Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

THE EFFECT OF POROSITY ON THE STRUCTURE AND PROPERTIES OF CALCIUM POLYPHOSPHATE BIOCERAMICS

Calcium polyphosphate (CPP) bioceramic with different porosities were prepared by controlling the concentration of the pore-foaming agent. Effect of porosity (0%, 15%, 30%, 45% and 60%) on the microstructure, pores interconnection, dissolution behavior and compressive strength of CPP bioceramic were investigated. Scanning electron microscope (SEM) and capillarity test results indicated that CPP with higher porosity (45% and 60%) exhibited three-dimensional interconnected pore structure with a pore size of about 200–400 μm, while the pores of lower porosity scaffold (0%, 15% and 30%) were isolated. The dissolution behavior in vitro indicated that the dissolution rate accelerated with the porosity increasing and the CPP with 60% porosity showed the highest dissolution velocity. The compressive strength of porosity CPP scaffolds were as much as the human cancellous bone, which decreased with the increase of porosity. While the dense CPP scaffolds lie in the same order of magnitude as compact bone

Preparation and evaluation of a biomimetic scaffold with porosity gradients in vitro

A novel biodegradable scaffold based on mimetic a natural bone tissue morphology with a porosity gradient structure was prepared in this paper. The result of surface morphology indicated that a graded porous structure was formed in the fabricated scaffold, where the dense layer (0%) was connected with the most porous layer (60%) by a middling porous layer (30%). To evaluate the degradability, graded porous scaffolds compared with homogeneous scaffolds were placed into a Tris-HCl buffer solution (pH = 7.4) for 28 days. It was found that both scaffolds presented the same degradation trend, and the graded porous structure did not change the original degradability of the scaffold. Moreover, the compressive strength of the graded porous scaffold was better than that of conventional homogeneous scaffold with the increase of degradation time, and the graded porous structure can enhanced the mechanical property of the scaffold. These findings suggest that this biodegradable and porosity-graded scaffold may be a new promising scaffold for loaded bone implant

Recognizing the Aggregation Characteristics of Extreme Precipitation Events Using Spatio-Temporal Scanning and the Local Spatial Autocorrelation Model

Precipitation is an essential climate variable in the hydrologic cycle. Its abnormal change would have a serious impact on the social economy, ecological development and life safety. In recent decades, many studies about extreme precipitation have been performed on spatio-temporal variation patterns under global changes; little research has been conducted on the regionality and persistence, which tend to be more destructive. This study defines extreme precipitation events by percentile method, then applies the spatio-temporal scanning model (STSM) and the local spatial autocorrelation model (LSAM) to explore the spatio-temporal aggregation characteristics of extreme precipitation, taking China in July as a case. The study result showed that the STSM with the LSAM can effectively detect the spatio-temporal accumulation areas. The extreme precipitation events of China in July 2016 have a significant spatio-temporal aggregation characteristic. From the spatial perspective, China’s summer extreme precipitation spatio-temporal clusters are mainly distributed in eastern China and northern China, such as Dongting Lake plain, the Circum-Bohai Sea region, Gansu, and Xinjiang. From the temporal perspective, the spatio-temporal clusters of extreme precipitation are mainly distributed in July, and its occurrence was delayed with an increase in latitude, except for in Xinjiang, where extreme precipitation events often take place earlier and persist longer

Degradation kinetics of calcium polyphosphate bioceramic: an experimental and theoretical study

In this work, the degradation kinetics of calcium polyphosphate bioceramic was studied. Liquid state31P nuclear magnetic resonance (NMR), X-ray diffraction (XRD) and scanning electron microscope (SEM) were used to characterize the product. The in vitro degradation test was carried out at 37 ºC for up to 48 hours for both the simulation solution and the extreme solution. The ion concentrations were measured and analyzed by establishing a mathematical model referring to the chemical reaction kinetics. The results indicated that the degradability of calcium polyphosphate increased with the decrease of pH value, and the sample showed a rapid loss of ion concentration within the initial period of immersion followed by a slower loss ratio. The relationship between ion concentration and the degradation time coincided with Boxlucas model

A novel bioceramic scaffold integrating silk fibroin in calcium polyphosphate for bone tissue-engineering

The advantages of bioceramics, such as biocompatibility and osteoconduction, have been widely used for bone repair and substitute as bone tissue-engineering materials. Bioceramic scaffolds however still need improvement to meet the requirements for complex bone repair. The aim of this study was to develop novel bioscaffolds for bone regeneration, based on the combination of silk fibroin (SF) and calcium polyphosphate (CPP) composite scaffolds. In this study, Bombyx mori silk fibroin (BMSF) and Antheraea pernyi silk fibroin (APSF) were prepared, and applied into CPP scaffolds with glutaraldehyde crosslinking to form the BMSF/CPP and APSF/CPP bioceramics. These scaffolds were then undergone the strength tests, morphology evaluation, and assessments for biodegradation and biocompatibility. Our results showed that the CPP-type bioceramics presented a higher compressive strength and enhanced degradation after the silk fibroin was doped into a CPP structure. Moreover, the BMSF/CPP and APSF/CPP-type scaffolds exhibited lower cellular toxicity than those of the CPP and HA types. Considering the improved mechanical characteristics and degradation as well as ready availability, SF/CPP may be considered a suitable bioceramic for bone tissue-engineering

Application of K/Sr co-doped calcium polyphosphate bioceramic as scaffolds for bone substitutes

Ion doping is one of the most important methods to modify the properties of bioceramics for better biodegrade abilities, biomechanical properties, and biocompatibilities. This paper presents a novel ion doping method applied in calcium polyphosphate (CPP)-based bioceramic scaffolds substituted by potassium and strontium ions (K/Sr) to form (K/Sr–CPP) scaffolds for bone tissue regeneration. The microstructure and crystallization of the scaffolds were detected by scanning electron microscopy and X-ray diffraction. Compressive strength and degradation tests were assessed to evaluate the mechanical and chemical stabilities of K/Sr–CPP in vitro. The cell biocompatibility was measured with respect to the cytotoxicity of the extractions of scaffolds. Muscle pouches and bone implantation were performed to evaluate the biodegradability and osteoconductivity of the scaffolds. The results indicated that the obtained K/Sr–CPP scaffolds had a single beta-CPP phase. The unit cell volume and average grain size increased but the crystallization decreased after the ions were doped into the CPP structure. The K/Sr–CPP scaffolds yielded a higher compressive strength and a better degradation property than the pure CPP scaffold. The MTT assay and in vivo results reveal that the K/Sr–CPP scaffolds exhibited a better cell biocompatibility and a tissue biocompatibility than CPP and hydroxyapatite scaffolds. This study proves the potential applications of K/Sr–CPP scaffolds in bone repair