Automatic knowledge graph population with model-complete text comprehension for pre-clinical outcomes in the field of spinal cord injury.

The paradigm of evidence-based medicine requires that medical decisions are made on the basis of the best available knowledge published in the literature. Existing evidence is often summarized in the form of systematic reviews and/or meta-reviews and is rarely available in a structured form. Manual compilation and aggregation is costly, and conducting a systematic review represents a high effort. The need to aggregate evidence arises not only in the context of clinical trials, but is also important in the context of pre-clinical animal studies. In this context, evidence extraction is important to support translation of the most promising pre-clinical therapies into clinical trials or to optimize clinical trial design. Aiming at developing methods that facilitate the task of aggregating evidence published in pre-clinical studies, in this paper a new system is presented that automatically extracts structured knowledge from such publications and stores it in a so-called domain knowledge graph. The approach follows the paradigm of model-complete text comprehension by relying on guidance from a domain ontology creating a deep relational data-structure that reflects the main concepts, protocol, and key findings of studies. Focusing on the domain of spinal cord injuries, a single outcome of a pre-clinical study is described by up to 103 outcome parameters. Since the problem of extracting all these variables together is intractable, we propose a hierarchical architecture that incrementally predicts semantic sub-structures according to a given data model in a bottom-up fashion. At the heart of our approach is a statistical inference method that relies on conditional random fields to infer the most likely instance of the domain model given the text of a scientific publication as input. This approach allows modeling dependencies between the different variables describing a study in a semi-joint fashion. We present a comprehensive evaluation of our system to understand the extent to which our system can capture a study in the depth required to enable the generation of new knowledge. We conclude the article with a brief description of some applications of the populated knowledge graph and show the potential implications of our work for supporting evidence-based medicine.

Low-pressure micro-mechanical re-adaptation device sustainably and effectively improves locomotor recovery from complete spinal cord injury.

Traumatic spinal cord injuries result in impairment or even complete loss of motor, sensory and autonomic functions. Recovery after complete spinal cord injury is very limited even in animal models receiving elaborate combinatorial treatments. Recently, we described an implantable microsystem (microconnector) for low-pressure re-adaption of severed spinal stumps in rat. Here we investigate the long-term structural and functional outcome following microconnector implantation after complete spinal cord transection. Re-adaptation of spinal stumps supports formation of a tissue bridge, glial and vascular cell invasion, motor axon regeneration and myelination, resulting in partial recovery of motor-evoked potentials and a thus far unmet improvement of locomotor behaviour. The recovery lasts for at least 5 months. Despite a late partial decline, motor recovery remains significantly superior to controls. Our findings demonstrate that microsystem technology can foster long-lasting functional improvement after complete spinal injury, providing a new and effective tool for combinatorial therapies.

Experimental Strategies to Bridge Large Tissue Gaps in the Injured Spinal Cord after Acute and Chronic Lesion.

After a spinal cord injury (SCI) a scar forms in the lesion core which hinders axonal regeneration. Bridging the site of injury after an insult to the spinal cord, tumor resections, or tissue defects resulting from traumatic accidents can aid in facilitating general tissue repair as well as regenerative growth of nerve fibers into and beyond the affected area. Two experimental treatment strategies are presented: (1) implantation of a novel microconnector device into an acutely and completely transected thoracic rat spinal cord to readapt severed spinal cord tissue stumps, and (2) polyethylene glycol filling of the SCI site in chronically lesioned rats after scar resection. The chronic spinal cord lesion in this model is a complete spinal cord transection which was inflicted 5 weeks before treatment. Both methods have recently achieved very promising outcomes and promoted axonal regrowth, beneficial cellular invasion and functional improvements in rodent models of spinal cord injury. The mechanical microconnector system (mMS) is a multi-channel system composed of polymethylmethacrylate (PMMA) with an outlet tubing system to apply negative pressure to the mMS lumen thus pulling the spinal cord stumps into the honeycomb-structured holes. After its implantation into the 1 mm tissue gap the tissue is sucked into the device. Furthermore, the inner walls of the mMS are microstructured for better tissue adhesion. In the case of the chronic spinal cord injury approach, spinal cord tissue - including the scar-filled lesion area - is resected over an area of 4 mm in length. After the microsurgical scar resection the resulting cavity is filled with polyethylene glycol (PEG 600) which was found to provide an excellent substratum for cellular invasion, revascularization, axonal regeneration and even compact remyelination in vivo.

