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Most parts of the Earth’s surface are situated in the deep ocean. To explore this visually rather adversarial environment with cameras, they have to be protected by pressure housings. These housings, in turn, need interfaces to the world, enduring extreme pressures within the water column. Commonly, a flat window or a half-sphere of glass, called flat-port or dome-port, respectively is used to implement such kind of interface. Hence, multi-media interfaces, between water, glass and air are introduced, entailing refraction effects in the images taken through them. To obtain unbiased 3D measurements and to yield a geometrically faithful reconstruction of the scene, it is mandatory to deal with the effects in a proper manner. Hence, we propose an optical digital twin of an underwater environment, which has been geometrically verified to resemble a real water lab tank that features the two most common optical interfaces. It can be used to develop, evaluate, train, test and tune refractive algorithms. Alongside this paper, we publish the model for further extension, jointly with code to dynamically generate samples from the dataset. Finally, we also publish a pre-rendered dataset ready for use at https://git.geomar.de/david-nakath/geodt.

Background China media reported infant deaths following hepatitis B vaccination in late 2013, leading to temporary suspension of hepatitis B vaccine (HepB Event) until the deaths were shown to be coincidental and the vaccine was of standard, good quality. In 2016, a criminal ring in Shandong province that had been purchasing, improperly storing, and reselling Category 2 vaccines (private-sector) to 60 (of 200,000) clinics for 5 years, was exposed, publicized, and prosecuted, and the potential health and epidemiological impacts were investigated to determine whether revaccination was necessary (Shandong Vaccine Event). Methods We assessed parental confidence in vaccines through 9 telephone surveys in 6 and 11 provinces before, during, and after the two events. Provider confidence was assessed through in-person interviews following each event. Vaccine utilization was assessed using Immunization Information Management System data from township clinics. Results In the early stages of each event, approximately 30% of parents indicated vaccine hesitancy and 18% said they would refuse routine immunization. Five and nine months after each event, hesitancy and refusal decreased, but not to pre-event levels. During the Shandong Vaccine Event, 49·1% of parents indicated refusal to use Category 2 vaccines; six months later, the rate was 32·8%. Use of HepB decreased by 21% during the first 2 weeks of the HepB Event and by 12·6% during the first 4 weeks of Shandong Vaccine Event, but returned to baseline in less than 3 months. Use of Category 2 vaccine decreased by 49·5% in the first 3 weeks of the Shandong Vaccine Event and by 28·7% 6 months later. After the Shandong Vaccine Event, 64% of clinicians held high confidence in routine immunization, lower than at baseline. Conclusions The two events caused mistrust, loss of confidence, and decreases in use of vaccines by parents and providers. In addition to ensuring immunization program integrity, effective communications and ongoing monitoring of vaccine use and confidence should be included to restore confidence and trust in vaccines.

Influenza A virus, the H9N2 subtype, is an avian influenza virus that has long been circulating in the worldwide poultry industry and is occasionally found to be transmissible to humans. Evidence from genomic analysis suggests that H9N2 provides the genes for the H5N1 and H7N9 subtypes, which have been found to infect mammals and pose a threat to human health. However, due to the lack of a structural model of the interaction between H9N2 and host cells, the mechanism of the extensive adaptability and strong transformation capacity of H9N2 is not fully understood. In this paper, we collected 40 representative H9N2 virus samples reported recently, mainly in China and neighboring countries, and investigated the interactions between H9N2 hemagglutinin and the mammalian receptor, the polysaccharide α-2,6-linked lactoseries tetrasaccharide c, at the atomic level using docking simulation tools. We categorized the mutations of studied H9N2 hemagglutinin according to their effects on ligand-binding interactions and the phylogenetic analysis. The calculations indicated that all the studied H9N2 viruses can establish a tight binding with LSTc although the mutations caused a variety of perturbations to the local conformation of the binding pocket. Our calculations suggested that a marginal equilibrium is established between the conservative ligand-receptor interaction and the conformational dynamics of the binding pocket, and it might be this equilibrium that allows the virus to accommodate mutations to adapt to a variety of environments. Our results provided a way to understand the adaptive mechanisms of H9N2 viruses, which may help predict its propensity to spread in mammals.

