Secure multiparty computation for privacy-preserving drug discovery

Motivation

Quantitative structure–activity relationship (QSAR) and drug–target interaction (DTI) prediction are both commonly used in drug discovery. Collaboration among pharmaceutical institutions can lead to better performance in both QSAR and DTI prediction. However, the drug-related data privacy and intellectual property issues have become a noticeable hindrance for inter-institutional collaboration in drug discovery.

Results

We have developed two novel algorithms under secure multiparty computation (MPC), including QSARMPC and DTIMPC, which enable pharmaceutical institutions to achieve high-quality collaboration to advance drug discovery without divulging private drug-related information. QSARMPC, a neural network model under MPC, displays good scalability and performance and is feasible for privacy-preserving collaboration on large-scale QSAR prediction. DTIMPC integrates drug-related heterogeneous network data and accurately predicts novel DTIs, while keeping the drug information confidential. Under several experimental settings that reflect the situations in real drug discovery scenarios, we have demonstrated that DTIMPC possesses significant performance improvement over the baseline methods, generates novel DTI predictions with supporting evidence from the literature and shows the feasible scalability to handle growing DTI data. All these results indicate that QSARMPC and DTIMPC can provide practically useful tools for advancing privacy-preserving drug discovery.

Availability and implementation

The source codes of QSARMPC and DTIMPC are available on the GitHub: https://github.com/rongma6/QSARMPC_DTIMPC.git.

Supplementary information

Supplementary data are available at Bioinformatics online.

ACME: pan-specific peptide–MHC class I binding prediction through attention-based deep neural networks

Motivation

Prediction of peptide binding to the major histocompatibility complex (MHC) plays a vital role in the development of therapeutic vaccines for the treatment of cancer. Algorithms with improved correlations between predicted and actual binding affinities are needed to increase precision and reduce the number of false positive predictions.

Results

We present ACME (Attention-based Convolutional neural networks for MHC Epitope binding prediction), a new pan-specific algorithm to accurately predict the binding affinities between peptides and MHC class I molecules, even for those new alleles that are not seen in the training data. Extensive tests have demonstrated that ACME can significantly outperform other state-of-the-art prediction methods with an increase of the Pearson correlation coefficient between predicted and measured binding affinities by up to 23 percentage points. In addition, its ability to identify strong-binding peptides has been experimentally validated. Moreover, by integrating the convolutional neural network with attention mechanism, ACME is able to extract interpretable patterns that can provide useful and detailed insights into the binding preferences between peptides and their MHC partners. All these results have demonstrated that ACME can provide a powerful and practically useful tool for the studies of peptide–MHC class I interactions.

Availability and implementation

ACME is available as an open source software at https://github.com/HYsxe/ACME.

Supplementary information

Supplementary data are available at Bioinformatics online.

[Shang Zhijun, a famous contemporary philogist in herbal literature research]

Mr. Shang is a famous herbalist in contemporary China and he devoted his life to the research of herbal literatures. During his lifetime, he has compiled and published a total 19 herbal literatures, 33 works of herbal literature, 268 academic papers, and more than 20 million words of handwritten herbal transcripts. In the field of herbal literature research, he has achieved fruitful results that are highly recognized by the academic communities. The research results can be roughly summarized as four aspects: the establishment of a two-line research network of herbal formulae, the research and collection of lost herbal works, the collation of the survived ancient herbal works and the textual research of famous herbal works. Many of his research results on herbal literature have been included in the modern higher education professional textbooks, and his outstanding academic achievements have opened the door for later scholars, influencing many scholars both home and abroad.

[Probe of the compiling stylistic rules and layout of Youyou Xin Shu]

Youyou Xin Shu(The New Book on Juveniles)《》is a great book of pediatrics in the Southern Song Dynasty. The book quotes a lot of literature.This paper makes an overall arrangement of the citation, sums up the features of the books cited, corrects some wrong compilations from different texts in various existing versions. Therefore, we can infer the publishing ages and time of some literature related.

