In Vivo Ultrasonic Detection of Polyurea Crosslinked Silica Aerogel Implants

Background

Polyurea crosslinked silica aerogels are highly porous, lightweight, and mechanically strong materials with great potential for in vivo applications. Recent in vivo and in vitro studies have demonstrated the biocompatibility of this type of aerogel. The highly porous nature of aerogels allows for exceptional thermal, electric, and acoustic insulating capabilities that can be taken advantage of for non-invasive external imaging techniques. Sound-based detection of implants is a low cost, non-invasive, portable, and rapid technique that is routinely used and readily available in major clinics and hospitals.

Methodology

In this study the first in vivo ultrasound response of polyurea crosslinked silica aerogel implants was investigated by means of a GE Medical Systems LogiQe diagnostic ultrasound machine with a linear array probe. Aerogel samples were inserted subcutaneously and sub-muscularly in a) fresh animal model and b) cadaveric human model for analysis. For comparison, samples of polydimethylsiloxane (PDMS) were also imaged under similar conditions as the aerogel samples.

Conclusion/significance

Polyurea crosslinked silica aerogel (X-Si aerogel) implants were easily identified when inserted in either of the regions in both fresh animal model and cadaveric model. The implant dimensions inferred from the images matched the actual size of the implants and no apparent damage was sustained by the X-Si aerogel implants as a result of the ultrasonic imaging process. The aerogel implants demonstrated hyperechoic behavior and significant posterior shadowing. Results obtained were compared with images acquired from the PDMS implants inserted at the same location.     

Investigation of polyurea-crosslinked silica aerogels as a neuronal scaffold: a pilot study

Background

Polymer crosslinked aerogels are an attractive class of materials for future implant applications particularly as a biomaterial for the support of nerve growth. The low density and nano-porous structure of this material combined with large surface area, high mechanical strength, and tunable surface properties, make aerogels materials with a high potential in aiding repair of injuries of the peripheral nervous system. However, the interaction of neurons with aerogels remains to be investigated.

Methodology

In this work the attachment and growth of neurons on clear polyurea crosslinked silica aerogels (PCSA) coated with: poly-L-lysine, basement membrane extract (BME), and laminin1 was investigated by means of optical and scanning electron microscopy. After comparing the attachment and growth capability of neurons on these different coatings, laminin1 and BME were chosen for nerve cell attachment and growth on PCSA surfaces. The behavior of neurons on treated petri dish surfaces was used as the control and behavior of neurons on treated PCSA discs was compared against it.

Conclusions/Significance

This study demonstrates that: 1) untreated PCSA surfaces do not support attachment and growth of nerve cells, 2) a thin application of laminin1 layer onto the PCSA discs adhered well to the PCSA surface while also supporting growth and differentiation of neurons as evidenced by the number of processes extended and b3-tubulin expression, 3) three dimensional porous structure of PCSA remains intact after fixing protocols necessary for preservation of biological samples and 4) laminin1 coating proved to be the most effective method for attaching neurons to the desired regions on PCSA discs. This work provides the basis for potential use of PCSA as a biomaterial scaffold for neural regeneration.     

The Improved Biological Performance of a Novel Low Elastic Modulus Implant

Background

The mismatch of the elastic modulus between implants and bone tissue can lead to stress shielding, bone resorption and poor osseointegration. Compared with normal bone tissue, this problem is much more serious in osteoporosis. The purpose of this study was designed to find out whether the novel Ti-24Nb-4Zr-7.9Sn (TNZS) implant with low elastic modulus and high strength was suitable for biomedical material, especially in osteoporosis.

Methodology

In vitro study, the viability and Alkaline phosphatase (ALP) activity of osteoblasts on the TNZS and Ti-6V-4V (TAV) were observed. In vivo study, 30 adult female New Zealand rabbits were selected and divided randomly into two groups: sham-operation (SHAM, n = 6) and ovariectomised in combination with methylprednisolone treatment (OVX+MP, n = 24). Two implants were then placed in the tibia of each OVX + MP group rabbit, one in each side (left: TAV; right: TNZS). The OVX + MP group rabbits were sacrificed at 4 and 12 weeks after the implantation. The osteoporotic bone responses to the TNZS and TAV implants were evaluated by pull-out test, Micro-CT analyses and histological observation.

Principal Findings

Compared with the TAV group, the TNZS group showed a significant increase (P<0.05) in cell viability and ALP activity, new bone formation and pull-out force.

