress related to osteochondral regeneration is reviewed, especially discussing the fabrication of biomimetic scaffolds and the regulation of biological factors for osteochondral defects.

Neurogenetic Heterochrony in Chick, Lizard, and Rat Mapped with Wholemount Acetylcholinesterase and the Prosomeric Model

In the developing brain, the phenomenon of neurogenesis is manifested heterotopically, that is, much the same neurogenetic steps occur at different places with a different timetable. This is due apparently to early molecular regionalization of the neural tube wall in the anteroposterior and dorsoventral dimensions, in a checkerboard pattern of more or less deformed quadrangular histogenetic areas. Their respective fate is apparently specified by a locally specific combination of active/repressed genes known as "molecular profile." This leads to position-dependent differential control of proliferation, neurogenesis, differentiation, and other aspects, eventually in a heterochronic manner across adjacent areal units with sufficiently different molecular profiles. It is not known how fixed these heterochronic patterns are. We reexamined here comparatively early patterns of forebrain and hindbrain neurogenesis in a lizard (Lacerta gallotia galloti), a bird (the chick), and a mammal (the rat), as demonstrated by activation of acetylcholinesterase (AChE). This is an early marker of postmitotic neurons, which leaves unlabeled the neuroepithelial ventricular cells, so that we can examine cleared wholemounts of the reacted brains to have a birds-eye view of the emergent neuronal pattern at each stage. There is overall heterochrony between the basal and alar plates of the brain, a known fact, but, remarkably, heterochrony occurs even within the precocious basal plate among its final anteroposterior neuromeric subdivisions and their internal microzonal subdivisions. Some neuromeric units or microzones are precocious, while others follow suit without any specific spatial order or gradient; other similar neuromeric units remain retarded in the midst of quite advanced neighbors, though they do produce similar neurogenetic patterns at later stages. It was found that some details of such neuromeric heterochrony are species-specific, possibly related to differential morphogenetic properties. Given the molecular causal underpinning of the updated prosomeric model used here for interpretation, we comment on the close correlation between some genetic patterns and the observed AChE differentiation patterns.

Multimodal Gradient Mapping of Rodent Hippocampus

The hippocampus plays a central role in supporting our coherent and enduring sense of self and our place in the world. Understanding its functional organisation is central to understanding this complex role. Previous studies suggest function varies along a long hippocampal axis, but there is disagreement about the presence of sharp discontinuities or gradual change along that axis. Other open questions relate to the underlying drivers of this variation and the conservation of organisational principles across species. Here, we delineate the primary organisational principles underlying patterns of hippocampal functional connectivity (FC) in the mouse using gradient analysis on resting state fMRI data. We further applied gradient analysis to mouse gene co-expression data to examine the relationship between variation in genomic anatomy and functional organisation. Two principal FC gradients along a hippocampal axis were revealed. The principal gradient exhibited a sharp discontinuity that divided the hippocampus into dorsal and ventral compartments. The second, more continuous, gradient followed the long axis of the ventral compartment. Dorsal regions were more strongly connected to areas involved in spatial navigation while ventral regions were more strongly connected to areas involved in emotion, recapitulating patterns seen in humans. In contrast, gene co-expression gradients showed a more segregated and discrete organisation. Our findings suggest that hippocampal functional organisation exhibits both sharp and gradual transitions and that hippocampal genomic anatomy exerts only a subtle influence on this organisation.

Insights into the present and future of cartilage regeneration and joint repair

Knee osteoarthritis is the most common joint disease. It causes pain and suffering for affected patients and is the source of major economic costs for healthcare systems. Despite ongoing research, there is a lack of knowledge regarding disease mechanisms, biomarkers, and possible cures. Current treatments do not fulfill patients' long-term needs, and it often requires invasive surgical procedures with subsequent long periods of rehabilitation. Researchers and companies worldwide are working to find a suitable cell source to engineer or regenerate a functional and healthy articular cartilage tissue to implant in the damaged area. Potential cell sources to accomplish this goal include embryonic stem cells, mesenchymal stem cells, or induced pluripotent stem cells. The differentiation of stem cells into different tissue types is complex, and a suitable concentration range of specific growth factors is vital. The cellular microenvironment during early embryonic development provides crucial information regarding concentrations of signaling molecules and morphogen gradients as these are essential inducers for tissue development. Thus, morphogen gradients implemented in developmental protocols aimed to engineer functional cartilage tissue can potentially generate cells comparable to those within native cartilage. In this review, we have summarized the problems with current treatments, potential cell sources for cell therapy, reviewed the progress of new treatments within the regenerative cartilage field, and highlighted the importance of cell quality, characterization assays, and chemically defined protocols.

A tale of two gradients: differences between the left and right hemispheres predict semantic cognition

Decomposition of whole-brain functional connectivity patterns reveals a principal gradient that captures the separation of sensorimotor cortex from heteromodal regions in the default mode network (DMN). Functional homotopy is strongest in sensorimotor areas, and weakest in heteromodal cortices, suggesting there may be differences between the left and right hemispheres (LH/RH) in the principal gradient, especially towards its apex. This study characterised hemispheric differences in the position of large-scale cortical networks along the principal gradient, and their functional significance. We collected resting-state fMRI and semantic, working memory and non-verbal reasoning performance in 175 + healthy volunteers. We then extracted the principal gradient of connectivity for each participant, tested which networks showed significant hemispheric differences on the gradient, and regressed participants’ behavioural efficiency in tasks outside the scanner against interhemispheric gradient differences for each network. LH showed a higher overall principal gradient value, consistent with its role in heteromodal semantic cognition. One frontotemporal control subnetwork was linked to individual differences in semantic cognition: when it was nearer heteromodal DMN on the principal gradient in LH, participants showed more efficient semantic retrieval—and this network also showed a strong hemispheric difference in response to semantic demands but not working memory load in a separate study. In contrast, when a dorsal attention subnetwork was closer to the heteromodal end of the principal gradient in RH, participants showed better visual reasoning. Lateralization of function may reflect differences in connectivity between control and heteromodal regions in LH, and attention and visual regions in RH.