Software to predict the change in protein stability upon point mutation is a valuable tool for a number of biotechnological and scientific problems. To facilitate the development of such software and provide easy access to the available experimental data, the ProTherm database was created. Biases in the methods and types of information collected has led to disparity in the types of mutations for which experimental data is available. For example, mutations to alanine are hugely overrepresented whereas those involving charged residues, especially from one charged residue to another, are underrepresented. ProTherm subsets created as benchmark sets that do not account for this often underrepresented certain mutational types. This issue introduces systematic biases into previously published protocols’ ability to accurately predict the change in folding energy on these classes of mutations. To resolve this issue, we have generated a new benchmark set with these problems corrected. We have then used the benchmark set to test a number of improvements to the point mutation energetics tools in the Rosetta software suite.

Objective To estimate the costs of routine immunization (RI) services in China in 2015, to provide objective data relevant to investment in the Expanded Program on Immunization, and to contribute to global data on costing and financing of RI. Methods The study was conducted between January and March 2016. We selected 276 villages, 138 townships, 46 counties, and 40 prefectures from 15 provinces as investigation sites at random, stratified by eastern, middle, and western regions. Direct cost items included vaccines, personnel, cold chain, surveillance, communication, training, and supervision at the national, provincial, prefecture, county, township, and village levels. We obtained financial data from governmental and external sources. Indirect costs of RI included parents’ transportation costs and productivity lost due to taking their children for vaccination. Results Total direct costs were $92.42 for each child fully immunized ($4.20/dose), which equates to $1529.55 million per birth cohort. RI costs were higher in the eastern region than in the western region, and higher than that of the central region. Vaccination coverage was positively associated with direct routine immunization costs. The cost of the recommended vaccines was $19.08/child and vaccine only accounted for 20.64% of total costs. Operational cost, including surveillance, communication, training and supervision, was $217.31/child, accounting for 14.21% of total cost. The indirect cost per child was $72.86; the total indirect cost was $1205.83 million for the birth cohort. Government investment in RI accounted for about 70% of total costs. Revenue from sales of private-sector vaccine supported the remaining 30% of RI costs. Conclusions While government financing has increased, some operating costs continue to be provided from revenue generated by sales of Category 2 (private-sector) vaccines to families. China could benefit from bringing new and underutilized vaccines into the EPI system based on evidence that includes routine immunization vaccine and operations costs.

Natural antisense transcripts (NAT) and alternative polyadenylation (APA) of messenger RNA (mRNA) are important contributors of transcriptome complexity, each playing a critical role in multiple biological processes. However, whether they have crosstalk and function collaboratively is unclear. We discovered that APA enriched in human sense-antisense (S-AS) gene pairs, and finally focused on RNASEH2C-KAT5 S-AS pair for further study. In cis but not in trans over-expression of the antisense KAT5 gene promoted the usage of distal polyA (pA) site in sense gene RNASEH2C, which generated longer 3′ untranslated region (3′UTR) and produced less protein, accompanying with slowed cell growth. Mechanistically, elevated Pol II occupancy coupled with SRSF3 could explain the higher usage of distal pA site. Finally, NAT-mediated downregulation of sense gene’s protein level in RNASEH2C-KAT5 pair was specific for human rather than mouse, which lacks the distal pA site of RNASEH2C. We provided the first evidence to support that certain gene affected phenotype may not by the protein of its own, but by affecting the expression of its overlapped gene through APA, implying an unexpected view for understanding the link between genotype and phenotype. Electronic supplementary material The online version of this article (10.1007/s13238-017-0497-0) contains supplementary material, which is available to authorized users.

Alternative polyadenylation (APA), a phenomenon that RNA molecules with different 3â² ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells. Then we summarized the main findings and advances so far based on these methods, including the preferences of alternative polyA (pA) site, the biological processes involved, and the corresponding consequences. We especially categorized the APA changes discovered so far and discussed their potential functions under given conditions, along with the possible underlying molecular mechanisms. With more in-depth studies on extensive samples, more signatures and functions of APA will be revealed, and its diverse roles will gradually heave in sight. Keywords: Alternative polyadenylation, Next-generation sequencing, 3â²UTR, Alternative splicing, Gene regulation

This prospective observational case series study aimed to observe the clinical characteristics of acute zonal occult outer retinopathy (AZOOR) and its prognosis in Chinese Han patients. Six eyes of 5 female patients diagnosed with AZOOR were followed up for 4 months to observe the natural disease course. All enrolled subjects underwent a series of ocular examinations at the onset and each return visit, including best corrected visual acuity (BCVA), split lamp microscopy, fundus photography, optical coherence tomography (OCT), perimetry, multifocal electroretinogram and fundus fluorescein angiography. Over the follow-up, all enrolled patients recovered on BCVA, perimetry and OCT in different degrees. Among them, one patient recovered completely since the ocular examination results returned to normal. AZOOR is a rare ocular disorder in Chinese population. Our results demonstrated that visual functions of enrolled patients significantly improved spontaneously, indicating that Chinese female Han patients with AZOOR have good visual outcomes during the follow-up period without any specific managements.