Conclusions

The novel TNZS implants show good biological performance both in vitro and in vivo, which suggests that the alloys are suitable for biomedical applications, especially in osteoporosis.     

Circadian rhythm and cartilage extracellular matrix genes in osseointegration: a genome-wide screening of implant failure by vitamin D deficiency

Background

Successful dental and orthopedic implants require the establishment of an intimate association with bone tissue; however, the mechanistic explanation of how biological systems accomplish osseointegration is still incomplete. We sought to identify critical gene networks involved in osseointegration by exploring the implant failure model under vitamin D deficiency.

Methodology

Adult male Sprague-Dawley rats were exposed to control or vitamin D-deficient diet prior to the osteotomy surgery in the femur bone and the placement of T-shaped Ti4Al6V implant. Two weeks after the osteotomy and implant placement, tissue formed at the osteotomy site or in the hollow chamber of T-shaped implant was harvested and total RNA was evaluated by whole genome microarray analyses.

Principal Findings

Two-way ANOVA of microarray data identified 103 genes that were significantly (>2 fold) modulated by the implant placement and vitamin D deficiency. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses assigned the highest z-score to the circadian rhythm pathway including neuronal PAS domain 2 (NPAS2), and period homolog 2 (Per2). NPAS2 and Aryl hydrocarbon receptor nuclear translocator-like (ARNTL/Bmal 1) were upregulated around implant and diminished by vitamin D deficiency, whereas the expression pattern of Per2 was complementary. Hierarchical cluster analysis further revealed that NPAS2 was in a group predominantly composed of cartilage extracellular matrix (ECM) genes. Whereas the expression of bone ECM genes around implant was not significantly affected by vitamin D deficiency, cartilage ECM genes were modulated by the presence of the implant and vitamin D status. In a proof-of-concept in vitro study, the expression of cartilage type II and X collagens was found upregulated when mouse mesenchymal stem cells were cultured on implant disk with 1,25D supplementation.

Conclusions

This study suggests that the circadian rhythm system and cartilage extracellular matrix may be involved in the establishment of osseointegration under vitamin D regulation.     

Evaluation of Biological Properties of Electron Beam Melted Ti6Al4V Implant with Biomimetic Coating In Vitro and In Vivo

Background

High strength porous titanium implants are widely used for the reconstruction of craniofacial defects because of their similar mechanical properties to those of bone. The recent introduction of electron beam melting (EBM) technique allows a direct digitally enabled fabrication of patient specific porous titanium implants, whereas both their in vitro and in vivo biological performance need further investigation.

Methods

In the present study, we fabricated porous Ti6Al4V implants with controlled porous structure by EBM process, analyzed their mechanical properties, and conducted the surface modification with biomimetic approach. The bioactivities of EBM porous titanium in vitro and in vivo were evaluated between implants with and without biomimetic apatite coating.

Results

The physical property of the porous implants, containing the compressive strength being 163 - 286 MPa and the Young’s modulus being 14.5–38.5 GPa, is similar to cortical bone. The in vitro culture of osteoblasts on the porous Ti6Al4V implants has shown a favorable circumstance for cell attachment and proliferation as well as cell morphology and spreading, which were comparable with the implants coating with bone-like apatite. In vivo, histological analysis has obtained a rapid ingrowth of bone tissue from calvarial margins toward the center of bone defect in 12 weeks. We observed similar increasing rate of bone ingrowth and percentage of bone formation within coated and uncoated implants, all of which achieved a successful bridging of the defect in 12 weeks after the implantation.

Conclusions

This study demonstrated that the EBM porous Ti6Al4V implant not only reduced the stress-shielding but also exerted appropriate osteoconductive properties, as well as the apatite coated group. The results opened up the possibility of using purely porous titanium alloy scaffolds to reconstruct specific bone defects in the maxillofacial and orthopedic fields.     

The role of pro- and anti-inflammatory responses in silica-induced lung fibrosis

Background

It has been generally well accepted that chronic inflammation is a necessary component of lung fibrosis but this concept has recently been challenged.

Methods

Using biochemical, histological, immunohistochemistry, and cellular analyses, we compared the lung responses (inflammation and fibrosis) to fibrogenic silica particles (2.5 and 25 mg/g lung) in Sprague-Dawley rats and NMRI mice.