Joining soft tissues to bone: Insights from modeling and simulations

Entheses are complex multi-tissue regions of the musculoskeletal system serving the challenging task of connecting highly dissimilar materials such as the compliant tendon to the much stiffer bone, over a very small region. The first aim of this review is to highlight mathematical and computational models that have been developed to investigate the many attachment strategies present at entheses at different length scales. Entheses are also relevant in the medical context due to the high prevalence of orthopedic injuries requiring the reattachment of tendons or ligaments to bone, which are associated with a rather poor long-term clinical outcome. The second aim of the review is to report on the computational works analyzing the whole tendon to bone complex as well as targeting orthopedic relevant issues. Modeling approaches have provided important insights on anchoring mechanisms and surgical repair strategies, that would not have been revealed with experiments alone. We intend to demonstrate the necessity of including, in future models, an enriched description of enthesis biomechanical behavior in order to unravel additional mechanical cues underlying the development, the functioning and the maintaining of such a complex biological interface as well as to enhance the development of novel biomimetic adhesive, attachment procedures or tissue engineered implants.

Components of a magnetic resonance imaging system and their relationship to safety and image quality

Magnetic resonance imaging (MRI) is a powerful diagnostic tool that can be optimized to display a wide range of clinical conditions. An MRI system consists of four major components: a main magnet formed by superconducting coils, gradient coils, radiofrequency (RF) coils, and computer systems. Each component has safety considerations. Unless carefully controlled, the MRI machine's strong static magnetic field could turn a ferromagnetic object into a harmful projectile or cause vertigo and headache. Switching magnetic fields in the gradients evokes loud noises in the scanner, which can be mitigated by ear protection. Gradients also generate varying magnetic fields that can cause peripheral nerve stimulation and muscle twitching. Magnetic fields produced by RF coils deposit energy in the body and can cause tissue heating (with the potential to cause skin burns). In this review, we provide an overview of the components of a typical clinical MRI scanner and its associated safety issues. We also discuss how the relationship between the scanning parameters can be manipulated to improve image quality while ensuring a safe operational environment for the patients and staff. Understanding the strengths and limitations of these parameters can enable users to choose optimal techniques for image acquisition, apply them in clinical practice, and improve the diagnostic accuracy of an MRI examination.

Mesoscale hierarchical organization of primary somatosensory cortex captured by resting-state-fMRI in humans

The primary somatosensory cortex (S1) plays a key role in the processing and integration of afferent somatosensory inputs along an anterior-to-posterior axis, contributing towards necessary human function. It is believed that anatomical connectivity can be used to probe hierarchical organization, however direct characterization of this principle in-vivo within humans remains elusive. Here, we use resting-state functional connectivity as a complement to anatomical connectivity to investigate topographical principles of human S1. We employ a novel approach to examine mesoscopic variations of functional connectivity, and demonstrate a topographic organisation spanning the region's hierarchical axis that strongly correlates with underlying microstructure while tracing along architectonic Brodmann areas. Our findings characterize anatomical hierarchy of S1 as a 'continuous spectrum' with evidence supporting a functional boundary between areas 3b and 1. The identification of this topography bridges the gap between structure and connectivity, and may be used to help further current understanding of sensorimotor deficits.

Natural History of Moderate Aortic Stenosis with Preserved and Low Ejection Fraction

BACKGROUND

There is a shortage of data concerning the natural history of patients with moderate aortic stenosis (AS). The aim of this study was to assess the effect of moderate AS on mortality in the general population and in the subgroups of patients with moderate AS and reduced ejection fractions (EF) and patients with moderate AS and low aortic valve gradients. The study was not designed to address the applicability of treatment in this population.

METHODS

Outcomes were compared between patients with moderate AS and a propensity-matched cohort (1:3 ratio) without AS. The primary outcome was survival until end of follow-up.

RESULTS

Among approximately 40,000 patients who underwent echocardiographic evaluations between 2011 and 2016, 952 had moderate AS. Median follow-up duration was 181 weeks (interquartile range, 179-182 weeks) for the entire cohort and 174 weeks (interquartile range, 169-179 weeks) for the propensity-matched groups. Propensity matching successfully balanced most preexisting clinical differences. Increased mortality was observed in the group of patients with moderate AS before propensity matching and persisted following propensity matching (median survival 4.1 vs 5.2 years, P = .008). Survival rates and corresponding standard errors at 1, 2, 3, and 5 years were 80 ± 1% versus 82 ± 0.7%, 70 ± 1.5% versus 74 ± 0.8%, 62 ± 1.7% versus 66 ± 0.9%, and 47 ± 2.4% versus 52 ± 1.3%, respectively. A survival difference was similarly observed for the subgroup analyses of moderate AS and reduced ejection fraction (P = .028) and moderate AS and low aortic valve gradients (P = .039).

CONCLUSIONS

Moderate AS is associated with increased mortality. The increased mortality was also observed in the subgroups of patients with either reduced ejection fraction or low aortic valve gradients.

Scaling of gene transcriptional gradients with brain size across mouse development

The structure of the adult brain is the result of complex physical mechanisms acting in three-dimensional space through development. Consequently, the brain's spatial embedding plays a key role in its organization, including the gradient-like patterning of gene expression that encodes the molecular underpinning of functional specialization. However, we do not yet understand how changes in brain shape and size that occur across development influence the brain's transcriptional architecture. Here we investigate the spatial embedding of transcriptional patterns of over 1800 genes across seven time points through mouse-brain development using data from the Allen Developing Mouse Brain Atlas. We find that transcriptional similarity decreases exponentially with separation distance across all developmental time points, with a correlation length scale that follows a power-law scaling relationship with a linear dimension of brain size. This scaling suggests that the mouse brain achieves a characteristic balance between local molecular similarity (homogeneous gene expression within a specialized brain area) and longer-range diversity (between functionally specialized brain areas) throughout its development. Extrapolating this mouse developmental scaling relationship to the human cortex yields a prediction consistent with the value measured from microarray data. We introduce a simple model of brain growth as spatially autocorrelated gene-expression gradients that expand through development, which captures key features of the mouse developmental data. Complementing the well-known exponential distance rule for structural connectivity, our findings characterize an analogous exponential distance rule for transcriptional gradients that scales across mouse brain development, providing new understanding of spatial constraints on the brain's molecular patterning.