Pharmacological Suppression of CNS Scarring by Deferoxamine Reduces Lesion Volume and Increases Regeneration in an In Vitro Model for Astroglial-Fibrotic Scarring and in Rat Spinal Cord Injury In Vivo.

Lesion-induced scarring is a major impediment for regeneration of injured axons in the central nervous system (CNS). The collagen-rich glial-fibrous scar contains numerous axon growth inhibitory factors forming a regeneration-barrier for axons. We demonstrated previously that the combination of the iron chelator 2,2'-bipyridine-5,5'-decarboxylic acid (BPY-DCA) and 8-Br-cyclic AMP (cAMP) inhibits scar formation and collagen deposition, leading to enhanced axon regeneration and partial functional recovery after spinal cord injury. While BPY-DCA is not a clinical drug, the clinically approved iron chelator deferoxamine mesylate (DFO) may be a suitable alternative for anti-scarring treatment (AST). In order to prove the scar-suppressing efficacy of DFO we modified a recently published in vitro model for CNS scarring. The model comprises a co-culture system of cerebral astrocytes and meningeal fibroblasts, which form scar-like clusters when stimulated with transforming growth factor-ß (TGF-ß). We studied the mechanisms of TGF-ß-induced CNS scarring and compared the efficiency of different putative pharmacological scar-reducing treatments, including BPY-DCA, DFO and cAMP as well as combinations thereof. We observed modulation of TGF-ß-induced scarring at the level of fibroblast proliferation and contraction as well as specific changes in the expression of extracellular matrix molecules and axon growth inhibitory proteins. The individual and combinatorial pharmacological treatments had distinct effects on the cellular and molecular aspects of in vitro scarring. DFO could be identified as a putative anti-scarring treatment for CNS trauma. We subsequently validated this by local application of DFO to a dorsal hemisection in the rat thoracic spinal cord. DFO treatment led to significant reduction of scarring, slightly increased regeneration of corticospinal tract as well as ascending CGRP-positive axons and moderately improved locomotion. We conclude that the in vitro model for CNS scarring is suitable for efficient pre-screening and identification of putative scar-suppressing agents prior to in vivo application and validation, thus saving costs, time and laboratory animals.

Long-lasting significant functional improvement in chronic severe spinal cord injury following scar resection and polyethylene glycol implantation.

We identified a suitable biomatrix that improved axon regeneration and functional outcome after partial (moderate) and complete (severe) chronic spinal cord injury (SCI) in rat. Five weeks after dorsal thoracic hemisection injury the lesion scar was resected via aspiration and the resulting cavity was filled with different biopolymers such as Matrigel™, alginate-hydrogel and polyethylene glycol 600 (PEG) all of which have not previously been used as sole graft-materials in chronic SCI. Immunohistological staining revealed marked differences between these compounds regarding axon regeneration, invasion/elongation of astrocytes, fibroblasts, endothelial and Schwann cells, revascularization, and collagen deposition. According to axon regeneration-supporting effects, the biopolymers could be ranked in the order PEG>>alginate-hydrogel>Matrigel™. Even after complete chronic transection, the PEG-bridge allowed long-distance axon regeneration through the grafted area and for, at least, 1cm beyond the lesion/graft border. As revealed by electron microscopy, bundles of regenerating axons within the matrix area received myelin ensheathment from Schwann cells. The beneficial effects of PEG-implantation into the resection-cavity were accompanied by long-lasting significant locomotor improvement over a period of 8months. Following complete spinal re-transection at the rostral border of the PEG-graft the locomotor recovery was aborted, suggesting a functional role of regenerated axons in the initial locomotor improvement. In conclusion, scar resection and subsequent implantation of PEG into the generated cavity leads to tissue recovery, axon regeneration, myelination and functional improvement that have not been achieved before in severe chronic SCI.

