DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function

MOTIVATION

Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there is a need for further improvements in the quality of detailed structures, such as side-chains, along with protein backbone structures.

RESULTS

Building upon the successes of AlphaFold2, the modifications we made include changing the losses of side-chain torsion angles and frame aligned point error, adding loss functions for side chain confidence and secondary structure prediction, and replacing template feature generation with a new alignment method based on conditional random fields. We also performed re-optimization by conformational space annealing using a molecular mechanics energy function which integrates the potential energies obtained from distogram and side-chain prediction. In the CASP15 blind test for single protein and domain modeling (109 domains), DeepFold ranked fourth among 132 groups with improvements in the details of the structure in terms of backbone, side-chain, and Molprobity. In terms of protein backbone accuracy, DeepFold achieved a median GDT-TS score of 88.64 compared with 85.88 of AlphaFold2. For TBM-easy/hard targets, DeepFold ranked at the top based on Z-scores for GDT-TS. This shows its practical value to the structural biology community, which demands highly accurate structures. In addition, a thorough analysis of 55 domains from 39 targets with publicly available structures indicates that DeepFold shows superior side-chain accuracy and Molprobity scores among the top-performing groups.

AVAILABILITY AND IMPLEMENTATION

DeepFold tools are open-source software available at https://github.com/newtonjoo/deepfold.

AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders

BACKGROUND

Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evolution of ligands by exponential enrichment (SELEX) method is a critical in vitro technique employed to identify aptamers that bind specifically to target proteins. While advanced SELEX-based methods such as Cell- and HT-SELEX are available, they often encounter issues such as extended time consumption and suboptimal accuracy. Several In silico aptamer discovery methods have been proposed to address these challenges. These methods are specifically designed to predict aptamer-protein interaction (API) using benchmark datasets. However, these methods often fail to consider the physicochemical interactions between aptamers and proteins within tertiary structures.

RESULTS

In this study, we propose AptaTrans, a pipeline for predicting API using deep learning techniques. AptaTrans uses transformer-based encoders to handle aptamer and protein sequences at the monomer level. Furthermore, pretrained encoders are utilized for the structural representation. After validation with a benchmark dataset, AptaTrans has been integrated into a comprehensive toolset. This pipeline synergistically combines with Apta-MCTS, a generative algorithm for recommending aptamer candidates.

CONCLUSION

The results show that AptaTrans outperforms existing models for predicting API, and the efficacy of the AptaTrans pipeline has been confirmed through various experimental tools. We expect AptaTrans will enhance the cost-effectiveness and efficiency of SELEX in drug discovery. The source code and benchmark dataset for AptaTrans are available at https://github.com/pnumlb/AptaTrans .

Intra-Operative Radiotherapy (IORT) in Breast Conserving Therapy in Early-Stage Breast Cancer and DCIS

PURPOSE/OBJECTIVE(S)

Initial breast intra-operative radiotherapy (IORT) results in clinical trials were encouraging though with longer follow up, increased local recurrences have been reported compared with whole breast radiation or other partial breast radiation including accelerated partial breast irradiation (APBI) methods. The goal of the study is to report our prospective single institution IORT breast study outcomes of local recurrence (LR) including true recurrence and breast elsewhere failures, breast cancer specific survival (BCSS), and overall survival (OS) with low energy x-ray IORT in early-stage breast cancer or ductal carcinoma in situ.

MATERIALS/METHODS

A total of 480 patients with early-stage breast cancer or DCIS were prospectively enrolled in an IRB approved single institution trial and treated with low energy X-ray IORT 20 Gy at time of breast-conserving surgery. Eligibility criteria included ≥ 45 years of age with unifocal tumors < 3 cm deemed candidates for partial mastectomy. Supplemental external beam radiation was recommended for patients with high-risk surgical pathology including multifocal disease, positive nodes, close margins < 2 mm, or lymphovascular invasion. Ipsilateral breast tumor recurrences were classified as true recurrence versus elsewhere failure by location and histology: same/different quadrant and similar/different histology. Kaplan-Meier methods were used to estimate survival probabilities across time.

RESULTS

Median age of enrolled patients was 64 years with the majority of patients having favorable phenotype with 94% ER+ and 93% Her-2 - disease. 110 patients (23%) had supplemental EBRT delivered; 103 to the whole breast and 7 to the breast and regional nodes. At a median follow up of 73 months (range 17 - 131 months), there were 23 (4.8%) ipsilateral breast tumor recurrences, of which 9 were true recurrences (1.9%) and 14 elsewhere failures (2.9%). One patient with true recurrence and 3 patients with elsewhere breast failures synchronously presented with clinical or radiographic regional node involvement. Seven patient developed contralateral breast cancer and 8 patients developed distant metastases during the follow-up period. There were 2 breast cancer related deaths. At 6-years, overall survival rate was 96.8% and breast cancer specific survival was 98.7%.

CONCLUSION

Our study outcomes reflect similar outcomes as other reported IORT studies with electron or low energy X-ray in breast cancer, with higher risk of local failure than historical whole breast and other partial breast radiation techniques. This supports current radiation society guidelines for IORT monotherapy for breast cancer to be optimally considered in the context of prospective clinical trials.

A Novel MR Imaging Sequence of 3D-ZOOMit Real Inversion-Recovery Imaging Improves Endolymphatic Hydrops Detection in Patients with Ménière Disease

BACKGROUND AND PURPOSE

The detection rate of premortem MR imaging endolymphatic hydrops is lower than that of postmortem endolymphatic hydrops in Ménière disease, indicating that current MR imaging techniques may underestimate endolymphatic hydrops. Therefore, we prospectively investigated whether a novel high-resolution MR imaging technique, the 3D zoomed imaging technique with parallel transmission real inversion-recovery (3D-ZOOMit real IR), would improve the detection of endolymphatic hydrops compared with conventional 3D TSE inversion-recovery with real reconstruction.