Results

Rats treated with silica particles developed chronic and progressive inflammation accompanied by an overproduction of TNF-α as well as an intense lung fibrosis. Dexamethasone or pioglitazone limited the amplitude of the lung fibrotic reaction to silica in rats, supporting the paradigm that inflammation drives lung fibrosis.In striking contrast, in mice, silica induced only a limited and transient inflammation without TNF-α overproduction. However, mice developed lung fibrosis of a similar intensity than rats. The fibrotic response in mice was accompanied by a high expression of the anti-inflammatory and fibrotic cytokine IL-10 by silica-activated lung macrophages. In mice, IL-10 was induced only by fibrotic particles and significantly expressed in the lung of silica-sensitive but not silica-resistant strains of mice. Anti-inflammatory treatments did not control lung fibrosis in mice.

Conclusion

These results indicate that, beside chronic lung inflammation, a pronounced anti-inflammatory reaction may also contribute to the extension of silica-induced lung fibrosis and represents an alternative pathway leading to lung fibrosis.     

Incidence and Risk Factors of Striae Distensae Following Breast Augmentation Surgery: A Cohort Study

Background

The significant increase in the popularity of breast augmentation surgeries has led to an increase in the number and types of complications; among these is the postoperative occurrence of Striae Distensae (SD). The objective of this study was to investigate the incidence of SD and describing its occurrence in association with age, breast implant volume, history of SD, history of pregnancies and breastfeeding, body mass index (BMI), changes in postoperative weight, smoking habits, and use of oral contraceptives.

Methods

A cohort study was conducted and the patient data from a specific social group that underwent augmentation mammaplasty with silicone breast implants in a private clinic was analyzed.

Results

563 patients entered the cohort, while 538 completed the study. The SD incidence was 7.06%. The risk was almost the double at 22–28 years of age and triple in women of 21 years of age or less. The women who did not use oral contraceptives were 2.59 times more likely of developing SD. A higher incidence of SD was observed among those with normal or low BMI values, smokers, and in those who had implants larger than 300 ml.

Conclusions

Young age, larger implant volumes, smoking, and normal or low BMI values were the risk factors responsible for the development of SD; while using oral contraceptives was found to be a protective factor.     

Worldwide Enucleation Techniques and Materials for Treatment of Retinoblastoma: An International Survey

Purpose

To investigate the current practice of enucleation with or without orbital implant for retinoblastoma in countries across the world.

Methods

A digital survey identifying operation techniques and material used for orbital implants after enucleation in patients with retinoblastoma.

Results

We received a response of 58 surgeons in 32 different countries. A primary artificial implant is routinely inserted by 42 (72.4%) surgeons. Ten (17.2%) surgeons leave the socket empty, three (5.2%) decide per case. Other surgeons insert a dermis fat graft as a standard primary implant (n=1), or fill the socket in a standard secondary procedure (n=2; one uses dermis fat grafts and one artificial implants). The choice for porous implants was more frequent than for non-porous implants: 27 (58.7%) and 15 (32.6%), respectively. Both porous and non-porous implant types are used by 4 (8.7%) surgeons. Twenty-five surgeons (54.3%) insert bare implants, 11 (23.9%) use separate wrappings, eight (17.4%) use implants with prefab wrapping and two insert implants with and without wrapping depending on type of implant. Attachment of the muscles to the wrapping or implant (at various locations) is done by 31 (53.4%) surgeons. Eleven (19.0%) use a myoconjunctival technique, nine (15.5%) suture the muscles to each other and seven (12.1%) do not reattach the muscles. Measures to improve volume are implant exchange at an older age (n=4), the use of Restylane SQ (n=1) and osmotic expanders (n=1). Pegging is done by two surgeons.

Conclusion

No (worldwide) consensus exists about the use of material and techniques for enucleation for the treatment of retinoblastoma. Considerations for the use of different techniques are discussed.     

Enhancement of implant osseointegration by high-frequency low-magnitude loading

Background

Mechanical loading is known to play an important role in bone remodelling. This study aimed to evaluate the effect of high- and low-frequency axial loading, applied directly to the implant, on peri-implant bone healing and implant osseointegration.

Methodology

Titanium implants were bilaterally installed in rat tibiae. For every animal, one implant was loaded (test) while the other one was not (control). The test implants were randomly divided into 8 groups according to 4 loading regimes and 2 experimental periods (1 and 4 weeks). The loaded implants were subject to an axial displacement. Within the high- (HF, 40 Hz) or low-frequency (LF, 8 Hz) loading category, the displacements varied 2-fold and were ranked as low- or high-magnitude (LM, HM), respectively. The strain rate amplitudes were kept constant between the two frequency groups. This resulted in the following 4 loading regimes: 1) HF-LM, 40 Hz-8 µm; 2) HF-HM, 40 Hz-16 µm; 3) LF-LM, 8 Hz-41 µm; 4) LF-HM, 8 Hz-82 µm. The tissue samples were processed for resin embedding and subjected to histological and histomorphometrical analyses. Data were analyzed statistically with the significance set at p<0.05.