Understanding gradients in industrial bioreactors

Gradients in industrial bioreactors have attracted substantial research attention since exposure to fluctuating environmental conditions has been shown to lead to changes in the metabolome, transcriptome as well as population heterogeneity in industrially relevant microorganisms. Such changes have also been found to impact key process parameters like the yield on substrate and the productivity. Hence, understanding gradients is important from both the academic and industrial perspectives. In this review the causes of gradients are outlined, along with their impact on microbial physiology. Quantifying the impact of gradients requires a detailed understanding of both fluid flow inside industrial equipment and microbial physiology. This review critically examines approaches used to investigate gradients including large-scale experimental work, computational methods and scale-down approaches. Avenues for future work have been highlighted, particularly the need for further coordinated development of both in silico and experimental tools which can be used to further the current understanding of gradients in industrial equipment.

rest2vec: Vectorizing the resting-state functional connectome using graph embedding

Resting-state functional magnetic resonance imaging (rs-fMRI) is widely used in connectomics for studying the functional relationships between regions of the human brain. rs-fMRI connectomics, however, has inherent analytical challenges, such as how to properly model negative correlations between BOLD time series. In addition, functional relationships between brain regions do not necessarily correspond to their anatomical distance, making the functional topology of the brain less well understood. Recent machine learning techniques, such as word2vec, have used embedding methods to map high-dimensional data into vector spaces, where words with more similar meanings are mapped closer to one another. Inspired by this approach, we have developed the graph embedding pipeline rest2vec for studying the vector space of functional connectomes. We demonstrate how rest2vec uses the phase angle spatial embedding (PhASE) method with dimensionality reduction to embed the connectome into lower dimensions, where the functional definition of a brain region is represented continuously in an intrinsic “functional space.” Furthermore, we show how the “functional distance” between brain regions in this space can be applied to discover biologically-relevant connectivity gradients. Interestingly, rest2vec can be conceptualized in the context of the recently proposed maximum mean discrepancy (MMD) metric, followed by a double-centering approach seen in kernel PCA. In sum, rest2vec creates a low-dimensional representation of the rs-fMRI connectome where brain regions are mapped according to their functional relationships, giving a more informed understanding of the functional organization of the brain.

Flow-following sensor devices: A tool for bridging data and model predictions in large-scale fermentations

Production-scale fermentation processes in industrial biotechnology experience gradients in process variables, such as dissolved gases, pH and substrate concentrations, which can potentially affect the production organism and therefore the yield and profitability of the processes. However, the extent of the heterogeneity is unclear, as it is currently a challenge at large scale to obtain representative measurements from different zones of the reactor volume. Computational fluid dynamics (CFD) models have proven to be a valuable tool for better understanding the environment inside bioreactors. Without detailed measurements to support the CFD predictions, the validity of CFD models is debatable. A promising technology to obtain such measurements from different zones in the bioreactors are flow-following sensor devices, whose development has recently benefitted from advancements in microelectronics and sensor technology. This paper presents the state of the art within flow-following sensor device technology and addresses how the technology can be used in large-scale bioreactors to improve the understanding of the process itself and to test the validity of detailed computational models of the bioreactors in the future.

Anchoring the human olfactory system within a functional gradient

Margulies et al. (2016) demonstrated the existence of at least five independent functional connectivity gradients in the human brain. However, it is unclear how these functional gradients might link to anatomy. The dual origin theory proposes that differences in cortical cytoarchitecture originate from two trends of progressive differentiation between the different layers of the cortex, referred to as the hippocampocentric and olfactocentric systems. When conceptualising the functional connectivity gradients within the evolutionary framework of the Dual Origin theory, the first gradient likely represents the hippocampocentric system anatomically. Here we expand on this concept and demonstrate that the fifth gradient likely links to the olfactocentric system. We describe the anatomy of the latter as well as the evidence to support this hypothesis. Together, the first and fifth gradients might help to model the Dual Origin theory of the human brain and inform brain models and pathologies.

A tutorial and tool for exploring feature similarity gradients with MRI data

There has been an increasing interest in examining organisational principles of the cerebral cortex (and subcortical regions) using different MRI features such as structural or functional connectivity. Despite the widespread interest, introductory tutorials on the underlying technique targeted for the novice neuroimager are sparse in the literature. Articles that investigate various "neural gradients" (for example based on region studied "cortical gradients," "cerebellar gradients," "hippocampal gradients" etc … or feature of interest "functional gradients," "cytoarchitectural gradients," "myeloarchitectural gradients" etc …) have increased in popularity. Thus, we believe that it is opportune to discuss what is generally meant by "gradient analysis". We introduce basics concepts in graph theory, such as graphs themselves, the degree matrix, and the adjacency matrix. We discuss how one can think about gradients of feature similarity (the similarity between timeseries in fMRI, or streamline in tractography) using graph theory and we extend this to explore such gradients across the whole MRI scale; from the voxel level to the whole brain level. We proceed to introduce a measure for quantifying the level of similarity in regions of interest. We propose the term "the Vogt-Bailey index" for such quantification to pay homage to our history as a brain mapping community. We run through the techniques on sample datasets including a brain MRI as an example of the application of the techniques on real data and we provide several appendices that expand upon details. To maximise intuition, the appendices contain a didactic example describing how one could use these techniques to solve a particularly pernicious problem that one may encounter at a wedding. Accompanying the article is a tool, available in both MATLAB and Python, that enables readers to perform the analysis described in this article on their own data. We refer readers to the graphical abstract as an overview of the analysis pipeline presented in this work.

Perlecan domain I gradients establish stable biomimetic heparin binding growth factor gradients for cell migration in hydrogels

Growth factor gradients orchestrate many biological processes including organogenesis, wound healing, cancer invasion, and metastasis. Heparin-binding growth factor (HBGF) gradients are established in living systems by proteoglycans including the extracellular matrix heparan sulfate proteoglycan, perlecan/HSPG2. Three potential HBGF-binding glycosaminoglycan attachment sites occur in N-terminal domain I of perlecan's five domains. Our overarching goal was to form stable, biomimetic non-covalently bound HBGF gradients surrounding cells encapsulated in hyaluronate-based hydrogels by first establishing perlecan domain I (PlnD1) gradients. A versatile multichannel gradient maker device (MGMD) was designed and 3D printed, then used to create desired gradients of microparticles in hydrogels. Next, we used the device to covalently incorporate gradients of PEGylated PlnD1 in hydrogels with high-low-high or high-medium-low concentrations across the hydrogel width. Fluorescently-labeled fibroblast growth factor-2 was delivered to hydrogels in phosphate-buffered saline and allowed to electrostatically bind to the covalently pre-incorporated PlnD1, producing stable non-covalent HBGF gradients. To test cell viability after flow through the MGMD, delicate primary human salivary stem/progenitor cells were encapsulated in gradient hydrogels where they showed high viability and continued to grow. Next, to test migratory behavior in response to HBGF gradients, two cell types, preosteoblastic MC3T3-E1 cell line and breast cancer cell line MDA-MB-231 were encapsulated in or adjacent to PlnD1-modified hydrogels. Both cell lines migrated toward HBGFs bound to PlnD1. We conclude that establishing covalently-bound PlnD1 gradients in hydrogels provides a new means to establish physiologically-relevant gradients of HBGFs that are useful for a variety of applications in tissue engineering and cancer biology. STATEMENT OF SIGNIFICANCE: Gradients of heparin binding growth factors (HBGFs) direct cell behavior in living systems. HBGFs bind electrostatically to gradients of HS proteoglycans in the extracellular matrix creating HBGF gradients. We recreated HBGF gradients in physiological hyaluronate-based hydrogels using a 3D-printed multichannel gradient maker device (MGMD) that created gradients of HS proteoglycan-derived perlecan/HSPG2 domain I. We demonstrated the ability of a variety of cells, including primary salivary stem/progenitor cells, pre-osteoblastic cells and an invasive breast cancer cell line, to be co-encapsulated in gradient hydrogels by flowing them together through the MGMD. The versatile device and the ability to create HBGF gradients in hydrogels for a variety of applications is innovative and of broad utility in both cancer biology and tissue engineering applications.

