bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the interaction biomolecule types for lncRNA: an ensemble deep learning approach
Authors: Zhang Yu , Jia Cangzhi , Kwoh Chee Keong 
Published: August 2020

Abstract
Long noncoding RNAs (lncRNAs) play significant roles in various physiological and pathological processes via their interactions with biomolecules like DNA, RNA and protein. The existing in silico methods used for predicting the functions of lncRNA mainly rely on calculating the similarity of lncRNA or investigating whether an lncRNA can interact with a specific biomolecule or disease. In this work, we explored the functions of lncRNA from a different perspective: we presented a tool for predicting the interaction biomolecule type for a given lncRNA. For this purpose, we first investigated the main molecular mechanisms of the interactions of lncRNA–RNA, lncRNA–protein and lncRNA–DNA. Then, we developed an ensemble deep learning model: lncIBTP (lncRNA Interaction Biomolecule Type Prediction). This model predicted the interactions between lncRNA and different types of biomolecules. On the 5-fold cross-validation, the lncIBTP achieves average values of 0.7042 in accuracy, 0.7903 and 0.6421 in macro-average area under receiver operating characteristic curve and precision–recall curve, respectively, which illustrates the model effectiveness. Besides, based on the analysis of the collected published data and prediction results, we hypothesized that the characteristics of lncRNAs that interacted with DNA may be different from those that interacted with only RNA.
Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation
Authors: Stammler Sebastian , Kussel Tobias , Schoppmann Phillipp , Stampe Florian , Tremper Galina , Katzenbeisser Stefan , Hamacher Kay , Lablans Martin 
Published: August 2020

Abstract

Motivation
Record Linkage has versatile applications in real-world data analysis contexts, where several datasets need to be linked on the record level in the absence of any exact identifier connecting related records. An example are medical databases of patients, spread across institutions, that have to be linked on personally identifiable entries like name, date of birth or ZIP code. At the same time, privacy laws may prohibit the exchange of this personally identifiable information (PII) across institutional boundaries, ruling out the outsourcing of the record linkage task to a trusted third party. We propose to employ privacy-preserving record linkage (PPRL) techniques that prevent, to various degrees, the leakage of PII while still allowing for the linkage of related records.

Results
We develop a framework for fault-tolerant PPRL using secure multi-party computation with the medical record keeping software Mainzelliste as the data source. Our solution does not rely on any trusted third party and all PII is guaranteed to not leak under common cryptographic security assumptions. Benchmarks show the feasibility of our approach in realistic networking settings: linkage of a patient record against a database of 10 000 records can be done in 48 s over a heavily delayed (100 ms) network connection, or 3.9 s with a low-latency connection.

Availability and implementation
The source code of the sMPC node is freely available on Github at https://github.com/medicalinformatics/SecureEpilinker subject to the AGPLv3 license. The source code of the modified Mainzelliste is available at https://github.com/medicalinformatics/MainzellisteSEL.

Supplementary information
Supplementary data are available at Bioinformatics online.
SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model
Authors: Zhang Dachuan , Zhang Tong , Liu Sheng , Sun Dandan , Ding Shaozhen , Cheng Xingxiang , Cai Pengli , Ren Ailin , Han Mengying , Liu Dongliang , Jia Cancan , Gong Linlin , Zhang Rui , Xing Huadong , Tu Weizhong , Chen Junni , Hu Qian-Nan 
Published: August 2020

Abstract

Motivation
The 2019 novel coronavirus outbreak has significantly affected global health and society. Thus, predicting biological function from pathogen sequence is crucial and urgently needed. However, little work has been conducted to identify viruses by the enzymes that they encode, and which are key to pathogen propagation.

Results
We built a comprehensive scientific resource, SARS2020, which integrates coronavirus-related research, genomic sequences and results of anti-viral drug trials. In addition, we built a consensus sequence-catalytic function model from which we identified the novel coronavirus as encoding the same proteinase as the severe acute respiratory syndrome virus. This data-driven sequence-based strategy will enable rapid identification of agents responsible for future epidemics.