Principal Findings

After loading for 4 weeks, HF-LM loading (40 Hz-8 µm) induced more bone-to-implant contact (BIC) at the level of the cortex compared to its unloaded control. No significant effect of the four loading regimes on the peri-implant bone fraction (BF) was found in the 2 experimental periods.

Conclusions

The stimulatory effect of immediate implant loading on bone-to-implant contact was only observed in case of high-frequency (40 Hz) low-magnitude (8 µm) loading. The applied load regimes failed to influence the peri-implant bone mass.     

Comparative Effects of Snoring Sound between Two Minimally Invasive Surgeries in the Treatment of Snoring: A Randomized Controlled Trial

Background

Minimally invasive surgeries of the soft palate have emerged as a less-invasive treatment for habitual snoring. To date, there is only limited information available comparing the effects of snoring sound between different minimally invasive surgeries in the treatment of habitual snoring.

Objective

To compare the efficacy of palatal implant and radiofrequency surgery, in the reduction of snoring through subjective evaluation of snoring and objective snoring sound analysis.

Patients and Method

Thirty patients with habitual snoring due to palatal obstruction (apnea-hypopnea index ≤15, body max index ≤30) were prospectively enrolled and randomized to undergo a single session of palatal implant or temperature-controlled radiofrequency surgery of the soft palate under local anesthesia. Snoring was primarily evaluated by the patient with a 10 cm visual analogue scale (VAS) at baseline and at a 3-month follow-up visit and the change in VAS was the primary outcome. Moreover, life qualities, measured by snore outcomes survey, and full-night snoring sounds, analyzed by a sound analytic program (Snore Map), were also investigated at the same time.

Results

Twenty-eight patients completed the study; 14 received palatal implant surgery and 14 underwent radiofrequency surgery. The VAS and snore outcomes survey scores were significantly improved in both groups. However, the good response (postoperative VAS ≤3 or postoperative VAS ≤5 plus snore outcomes survey score ≥60) rate of the palatal implant group was significantly higher than that of the radiofrequency group (79% vs. 29%, P = 0.021). The maximal loudness of low-frequency (40–300 Hz) snores was reduced significantly in the palatal implant group. In addition, the snoring index was significantly reduced in the radiofrequency group.

Conclusions

Both palatal implants and a single-stage radiofrequency surgery improve subjective snoring outcomes, but palatal implants have a greater effect on most measures of subjective and objective snoring. Multi-stage radiofrequency surgery was not tested.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01955083","term_id":"NCT01955083"}}NCT01955083     

Electrochemical disinfection of dental implants--a proof of concept

Background

Peri-implantitis has gained significant clinical attention in recent years. This disease is an inflammatory reaction to microorganisms around dental implants. Due to the limited accessibility, non-invasive antimicrobial strategies are of high interest. An unexpected approach to implant disinfection may evolve from electrolysis. Given the electrical conductivity of titanium implants, alkalinity or active oxidants can be generated in body fluids. We investigated the use of dental titanium implants as electrodes for the local generation of disinfectants. Our hypothesis was that electrolysis can reduce viable counts of adhering bacteria, and that this reduction should be greater if active oxidative species are generated.

Methodology/Principal Findings

As model systems, dental implants, covered with a mono-species biofilm of Escherichia coli C43, were placed in photographic gelatin prepared with physiological saline. Implants were treated by a continuous current of 0 - 10 mA for 15 minutes. The reduction of viable counts was investigated on cathodes and anodes. In separate experiments, the local change in pH was visualized using color indicators embedded in the gelatin. Oxidative species were qualitatively detected by potassium iodide-starch paper. The in situ generated alkaline environment around cathodic implants caused a reduction of up to 2 orders of magnitude in viable E. coli counts. On anodic implants, in contrast to cathodic counterparts, oxidative species were detected. Here, a current of merely 7.5 mA caused complete kill of the bacteria.

Conclusions/Significance

This laboratory study shows that electrochemical treatment may provide access to a new way to decontaminate dental implants in situ.     

KaBOB: ontology-based semantic integration of biomedical databases

Background

The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources.

Results

We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license.

Conclusions

KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for formal reasoning over a wealth of integrated biomedical data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0559-3) contains supplementary material, which is available to authorized users.     