Idiopathic renal hypouricemia is a rare hereditary condition. Type 2 renal hyperuricemia (RHUC2) is caused by a mutation in the SLC2A9 gene, which encodes a high-capacity glucose and urate transporter, glucose transporter (GLUT)9. RHUC2 predisposes to exercise-induced acute renal failure (EIARF) and nephrolithiasis, which is caused by a defect in renal tubular urate transport and is characterized by increased clearance of renal uric acid. In the present study a case of a 35-year-old Chinese man with EIARF is reported. The patient had isolated renal hypouricemia, with a serum uric acid level of 21 µmol/l and a fractional excretion of uric acid of 200%. The mutational analysis revealed a homozygous mutation (c.857G>A in exon 8) in the SLC2A9 gene. The patient's family members carried the same mutation, but were heterozygous and clinically asymptomatic. In conclusion, to the best of our knowledge, this is the first report of a RHUC2 patient with a GLUT9 mutation, p.W286X, which may be a pathogenic mutation of RHUC2. Further investigation into the functional role of GLUT9 in this novel SLC2A9 mutation is required.

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at ., This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.

To investigate the efficacy of non-tranexamic acid (TXA) on reducing blood loss and requirements of allogeneic blood transfusion (ABT) in total knee arthroplasty (TKA). The PubMed, EMBASE, and the Cochrane Library databases were researched since incipiency to June 2018. Only randomized controlled trials (RCTs) involved with non-TXA hemostatic techniques in TKA met the inclusion criteria. A total of 36 RCTs, including 1511 patients, were recruited for analysis. The results of subgroup analysis revealed that hemostatic techniques, which could substantially decrease the rate of ABT, were cell salvage with the transfusion trigger of 9 mg/dl, fibrin sealant with a dosage of 10 ml, and postoperative flexion position. The available evidence in this meta-analysis suggests that postoperative flexion position, fibrin sealant, and cell salvage can substantially decrease the rate of ABT in TKA. Further studies, including more hemostatic methods and high-quality research, are expected.

BACKGROUND Trochlear dysplasia is an important pathological factor in patellofemoral instability. Quantitative evaluation of the severity of trochlear dysplasia is rare and remains unclear. MATERIAL AND METHODS Computed tomography (CT) data on 136 knees (95 patients) with trochlear dysplasia in the case group and an age- and sex-matched cohort of 120 knees (70 patients) in the control group were collected for this retrospective study. All participants had undergone CT scans in the supine position. The trochlear angles (TA) formed by the posterior condylar line and the trochlear line were calculated and compared. The threshold for statistical significance was set at p

Objective: The double-bundle (DB) techniques are considered to yield better stability of the knee compared with single-bundle (SB) for anterior cruciate ligament (ACL) reconstruction. However, most studies followed up patients in short to middle-term within 5 years, and the longer-term efficacy of SB and DB ACL reconstruction is still beyond consensus. The purpose of this meta-analysis is to compare the longer-term efficacy between double-bundle (DB) and single-bundle (SB) techniques. Methods: PubMed, EMBASE, and Cochrane Library databases were searched for relevant articles published up to November, 2017 with an English language restriction. The searches were limited to human subjects and randomized controlled trials (RCTs). In addition, the reference lists of identified articles were checked manually to avoid missing other potentially eligible studies. This process was performed iteratively until no additional articles could be included. The quality of the included studies was assessed using The Cochrane Collaboration's risk of bias tool. All statistical analyses were performed with Review Manager soft-ware. Results: A total of five RCTs involving 294 patients were included finally. No studies were excluded due to insufficient data or low quality. The pooled results showed no statistically significant difference between SB and double bundle DB reconstructions for Lysholm, IKDC, pivot shift, KT scores, and the development of osteoarthritis at a minimum of 5 years. No significant heterogeneity was found across all outcomes. Conclusion: The best available evidence demonstrated that SB and DB techniques could yield similar efficacy for ACL reconstruction. And no superiority was founded in DB ACL reconstruction with a minimal 5-year follow-up. Given that, the relatively simple and proven techniques of SB ACL reconstruction may be preferable for orthopedic surgeons.Level of evidence: Level I, Therapeutic Study. Keywords: Anterior cruciate ligament, Reconstruction, Single bundle, Double bundle

