BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License

Hemifacial Spasm and Neurovascular Compression

Hemifacial spasm (HFS) is characterized by involuntary unilateral contractions of the muscles innervated by the ipsilateral facial nerve, usually starting around the eyes before progressing inferiorly to the cheek, mouth, and neck. Its prevalence is 9.8 per 100,000 persons with an average age of onset of 44 years. The accepted pathophysiology of HFS suggests that it is a disease process of the nerve root entry zone of the facial nerve. HFS can be divided into two types: primary and secondary. Primary HFS is triggered by vascular compression whereas secondary HFS comprises all other causes of facial nerve damage. Clinical examination and imaging modalities such as electromyography (EMG) and magnetic resonance imaging (MRI) are useful to differentiate HFS from other facial movement disorders and for intraoperative planning. The standard medical management for HFS is botulinum neurotoxin (BoNT) injections, which provides low-risk but limited symptomatic relief. The only curative treatment for HFS is microvascular decompression (MVD), a surgical intervention that provides lasting symptomatic relief by reducing compression of the facial nerve root. With a low rate of complications such as hearing loss, MVD remains the treatment of choice for HFS patients as intraoperative technique and monitoring continue to improve

Social Networks, High-Risk anal Hpv and Coinfection With Hiv in Young Sexual Minority Men

OBJECTIVES: Young sexual minority men (SMM) exhibit a high prevalence and incidence of high-risk genotypes of human papillomavirus (hrHPV) anal infections and a confluence of a high prevalence of HIV and rectal STIs. Social determinants of health (SDOHs) are linked to social network contexts that generate and maintain racial disparities in HIV and STIs. A network perspective was provided to advance our knowledge of drivers of genotype-specific hrHPV infection and coinfection with HIV. The study also examined whether socially connected men are infected with the same high-risk HPV genotypes and, if so, whether this tendency is conditioned on coinfection with HIV. METHODS: Our sample included 136 young SMM of predominantly black race and their network members of other races and ethnicities, aged 18-29 years, who resided in Houston, Texas, USA. These participants were recruited during 2014-2016 at the baseline recruitment period by network-based peer referral, where anal exfoliated cells and named social and sexual partners were collected. Exponential random graph models were estimated to assess similarity in genotype-specific hrHPV anal infection in social connections and coinfection with HIV in consideration of the effects of similarity in sociodemographic, sexual behavioural characteristics, SDOHs and syphilis infection. RESULTS: Pairs of men socially connected to each other tend to be infected with the same hrHPV genotypes of HPV-16, HPV-45 and HPV-51 or HPV-16 and/or HPV-18. The tendency of social connections between pairs of men who were infected with either HPV-16 or HPV-18 were conditioned on HIV infection. CONCLUSIONS: Networked patterns of hrHPV infection could be amenable to network-based HPV prevention interventions that engage young SMM of predominantly racial minority groups who are out of HIV care and vulnerable to high-risk HPV acquisition

Synthesis and self-assembly of tetraphenylethene and biphenyl based AIE-active triazoles

Self-assembly of fluorescent functional materials has attracted increasing interest in the fabrication of optoelectronic and biological nanodevices. Tetraphenylethene (TPE) is a typical dye molecule with aggregation-induced-emission (AIE) characteristics. Melding TPE carrying triple-bond functionality with diazide-containing biphenyl through ''click'' chemistry generates AIE-active luminogens [1,1'-biphenyl]-4,4'-diyl bis(6-(4-(4-(1,2,2-triphenylvinyl)phenyl)-1H-1,2,3-triazol-1-yl) hexanoate) [1(5)] and[1,1'-biphenyl]-4,4'-diyl bis(11-(4-(4-(1,2,2-triphenylvinyl)phenyl)-1H-1,2,3-triazol-1-yl) undecanoate)[1(10)] with solid state efficiencies up to unity. Slow addition of dilute THF solutions of 1(m) (m ¼ 5, 10) into nonsolvents such as n-hexane and water yields self-assembled white wooly solids. TEM and SEM observations reveal the (helical) nanofibrous structure of the aggregates. Upon cooling from their concentrated hot solutions, 1(m) readily precipitate. Meanwhile, they can also form gels at high concentrations. Both precipitates and gels of 1(m) exhibit structures similar to those of the aggregates formed in nonsolvents. These results indicate that 1(m) can facilely self-assemble into high emission efficiency (helical) nanofibers, thus paving the way for their optoelectronic and biological applications