Availabilityand implementation
SARS2020 is available at http://design.rxnfinder.org/sars2020/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Increased FOXL2 expression alters uterine structures and functions†
Authors: Li Rong , Wu San-Pin , Zhou Lecong , Nicol Barbara , Lydon John P , Yao Humphrey H-C , DeMayo Francesco J 
Published: August 2020

AbstractThe transcription factor forkhead box L2 (FOXL2) regulates sex differentiation and reproductive function. Elevated levels of this transcription factor have been observed in the diseases of the uterus, such as endometriosis. However, the impact of elevated FOXL2 expression on uterine physiology remains unknown. In order to determine the consequences of altered FOXL2 in the female reproductive axis, we generated mice with over-expression of FOXL2 (FOXL2OE) by crossing Foxl2LsL/+ with the Progesterone receptor Pgrcre model. FOXL2OE uterus showed severe morphological abnormality including abnormal epithelial stratification, blunted adenogenesis, increased endometrial fibrosis, and disrupted myometrial morphology. In contrast, increasing FOXL2 levels specifically in uterine epithelium by crossing the Foxl2LsL/+ with the lactoferrin Ltficre mice resulted in the eFOXL2OE mice with uterine epithelial stratification but without defects in endometrial fibrosis and adenogenesis, demonstrating a role of the endometrial stroma in the uterine abnormalities of the FOXL2OE mice. Transcriptomic analysis of 12 weeks old Pgrcre and FOXL2OE uterus at diestrus stage showed multiple signaling pathways related with cellular matrix, wnt/β-catenin, and altered cell cycle. Furthermore, we found FOXL2OE mice were sterile. The infertility was caused in part by a disruption of the hypophyseal ovarian axis resulting in an anovulatory phenotype. The FOXL2OE mice failed to show decidual responses during artificial decidualization in ovariectomized mice demonstrating the uterine contribution to the infertility phenotype. These data support that aberrantly increased FOXL2 expressions in the female reproductive tract can disrupt ovarian and uterine functions.
Aberrant and constitutive expression of FOXL2 impairs ovarian development and functions in mice
Authors: Nicol Barbara , Rodriguez Karina , Yao Humphrey H-C 
Published: August 2020

Abstract
Development and functions of the ovary rely on appropriate signaling and communication between various ovarian cell types. FOXL2, a transcription factor that plays a key role at different stages of ovarian development, is associated with primary ovarian insufficiency and ovarian cancer as a result of its loss-of-function or mutations. In this study, we investigated the impact of aberrant, constitutive expression of FOXL2 in somatic cells of the ovary. Overexpression of FOXL2 that started during fetal life resulted in defects in nest breakdown and consequent formation of polyovular follicles. Granulosa cell differentiation was impaired and recruitment and differentiation of steroidogenic theca cells was compromised. As a consequence, adult ovaries overexpressing FOXL2 exhibited defects in compartmentalization of granulosa and theca cells, significant decreased steroidogenesis and lack of ovulation. These findings demonstrate that fine-tuned expression of FOXL2 is required for proper folliculogenesis and fertility.
Introduction to the Symposium on Legal Dimensions of Chinese Globalization: China and Global Health Governance
Authors: Erie Matthew S 
Published: August 2020

Abstract
China has emerged as a champion of economic globalization, particularly through building global supply chains, financing overseas infrastructure and energy projects, and exporting labour to developing countries throughout the world. The Belt and Road Initiative (BRI), announced in 2013, is a keystone in China’s economic globalization. The BRI emphasizes connectivity: policy, infrastructure, trade, financial, and ‘people-to-people’. Despite the broad significance of Chinese economic globalization, its legal dimensions are still poorly understood. China, Law and Development (CLD) is an international and multi-disciplinary research project that aims to study the legal and regulatory aspects of this stage of globalization. This symposium is comprised of articles by CLD research associates who investigate various questions, including labour rights, skilled migration facilitation, investment review, multilateralism, and patronage and clientelism. This article introduces the symposium, and it does so through the example of China’s role in global health governance. The outbreak of the novel coronavirus (Covid-19) epidemic in late 2019 in China, which has since become a worldwide pandemic, has obstructed BRI connectivity through delinking global supply chains, blocking labour migration, freezing markets, and exacerbating Sinophobia. In response, China has sought to lead an effort in improving global health governance through participation in international organizations and strengthening its bilateral ties through health aid and technology export. The coronavirus pandemic may offer the Chinese an opportunity to lead a more circumscribed re-globalization, although China faces significant challenges.
A Blockchain-Based Framework for IoT Data Monetization Services
Authors: Ali Muhammad Salek , Vecchio Massimo , Antonelli Fabio 
Published: August 2020