A mechanical microconnector system for restoration of tissue continuity and long-term drug application into the injured spinal cord.

Complete transection of the spinal cord leaves a gap of several mm which fills with fibrous scar tissue. Several approaches in rodent models have used tubes, foams, matrices or tissue implants to bridge this gap. Here, we describe a mechanical microconnector system (mMS) to re-adjust the retracted spinal cord stumps. The mMS is a multi-channel system of polymethylmethacrylate (PMMA), designed to fit into the spinal cord tissue gap after transection, with an outlet tubing system to apply negative pressure to the mMS thus sucking the spinal cord stumps into the honeycomb-structured holes. The stumps adhere to the microstructure of the mMS walls and remain in the mMS after removal of the vacuum. We show that the mMS preserves tissue integrity and allows axonal regrowth at 2, 5 and 19 weeks post lesion with no adverse tissue effects like in-bleeding or cyst formation. Preliminary assessment of locomotor function in the open field suggested beneficial effects of the mMS. Additional inner micro-channels enable local substance delivery into the lesion center via an attached osmotic minipump. We suggest that the mMS is a suitable device to adapt and stabilize the injured spinal cord after surgical resection of scar tissue (e.g., for chronic patients) or traumatic injuries with large tissue and bone damages.

Defeating inhibition of regeneration by scar and myelin components.

Axon regeneration and the sprouting processes that underlie plasticity are blocked by inhibitory factors in the central nervous system (CNS) environment, several of which are upregulated after injury. The major inhibitory molecules are those associated with myelin and those associated with the glial scar. In myelin, NogoA, MAG, and OMgp are present on normal oligodendrocytes and on myelin debris. They act partly via the Nogo receptor, partly via an unidentified amino-Nogo receptor. In the glial scar, chondroitin sulphate proteoglycans, semaphorins, and the formation of a collagen-based membrane are all inhibitory. Methods to counteract these forms of inhibition have been identified, and these treatments promote axon regeneration in the damaged spinal cord, and in some cases recovery of function through enhanced plasticity.

Cortical gene expression in spinal cord injury and repair: insight into the functional complexity of the neural regeneration program.

Traumatic spinal cord injury (SCI) results in the formation of a fibrous scar acting as a growth barrier for regenerating axons at the lesion site. We have previously shown (Klapka et al., 2005) that transient suppression of the inhibitory lesion scar in rat spinal cord leads to long distance axon regeneration, retrograde rescue of axotomized cortical motoneurons, and improvement of locomotor function. Here we applied a systemic approach to investigate for the first time specific and dynamic alterations in the cortical gene expression profile following both thoracic SCI and regeneration-promoting anti-scarring treatment (AST). In order to monitor cortical gene expression we carried out microarray analyses using total RNA isolated from layer V/VI of rat sensorimotor cortex at 1-60 days post-operation (dpo). We demonstrate that cortical neurons respond to injury by massive changes in gene expression, starting as early as 1 dpo. AST, in turn, results in profound modifications of the lesion-induced expression profile. The treatment attenuates SCI-triggered transcriptional changes of genes related to inhibition of axon growth and impairment of cell survival, while upregulating the expression of genes associated with axon outgrowth, cell protection, and neural development. Thus, AST not only modifies the local environment impeding spinal cord regeneration by reduction of fibrous scarring in the injured spinal cord, but, in addition, strikingly changes the intrinsic capacity of cortical pyramidal neurons toward enhanced cell maintenance and axonal regeneration.

Enhanced regenerative axon growth of multiple fibre populations in traumatic spinal cord injury following scar-suppressing treatment.