MATERIALS AND METHODS

Fifty patients with definite unilateral Ménière disease were enrolled and underwent 3D-ZOOMit real IR and 3D TSE inversion-recovery with real reconstruction 6 hours after IV gadolinium injection. The endo- and perilymph spaces were scored separately. The contrast-to-noise ratio, SNR, and signal intensity ratio of the 2 sequences were respectively calculated and compared. The presence of endolymphatic hydrops was evaluated.

RESULTS

The endolymphatic space in the cochlea and vestibule was better visualized with 3D-ZOOMit real IR than with conventional 3D TSE inversion-recovery with real reconstruction (P < .001). There were differences between the 2 sequences in the evaluation of no cochlear hydrops and cochlear hydrops (both, P < .017). All contrast-to-noise ratio, SNR, and signal intensity ratio values of 3D-ZOOMit real IR images were statistically higher than those of conventional 3D TSE inversion-recovery with real reconstruction (all, P < .001).

CONCLUSIONS

The 3D-ZOOMit real IR sequences are superior to conventional 3D TSE inversion-recovery with real reconstruction sequences in visualizing the endolymphatic space, detecting endolymphatic hydrops, and discovering contrast permeability.

BACH1 regulates the proliferation and odontoblastic differentiation of human dental pulp stem cells

Background

The preservation of biological and physiological vitality as well as the formation of dentin are among the main tasks of human dental pulp for a life time. Odontoblastic differentiation of human dental pulp stem cells (hDPSCs) exhibits the capacity of dental pulp regeneration and dentin complex rebuilding. Exploration of the mechanisms regulating differentiation and proliferation of hDPSCs may help to investigate potential clinical applications. BTB and CNC homology 1 (BACH1) is a transcription repressor engaged in the regulation of multiple cellular functions. This study aimed to investigate the effects of BACH1 on the proliferation and odontoblastic differentiation of hDPSCs in vitro.

Methods

hDPSCs and pulpal tissues were obtained from extracted human premolars or third molars. The distribution of BACH1 was detected by immunohistochemistry. The mRNA and protein expression of BACH1 were examined by qRT-PCR and Western blot analysis. BACH1 expression was regulated by stable lentivirus-mediated transfection. Cell proliferation and cell cycle were assessed by cell counting kit-8 assay, 5-Ethynyl-2'-deoxyuridine assay and flow cytometry. The expression of mineralization markers, alkaline phosphatase (ALP) activity and alizarin red S staining were conducted to assess the odontoblastic differentiation ability.

Results

BACH1 expression was stronger in the odontoblast layer than in the cell rich zone. The total and nuclear protein level of BACH1 during odontoblastic differentiation was downregulated initially and then upregulated gradually. Knockdown of BACH1 greatly inhibited cell proliferation, arrested cell cycle, upregulated the heme oxygenase-1 (HO-1) expression and attenuated ALP activity, decreased calcium deposits and downregulated the expression of mineralization markers. Treatment of Tin-protoporphyrin IX, an HO-1 inhibitor, failed to rescue the impaired odonto/osteogenic differentiation capacity. Overexpression of BACH1 increased cell proliferation, ALP activity and the expression of mineralization markers.

Conclusions

Our findings suggest that BACH1 is an important regulator of the proliferation and odontoblastic differentiation of hDPSCs in vitro. Manipulation of BACH1 expression may provide an opportunity to promote the regenerative capacity of hDPSCs.

FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model

MOTIVATION

Over the past decades, vast amounts of genome sequencing data have been produced, requiring an enormous level of storage capacity. The time and resources needed to store and transfer such data cause bottlenecks in genome sequencing analysis. To resolve this issue, various compression techniques have been proposed to reduce the size of original FASTQ raw sequencing data, but these remain suboptimal. Long-read sequencing has become dominant in genomics, whereas most existing compression methods focus on short-read sequencing only.

RESULTS

We designed a compression algorithm based on read reordering using a novel scoring model for reducing FASTQ file size with no information loss. We integrated all data processing steps into a software package called FastqCLS and provided it as a Docker image for ease of installation and execution to help users easily install and run. We compared our method with existing major FASTQ compression tools using benchmark datasets. We also included new long-read sequencing data in this validation. As a result, FastqCLS outperformed in terms of compression ratios for storing long-read sequencing data.

AVAILABILITY AND IMPLEMENTATION

FastqCLS can be downloaded from https://github.com/krlucete/FastqCLS.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

DNN-Boost: Somatic mutation identification of tumor-only whole-exome sequencing data using deep neural network and XGBoost

Detection of somatic mutation in whole-exome sequencing data can help elucidate the mechanism of tumor progression. Most computational approaches require exome sequencing for both tumor and normal samples. However, it is more common to sequence exomes for tumor samples only without the paired normal samples. To include these types of data for extensive studies on the process of tumorigenesis, it is necessary to develop an approach for identifying somatic mutations using tumor exome sequencing data only. In this study, we designed a machine learning approach using Deep Neural Network (DNN) and XGBoost to identify somatic mutations in tumor-only exome sequencing data and we integrated this into a pipeline called DNN-Boost. The XGBoost algorithm is used to extract the features from the results of variant callers and these features are then fed into the DNN model as input. The XGBoost algorithm resolves issues of missing values and overfitting. We evaluated our proposed model and compared its performance with other existing benchmark methods. We noted that the DNN-Boost classification model outperformed the benchmark method in classifying somatic mutations from paired tumor-normal exome data and tumor-only exome data.