RF shielding and eddy currents in NMR probes

Shielding of the NMR sample by a thin coating of metal between the sample and the rf coil arises in some geometries. The shielding may be used for rf heating of the sample tube or for a high infrared reflectivity coating in cryoprobe applications. An important application is for a shield that prevents noise from entering the rf probe circuit while allowing pulsed magnetic field gradients or field modulation to pass. We show by simple, approximate derivations that the criterion for shielding is not whether the coating exceeds the classical electromagnetic skin depth δ at the operating frequency (as is often stated), but whether the geometric mean between the thickness and an appropriate radius r exceeds δ. Thus, because r is typically much larger than δ, conducting layers substantially thinner than δ may still be good shields. Measurements are performed at high audio frequencies to confirm the calculations, using geometries relevant to rf saddle coils and to rf solenoids. Measurements of the slowing of the edges of a pulsed field gradient are also in accord with the calculations.

Label-free cell sorting strategies via biophysical and biochemical gradients

Isolating active mesenchymal stem cells from a heterogeneous population is an essential step that determines the efficacy of stem cell therapy such as for osteoarthritis. Nowadays, the gold standard of cell sorting, fluorescence-activated cell sorting, relies on labelling surface markers via antibody-antigen reaction. However, sorting stem cells with high stemness usually requires the labelling of multiple biomarkers. Moreover, the labelling process is costly, and the high operating pressure is harmful to cell functionality and viability. Although label-free cell sorting, based on physical characteristics, has gained increasing interest in the past decades, it has not shown the ability to eliminate stem cells with low stemness. Cell motility, as a novel sorting marker, is hence proposed for label-free sorting active stem cells. Accumulating evidence has demonstrated the feasibility in manipulating directional cell migration through patterning the biophysical, biochemical or both gradients of the extracellular matrix. However, applying those findings to label-free cell sorting has not been well discussed and studied. This review thus first provides a brief overview about the effect of biophysical and biochemical gradients of the extracellular matrix on cell migration. State-of-the-art fabrication techniques for generating such gradients of hydrogels are then introduced. Among current research, the authors suggest that hydrogels with dual-gradients of biochemistry and biophysics are potential tools for accurate label-free cell sorting with satisfactory selectivity and efficiency.

TRANSLATIONAL POTENTIAL OF THIS ARTICLE

The reviewed label-free cell sorting approaches enable us to isolate active cell for cytotherapy. The proposed system can be further modified for single-cell analysis and drug screening.

Engineering of gradient osteochondral tissue: From nature to lab

The osteochondral tissue is an interface between two distinct tissues: articular cartilage and bone. These two tissues are significantly diverse with regard to their chemical compositions, mechanical properties, structure, electrical properties, and the amount of nutrient and oxygen consumption. Thus, transition from the surface of the articular cartilage to the subchondral bone needs to face several smooth gradients. These gradients are imperative to study to generate a scaffold suitable for the reconstruction of the cartilaginous and osseous layers of a defected osteochondral tissue, simultaneously. The aim of this review is to peruse the alternation of biochemical, biomechanical, structural, electrical, and metabolic properties of the osteochondral tissue moving from the surface of the articular cartilage to the subchondral bone. Moreover, this review also discusses currently developed approaches and ideal techniques with a focus on gradients present in the interface of the cartilage and bone. STATEMENT OF SIGNIFICANCE: The submitted review paper entitled as "Engineering of the gradient osteochondral tissue: from nature to lab" is a complete review with regard to the osteochondral tissue and transition of different properties between the cartilage and bone tissues. Moreover, previous studies on the osteochondral tissue engineering have been reviewed in this paper. This complete information can be a valuable and useful source for current and future researchers and scientists. Considering the scope of the submitted paper, Acta Biomaterialia would be a suitable journal for publishing this article.

Urban heat islands advance the timing of reproduction in a social insect

For many species, the timing of life cycle events is advancing under contemporary global climate change. However, much less is known regarding phenological shifts as a result of other sources of anthropogenic change, such as urban warming. In both cases, progress has been hampered by a focus on phenological traits such as the timing of emergence, rather than the phenology of more directly related fitness traits such as the timing of reproduction. Here we explore how urban heat island effects shape the timing of reproduction in an acorn-dwelling ant. We used a common garden experiment with acorn ants collected from three cities in the eastern United States along a latitudinal gradient and reared long-term in the laboratory under five temperature treatments. This allowed us to quantify the effects of temperature on reproductive phenology across three scales-a biogeographic temperature cline, three urban vs. rural temperature comparisons, and five laboratory rearing temperatures. At our northernmost and southernmost cities (spanning 6° of latitude), we found both urbanization and warmer laboratory rearing temperature significantly advanced reproductive phenology; ants from the lowest latitude city also had earlier reproductive phenology compared with the higher latitude cities. In the field, the differences in urban versus rural acorn ant reproductive phenology translate to approximately one month earlier reproduction in the urban populations. For insects with synchronous mating events, such as ants, shifts in the already short window of time to reproduce could limit mating across environments, potentially leading to reproductive isolation between urban and rural populations.

Network convergence zones in the anterior midcingulate cortex

Situated medially and centrally in the brain, the anterior midcingulate cortex (aMCC) is a nexus of control. This specialized neocortical brain region participates in large-scale brain networks underlying attention, motor, and limbic processes. The functional diversity and proximity of cognitive and affective subdivisions within this region are its distinguishing features, rendering it an effective site for integration across domains. Here we review comparative neuroanatomic, meta-analytic, and connectomic analyses contributing to the emerging picture of the aMCC as comprising functionally diverse, flexible network nodes involved in multiple regulatory behaviors. We further present data providing evidence for an organizing gradient along the anterior and midcingulate cortex and explore the implications of these findings for understanding the functional role of the anterior midcingulate within this spectrum. We conclude by highlighting open questions and proposing future directions for investigations into the functional role of this important network convergence zone.