Laboratory comparison of two Aphelinus mali clades for control of woolly apple aphid from Hebei Province, China

Aphelinus mali (Haldeman) is an effective natural enemy of woolly apple aphid (WAA), Eriosoma lanigerum (Hausmann). Previous studies have found that, with WAA from Shandong Province (Qingdao) as the host, there are significant differences in various biological characteristics between a Shandong clade and Liaoning clade of A. mali. The ability of the Shandong clade to control this aphid was significantly higher than that of the Liaoning clade in Shandong Province. In order to determine whether differences were caused by better adaptation of the Shandong parasitoid clade to the population of the host in that province or if it represents a more general fitness of this clade to control the host regardless of location, we compared the same parasitoid clades with hosts from Hebei Province. We found no significant differences in the developmental threshold temperature, effective accumulated temperature, fecundity, longevity, and oviposition period of the two clades, but the duration of host searching of the Shandong clade was significantly longer than that of the Liaoning clade. The instantaneous attack rate, the control ability (a/Th), the search parameter (Q) of the Shandong clade (0.0946, 0.543, 0.0725) of A. mali were higher than that of the Liaoning clade (0.0713, 0.382, 0.0381), and therefore, with WAA from Hebei Province as the host, the host adaptability of the Shandong clade of A. mali was not worse than that of the Liaoning clade, while the pest control ability of the Shandong clade was still greater than that of the Liaoning clade.

[Comparison of outcomes of two minimally invasive approaches for multi-vessel coronary revascularization]

OBJECTIVE

To compare the safety and effectiveness of two minimally invasive approaches for multi-vessel coronary revascularization.

METHODS

From August 2014 to February 2017, 70 consecutive patients who underwent minimally invasive coronary artery bypass grafting in Peking University Third Hospital were randomly divided into two groups. In one group, 40 patients underwent staged-hybrid coronary revascularization (staged-HCR) treatment; in the other group, 30 patients underwent minimally invasive total arterial revascularization with bilateral internal thoracic artery (BITA). In staged -HCR group, the patients underwent minimally invasive direct coronary artery bypass grafting (MIDCAB) and percutaneous coronary intervention (PCI) procedure for treatment of multi-vessel disease. In BITA group, the patients underwent total arterial coronary artery bypass grafting with composite "Y" BITA graft. Preoperative and postoperative data of the two groups, including postoperative blood usage, mechanical ventilation time, domiciling duration in intensive care unit (ICU), major adverse cerebral and cardiovascular event (MACCE), and postoperative coronary angiography results were compared, in order to evaluate the safety and effectiveness of these surgical approaches.

RESULTS

The preoperative characteristics of 70 patients in the two groups showed no significant difference. All the patients underwent successfully, elective minimally invasive multi-vessel coronary artery bypass grafting as scheduled preoperatively. Postoperative result showed the patients in staged-HCR group took advantages in less postoperative mechanical ventilation time [Staged-HCR group (11.2±8.7) h vs. BITA group (18.3±9.1) h, P=0.013], shorter domiciling duration in ICU [Staged-HCR group (26.29±4.05) h vs. BITA group (44.74±28.75) h, P=0.022], and less total drainage [Staged-HCR group (695.57±250.46) mL vs. BITA group (1 103.26±547.44) mL, P=0.03] than the patients in the group of minimally invasive total arterial revascularization with BITA. Postoperative in hospital coronary angiography showed satisfactory graft patency rates in both groups [97.5% in Staged-HCR group vs. 97.8% in BITA group]. No MACCE occurred in both groups during hospitalization.

CONCLUSION

Staged-HCR is a feasible method for the treatment of multi-vessel revascularization involving right coronary artery. Minimally coronary revascularization with BITA is associated with superior long-term graft patency and it's recommended for patients who could not tolerate dual-antiplatelet therapy. This study shows that both minimally invasive surgical approaches are safe and effective for treatment of patients with multi-vessel coronary artery disease.