[The Mongolian physicians in the Chuo Ban Chu of the Shang Si Yuan in the Qing Dynasty]

The Chuo Ban Chu of Shang Si Yuan in the Qing Dynasty was an institution for Mongolian physicians who provided bone injury diagnosis and treatment for the royal family. This paper reports on an examination of the archives at the First Historical Archives of China, where 171 relevant archives were obtained. Based on this data, the paper summarises and verifies the directories of 112 Mongolian physicians, the authenticity and inheritance of 26 of these physicians, and a brief biography of 16 of them in each period of the Qing Dynasty.

Effective Model of Food Allergy in Mice Sensitized with Ovalbumin and Freud's Adjuvant

To better explore the pathophysiology of FA and its therapy, we aimed to establish a simple and practicable FA model with Freund's adjuvant and introduce an easy and reliable laboratory evaluation method for assessment of inflammation in intestinal segments at different anatomical locations. BALB/c mice were sensitized with ovalbumin combined with Freund's adjuvant. Complete Freund's adjuvant was chosen for the first sensitization and two weeks later incomplete Freund's adjuvant was used for a second sensitization. Two weeks later, the sensitized mice were challenged with 50 mg ovalbumin every other day. After the 6 challenge, all mice were assessed for systemic anaphylaxis, and then sacrificed for sample collection. All sensitized mice showed anaphylactic symptoms and markedly increased levels of serum ovalbumin-specific IgE and IgG1. The activity of mast cell protease-1 (mMCPT-1) was significantly increased in the serum and interstitial fluid of the duodenum, jejunum, ileum, and colon. A successful FA model was established, of which inflammation occurred in the duodenum, jejunum, ileum, and colon. This model provides a reliable and simple tool for analysis of the mechanism of FA and methods of immunotherapy. Moreover, combined detection of ovalbumin-specific antibody and local mMCPT-1 levels could potentially be used as the major indicator for assessment of food allergy.

Authentication of differential gene expression in oral squamous cell carcinoma using machine learning applications

BACKGROUND

Recently, the possibility of tumour classification based on genetic data has been investigated. However, genetic datasets are difficult to handle because of their massive size and complexity of manipulation. In the present study, we examined the diagnostic performance of machine learning applications using imaging-based classifications of oral squamous cell carcinoma (OSCC) gene sets.

METHODS

RNA sequencing data from SCC tissues from various sites, including oral, non-oral head and neck, oesophageal, and cervical regions, were downloaded from The Cancer Genome Atlas (TCGA). The feature genes were extracted through a convolutional neural network (CNN) and machine learning, and the performance of each analysis was compared.

RESULTS

The ability of the machine learning analysis to classify OSCC tumours was excellent. However, the tool exhibited poorer performance in discriminating histopathologically dissimilar cancers derived from the same type of tissue than in differentiating cancers of the same histopathologic type with different tissue origins, revealing that the differential gene expression pattern is a more important factor than the histopathologic features for differentiating cancer types.

CONCLUSION

The CNN-based diagnostic model and the visualisation methods using RNA sequencing data were useful for correctly categorising OSCC. The analysis showed differentially expressed genes in multiwise comparisons of various types of SCCs, such as KCNA10, FOSL2, and PRDM16, and extracted leader genes from pairwise comparisons were FGF20, DLC1, and ZNF705D.

[Effects of interpregnancy interval on pregnancy outcomes of subsequent pregnancy: a multicenter retrospective study]

Objective: To explore the effects of interpregnancy interval (IPI) on pregnancy outcomes of subsequent pregnancy. Methods: A multicenter retrospective study was conducted in 21 hospitals in China. Information of age, height, pre-pregnancy weight, IPI, history of diseases, complications of pregnancy, gestational age of delivery, delivery mode, and pregnancy outcomes of the participants were collected by consulting medical records of pregnant women who had two consecutive deliveries in the same hospital during 2011 to 2018. The participants were divided into 4 groups according to IPI:<18 months, 18-23 months, 24-59 months and ≥60 months. According to the WHO's recommendation, with the IPI of 24-59 months group as a reference, to the effects of IPI on pregnancy outcomes of subsequent pregnancy were analyzed. Stratified analysis was further carried out based on age, history of gestational diabetes mellitus (GDM), macrosomia, and premature delivery, to explore the differences in the effects of IPI on pregnancy outcomes among women with different characteristics. Results: A total of 8 026 women were included in this study. There were 423, 623, 5 512 and 1 468 participants in <18 months group, 18-23 months group, 24-59 months group and ≥60 months group, respectively. (1) The age, pre-pregnancy body mass index (BMI), history of cesarean section, GDM, gestational hypertension and cesarean section delivery rate of <18 months group, 18-23 months group, 24-59 months group and ≥60 months group were gradually increased, and the differences were statistically significant (P<0.05). (2) After adjusting for potential confounding factors, compared with women in the IPI of 24-59 months group, the risk of premature delivery, premature rupture of membranes, and oligohydramnios were increased by 42% (OR=1.42, 95%CI: 1.07-1.88, P=0.015), 46% (OR=1.46, 95%CI: 1.13-1.88, P=0.004), and 64% (OR=1.64, 95%CI: 1.13-2.38, P=0.009) respectively for women in the IPI≥60 months group. No effects of IPI on other pregnancy outcomes were found in this study (P>0.05). (3) After stratified by age and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months would significantly increase the risk of oligohydramnios for women with advanced age (OR=2.87, 95%CI: 1.41-5.83, P=0.004); and <18 months could increase the risk of premature rupture of membranes for women under the age of 35 (OR=1.59, 95%CI: 1.04-2.43, P=0.032). Both the risk of premature rupture of membranes (OR=1.58, 95%CI: 1.18-2.13, P=0.002) and premature delivery (OR=1.52, 95%CI: 1.07-2.17, P=0.020) were significantly increased in the IPI≥60 months group. After stratified by history of GDM and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months would lead to an increased risk of postpartum hemorrhage for women with a history of GDM (OR=5.34, 95%CI: 1.45-19.70, P=0.012) and an increased risk of premature rupture of membranes for women without a history of GDM (OR=1.44, 95%CI: 1.10-1.90, P=0.009). After stratified by history of macrosomia and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months could increase the proportion of cesarean section for women with a history of macrosomia (OR=4.11, 95%CI: 1.18-14.27, P=0.026) and the risk of premature rupture of membranes for women without a history of macrosomia (OR=1.46, 95%CI: 1.12-1.89, P=0.005). After stratified by history of premature delivery and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months would significantly increase the risk of premature rupture of membranes for women without a history of premature delivery (OR=1.47, 95%CI: 1.13-1.92, P=0.004). Conclusions: Both IPI≥60 months and <18 months would increase the risk of adverse pregnancy outcomes in the subsequent pregnancy. Healthcare education and consultation should be conducted for women of reproductive age to maintain an appropriate IPI when they plan to pregnant again, to reduce the risk of adverse pregnancy outcomes in the subsequent pregnancy.