Identifying protein functional sites (PFSs) and, particularly, the physicochemical interactions at these sites is critical to understanding protein functions and the biochemical reactions involved. Several knowledge-based methods have been developed for the prediction of PFSs; however, accurate methods for predicting the physicochemical interactions associated with PFSs are still lacking. In this paper, we present a sequence-based method for the prediction of physicochemical interactions at PFSs. The method is based on a functional site and physicochemical interaction-annotated domain profile database, called fiDPD, which was built using protein domains found in the Protein Data Bank. This method was applied to 13 target proteins from the very recent Critical Assessment of Structure Prediction (CASP10/11), and our calculations gave a Matthews correlation coefficient (MCC) value of 0.66 for PFS prediction and an 80% recall in the prediction of the associated physicochemical interactions. Our results show that, in addition to the PFSs, the physical interactions at these sites are also conserved in the evolution of proteins. This work provides a valuable sequence-based tool for rational drug design and side-effect assessment. The method is freely available and can be accessed at http://202.119.249.49 .

Background Intron retention (IR), the most prevalent alternative splicing form in plants, plays a critical role in gene expression during plant development and stress response. However, the molecular mechanisms underlying IR regulation remain largely unknown. Results Knockdown of SDG725, a histone H3 lysine 36 (H3K36)-specific methyltransferase in rice, leads to alterations of IR in more than 4700 genes. Surprisingly, IR events are globally increased at the 5′ region but decreased at the 3′ region of the gene body in the SDG725-knockdown mutant. Chromatin immunoprecipitation sequencing analyses reveal that SDG725 depletion results in a genome-wide increase of the H3K36 mono-methylation (H3K36me1) but, unexpectedly, promoter-proximal shifts of H3K36 di- and tri-methylation (H3K36me2 and H3K36me3). Consistent with the results in animals, the levels of H3K36me1/me2/me3 in rice positively correlate with gene expression levels, whereas shifts of H3K36me2/me3 coincide with position-specific alterations of IR. We find that either H3K36me2 or H3K36me3 alone contributes to the positional change of IR caused by SDG725 knockdown, although IR shift is more significant when both H3K36me2 and H3K36me3 modifications are simultaneously shifted. Conclusions Our results revealed that SDG725 modulates IR in a position-specific manner, indicating that H3K36 methylation plays a role in RNA splicing, probably by marking the retained introns in plants. Electronic supplementary material The online version of this article (10.1186/s12915-018-0513-8) contains supplementary material, which is available to authorized users.

Cellular senescence has been viewed as a tumor suppression mechanism and also as a contributor to individual aging. Widespread shortening of 3′ untranslated regions (3′ UTRs) in messenger RNAs (mRNAs) by alternative polyadenylation (APA) has recently been discovered in cancer cells. However, the role of APA in the process of cellular senescence remains elusive. Here, we found that hundreds of genes in senescent cells tended to use distal poly(A) (pA) sites, leading to a global lengthening of 3′ UTRs and reduced gene expression. Genes that harbor longer 3′ UTRs in senescent cells were enriched in senescence-related pathways. Rras2, a member of the Ras superfamily that participates in multiple signal transduction pathways, preferred longer 3′ UTR usage and exhibited decreased expression in senescent cells. Depletion of Rras2 promoted senescence, while rescue of Rras2 reversed senescence-associated phenotypes. Mechanistically, splicing factor TRA2B bound to a core “AGAA” motif located in the alternative 3′ UTR of Rras2, thereby reducing the RRAS2 protein level and causing senescence. Both proximal and distal poly(A) signals showed strong sequence conservation, highlighting the vital role of APA regulation during evolution. Our results revealed APA as a novel mechanism in regulating cellular senescence.