Abstract
Within internet of things (IoT) research, there is a growing interest in leveraging the decentralization properties of blockchains, towards developing IoT authentication and authorization mechanisms that do not inherently require centralized third-party intermediaries. This paper presents a framework for sharing IoT data in a decentralized and private-by-design manner in exchange for monetary services. The framework is built on a tiered blockchain architecture, along with InterPlanetary File System for IoT data storage and transfer. The goal is to enable IoT data users to exercise fine-grained control on how much data they share with entities authenticated through blockchains. To highlight how the framework would be used in real-life scenarios, this paper presents two use cases, namely an IoT data marketplace and a decentralized connected vehicle insurance. These examples showcase how the proposed framework can be used for varying smart contract-based applications involving exchanges of IoT data and cryptocurrency. Following the discussion about the use cases, the paper outlines a detailed security analysis performed on the proposed framework, based on multiple attack scenarios. Finally, it presents and discusses extensive evaluations, in terms of various performance metrics obtained from a real-world implementation.
Dunlin subspecies exhibit regional segregation and high site fidelity along the East Asian–Australasian Flyway
Authors: Lagassé Benjamin J , Lanctot Richard B , Barter Mark , Brown Stephen , Chiang Chung-Yu , Choi Chi-Yeung , Gerasimov Yuri N , Kendall Steve , Liebezeit Joseph R , Maslovsky Konstantin S , Matsyna Alexander I , Matsyna Ekaterina L , Payer David C , Saalfeld Sarah T , Shigeta Yoshimitsu , Tiunov Ivan M , Tomkovich Pavel S , Valchuk Olga P , Wunder Michael B 
Published: August 2020

Abstract
The degree to which individuals migrate among particular breeding, migration, and wintering sites can have important implications for prioritizing conservation efforts. Four subspecies of Dunlin (Calidris alpina) migrate along the East Asian−Australasian Flyway. Each subspecies has a distinct and well-defined breeding range, but their migration and winter ranges are poorly defined or unknown. We assessed the migratory connectivity of 3 of these subspecies by evaluating a dataset that encompasses 57 yr (1960–2017), and comprises more than 28,000 Dunlin banding records and 818 observations (71 recaptures and 747 band resightings). We present some of the first evidence that subspecific segregation likely occurs, with arcticola Dunlin wintering in areas of Japan, and other arcticola, actites, and sakhalina Dunlin wintering in areas of the Yellow and China seas. Observations indicate that whether an arcticola Dunlin winters in Japan or the Yellow and China seas is independent of their breeding location, sex, or age. Furthermore, observations indicate that ≥83% of arcticola Dunlin exhibit interannual site fidelity to specific wintering sites. This suggests that the degradation of specific wetland areas may negatively affect particular individuals of a particular subspecies (or combination of subspecies), and, if widespread, could result in population declines. Given the possible biases inherent in analyzing band recovery data, we recommend additional flyway-wide collaboration and the use of lightweight tracking devices and morphological and genetic assignment techniques to better quantify subspecies’ migratory movements and nonbreeding distributions. This information, when combined, will enable effective conservation efforts for this species across the East Asian−Australasian Flyway.
A combined microRNA and target protein-based panel for predicting the probability and severity of uraemic vascular calcification: a translational study
Authors: Chao Chia-Ter , Yeh Hsiang-Yuan , Tsai You-Tien , Chiang Chih-Kang , Chen Huei-Wen 
Published: August 2020

Abstract

Aims
Vascular calcification (VC) increases the future risk of cardiovascular events in uraemic patients, but effective therapies are still unavailable. Accurate identification of those at risk of developing VC using pathogenesis-based biomarkers is of particular interest and may facilitate individualized risk stratification. We aimed to uncover microRNA (miRNA)-target protein-based biomarker panels for evaluating uraemic VC probability and severity.