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

BACKGROUND

Macaque species share >93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g., HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort.

RESULTS

To close this gap and enhance functional genomics approaches, we used a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells derived from the same animal. Reconstruction of the evolutionary tree using whole-genome annotation and orthologous comparisons among 3 macaque species, human, and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques.

CONCLUSIONS

These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection

ChIP-seq is one of the core experimental resources available to understand genome-wide epigenetic interactions and identify the functional elements associated with diseases. The analysis of ChIP-seq data is important but poses a difficult computational challenge, due to the presence of irregular noise and bias on various levels. Although many peak-calling methods have been developed, the current computational tools still require, in some cases, human manual inspection using data visualization. However, the huge volumes of ChIP-seq data make it almost impossible for human researchers to manually uncover all the peaks. Recently developed convolutional neural networks (CNN), which are capable of achieving human-like classification accuracy, can be applied to this challenging problem. In this study, we design a novel supervised learning approach for identifying ChIP-seq peaks using CNNs, and integrate it into a software pipeline called CNN-Peaks. We use data labeled by human researchers who annotate the presence or absence of peaks in some genomic segments, as training data for our model. The trained model is then applied to predict peaks in previously unseen genomic segments from multiple ChIP-seq datasets including benchmark datasets commonly used for validation of peak calling methods. We observe a performance superior to that of previous methods.

Pregnancy outcomes after a mass vaccination campaign with an oral cholera vaccine: a systematic review and meta-analysis

BACKGROUND

Cholera has harmful effects on the fetus but safety data on the oral cholera vaccine in pregnant women are controversial.

OBJECTIVES

We conducted the first meta-analysis of studies in pregnant women comparing the effect of oral cholera vaccination on pregnancy outcomes with unvaccinated women. Outcomes of interest were adverse pregnancy outcome, miscarriage, stillbirth, preterm delivery, low birthweight, abortion and malformation.

SEARCH STRATEGY

The search was run in MEDLINE/PubMed, SCOPUS and Embase databases from inception up to December 2019.

SELECTION CRITERIA

Inclusion criteria were: (1) studies that investigated the association between oral cholera vaccines and adverse pregnancy outcomes; (2) studies that reported outcomes with appropriate estimates; and (3) studies that contained an unvaccinated control group.

DATA COLLECTION AND ANALYSIS

A random-effects model (DerSimonian and Laird) was run to evaluate the overall treatment effect (relative risk, RR). The PRISMA statement was followed in reporting this meta-analysis.

MAIN RESULTS

Five studies included in meta-analysis with 5584 women (2920 exposed and 2664 not exposed). No significant increase in adverse pregnancy outcome (RR 1.03, 95% CI 0.79-1.34), miscarriage (RR 1.15, 95% CI 0.84-1.57) or stillbirth (RR 1.11, 95% CI 0.69-1.80) following cholera vaccine administration was found compared with control group. There was also no association with an increased risk of preterm delivery (RR 0.61, 95% CI 0.35-1.06) low birthweight (RR 0.84, 95% CI 0.56- 1.26), accidental abortion (RR 1.02, 95% CI 0.77-1.35) or malformation (RR 0.70, 95% CI 0.22-2.25).

CONCLUSIONS

This study shows no evidence of an association between oral cholera vaccination and adverse pregnancy outcomes. The findings do not rigorously exclude the possibility that the vaccine protocol may result in some degree of harm.

TWEETABLE ABSTRACT

There is no evidence of an association between oral cholera vaccination and adverse pregnancy outcomes. The findings do not rigorously exclude the possibility that the vaccine protocol may result in some degree of harm.

International Nosocomial Infection Control Consortium (INICC) report, data summary of 45 countries for 2012-2017: Device-associated module

BACKGROUND

We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2012 to December 2017 in 523 intensive care units (ICUs) in 45 countries from Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific.

METHODS

During the 6-year study period, prospective data from 532,483 ICU patients hospitalized in 242 hospitals, for an aggregate of 2,197,304 patient days, were collected through the INICC Surveillance Online System (ISOS). The Centers for Disease Control and Prevention-National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI) were applied.