Gradients in compositions in the starchy endosperm of wheat have implications for milling and processing

BACKGROUND

Wheat is the major food grain consumed in temperate countries. Most wheat is consumed after milling to produce white flour, which corresponds to the endosperm storage tissue of the grain. Because the starchy endosperm accounts for about 80% of the grain dry weight, the miller aims to achieve flour yields approaching this value.

SCOPE AND APPROACH

Bioimaging can be combined with biochemical analysis of fractions produced by sequential pearling of whole grains to determine the distributions of components within the endosperm tissue.

KEY FINDINGS AND CONCLUSIONS

This reveals that endosperm is not homogeneous, but exhibits gradients in composition from the outer to the inner part. These include gradients in both amount and composition. For example, the content of gluten proteins decreases but the proportion of glutenin polymers increases from the outside to the centre of the tissue. However, the content of starch increases with changes in the granule size distribution, the proportions of amylose and amylopectin, and their thermal properties. Hence these parts of the endosperm differ in the functional properties for food processing. Gradients also exist in minor components which may affect health and processing, such as dietary fibre and lipids. The gradients in grain composition are reflected in differences in the compositions of the mill streams which are combined to give white flour (which may number over 20). These differences could therefore be exploited by millers and food processors to develop flours with compositions and properties for specific end uses.

Geoelectrodes and Fuel Cells for Simulating Hydrothermal Vent Environments

Gradients generated in hydrothermal systems provide a significant source of free energy for chemosynthetic life and may play a role in present-day habitability on ocean worlds. Electron/proton/ion gradients, particularly in the context of hydrothermal chimney structures, may also be relevant to the origins of life on Earth. Hydrothermal vents are similar in some ways to typical fuel cell devices: redox/pH gradients between seawater and hydrothermal fluid are analogous to the fuel cell oxidant and fuel reservoirs; the porous chimney wall is analogous to a separator or ion-exchange membrane and is also a conductive path for electrons; and the hydrothermal minerals are analogous to electrode catalysts. The modular and scalable characteristics of fuel cell systems make for a convenient planetary geology test bed in which geologically relevant components may be assembled and investigated in a controlled simulation environment. We have performed fuel cell experiments and electrochemical studies to better understand the catalytic potential of seafloor minerals and vent chimneys, using samples from a black smoker vent chimney as an initial demonstration. In a fuel cell with Na⁺-conducting Nafion^® membranes and liquid fuel/oxidant reservoirs (simulating the vent environment), the black smoker mineral catalyst in the membrane electrode assembly was effective in reducing O₂ and oxidizing sulfide. In a H₂/O₂ polymer electrolyte membrane (PEM) fuel cell with H⁺-conducting Nafion membranes, the black smoker catalyst was effective in reducing O₂ but not in oxidizing H₂. These fuel cell experiments accurately simulated the redox reactions that could occur in a geological setting with this particular catalyst, and also tested whether the minerals are sufficiently active to replace a commercial fuel cell catalyst. Similar experiments with other geocatalysts could be utilized to test which redox reactions could be driven in other hydrothermal systems, including hypothesized vent systems on other worlds.

Glycosylated superparamagnetic nanoparticle gradients for osteochondral tissue engineering

In developmental biology, gradients of bioactive signals direct the formation of structural transitions in tissue that are key to physiological function. Failure to reproduce these native features in an in vitro setting can severely limit the success of bioengineered tissue constructs. In this report, we introduce a facile and rapid platform that uses magnetic field alignment of glycosylated superparamagnetic iron oxide nanoparticles, pre-loaded with growth factors, to pattern biochemical gradients into a range of biomaterial systems. Gradients of bone morphogenetic protein 2 in agarose hydrogels were used to spatially direct the osteogenesis of human mesenchymal stem cells and generate robust osteochondral tissue constructs exhibiting a clear mineral transition from bone to cartilage. Interestingly, the smooth gradients in growth factor concentration gave rise to biologically-relevant, emergent structural features, including a tidemark transition demarcating mineralized and non-mineralized tissue and an osteochondral interface rich in hypertrophic chondrocytes. This platform technology offers great versatility and provides an exciting new opportunity for overcoming a range of interfacial tissue engineering challenges.

Trends in Education-Specific Life Expectancy, Data Quality, and Shifting Education Distributions: A Note on Recent Research

Several recent articles have reported conflicting conclusions about educational differences in life expectancy, and this is partly due to the use of unreliable data subject to a numerator-denominator bias previously reported as ranging from 20 % to 40 %. This article presents estimates of life expectancy and lifespan variation by education in the United States using more reliable data from the National Health Interview Survey. Contrary to prior conclusions in the literature, I find that life expectancy increased or stagnated since 1990 among all education-race-sex groups except for non-Hispanic white women with less than a high school education; there has been a robust increase in life expectancy among white high school graduates and a smaller increase among black female high school graduates; lifespan variation did not increase appreciably among high school graduates; and lifespan variation plays a very limited role in explaining educational gradients in mortality. I also discuss the key role that educational expansion may play in driving future changes in mortality gradients. Because of shifting education distributions, within an education-specific synthetic cohort, older age groups are less negatively selected than younger age groups. We could thus expect a greater concentration of mortality at younger ages among people with a high school education or less, which would be reflected in increasing lifespan variability for this group. Future studies of educational gradients in mortality should use more reliable data and should be mindful of the effects of shifting education distributions.

Systems for localized release to mimic paracrine cell communication in vitro

Paracrine cell communication plays a pivotal role for signal exchange between proximal cells in vivo. However, this localized, gradient type release of mediators at very low concentrations (pg/ml), relevant during physiological and pathological processes, is rarely reflected within in vitro approaches. This review gives an overview on state-of-the-art approaches, which transfer the paracrine cell-to-cell communication into in vitro cell culture model setups. The traditional methods like trans-well assays and more advanced microfluidic approaches are included. The review focusses on systems for localized release, mostly based on microparticles, which tightly mimic the paracrine interaction between single cells in 3D microenvironments. Approaches based on single microparticles, with the main focus on affinity-controlled storage and release of cytokines, are reviewed and their importance for understanding paracrine communication is highlighted. Various methods to study the cytokine release and their advantages and disadvantages are discussed. Basic principles of the release characteristics, like diffusion mechanisms, are quantitatively described, including the formation of resulting gradients around the local sources. In vitro cell experiments using such localized microparticle release systems in approaches to increase understanding of stem cell behavior within their niches and regulation of wound healing are highlighted as examples of successful localized release systems for mimicking paracrine cell communication.