Methods and results
We created a three-tiered in vitro VC model and an in vivo uraemic rat model receiving high phosphate diet to mimic uraemic VC. RNAs from the three-tiered in vitro and in vivo uraemic VC models underwent miRNA and mRNA microarray, with results screened for differentially expressed miRNAs and their target genes as biomarkers. Findings were validated in original models and additionally in an ex vivo VC model and human cells, followed by functional assays of identified miRNAs and target proteins, and tests of sera from end-stage renal disease (ESRD) and non-dialysis-dependent chronic kidney disease (CKD) patients without and with VC. Totally 122 down-regulated and 119 up-regulated miRNAs during calcification progression were identified initially; further list narrowing based on miRNA–mRNA pairing, anti-correlation, and functional enrichment left 16 and 14 differentially expressed miRNAs and mRNAs. Levels of four miRNAs (miR-10b-5p, miR-195, miR-125b-2-3p, and miR-378a-3p) were shown to decrease throughout all models tested, while one mRNA (SULF1, a potential target of miR-378a-3p) exhibited the opposite trend concurrently. Among 96 ESRD (70.8% with VC) and 59 CKD patients (61% with VC), serum miR-125b2-3p and miR-378a-3p decreased with greater VC severity, while serum SULF1 levels increased. Adding serum miR-125b-2-3p, miR-378a-3p, and SULF1 into regression models for VC substantially improved performance compared to using clinical variables alone.

Conclusion
Using a translational approach, we discovered a novel panel of biomarkers for gauging the probability/severity of uraemic VC based on miRNAs/target proteins, which improved the diagnostic accuracy.
Role of interleukin-23/interleukin-17 axis in T-cell-mediated actions in hypertension
Authors: Higaki Akinori , Mahmoud Ahmad U M , Paradis Pierre , Schiffrin Ernesto L 
Published: August 2020

Abstract
Current knowledge suggests that hypertension is in part mediated by immune mechanisms. Both interleukin (IL)-23 and IL-17 are up-regulated in several experimental hypertensive rodent models, as well as in hypertensive humans in observational studies. Recent preclinical studies have shown that either IL-23 or IL-17A treatment induce blood pressure elevation. However, the IL-23/IL-17 axis has not been a major therapeutic target in hypertension, unlike in other autoimmune diseases. In this review, we summarize current knowledge on the role of these cytokines in immune mechanisms contributing to hypertension, and discuss the potential of IL-23/IL-17-targeted therapy for treatment of hypertension.
Interaction between Lactobacillus reuteri and periodontopathogenic bacteria using in vitro and in vivo (G. mellonella) approaches
Authors: Santos Thaís Aguiar , Scorzoni Liliana , Correia Raquel , Junqueira Juliana Campos , Anbinder Ana Lia 
Published: August 2020

ABSTRACT
Periodontitis is a multifactorial inflammatory disease, and the major cause of tooth loss in adults. New therapies have been proposed for its treatment, including the use of probiotics such as Lactobacillus reuteri. The objective of this study was to evaluate the antimicrobial effects of L. reuteri: live, heat-killed and culture filtrate (cell-free supernatant), on periodontopathogenic bacteria (Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans) in vitro, as well as the in vivo survival curve, hemocyte density and microbial recovery using Galleria mellonella. For in vitro assays, all preparations reduced colony forming units of F. nucleatum, while only live L. reuteri reduced the growth of A. actinomycetemcomitans. All treatments reduced periodontopathogenic bacteria growth in vivo. The treatment with the supernatant increased the survival of larvae infected with F. nucleatum more than the treatment with live L. reuteri, and none of the treatments altered the survival of A. actinomycetemcomitans-infected larvae. In addition, the treatment with L. reuteri preparations did not alter the hemocyte count of F. nucleatum- and A. actinomycetemcomitans-infected larvae. This study demonstrated that L. reuteri preparations exerted antimicrobial effects and increased the survival of G. mellonella infected by F. nucleatum, although only live L. reuteri was able to reduce the growth of A. actinomycetemcomitans in vitro.
Adipose Tissue Inflammation Is Directly Linked to Obesity-Induced Insulin Resistance, while Gut Dysbiosis and Mitochondrial Dysfunction Are Not Required
Authors: Petrick Heather L , Foley Kevin P , Zlitni Soumaya , Brunetta Henver S , Paglialunga Sabina , Miotto Paula M , Politis-Barber Valerie , O’Dwyer Conor , Philbrick Diana J , Fullerton Morgan D , Schertzer Jonathan D , Holloway Graham P 
Published: August 2020