RESULTS

Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the medical-surgical ICUs, the pooled central line-associated bloodstream infection rate was higher (5.05 vs 0.8 per 1,000 central line-days); the ventilator-associated pneumonia rate was also higher (14.1 vs 0.9 per 1,000 ventilator-days,), as well as the rate of catheter-associated urinary tract infection (5.1 vs 1.7 per 1,000 catheter-days). From blood cultures samples, frequencies of resistance, such as of Pseudomonas aeruginosa to piperacillin-tazobactam (33.0% vs 18.3%), were also higher.

CONCLUSIONS

Despite a significant trend toward the reduction in INICC ICUs, DA-HAI rates are still much higher compared with CDC-NHSN's ICUs representing the developed world. It is INICC's main goal to provide basic and cost-effective resources, through the INICC Surveillance Online System to tackle the burden of DA-HAIs effectively.

Rapid Identification of Four New Synthetic Cannabinoids in Whole Blood

Objective To establish accurate and rapid methods to identify four new synthetic cannabinoids （JWH-203, JWH-122, 5F-APINACA and AB-CHMINACA） in blood samples. Methods The whole blood samples were extracted by acetonitrile and methanol, screened by gas chromatography-mass spectrometry （GC-MS） then confirmed by liquid chromatography-tandem mass spectrometry （LC-MS/MS） method, and multiple reaction monitoring （MRM） mode was used for quantitative analysis. Results The GC-MS method needed 21 min to complete the analysis, while the LC-MS/MS method needed 5 min. The AB-CHMINACA, JWH-203, 5F-APINACA and JWH-122 all used quasi molecular ion peak as a parent ion. The precursor-product ion combinations were m/z 357.4→312.2, m/z 340.2→125.0, m/z 384.1→135.1 and m/z 356.4→169.2. The four synthetic cannabinoids in blood samples had good linearity in the 1-250 ng/mL mass concentration range （r>0.99）. The limits of detection （LODs） were in the range of 0.1-0.5 ng/mL, the recovery rate was 85.4%-95.2%, the RSD less than 10.0%, and the matrix effect was 80.3%-92.8%. Conclusion The GC-MS and LC-MS/MS chromatographic behaviors and mass spectrometry analysis information of four synthetic cannabinoids were obtained in this study, and the possible causes of differences in chromatographic behaviors were discussed preliminarily. Therefore this study has a suggestive effect on judging the development trend of synthetic cannabinoids. This method can be used for rapid identification of four synthetic cannabinoids in blood, which can provide reference for identification of new synthetic cannabinoids when they are proliferating at present.

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

HepG2 is one of the most widely used human cancer cell lines in biomedical research and one of the main cell lines of ENCODE. Although the functional genomic and epigenomic characteristics of HepG2 are extensively studied, its genome sequence has never been comprehensively analyzed and higher order genomic structural features are largely unknown. The high degree of aneuploidy in HepG2 renders traditional genome variant analysis methods challenging and partially ineffective. Correct and complete interpretation of the extensive functional genomics data from HepG2 requires an understanding of the cell line’s genome sequence and genome structure. Using a variety of sequencing and analysis methods, we identified a wide spectrum of genome characteristics in HepG2: copy numbers of chromosomal segments at high resolution, SNVs and Indels (corrected for aneuploidy), regions with loss of heterozygosity, phased haplotypes extending to entire chromosome arms, retrotransposon insertions and structural variants (SVs) including complex and somatic genomic rearrangements. A large number of SVs were phased, sequence assembled and experimentally validated. We re-analyzed published HepG2 datasets for allele-specific expression and DNA methylation and assembled an allele-specific CRISPR/Cas9 targeting map. We demonstrate how deeper insights into genomic regulatory complexity are gained by adopting a genome-integrated framework.

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

Background

Genomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional and evolutionary genetic studies, including human diseases, such as cancers. Recently, a large number of whole genomes of evolving populations of yeast (Saccharomyces cerevisiae W303 strain) were sequenced in a time-dependent manner to identify temporal evolutionary patterns. For this type of study, a chromosome-level sequence assembly of the strain or population at time zero is required to compare with the genomes derived later. However, there is no fully automated computational approach in experimental evolution studies to establish the chromosome-level genome assembly using unique features of sequencing data.

Methods and results

In this study, we developed a new software pipeline, the integrative meta-assembly pipeline (IMAP), to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data. We significantly improved the continuity and accuracy of the genome assembly using a large collection of sequencing data and hybrid assembly approaches. We validated our pipeline by generating chromosome-level assemblies of yeast strains W303 and SK1, and compared our results with assemblies built using long-read sequencing and various assembly evaluation metrics. We also constructed chromosome-level sequence assemblies of S. cerevisiae strain Sigma1278b, and three commonly used fungal strains: Aspergillus nidulans A713, Neurospora crassa 73, and Thielavia terrestris CBS 492.74, for which long-read sequencing data are not yet available. Finally, we examined the effect of IMAP parameters, such as reference and resolution, on the quality of the final assembly of the yeast strains W303 and SK1.

Conclusions

We developed a cost-effective pipeline to generate chromosome-level sequence assemblies using only short-read sequencing data. Our pipeline combines the strengths of reference-guided and meta-assembly approaches. Our pipeline is available online at http://github.com/jkimlab/IMAP including a Docker image, as well as a Perl script, to help users install the IMAP package, including several prerequisite programs. Users can use IMAP to easily build the chromosome-level assembly for the genome of their interest.