Sephadex filtration as successful alternative to density-gradient centrifugation procedures for ram sperm selection with improved kinetics

Density-gradients centrifugation (DGC) and filtration columns (FC) are used to separate deformed or dead sperm, debris, and other cells that may negatively affect the fertilizing capacity of sperm in fresh, chilled and frozen/thawed semen. The present study was conducted to evaluate the suitability of DGC (BoviPure®, Percoll® and Accudenz®) and FC (Sephadex G-15®) sperm selection procedures for fresh-extended and cold-stored ram semen by assessment of post-treatment sperm quality variables. Twenty normospermic ejaculates from ten adult Merino rams were used. Sperm concentration of recovered cells was greater (P < 0.001) after BoviPure treatment than other procedures in both fresh and cold semen. With the Sephadex method, there were more desirable values than with use of DGC procedures in several sperm motility variables measured by using the CASA system. In non-refrigerated semen samples, the percentage of progressive sperm motility (%PSM) after Sephadex filtration was greater (P < 0.05) than after BoviPure treatment; the straightline velocity (VSL) value after Sephadex filtration was greater (P < 0.01) than after Accudenz treatment; the amplitude of lateral head displacement (ALH) after Sephadex and Accudenz treatment was less than non-filtered semen (P < 0.001) and after Percoll (P < 0.01) and BoviPure (P < 0.05) treatments. In cold-stored semen samples, the %PSM after Sephadex filtration was greater than non-filtered (P < 0.05) semen and after BoviPure (P < 0.05), Percoll (P < 0.05) and Accudenz (P < 0.001) treatments. It is concluded that Sephadex column filtration can be used to select ram sperm in non-refrigerated and cooled semen, because percentage progressively motile sperm and some other sperm motility characteristics are greater with use of this techniques as compared with use of DGC methods.

Gradient and shim technologies for ultra high field MRI

Ultra High Field (UHF) MRI requires improved gradient and shim performance to fully realize the promised gains (SNR as well as spatial, spectral, diffusion resolution) that higher main magnetic fields offer. Both the more challenging UHF environment by itself, as well as the higher currents used in high performance coils, require a deeper understanding combined with sophisticated engineering modeling and construction, to optimize gradient and shim hardware for safe operation and for highest image quality. This review summarizes the basics of gradient and shim technologies, and outlines a number of UHF-related challenges and solutions. In particular, Lorentz forces, vibroacoustics, eddy currents, and peripheral nerve stimulation are discussed. Several promising UHF-relevant gradient concepts are described, including insertable gradient coils aimed at higher performance neuroimaging.

Photo-immobilized EGF chemical gradients differentially impact breast cancer cell invasion and drug response in defined 3D hydrogels

Breast cancer cell invasion is influenced by growth factor concentration gradients in the tumor microenvironment. However, studying the influence of growth factor gradients on breast cancer cell invasion is challenging due to both the complexities of in vivo models and the difficulties in recapitulating the tumor microenvironment with defined gradients using in vitro models. A defined hyaluronic acid (HA)-based hydrogel crosslinked with matrix metalloproteinase (MMP) cleavable peptides and modified with multiphoton labile nitrodibenzofuran (NDBF) was synthesized to photochemically immobilize epidermal growth factor (EGF) gradients. We demonstrate that EGF gradients can differentially influence breast cancer cell invasion and drug response in cell lines with different EGF receptor (EGFR) expression levels. Photopatterned EGF gradients increase the invasion of moderate EGFR expressing MDA-MB-231 cells, reduce invasion of high EGFR expressing MDA-MB-468 cells, and have no effect on invasion of low EGFR-expressing MCF-7 cells. We evaluate MDA-MB-231 and MDA-MB-468 cell response to the clinically tested EGFR inhibitor, cetuximab. Interestingly, the cellular response to cetuximab is completely different on the EGF gradient hydrogels: cetuximab decreases MDA-MB-231 cell invasion but increases MDA-MB-468 cell invasion and cell number, thus demonstrating the importance of including cell-microenvironment interactions when evaluating drug targets.

Bioengineered Systems and Designer Matrices That Recapitulate the Intestinal Stem Cell Niche

The relationship between intestinal stem cells (ISCs) and the surrounding niche environment is complex and dynamic. Key factors localized at the base of the crypt are necessary to promote ISC self-renewal and proliferation, to ultimately provide a constant stream of differentiated cells to maintain the epithelial barrier. These factors diminish as epithelial cells divide, migrate away from the crypt base, differentiate into the postmitotic lineages, and end their life span in approximately 7 days when they are sloughed into the intestinal lumen. To facilitate the rapid and complex physiology of ISC-driven epithelial renewal, in vivo gradients of growth factors, extracellular matrix, bacterial products, gases, and stiffness are formed along the crypt-villus axis. New bioengineered tools and platforms are available to recapitulate various gradients and support the stereotypical cellular responses associated with these gradients. Many of these technologies have been paired with primary small intestinal and colonic epithelial cells to re-create select aspects of normal physiology or disease states. These biomimetic platforms are becoming increasingly sophisticated with the rapid discovery of new niche factors and gradients. These advancements are contributing to the development of high-fidelity tissue constructs for basic science applications, drug screening, and personalized medicine applications. Here, we discuss the direct and indirect evidence for many of the important gradients found in vivo and their successful application to date in bioengineered in vitro models, including organ-on-chip and microfluidic culture devices.

Planarians and the History of Animal Regeneration: Paradigm Shifts and Key Concepts in Biology

Regeneration has captured human imagination for much of recorded history. Its sociological influence is evident in ancient and modern folklore, art, politics, and even language. In many ways, the study of regeneration helped establish the field of biology as a legitimate scientific discipline. Furthermore, regeneration research yielded critical insights that challenged flawed scientific models and uncovered fundamental principles underpinning the workings of life on this planet. This chapter details some ways in which the study of animal regeneration-with special emphasis on planarian regeneration-influenced the evolution of thought in biology. This includes contributions to the discovery of stem cells, the nature of heredity, and key concepts in pattern formation.