Objective To describe the prevalence and severity of diabetic retinopathy (DR) and sight-threatening DR (STDR) among Chinese adults with diabetes. Design, setting and participants A cross-sectional epidemiological survey across Mainland China (N=13 473). Participants were diagnosed with diabetes mellitus by physicians and transferred to our screening clinics (1/3 from hospital patients, 1/3 from city residents, the other 1/3 from rural residents). 2 fundus photographs were taken of each eye with a colourful, non-mydriatic and non-stereoscopic camera and were graded according to the UK guidelines. Main outcomes and measures The prevalence and severity of DR and STDR. Results Of the 13 473 participants with diabetes participating in the study, 4591 had DR and 1769 had STDR, for an overall prevalence of 34.08% (95% CI 33.28% to 34.88%) and 13.13% (95% CI 12.56% to 13.70%), respectively. Among these, gradable photographs were available for 12 780 participants (94.86%). Participants who were aged >65 years were less likely to suffer from DR or STDR (p0.05). Participants with STDR suffered from more severe visual impairment compared with those without STDR (p

We generalize the cryptographic notion of Order Revealing Encryption (ORE) to arbitrary functions and we present a construction that allows to determine the (partial) ordering of two vectors i.e., given \(E(\varvec{x})\) and \(E(\varvec{y})\) it is possible to learn whether \(\varvec{x}=\varvec{y}\), \(\varvec{x}>\varvec{y}\), \(\varvec{x}

We describe the identification and characterization of novel homing endonucleases using genome database mining to identify putative target sites, followed by high throughput activity screening in a bacterial selection system. We characterized the substrate specificity and kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The endonuclease specificities revealed by these experiments can be partially recapitulated using 3D structure-based computational models. Analysis of these models together with genome sequence data provide insights into how alternative endonuclease specificities were generated during natural evolution.

SummaryBecause apoptosis of infected cells can limit virus production and spread, some viruses have co-opted prosurvival genes from the host. This includes the Epstein-Barr virus (EBV) gene BHRF1, a homolog of human Bcl-2 proteins that block apoptosis and are associated with cancer. Computational design and experimental optimization were used to generate a novel protein called BINDI that binds BHRF1 with picomolar affinity. BINDI recognizes the hydrophobic cleft of BHRF1 in a manner similar to other Bcl-2 protein interactions but makes many additional contacts to achieve exceptional affinity and specificity. BINDI induces apoptosis in EBV-infected cancer lines, and when delivered with an antibody-targeted intracellular delivery carrier, BINDI suppressed tumor growth and extended survival in a xenograft disease model of EBV-positive human lymphoma. High-specificity-designed proteins that selectively kill target cells may provide an advantage over the toxic compounds used in current generation antibody-drug conjugates.

Cucurbitacin IIa (CuIIa), a tetracyclic triterpenoid harboring anticancer activity, was investigated in A549 cells to reveal its mechanism of targeting on epidermal growth factor receptor (EGFR) signaling pathway. Results showed that CuIIa was capable of inducing apoptosis and cell cycle arrest at G2/M phase. The transcription of EGFR pathway genes and their proteins accumulation was inconsistently influenced by CuIIa. Notably, transcription of Raf1 was significantly upregulated, nevertheless, MEK1 and ERK1 were significantly downregulated. On the other hand, the accumulation of the total and phosphorylated proteins of the most members in EGFR-mitogen-activated protein kinase (MAPK) pathway, as well as CylclinB1 and survivin were also shifted by CuIIa treatment. Remarkably, total MEK remained constant but survivin completely degraded. Moreover, phosphorylated BRAF continuously increased while Raf1 and MEK decreased continuously. CuIIa was further confirmed to be a tyrosine kinase inhibitor (TKI) of EGFR by kinase inhibition assay. The results of molecular simulation showed that the long side chain of CuIIa occupied the binding pocket of EGFR and the ligand was stabilized at the active site of EGFR. In view of the results above, it is suggested that CuIIa inhibits cell proliferation by interfering the EGFR-MAPK signaling pathway.

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3–4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps. DOI: http://dx.doi.org/10.7554/eLife.17219.001

Predicting the outcome of engineered and naturally occurring sequence perturbations to protein-DNA interfaces requires accurate computational modeling technologies. It has been well established that computational design to accommodate small numbers of DNA target site substitutions is possible. This chapter details the basic method of design used in the Rosetta macromolecular modeling program that has been successfully used to modulate the specificity of DNA-binding proteins. More recently, combining computational design and directed evolution has become a common approach for increasing the success rate of protein engineering projects. The power of such high-throughput screening depends on computational methods producing multiple potential solutions. Therefore, this chapter describes several protocols for increasing the diversity of designed output. Lastly, we describe an approach for building comparative models of protein-DNA complexes in order to utilize information from homologous sequences. These models can be used to explore how nature modulates specificity of protein-DNA interfaces and potentially can even be used as starting templates for further engineering.

SummaryWe describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%.