Assessing children's exposure to manganese in drinking water using a PBPK model

A previously published human PBPK model for manganese (Mn) in infants and children has been updated with Mn in drinking water as an additional exposure source. Built upon the ability to capture differences in Mn source-specific regulation of intestinal uptake in nursing infants who are breast-fed and formula-fed, the updated model now describes the bioavailability of Mn from drinking water in children of ages 0-18. The age-related features, including the recommended age-specific Mn dietary intake, age-specific water consumption rates, and age-specific homeostasis of Mn, are based on the available human data and knowledge of the biology of essential-metal homeostasis. Model simulations suggest that the impact of adding drinking-water exposure to daily Mn exposure via dietary intake and ambient air inhalation in children is not greater than the impacts in adults, even at a drinking-water concentration that is 2 times higher than the USEPA's lifetime health advisory value. This conclusion was also valid for formula-fed infants who are considered at the highest potential exposure to Mn from drinking water compared to all other age groups. Our multi-route, multi-source Mn PBPK model for infants and children provides insights about the potential for Mn-related health effects on growing children and will thereby improve the level of confidence in properly interpreting Mn exposure-health effects relationships in children in human epidemiological studies.

Effectiveness of an advanced practice nurse-led delirium education and training programme

AIM

To develop an education and training programme to enhance bedside nurses' knowledge, competency and compliance in accurately performing delirium screening in intensive care units.

BACKGROUND

Delirium in intensive care units is associated with several poor patient outcomes. Delirium detection can be improved by enhancing nurses' knowledge, competency and compliance in accurately performing delirium screening.

METHODS

A descriptive quantitative study with pretest-post-test design was adopted. There were 245 nurses from five intensive care units who participated in the study. Multiple-choice questions were used to assess nurses' knowledge change before and after the education programme. Competency was assessed before and 2 months after the programme by simulation with a standardized patient, followed by real patients at the bedside. Compliance data on screening were collected from the documentation of the Richmond Agitation-Sedation Scale and the Confusion Assessment Method for the ICU before and 3 and 10 months after the programme. Data collection took 1 year, from June 2014 to May 2015.

RESULTS

Despite nurses' improved knowledge and good competency, delirium screening documentations after 3 months were poor. However, screening documentations subsequently improved when measured at 10 months, following further emphasis by the senior nursing staff.

IMPLICATIONS FOR NURSING PRACTICE AND POLICY

Nursing administrators and bedside nurses need to be involved in the policy-making process and plan a training programme for the new nursing staff in the high-risk areas. A short refreshment course should be offered to the nursing staff 3 months after the initial training programme.

CONCLUSIONS

Improved knowledge and competency in assessment did not improve compliance and documentation of delirium screening. Therefore, it is important to reinforce nurses' compliance of delirium screening over time.

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed. Such information is essential for the correct interpretation and understanding of the vast troves of existing functional genomics and epigenomics data for K562. We performed and integrated deep-coverage whole-genome (short-insert), mate-pair, and linked-read sequencing as well as karyotyping and array CGH analysis to identify a wide spectrum of genome characteristics in K562: copy numbers (CN) of aneuploid chromosome segments at high-resolution, SNVs and indels (both corrected for CN in aneuploid regions), loss of heterozygosity, megabase-scale phased haplotypes often spanning entire chromosome arms, structural variants (SVs), including small and large-scale complex SVs and nonreference retrotransposon insertions. Many SVs were phased, assembled, and experimentally validated. We identified multiple allele-specific deletions and duplications within the tumor suppressor gene FHIT. Taking aneuploidy into account, we reanalyzed K562 RNA-seq and whole-genome bisulfite sequencing data for allele-specific expression and allele-specific DNA methylation. We also show examples of how deeper insights into regulatory complexity are gained by integrating genomic variant information and structural context with functional genomics and epigenomics data. Furthermore, using K562 haplotype information, we produced an allele-specific CRISPR targeting map. This comprehensive whole-genome analysis serves as a resource for future studies that utilize K562 as well as a framework for the analysis of other cancer genomes.

A Review of Magnetic Particle Imaging and Perspectives on Neuroimaging

Magnetic particle imaging is an emerging tomographic technique with the potential for simultaneous high-resolution, high-sensitivity, and real-time imaging. Magnetic particle imaging is based on the unique behavior of superparamagnetic iron oxide nanoparticles modeled by the Langevin theory, with the ability to track and quantify nanoparticle concentrations without tissue background noise. It is a promising new imaging technique for multiple applications, including vascular and perfusion imaging, oncology imaging, cell tracking, inflammation imaging, and trauma imaging. In particular, many neuroimaging applications may be enabled and enhanced with magnetic particle imaging. In this review, we will provide an overview of magnetic particle imaging principles and implementation, current applications, promising neuroimaging applications, and practical considerations.

Efficacy of needleless transcutaneous electroacupuncture in synchronization with breathing for symptomatic idiopathic gastroparesis: A blinded and controlled acute treatment trial

BACKGROUND

Needleless transcutaneous electroacupuncture (TEA) improves nausea and myoelectrical activity in diabetic gastroparesis (GP). Synchronized TEA (STEA), which combines synchronized breathing with TEA, is more potent than TEA in enhancing vagal activity in healthy subjects.

AIMS

To investigate whether STEA improves symptoms, electrogastrogram (EGG) and vagal activity in idiopathic gastroparesis (IGP).

METHODS

Eighteen IGP subjects underwent 2 randomized visits (sham at non-acupoints or real STEA at acupoints) consisted of a 30-minute baseline, an Ensure challenge to provoke nausea, followed by 60-minute treatment with sham or real STEA, and 15-minute observation period. Severity of nausea, EGG, and vagal activity (based on electrocardiogram and serum Pancreatic Polypeptide, PP) were recorded.