Architecture and Transport Properties of Multifilamentary MgB2 Strands for MRI and Low AC Loss Applications

Standard in-situ type MgB2 strands manufactured by Hyper Tech Inc have 19 - 36 subelements, a monel outer sheath, and a Cu interfilamentary matrix. Typical transport Jc s of the strands are 2×105 A/cm2 with n-values of 20 - 30 at 4.2 K and 5 T. This work introduces two new MgB2 conductor designs. First, a new class of MgB2 strand is designed for magnetic resonance imaging applications. This type has a higher Cu content designed to enhance protection of a magnet wound with it, and a larger diameter to increase the critical current. Second, a new class of low AC loss MgB2 strand with high filament count and a high resistance matrix is discussed. Transport properties at 4.2 K and fields up to 10 T are reported. Optical techniques are used to study the macro- and micro-structures of these MgB2 strands.

Identification of the crucial genes in the elimination and survival process of Salmonella enterica ser. Pullorum in the chicken spleen

Salmonella enterica ser. Pullorum is one of the most easily re-infecting pathogens in poultry production because of its mechanism of escaping from immune elimination. We used the transcriptome method to investigate the variation in gene expression in chicken spleen resulting from the interaction between hosts and S. Pullorum in the survival process. The expression of various genes related to the maturation and activation of B cells was activated before S. Pullorum was eliminated, which might help S. Pullorum escape from the elimination process. The suppression of some genes involved in the fusion of autophagosomes and lysosomes, such as MYO6, was identified and may be regulated by the secretion systems of S. Pullorum. In addition, a large proportion of these differentially expressed genes could be localized in the identified quantitative trait loci regions associated with the antibody response to bacteria. Collectively, these identified genes provided an outline for further understanding the interaction between chicken immune cells and S. Pullorum in chicken spleen.

DTC chemotherapy regimen is associated with higher incidence of premature ovarian failure in women of reproductive age with breast cancer

OBJECTIVE

Different chemotherapy regimens may contribute differently to the development of Premature Ovarian Failure (POF) in women of reproductive age with breast cancer. Here we evaluated how two different chemotherapy regimens, CAF (tegafur + pirarubicin + ifosfamide) and DTC (docetaxel + pirarubicin + ifosfamide), affect the development of POF.

PATIENTS AND METHODS

We enrolled 164 women of reproductive age with breast cancer (mean ± SD age of 34.56 ± 9.48 years). The patients were divided into two groups, which were respectively treated with CAF (n = 89) or DTC (n = 75) chemotherapy regimen. Both study groups were comparable in all analyzed characteristics at baseline. Patients were treated with respective chemotherapy regimen for 6 months and followed up for over 12 months after completion of chemotherapy. Study outcomes were occurrence rates of POF, menstrual status and recovery after completion of chemotherapy, and serum levels of follicle stimulating hormone (FSH), luteinizing hormone (LH), and oestradiol (E2).

RESULTS

At 6 months after completion of chemotherapy, POF incidence rates were significantly lower in the CAF group. Furthermore, the proportion of patients with eumenorrhea, menstrual disorders or chemotherapy-induced amenorrhea in this study group was also significantly different from the DTC group. Similarly, adverse changes of serum levels of FSH, LH and E2 were less pronounced in the CAF group.

CONCLUSIONS

Both tested chemotherapy regimens can cause POF; however, adverse effects of DCT chemotherapy regimen on ovarian function are more pronounced than those by CAF chemotherapy regimen.

Single nucleotide polymorphism screening, molecular characterization, and evolutionary aspects of chicken Piwi genes

The P-element-induced wimpy testis (Piwi) gene is involved in germline stem cell self-renewal, meiosis, RNA silencing, and transcriptional regulation. Piwi genes are relatively well conserved in many species, but their function in poultry species is unclear. In this study, Piwi genes were sequenced using a target-sequence capture assay in quail and 28 breeds of chicken. Single nucleotide polymorphisms (SNPs) and evolutionary aspects of these chicken breeds were then analyzed. We found that SNP sites existed mainly in the introns of a few chicken breeds, and we selected an SNP on intron 4 for further verification by Sanger sequencing, the results of which were similar to those obtained by the target-capture sequencing assay. The evolutionary analysis revealed that there were more mutations in the Chahua and Leghorn breeds than in the other breeds, and that the phylogenetic tree was divided into four main categories that suggested that Piwi is evolutionarily conserved, and mutations in the introns might be associated with gametogenesis. The screened SNPs can be used as candidate markers for Piwi, and our results provide basic information for the further study of Piwi function in poultry.