Specific recruitment of circulating angiogenic cells using biomaterials as filters

Endogenous recruitment of circulating angiogenic cells (CACs) is an emerging strategy to induce angiogenesis within a defect site, and multiple recent strategies have deployed soluble protein releasing biomaterials for this purpose. However, the way in which the design of biomaterials affects CAC recruitment and invasion are poorly understood. Here we used an enhanced-throughput cell invasion assay to systematically examine the effects of biomaterial design on CAC recruitment. The screens co-optimized hydrogel presentation of a stromal-derived factor-1α (SDF-1α) gradient, hydrogel degradability, and hydrogel stiffness for maximal CAC invasion. We also examined the specificity of this invasion by assessing dermal fibroblast, mesenchymal stem cell, and lymphocyte invasion individually and in co-culture with CACs to identify hydrogels specific to CAC invasion. These screens suggested a subset of MMP-degradable hydrogels presenting a specific range of SDF-1α gradient slopes that induced specific invasion of CACs, and we posit that the design parameters of this subset of hydrogels may serve as instructive templates for the future design of biomaterials to specifically recruit CACs. We also posit that this design concept may be applied more broadly in that it may be possible to utilize these specific subsets of biomaterials as "filters" to control which types of cell populations invade into and populate the biomaterial.

STATEMENT OF SIGNIFICANCE

The recruitment of specific cell types for cell-based therapies in vivo is of great interest to the regenerative medicine community. Circulating angiogenic cells (CACs), CD133+ cells derived from the blood stream, are of particular interest for induction of angiogenesis in ischemic tissues, and recent studies utilizing soluble-factor releasing biomaterials to recruit these cells in vivo show great promise. However, these studies are largely "proof of concept" and are not systematic in nature. Thus, little is currently known about how biomaterial design affects the recruitment of CACs. In the present work, we use a high throughput cell invasion screening platform to systematically examine the effects of biomaterial design on circulating angiogenic cell (CAC) recruitment, and we successfully screened 263 conditions at 3 replicates each. Our results identify a particular subset of conditions that robustly recruit CACs. Additionally, we found that these conditions also specifically recruited CACs and excluded the other tested cells types of dermal fibroblasts, mesenchymal stem cells, and lymphocytes. This suggests an intriguing new role for biomaterials as "filters" to control the types of cells that invade and populate that biomaterial.

Lateral cortical Cdca7 expression levels are regulated by Pax6 and influence the production of intermediate progenitors

Background

We studied whether regulation of Cdca7 (Cell division cycle associated 7) expression by transcription factor Pax6 contributes to Pax6’s cellular actions during corticogenesis. The function of Cdca7 in mediating Pax6’s effects during corticogenesis has not been explored. Pax6 is expressed by radial glial progenitors in the ventricular zone of the embryonic cortical neuroepithelium, where it is required for the development of a normal complement of Tbr2-expressing intermediate progenitor cells in the subventricular zone. Pax6’s expression levels are graded across the ventricular zone, with highest levels laterally where Tbr2-expressing progenitors are generated in greatest numbers at early stages of corticogenesis.

Methods

We used in situ hybridization and immunohistochemistry to analyse patterns of Cdca7 and Pax6 expression in cortical tissue from wild-type and Pax6^−/− embryos. In each genotype we compared the graded expression of the two genes quantitatively at several ages. To test whether defects in Cdca7 expression in lateral cortical cells might contribute to the cellular defects in this region caused by Pax6 loss, we electroporated a Cdca7 expression vector into wild-type lateral cortex and examined the effect on the production of Tbr2-expressing cells.

Results

We found that Cdca7 is co-expressed with Pax6 in cortical progenitors, at levels opposite to those of Pax6. Lowest levels of Cdca7 are found in the radial glial progenitors of lateral cortex, where Pax6 levels are highest. Higher levels of Cdca7 are found in ventral telencephalon, where Pax6 levels are low. Loss of Pax6 causes Cdca7 expression to increase in the lateral cortex. Elevating Cdca7 in normal lateral cortical progenitors to levels close to those normally found in ventral telencephalon reduces their production of Tbr2-expressing cells early in lateral cortical formation.

Conclusion

Our results suggest that Pax6 normally represses Cdca7 expression in the lateral cortex and that repression of Cdca7 in cells of this region is required for their production of a normal complement of Tbr2-expressing intermediate progenitors.

Planning for the Maintenance of Floristic Diversity in the Face of Land Cover and Climate Change

Habitat loss and climate change are primary drivers of global biodiversity loss. Species will need to track changing environmental conditions through fragmented and transformed landscapes such as KwaZulu-Natal, South Africa. Landscape connectivity is an important tool for maintaining resilience to global change. We develop a coarse-grained connectivity map between protected areas to aid decision-making for implementing corridors to maintain floristic diversity in the face of global change. The spatial location of corridors was prioritised using a biological underpinning of floristic composition that incorporated high beta diversity regions, important plant areas, climate refugia, and aligned to major climatic gradients driving floristic pattern. We used Linkage Mapper to develop the connectivity network. The resistance layer was based on land-cover categories with natural areas discounted according to their contribution towards meeting the biological objectives. Three corridor maps were developed; a conservative option for meeting minimum corridor requirements, an optimal option for meeting a target amount of 50% of the landscape and an option including linkages in highly transformed areas. The importance of various protected areas and critical linkages in maintaining landscape connectivity are discussed, disconnected protected areas and pinch points identified where the loss of small areas could compromise landscape connectivity. This framework is suggested as a way to conserve floristic diversity into the future and is recommended as an approach for other global connectivity initiatives. A lack of implementation of corridors will lead to further habitat loss and fragmentation, resulting in further risk to plant diversity.

Analysis of Semaphorin-Induced Growth Cone Collapse and Axon Growth Inhibition

The axonal growth cone is a specialized structure enabling axon extension and proper guidance to its target by sensing the extracellular environment. A growth cone collapse assay is a popular approach designed to characterize the inhibitory effect of secreted guidance cues in vitro. However, the actin cytoskeleton of the growth cone is very sensitive to various factors like physical impact, temperature, and acidity of environment that may also induce responses resembling those of guidance signals. Herein, we provide an easy and reproducible method to analyze growth cone sensitivity to the prototypic guidance molecule family class 3 semaphorin. This protocol is intended to present a systematic approach that is easy to apply to any soluble factors with a potential to impact axon elongation.