RESULTS

In sham or STEA, the nausea scores of 2.7 ± 0.5 and 1.9 ± 0.5 at fasting baseline, respectively, increased to 5.9 ± 0.4 and 5.8 ± 0.3 during Ensure test (P < .05, vs baseline), subsequently reduced to 3.4 ± 0.6 with sham or 3.6 ± 0.6 with STEA, respectively (P < .05, vs Ensure period). Experiments with sham and STEA started with similar % of normal waves on EGG (66.4 ± 3.9 and 61.8 ± 3.0, respectively); decreased to 63. 5 ± 4.1 and 58.2 ± 2.8 during the Ensure test. After STEA, there was ~24% increase in % of normal waves, significantly different from the sham (6.0%) (P < .01). In sham or STEA, vagal activity was identical at baseline and after the Ensure. STEA induced a 3-fold increase in vagal activity compared with sham (P < .01). Ensure increased serum PP levels, and both treatments decreased the PP CONCLUSIONS: In IGP, STEA is not superior to Sham in decreasing nausea, but is more effective in improving gastric dysrhythmia.

[Developing a Chinese PI-RADS v2-based nomogram for predicting clinically significant prostate cancer in patients with a prior negative biopsy]

Objective: To develop a nomogram based on prostate imaging reporting and data system version 2 (PI-RADS v2) to predict clinically significant prostate cancer in patients with a prior negative prostate biopsy. Methods: The clinical and pathological data of 231 patients who underwent repeat prostate biopsy and multiparametric MRI (mpMRI) were reviewed. Based on PI-RADS v2, the mpMRI results were assigned as PI-RADS grade from 0 to 2. A Logistic regression nomogram for predicting the probabilities of clinically significant prostate cancer were constructed. The performances of the nomogram were assessed using area under the receiver operating characteristic (ROC) curve, calibrations and decision curve analysis. Results: Of the total 231 repeat prostate biopsy patients, clinically significant prostate cancer was detected in 59 cases(25.5%). In multivariate Logistic regression analysis, age, prostate specific antigen (PSA), prostate volume (PV), digital rectal examination (DRE) and mpMRI results were significant independent predictors of the diagnosis of clinically significant prostate cancer (P<0.05). The nomogram with super predictive accuracy were constructed (AUC=0.927, P<0.001), and exhibited excellent calibration. Decision curve analysis also demonstrated a high net benefit across a wide range of threshold probabilities . Conclusions: PI-RADS v2 combined with age, PSA, PV and DRE can predict the probability of clinically significant prostate cancer in patients with negative initial biopsies. The nomogram generated may help the decision-making process in patients with prior benign histology before the performance of repeat biopsy.

Adiponectin: A prosurvival and proproliferation signal that increases bovine mammary epithelial cell numbers and protects them from endoplasmic reticulum stress responses

Cell-cell interactions between epithelial and stromal cells are predominant in the mammary gland, and various stromal cell-derived factors can elicit mitogenic responses in adjacent epithelial cells. Adiponectin is a hormone secreted mainly by adipocytes that mediates stromal-epithelial interactions in a number of tissues. Adiponectin receptors are expressed by bovine mammary epithelial cells, but the regulatory effects of adiponectin on the development and function of the mammary gland remain unclear. We therefore sought to investigate the effects of adiponectin on bovine mammary epithelial (MAC-T) cells and the regulatory mechanisms that underlie these adiponectin-induced actions. Our results revealed an increase in MAC-T cell proliferation and cell cycle progression in response to adiponectin. The expression of nuclear proliferating cell nuclear antigen (PCNA) and cyclin D1 was induced in MAC-T cells, and intracellular signaling molecules such as serine/threonine protein kinase (AKT), 70 kDa ribosomal S6 kinase (P70S6K), ribosomal protein S6 (S6), extracellular signal-regulated kinases 1 and 2 (ERK1/2), 90 kDa ribosomal S6 kinase (P90S6K), and cyclin D1 were activated in a dose-dependent manner. The abundance of adiponectin-induced signaling proteins was suppressed following inhibition of AKT or ERK1/2 mitogen-activated protein kinase (MAPK) signaling. In addition, inhibition of AKT or ERK1/2 signaling significantly reduced adiponectin-stimulated MAC-T cell proliferation. Furthermore, adiponectin reduced tunicamycin-induced expression and activation of endoplasmic reticulum stress-related proteins in MAC-T cells and attenuated the repressive effect of tunicamycin on proliferation of MAC-T cells. Collectively, these results suggest that adiponectin-mediated signaling may affect the development and function of the mammary gland in dairy cows by increasing mammary epithelial cell numbers. These findings may result in important implications for improving our fundamental understanding of lactation physiology in livestock species.

The functional effects and mechanisms by which fibroblast growth factor 2 (FGF2) controls bovine mammary epithelial cells: Implications for the development and functionality of the bovine mammary gland