Molecular anchors in the solid state: Restriction of intramolecular rotation boosts emission efficiency of luminogen aggregates to unity

Introduction of freely rotatable tetraphenylethene (TPE) to conventional luminophors quenches their light emissions in the solutions but endows the resultant molecules (TPEArs) with aggregation-induced emission characteristics in the condensed phase due to the restriction of intramolecular rotation. High fluorescence quantum yields up to 100% have been achieved in the films of TPEArs

S100A12 in Digestive Diseases and Health: A Scoping Review

Calgranulin proteins are an important class of molecules involved in innate immunity. These members of the S100 class of the EF-hand family of calcium-binding proteins have numerous cellular and antimicrobial functions. One protein in particular, S100A12 (also called EN-RAGE or calgranulin C), is highly abundant in neutrophils during acute inflammation and has been implicated in immune regulation. Structure-function analyses reveal that S100A12 has the capacity to bind calcium, zinc, and copper, processes that contribute to nutritional immunity against invading microbial pathogens. S100A12 is a ligand for the receptor for advanced glycation end products (RAGE), toll-like receptor 4 (TLR4), and CD36, which promote cellular and immunological pathways to alter inflammation. We conducted a scoping review of the existing literature to define what is known about the association of S100A12 with digestive disease and health. Results suggest that S100A12 is implicated in gastroenteritis, necrotizing enterocolitis, gastritis, gastric cancer, Crohn’s disease, irritable bowel syndrome, inflammatory bowel disease, and digestive tract cancers. Together, these results reveal S100A12 is an important molecule broadly associated with the pathogenesis of digestive diseases

What makes efficient circularly polarised luminescence in the condensed phase: aggregation-induced circular dichroism and light emission

In this contribution, we conceptually present a new avenue to construction of molecular functional materials with high performance of circularly polarised luminescence (CPL) in the condensed phase. A molecule (1) containing luminogenic silole and chiral sugar moieties was synthesized and thoroughly characterized. In a solution of 1, no circular dichroism (CD) and fluorescence emission are observed, but upon molecular aggregation, both the CD and fluorescence are simultaneously turned on, showing aggregation-induced CD (AICD) and emission (AIE) effects. The AICD effect is supported by the fact that the molecules readily assemble into right-handed helical nanoribbons and superhelical ropes when aggregated. The AIE effect boosts the fluorescence quantum efficiency (ΦF) by 136 fold (ΦF, ∼0.6% in the solution versus ∼81.3% in the solid state), which surmounts the serious limitations of aggregation-caused quenching effect encountered by conventional luminescent materials. Time-resolved fluorescence study and theoretical calculation from first principles conclude that restriction of the low-frequency intramolecular motions is responsible for the AIE effect. The helical assemblies of 1 prefer to emit right-handed circularly polarised light and display large CPL dissymmetry factors (gem), whose absolute values are in the range of 0.08–0.32 and are two orders of magnitude higher than those of commonly reported organic materials. We demonstrate for the first time the use of a Teflon-based microfluidic technique for fabrication of the fluorescent pattern. This shows the highest gem of −0.32 possibly due to the enhanced assembling order in the confined microchannel environment. The CPL performance was preserved after more than half year storage under ambient conditions, revealing the excellent spectral stability. Computational simulation was performed to interpret how the molecules in the aggregates interact with each other at the molecular level. Our designed molecule represents the desired molecular functional material for generating efficient CPL in the solid state, and the current study shows the best results among the reported organic conjugated molecular systems in terms of emission efficiency, dissymmetry factor, and spectral stability

Learning and innovation of Chinese Firms along the paths of “Bring In” to “Go Global”

Over the past several decades, the “Bring In” and “Go Global” policies implemented in China have encouraged an unprecedented level of investment in and out of the country, creating unique opportunities for Chinese firms to learn and innovate along the paths of inward and outward internationalization. The international business (IB) literature has yet to satisfactorily explain what has been learnt by the Chinese firms and whether and how their learning and innovation have taken place over time. This special issue examines the specific content, nature, mechanisms, processes, and internal and external conditions and contexts of learning and innovation of Chinese firms during the course of inward and outward internationalization. We provide an overview of the “Bring In” and “Go Global” policies, assess the current state of the field, and explicate how the research articles in the special issue contribute to the understanding of learning and innovation of Chinese firms along the paths of inward and outward internationalization