AbstractObesity is associated with adipose tissue hypertrophy, systemic inflammation, mitochondrial dysfunction, and intestinal dysbiosis. Rodent models of high-fat diet (HFD)-feeding or genetic deletion of multifunctional proteins involved in immunity and metabolism are often used to probe the etiology of obesity; however, these models make it difficult to divorce the effects of obesity, diet composition, or immunity on endocrine regulation of blood glucose. We, therefore, investigated the importance of adipose inflammation, mitochondrial dysfunction, and gut dysbiosis for obesity-induced insulin resistance using a spontaneously obese mouse model. We examined metabolic changes in skeletal muscle, adipose tissue, liver, the intestinal microbiome, and whole-body glucose control in spontaneously hyperphagic C57Bl/6J mice compared to lean littermates. A separate subset of lean and obese mice was subject to 8 weeks of obesogenic HFD feeding, or to pair feeding of a standard rodent diet. Hyperphagia, obesity, adipose inflammation, and insulin resistance were present in obese mice despite consuming a standard rodent diet, and these effects were blunted with caloric restriction. However, hyperphagic obese mice had normal mitochondrial respiratory function in all tissues tested and no discernable intestinal dysbiosis relative to lean littermates. In contrast, feeding mice an obesogenic HFD altered the composition of the gut microbiome, impaired skeletal muscle mitochondrial bioenergetics, and promoted poor glucose control. These data show that adipose inflammation and redox stress occurred in all models of obesity, but gut dysbiosis and mitochondrial respiratory dysfunction are not always required for obesity-induced insulin resistance. Rather, changes in the intestinal microbiome and mitochondrial bioenergetics may reflect physiological consequences of HFD feeding.
Birth outcomes are superior after transfer of fresh versus frozen embryos for donor oocyte recipients
Authors: Roeca Cassandra , Johnson Rachel L , Truong Tracy , Carlson Nichole E , Polotsky Alex J 
Published: August 2020

Abstract

STUDY QUESTION
For donor oocyte recipients, are birth outcomes superior for fresh versus frozen embryos?

SUMMARY ANSWER
Among fresh donor oocyte recipients, fresh embryos are associated with better birth outcomes when compared with frozen embryos.

WHAT IS KNOWN ALREADY
Frozen embryo transfer (ET) with vitrification has been associated with improved pregnancy rates, but also increased rates of large for gestational age infants. Donor oocyte recipients represent an attractive biological model to attempt to isolate the impact of embryo cryopreservation on IVF outcomes, yet there is a paucity of studies in this population.

STUDY DESIGN, SIZE, DURATION
A retrospective cohort of the US national registry, the Society for Assisted Reproductive Technology Clinic Outcome Reporting System, of IVF cycles of women using fresh donor oocytes resulting in ET between 2013 and 2015. Thawed oocytes were excluded.

PARTICIPANTS/MATERIALS, SETTINGS, METHODS
Good obstetric outcome (GBO), defined as a singleton, term, live birth with appropriate for gestational age birth weight, was the primary outcome measure. Secondary outcomes included live birth, clinical pregnancy, spontaneous abortion, preterm birth, multiple births and gestational age-adjusted weight. Outcomes were modeled using the generalized estimating equation approach.

MAIN RESULTS AND THE ROLE OF CHANCE
Data are from 25 387 donor oocyte cycles, in which 14 289 were fresh and 11 098 were frozen ETs. A GBO was 27% more likely in fresh ETs (26.3%) compared to frozen (20.9%) (adjusted risk ratio 1.27; 95% confidence interval (CI) 1.21–1.35; P &lt; 0.001). Overall, fresh transfer was more likely to result in a live birth (55.7% versus 39.5%; adjusted risk ratio 1.21; 95% CI 1.18–1.26; P &lt; 0.001). Among singleton births, there was no difference in gestational age-adjusted birth weight between groups.

LIMITATION, REASONS FOR CAUTION
Our cohort findings contrast with data from autologous oocytes. Prospective studies with this population are warranted.

WIDER IMPLICATIONS OF THE FINDINGS
Among donor oocyte recipients, fresh ETs may be associated with better birth outcomes. Reassuringly, given its prevalent use, modern embryo cryopreservation does not appear to result in phenotypically larger infants.

STUDY FUNDING/COMPETING INTEREST(S)
None.

TRIAL REGISTRATION NUMBER
N/A.