Fertility clinicians and infertile patients in China have different preferences in fertility care

STUDY QUESTION

Do the preferences for fertility care of infertile Chinese patients differ from those of fertility care providers?

SUMMARY ANSWER

Infertile Chinese patients attached the greatest importance to physicians' attitude but, in contrast, fertility care providers in China considered treatment effectiveness to be the most important factor in fertility care.

WHAT IS KNOWN ALREADY

In Europe, physicians underestimate the importance of patient-centred infertility care.

STUDY DESIGN, SIZE, DURATION

A conjoint survey was distributed among 417 female infertile Chinese patients and 83 fertility care providers from February 2013 to August 2013.

PARTICIPANTS/MATERIALS, SETTING, METHODS

In this pilot study, 389 patients and 83 fertility care providers completed the survey at three reproductive medicine centres. Rating-based conjoint analysis was performed to elicit patients' and their caregivers' preferences regarding fertility care. Cluster analysis was used to explore the heterogeneity among patients' preferences.

MAIN RESULTS AND THE ROLE OF CHANCE

When searching for fertility care, patients valued the physicians' attitude the most, followed by success rates, distance from home to the fertility centre, physician continuity throughout the treatment period and type of fertility centre. Fertility care providers considered success rates (effectiveness) to be the most important factor when recommending a fertility centre. Fertility patients and care providers had significantly different views on the value of treatment effectiveness, physician attitude and physician continuity (P-values <0.05). Cluster analysis revealed that patients' preferences were heterogeneous.

LIMITATIONS, REASONS FOR CAUTION

The sample size is relatively small, and there is insufficient power for heterogeneity analysis. Two levels for each of five design factors (2(5)) may not fully capture the characteristics of realistic fertility centres. Rating-based conjoint analysis could be inferior to choice-based conjoint analysis in terms of predictive accuracy.

WIDER IMPLICATIONS OF THE FINDINGS

Fertility care providers in China significantly underestimate the importance of patient-centredness to infertile patients. To deliver optimal fertility care to infertile Chinese patients, fertility care providers need to understand the importance of patient-centred care, such as a friendly attitude, sympathy for patients' suffering, respect for patients' right to informed consent and a transparent treatment process.

STUDY FUNDING/COMPETING INTEREST(S)

This study was not funded, and there are no conflicts of interest.

TRIAL REGISTRATION NUMBER

None.

Comparison of three lymph node staging schemes for predicting outcome in patients with gastric cancer

BACKGROUND

Several node staging schemes have been proposed for gastric cancer. The optimal system remains controversial.

METHODS

Patients with gastric cancer were identified from the Surveillance, Epidemiology, and End Results (SEER) database, and a Chinese patient cohort was used for independent validation. The prognostic performance of three node staging schemes was compared, involving a number-based scheme (pN), ratio-based scheme (rN) and log odds of positive lymph nodes scheme (LODDS).

RESULTS

There were 12 443 patients in the SEER database and 866 in the Chinese cohort. LODDS provided better discriminatory capacity and higher predictive accuracy than either pN or rN, for patients with gastric cancer in both the SEER database and the Chinese cohort. The multivariable model using the LODDS classification was significantly more predictive than the pN classification. LODDS suffered much less from stage migration and was able efficiently to discriminate the heterogeneity for patients with no nodes involved or all nodes involved, whereas the pN and rN schemes could not.

CONCLUSION

LODDS showed a clear prognostic superiority over both pN and rN schemes. It could serve as an important reference for the tumour node metastasis (TNM) node classification.