Fibroblast growth factor (FGF) signaling plays essential roles in tissue development and homeostasis. Accumulating evidence reveals that fibroblast growth factor 2 (FGF2) regulates ductal elongation, which requires cell proliferation and epithelial expansion in the mammary gland. However, the function and mechanisms by which FGF2 controls functionality of epithelial cells is less well defined. Here, we demonstrate the functional effects of FGF2 on bovine mammary epithelial (MAC-T) cells and the intracellular signaling mechanisms for these FGF2-induced actions. The current results show that treatment of MAC-T cells with a recombinant FGF2 induced cell proliferation and cell-cycle progression with increased expression of proliferating cell nuclear antigen and cyclin D1. Moreover, FGF2 increased phosphorylation of serine/threonine protein kinase (protein kinase B [AKT]), extracellular signal-regulated kinases 1 and 2 (ERK1/2), Jun N-terminal kinase (JNK), 70 kDa ribosomal S6 kinase (P70S6K), 90 kDa ribosomal S6 kinase (P90S6K), ribosomal protein S6 (S6), and cyclin D1 proteins. These FGF2-induced activations of signaling pathway proteins were inhibited by blocking AKT, ERK1/2, or JNK phosphorylation. The effect of FGF2 to stimulate MAC-T cell proliferation was mediated by activation of FGF receptors (FGFR) and AKT, ERK1/2, and JNK mitogen-activated protein kinase pathways in response to FGF2 stimulation. Furthermore, expression and activation of endoplasmic reticulum (ER) stress-related factors and ER stress-induced MAC-T cell death was reduced by FGF2. Together, these results suggest that the FGF2-FGFR-intracellular signaling cascades may contribute to maintaining and/or increasing numbers of mammary epithelial cells by inducing proliferation of mammary epithelial cells and by protecting cells from ER stress responses. Therefore, this study provides evidence that FGF2 signaling is a positive factor for mammary gland remodeling and for increasing persistency of milk production.

Dicer1, AGO3, and AGO4 microRNA machinery genes are differentially expressed in developing female reproductive organs and overexpressed in cancerous ovaries of chickens

MicroRNA (miRNA)-mediated gene silencing is a key mechanism regulating numerous biological processes such as development of organs and tumorigenesis. The expression of miRNA machinery genes linked to miRNA biogenesis and processing is finely regulated. Despite accumulating evidence for chicken miRNA in the female reproduction system, precise regulatory mechanisms are largely unknown. Therefore, the objective of this study was to determine changes in expression levels of miRNA machinery genes in developmental stages of the oviduct and ovarian carcinogenesis of laying hens. In the present study, differential expression of miRNA machinery genes during ovarian carcinogenesis was determined using cancerous and normal ovaries collected from normal laying hens and hens with cancer. Our results showed that 3 miRNA machinery genes (, , and ) were differentially expressed as laying hens' reproductive organs developed. These genes were simultaneously upregulated in cancerous ovaries compared with those in normal ovaries. Their transcripts were abundantly localized in glandular epithelial cells of cancerous ovaries. Our results indicate that , , and play critical roles in the development of reproductive organs and ovarian carcinogenesis in laying hens, suggesting that simultaneous overexpression of these genes might serve as a prognostic factor for ovarian cancer.

Differential expression of neuregulin 1 (NRG1) and candidate miRNA regulating NRG1 transcription in the chicken oviduct in response to hormonal changes

Neuregulin 1 (NRG1), a signaling protein that binds to members of the erythroblastoma (ErbB) family, is known to play essential biological roles in mediating cell-cell interactions and orchestrating vital cell functions in the heart and nervous system. NRG1 is closely associated with developmental processes in various organs and expression of several NRG1 isoforms are regulated by estrogen. However, expression and its hormonal regulation during development of the female reproductive tract remain unknown. The reproductive system of chickens undergoes dynamic morphological and functional changes in response to estrogen and the molting process. Therefore, in the current study, we found differential expression of and candidate microRNA regulating chicken transcription in response to estrogen stimulation and/or the molting process. The results revealed that relative expression of mRNA increased in the oviducts of chicks treated with diesthylstilbestrol (DES; a synthetic non-steroidal estrogen). Additionally, abundant NRG1 mRNA expression was primarily in the glandular (GE) and luminal (LE) epithelia of the magnum in the developing chick oviduct in response to exogenous estrogen. Also, expression decreased during regression of the oviduct following induced molting by feeding high levels of zinc in the diet, and then gradually resurged as the oviduct underwent remodeling and recrudescence in laying hens. In addition, the present results revealed changes in relative expression of candidate chicken microRNA (, and ) targeting transcription in chicken oviducts in response to exogenous estrogen. In conclusion, these results provide the first evidence that is a novel estrogen-responsive gene closely correlated with the estrogen-dependent development of the oviduct of chicks and regeneration of the oviduct after molting. Further, regulation of expression involving at least 3 chicken miRNA is likely a prerequisite for those estrogen regulated developmental events.

[Development of a Chinese nomogram based on muti-parametric magnetic resonance for predicting the probability of prostate cancer in patients after initial negative biopsy]

Objective: To develop a predictive nomogram based on multi-parametric magnetic resonance imaging (mpMRI) information to identify men more likely to have a cancer diagnosed on repeat prostate biopsy. Methods: The clinical data of 237 patients who received repeat prostate biopsy after initial negative biopsy from Department of Urology of Peking University First Hospital between January 2001 and August 2016 was reviewed. Patient age, body mass index (BMI), serum total prostate-specific antigen (PSA), percent free PSA (f/t), prostate volume (PV), PSA density (PSAD), PSA velocity (PSAV), digital rectal examination (DRE), transrectal ultrasound (TRUS)and mpMRI results were included in the univariate and multivariate analysis. A nomogram was developed using selected variables and the area under the receiver operating characteristic (ROC) curve was calculated as a measure of discrimination. Results: A total of 76 patients (32.07%) had prostate cancer (PCa) detected on repeat biopsy. Based on univariate and multivariate logistic regression analysis, the patient age, PSA, PV, DRE and mpMRI results were independent predictors for the diagnosis of PCa on repeat biopsy. The current nomogram performed well (AUC=0.910) and showed excellent calibration. Conclusions: Multi-parametric magnetic resonance imaging combined with age, PSA, PV and DRE can predict the probability of PCa in patients with initial negative biopsy. The nomogram might help in decision-making for men with prior benign histology before the performance of repeat biopsy.