We analysed the effect of scar-suppressing treatment (anti-scarring treatment; AST) on augmenting axonal regeneration of various neuronal populations following spinal cord injury (SCI) in adult rat. AST included local iron chelator (2,2'-dipyridine-5,5'-dicarboxylic acid) injection and 8-bromo-cyclic adenosine monophosphate application to the lesion core. In previous studies, this treatment promoted long-distance regeneration of cut corticospinal tract axons, neuroprotection of projecting cortical neurons and functional improvement of treated rats [N. Klapka et al. (2005)Eur. J. Neurosci., 22, 3047-3058]. Treatment yielded significantly enhanced regrowth of descending serotonergic (5-HT), catecholaminergic (tyrosine hydroxylase; TH), corticospinal and rubrospinal axons into the lesion zone, as assessed by anterograde tracing and immunohistochemistry followed by quantification of axon profiles at 5 and 12 weeks post-injury. In addition, the determination of axons crossing the proximal borderline from uninjured tissue into fibrous scar area revealed a significant AST-promoted increase of intersecting fibres for 5-HT, TH and calcitonin gene-related peptide containing ascending sensory fibres. For a prolonged time period after lesion, the delayed (secondary) scar developing in treated rats is significantly more permeable for all analysed axon tracts than the initial (primary) scar forming in injured control animals lacking treatment. Furthermore, enhanced outgrowth of descending axons from fibrous scar into distal healthy spinal tissue was achieved in treated animals, and is in line with previous functional studies [S. Hermanns et al. (2001) Restor. Neurol. Neurosci., 19,139-148; N. Klapka et al. (2005)Eur. J. Neurosci., 22, 3047-3058]. Our findings indicate that AST exerts a prolonged beneficial effect on fibrous scarring allowing enhanced axonal regrowth of different fibre tracts in SCI regardless of their distinct regenerative demands.

Pharmacological modification of the extracellular matrix to promote regeneration of the injured brain and spinal cord.

This chapter focuses on the role of the fibrous lesion scar as a major impediment for axonal regeneration in the injured central nervous system (CNS). We describe the appearance and complementary distribution of the glial and fibrous scar components in spinal cord lesions focusing on the morphology as well as on axon growth inhibitory molecular components accumulating in the collagenous and basement membrane-rich fibrous scar. We further report on the differential responses to fibrous scar of distinct fiber tracts in the injured spinal cord including the rubrospinal and corticospinal tracts as well as serotonergic, dopaminergic, and calcitonin gene-related peptide (CGRP) systems. Finally, we discuss therapeutic strategies to suppress fibrous scarring in traumatic CNS injury with particular emphasis on a unique pharmacological treatment using iron chelators and cyclic adenosine monophosphate (cAMP) to inhibit collagen biosynthesis. The latter treatment has been shown to promote long-distance axon growth, retrograde protection of injured neurons, and significant functional improvement.

SDF-1 stimulates neurite growth on inhibitory CNS myelin.

Impaired axonal regeneration is a common observation after central nervous system (CNS) injury. The stromal cell-derived factor-1, SDF-1/CXCL12, has previously been shown to promote axonal growth in the presence of potent chemorepellent molecules known to be important in nervous system development. Here, we report that treatment with SDF-1alpha is sufficient to overcome neurite outgrowth inhibition mediated by CNS myelin towards cultured postnatal dorsal root ganglion neurons. While we found both cognate SDF-1 receptors, CXCR4 and CXCR7/RDC1, to be coexpressed on myelin-sensitive dorsal root ganglion neurons, the distinct expression pattern of CXCR4 on growth cones and branching points of neurites suggests a function of this receptor in chemokine-mediated growth promotion and/or arborization. These in vitro findings were further corroborated as local intrathecal infusion of SDF-1 into spinal cord injury following thoracic dorsal hemisection resulted in enhanced sprouting of corticospinal tract axons into white and grey matter. Our findings indicate that SDF-1 receptor activation might constitute a novel therapeutic approach to promote axonal growth in the injured CNS.