Influencing chondrogenic differentiation of human mesenchymal stromal cells in scaffolds displaying a structural gradient in pore size

Articular cartilage lesions have a limited ability to heal by themselves. Yet, golden standard treatments for cartilage repair such as drilling, microfracture and mosaicplasty provide further damage and an unstable solution that degenerates into fibrocartilage in time. Articular cartilage presents a number of gradients in cell number and size along with structural gradients in extra cellular matrix (ECM) composition. Therefore, creating scaffolds that display a structural gradient can be an appealing strategy for cartilage tissue regeneration treatments. In the present study, a scaffold with an in-built discrete gradient in pore size was produced by additive manufacturing. Human mesenchymal stromal cells (hMSCs) were seeded within the gradient scaffolds and their proliferation, differentiation and ECM deposition was evaluated with respect to 2 non-gradient scaffolds. Glycosaminoglycan (GAG) deposition was significantly higher in gradient scaffolds and non-gradient scaffolds with the smallest pore size compared to non-gradient scaffolds with the largest pore size. A gradual increase of chondrogenic markers was observed within the gradient structures with decreasing pore size, which was also accompanied by an increasingly compact ECM formation. Therefore, scaffolds displaying a structural gradient in pore size seem to be a promising strategy to aid in the process of hMSC chondrogenic differentiation and could be considered for improved cartilage tissue regeneration applications.

STATEMENT OF SIGNIFICANCE

We present the development of a novel hierarchical scaffold obtained by additive manufacturing. Structural hierarchy is obtained by changing pore size within the pore network characterizing the fabricated scaffolds and proves to be a functional element in the scaffold to influence adult stem cell differentiation in the chondrogenic lineage. Specifically, in regions of the scaffolds presenting smaller pores an increasing differentiation of stem cells toward the chondrogenic differentiation is displayed. Taking inspiration from the zonal organization of articular cartilage tissue, pore size gradients could, therefore, be considered as a new and important element in designing 3D scaffolds for regenerative medicine applications, in particular for all those tissues where gradient physical properties are present.

An experimental approach to addressing ecological questions related to the conservation of plant biodiversity in China

We briefly introduce and describe seven questions related to community structure and biodiversity conservation that can be addressed using field experiments, and provide the context for using the vast geographic diversity, biodiversity, and network of Nature Reserves in China to perform these experiments. China is the world's third largest country, has a diverse topography, covers five climatic zones from cold-temperate to tropical, has 18 vegetation biomes ranging from Arctic/alpine tundra and desert to Tropical rain forest, and supports the richest biodiversity in the temperate northern hemisphere (>10% of the world total). But this tremendous natural resource is under relentless assault that threatens to destroy biodiversity and negatively impact the services ecosystems provide. In an attempt to prevent the loss of biodiversity, China has established 2729 nature reserves which cover 14.84% of the nation's area. Unfortunately underfunding, mismanagement, illegal activities, invasive species and global climate change threaten the effectiveness of these protected areas. Attention has focused on protecting species and their habitats before degradation and loss of either species or habitats occur. Here we argue that we must move beyond the simple protection of ecosystems, beyond their description, and by using experiments, try to understand how ecosystems work. This new understanding will allow us to design conservation programs, perform restoration of damaged or degraded areas, and address resource management concerns (e.g., agriculture, logging, mining, hunting) more effectively than with the current approach of ad hoc reactions to ecological and environmental problems. We argue that improving our understanding of nature can best be done using well designed, replicated, and typically manipulative field experiments.

Positional Information and Pattern Formation

The concept of positional information proposes that cells acquire positional values as in a coordinate system, which they interpret by developing in particular ways to give rise to spatial patterns. Some of the best evidence for positional information comes from regeneration experiments, and the patterning of the leg and antenna in Drosophila, and the vertebrate limb. Central problems are how positional information is set up, how it is recorded, and then how it is interpreted by the cells. A number of models have been proposed for the setting up of positional gradients, and most are based on diffusion of a morphogen and its interactions with extracellular molecules; however, diffusion may not be reliable mechanism. There are also mechanisms based on timing. There is no good evidence for the quantitative aspects of any of the proposed gradients and details how they are set up. The way in which a signaling gradient regulates differential gene expression in a concentration-dependent manner also raises several technical and quite difficult issues. A key feature of positional information being the basis for pattern formation is that there is no prepattern in the embryo.

Heteroscedastic CAR models for areally referenced temporal processes for analyzing California asthma hospitalization data

Often in regionally aggregated spatiotemporal models, a single variance parameter is used to capture variability in the spatial structure of the model, ignoring the impact that spatially-varying factors may have on the variability in the underlying process. We extend existing methodologies to allow for region-specific variance components in our analysis of monthly asthma hospitalization rates in California counties, introducing a heteroscedastic CAR model that can greatly improve the fit of our spatiotemporal process. After demonstrating the effectiveness of our new model via simulation, we reanalyze the asthma hospitalization data and note a number of important findings.

Bayesian modeling and analysis for gradients in spatiotemporal processes

Stochastic process models are widely employed for analyzing spatiotemporal datasets in various scientific disciplines including, but not limited to, environmental monitoring, ecological systems, forestry, hydrology, meteorology, and public health. After inferring on a spatiotemporal process for a given dataset, inferential interest may turn to estimating rates of change, or gradients, over space and time. This manuscript develops fully model-based inference on spatiotemporal gradients under continuous space, continuous time settings. Our contribution is to offer, within a flexible spatiotemporal process model setting, a framework to estimate arbitrary directional gradients over space at any given timepoint, temporal derivatives at any given spatial location and, finally, mixed spatiotemporal gradients that reflect rapid change in spatial gradients over time and vice-versa. We achieve such inference without compromising on rich and flexible spatiotemporal process models and use nonseparable covariance structures. We illustrate our methodology using a simulated data example and subsequently apply it to a dataset of daily PM2.5 concentrations in California, where the spatiotemporal gradient process reveals the effects of California's unique topography on pollution and detects the aftermath of a devastating series of wildfires.

Monoplanar gradient system for imaging with nonlinear gradients

OBJECT

In this paper we present a monoplanar gradient system capable of imaging a volume comparable with that covered by linear gradient systems. Such a system has been designed and implemented.

MATERIALS AND METHODS

Building such a system was made possible by relaxing the constraint of global linearity and replacing it with a requirement for local orthogonality. A framework was derived for optimization of local orthogonality within the physical boundaries and geometric constraints. Spatial encoding of magnetic fields was optimized for their local orthogonality over a large field of view.

RESULTS

A coil design consisting of straight wire segments was optimized, implemented, and integrated into a 3T human scanner to show the feasibility of this approach. Initial MR images are shown and further applications of the derived optimization method and the nonlinear planar gradient system are discussed.

CONCLUSION

Encoding fields generated by the prototype encoding system were shown to be locally orthogonal and able to encode a cylindrical volume sufficient for some abdomen imaging applications for humans.