The effect of visual cues on difficulty ratings for segregation of musical streams in listeners with impaired hearing

Background

Enjoyment of music is an important part of life that may be degraded for people with hearing impairments, especially those using cochlear implants. The ability to follow separate lines of melody is an important factor in music appreciation. This ability relies on effective auditory streaming, which is much reduced in people with hearing impairment, contributing to difficulties in music appreciation. The aim of this study was to assess whether visual cues could reduce the subjective difficulty of segregating a melody from interleaved background notes in normally hearing listeners, those using hearing aids, and those using cochlear implants.

Methodology/Principal Findings

Normally hearing listeners (N = 20), hearing aid users (N = 10), and cochlear implant users (N = 11) were asked to rate the difficulty of segregating a repeating four-note melody from random interleaved distracter notes. The pitch of the background notes was gradually increased or decreased throughout blocks, providing a range of difficulty from easy (with a large pitch separation between melody and distracter) to impossible (with the melody and distracter completely overlapping). Visual cues were provided on half the blocks, and difficulty ratings for blocks with and without visual cues were compared between groups. Visual cues reduced the subjective difficulty of extracting the melody from the distracter notes for normally hearing listeners and cochlear implant users, but not hearing aid users.

Conclusion/Significance

Simple visual cues may improve the ability of cochlear implant users to segregate lines of music, thus potentially increasing their enjoyment of music. More research is needed to determine what type of acoustic cues to encode visually in order to optimise the benefits they may provide.     

Development of Implant/Interconnected Porous Hydroxyapatite Complex as New Concept Graft Material

Background

Dental implant has been successfully used to replace missing teeth. However, in some clinical situations, implant placement may be difficult because of a large bone defect. We designed novel complex biomaterial to simultaneously restore bone and place implant. This complex was incorporated implant into interconnected porous calcium hydroxyapatite (IP-CHA). We then tested this Implant/IP-CHA complex and evaluated its effect on subsequent bone regeneration and implant stability in vivo.

Methodology/Principal Findings

A cylinder-type IP-CHA was used in this study. After forming inside of the cylinder, an implant was placed inside to fabricate the Implant/IP-CHA complex. This complex was then placed into the prepared bone socket in the femur of four beagle-Labrador hybrid dogs. As a control, implants were placed directly into the femur without any bone substrate. Bone sockets were allowed to heal for 2, 3 and 6 months and implant stability quotients (ISQ) were measured. Finally, tissue blocks containing the Implant/IP-CHA complexes were harvested. Specimens were processed for histology and stained with toluidine blue and bone implant contact (BIC) was measured. The ISQs of complex groups was 77.8±2.9 in the 6-month, 72.0±5.7 in the 3-month and 47.4±11.0 in the 2-month. There was no significant difference between the 3- or 6-month complex groups and implant control groups. In the 2-month group, connective tissue, including capillary angiogenesis, was predominant around the implants, although newly formed bone could also be observed. While, in the 3 and 6-month groups, newly formed bone could be seen in contact to most of the implant surface. The BICs of complex groups was 2.18±3.77 in the 2-month, 44.03±29.58 in the 3-month, and 51.23±8.25 in the 6-month. Significant difference was detected between the 2 and 6-month.

Conclusions/Significance

Within the results of this study, the IP-CHA/implant complex might be able to achieve both bone reconstruction and implant stability.     

Chronic delivery of antibody fragments using immunoisolated cell implants as a passive vaccination tool

Background

Monoclonal antibodies and antibody fragments are powerful biotherapeutics for various debilitating diseases. However, high production costs, functional limitations such as inadequate pharmacokinetics and tissue accessibility are the current principal disadvantages for broadening their use in clinic.

Methodology and Principal Findings

We report a novel method for the long-term delivery of antibody fragments. We designed an allogenous immunoisolated implant consisting of polymer encapsulated myoblasts engineered to chronically release scFv antibodies targeted against the N-terminus of the Aβ peptide. Following a 6-month intracerebral therapy we observed a significant reduction of the production and aggregation of the Aβ peptide in the APP23 transgenic mouse model of Alzheimer''s disease. In addition, functional assessment showed prevention of behavioral deficits related to anxiety and memory traits.

Conclusions and Significance

The chronic local release of antibodies using immunoisolated polymer cell implants represents an alternative passive vaccination strategy in Alzheimer''s disease. This novel technique could potentially benefit other diseases presently treated by local and systemic antibody administration.     

Population-based rates of revision of primary total hip arthroplasty: a systematic review

Background

Most research on failure leading to revision total hip arthroplasty (THA) is reported from single centers. We searched PubMed between January 2000 and August 2010 to identify population- or community-based studies evaluating ten-year revision risks. We report ten-year revision risk using the Kaplan-Meier method, stratifying by age and fixation technique.

Results

Thirteen papers met the inclusion criteria. Cemented prostheses had Kaplan-Meier estimates of revision-free implant survival of ten years ranging from 88% to 95%; uncemented prostheses had Kaplan-Meier estimates from 80% to 85%. Estimates ranged from 72% to 86% in patients less than 60 years old and from 90 to 96% in older patients.

Conclusion

Data reported from national registries suggest revision risks of 5 to 20% ten years following primary THA. Revision risks are lower in older THA recipients. Uncemented implants may have higher ten-year rates of revision, regardless of age.     

Using a Search Engine-Based Mutually Reinforcing Approach to Assess the Semantic Relatedness of Biomedical Terms

Background

Determining the semantic relatedness of two biomedical terms is an important task for many text-mining applications in the biomedical field. Previous studies, such as those using ontology-based and corpus-based approaches, measured semantic relatedness by using information from the structure of biomedical literature, but these methods are limited by the small size of training resources. To increase the size of training datasets, the outputs of search engines have been used extensively to analyze the lexical patterns of biomedical terms.

Methodology/Principal Findings

In this work, we propose the Mutually Reinforcing Lexical Pattern Ranking (ReLPR) algorithm for learning and exploring the lexical patterns of synonym pairs in biomedical text. ReLPR employs lexical patterns and their pattern containers to assess the semantic relatedness of biomedical terms. By combining sentence structures and the linking activities between containers and lexical patterns, our algorithm can explore the correlation between two biomedical terms.

Conclusions/Significance

The average correlation coefficient of the ReLPR algorithm was 0.82 for various datasets. The results of the ReLPR algorithm were significantly superior to those of previous methods.     

All That Glitters Isn't Gold: A Survey on Acknowledgment of Limitations in Biomedical Studies

Background

Acknowledgment of all serious limitations to research evidence is important for patient care and scientific progress. Formal research on how biomedical authors acknowledge limitations is scarce.

Objectives

To assess the extent to which limitations are acknowledged in biomedical publications explicitly, and implicitly by investigating the use of phrases that express uncertainty, so-called hedges; to assess the association between industry support and the extent of hedging.

Design

We analyzed reporting of limitations and use of hedges in 300 biomedical publications published in 30 high and medium -ranked journals in 2007. Hedges were assessed using linguistic software that assigned weights between 1 and 5 to each expression of uncertainty.

Results

Twenty-seven percent of publications (81/300) did not mention any limitations, while 73% acknowledged a median of 3 (range 1–8) limitations. Five percent mentioned a limitation in the abstract. After controlling for confounders, publications on industry-supported studies used significantly fewer hedges than publications not so supported (p = 0.028).

Limitations

Detection and classification of limitations was – to some extent – subjective. The weighting scheme used by the hedging detection software has subjective elements.

Conclusions

Reporting of limitations in biomedical publications is probably very incomplete. Transparent reporting of limitations may protect clinicians and guideline committees against overly confident beliefs and decisions and support scientific progress through better design, conduct or analysis of new studies.     

Accommodating ontologies to biological reality--top-level categories of cumulative-constitutively organized material entities

Background

The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO''s three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity.

Methodology/Principal Findings

Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities.

Conclusions/Significance

We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle.     

A novel mechanism by which silica defends grasses against herbivory

Background and Aims

Previous studies have shown that silica in grass leaves defends them against small herbivores, which avoid high-silica grasses and digest them less efficiently. This study tested the idea that silica can reduce digestibility by preventing the mechanical breakdown of chlorenchyma cells.

Methods

Both the percentage of total chlorophyll liberated from high- and low-silica grass leaves by mechanical grinding and the chlorophyll content of locust faeces were measured.

Key Results

High-silica grasses released less chlorophyll after grinding and retained more after passing through the gut of locusts, showing that silica levels correlated with increased mechanical protection.

Conclusions

These results suggest that silica may defend grasses at least in part by reducing mechanical breakdown of the leaf, and that mechanical protection of resources in chlorenchyma cells is a novel and potentially important mechanism by which silica protects grasses.Key words: Grass, silica, locust, digestibility, defence, Lolium perenne, Festuca ovina