bluuebunny/crossref_metadata_2025_split huggingface dataset:
MGPLI: exploring multigranular representations for protein–ligand interaction prediction
Authors: Wang Junjie , Hu Jie , Sun Huiting , Xu MengDie , Yu Yun , Liu Yun , Cheng Liang 
Published: September 2022

Abstract

Motivation
The capability to predict the potential drug binding affinity against a protein target has always been a fundamental challenge in silico drug discovery. The traditional experiments in vitro and in vivo are costly and time-consuming which need to search over large compound space. Recent years have witnessed significant success on deep learning-based models for drug-target binding affinity prediction task.

Results
Following the recent success of the Transformer model, we propose a multigranularity protein–ligand interaction (MGPLI) model, which adopts the Transformer encoders to represent the character-level features and fragment-level features, modeling the possible interaction between residues and atoms or their segments. In addition, we use the convolutional neural network to extract higher-level features based on transformer encoder outputs and a highway layer to fuse the protein and drug features. We evaluate MGPLI on different protein–ligand interaction datasets and show the improvement of prediction performance compared to state-of-the-art baselines.

Availability and implementation
The model scripts are available at https://github.com/IILab-Resource/MGDTA.git
PHi-C2: interpreting Hi-C data as the dynamic 3D genome state
Authors: Shinkai Soya , Itoga Hiroya , Kyoda Koji , Onami Shuichi 
Published: September 2022

Abstract

Summary
High-throughput chromosome conformation capture (Hi-C) is a widely used assay for studying the three-dimensional (3D) genome organization across the whole genome. Here, we present PHi-C2, a Python package supported by mathematical and biophysical polymer modeling that converts input Hi-C matrix data into the polymer model’s dynamics, structural conformations and rheological features. The updated optimization algorithm for regenerating a highly similar Hi-C matrix provides a fast and accurate optimal solution compared to the previous version by eliminating the factors underlying the inefficiency of the optimization algorithm in the iterative optimization process. In addition, we have enabled a Google Colab workflow to run the algorithm, wherein users can easily change the parameters and check the results in the notebook. Overall, PHi-C2 represents a valuable tool for mining the dynamic 3D genome state embedded in Hi-C data.

Availability and implementation
PHi-C2 as the phic Python package is freely available under the GPL license and can be installed from the Python package index. The source code is available from GitHub at https://github.com/soyashinkai/PHi-C2. Moreover, users do not have to prepare a Python environment because PHi-C2 can run on Google Colab (https://bit.ly/3rlptGI).

Supplementary information
Supplementary data are available at Bioinformatics online.
CANTATA—prediction of missing links in Boolean networks using genetic programming
Authors: Müssel Christoph , Ikonomi Nensi , Werle Silke D , Weidner Felix M , Maucher Markus , Schwab Julian D , Kestler Hans A 
Published: September 2022

AbstractMotivationBiological processes are complex systems with distinct behaviour. Despite the growing amount of available data, knowledge is sparse and often insufficient to investigate the complex regulatory behaviour of these systems. Moreover, different cellular phenotypes are possible under varying conditions. Mathematical models attempt to unravel these mechanisms by investigating the dynamics of regulatory networks. Therefore, a major challenge is to combine regulations and phenotypical information as well as the underlying mechanisms. To predict regulatory links in these models, we established an approach called CANTATA to support the integration of information into regulatory networks and retrieve potential underlying regulations. This is achieved by optimizing both static and dynamic properties of these networks.ResultsInitial results show that the algorithm predicts missing interactions by recapitulating the known phenotypes while preserving the original topology and optimizing the robustness of the model. The resulting models allow for hypothesizing about the biological impact of certain regulatory dependencies.Availability and implementationSource code of the application, example files and results are available at https://github.com/sysbio-bioinf/Cantata.Supplementary informationSupplementary data are available at Bioinformatics online.
Peptidylarginine deiminase enzymes and citrullinated proteins in female reproductive physiology and associated diseases
Authors: Christensen Amanda O , Li Guangyuan , Young Coleman H , Snow Bryce , Khan Shaihla A , DeVore Stanley B , Edwards Sydney , Bouma Gerrit J , Navratil Amy M , Cherrington Brian D , Rothfuss Heather M 
Published: September 2022

AbstractCitrullination, the post-translational modification of arginine residues, is catalyzed by the four catalytically active peptidylarginine deiminase (PAD or PADI) isozymes and alters charge to affect target protein structure and function. PADs were initially characterized in rodent uteri and, since then, have been described in other female tissues including ovaries, breast, and the lactotrope and gonadotrope cells of the anterior pituitary gland. In these tissues and cells, estrogen robustly stimulates PAD expression resulting in changes in levels over the course of the female reproductive cycle. The best-characterized targets for PADs are arginine residues in histone tails, which, when citrullinated, alter chromatin structure and gene expression. Methodological advances have allowed for the identification of tissue-specific citrullinomes, which reveal that PADs citrullinate a wide range of enzymes and structural proteins to alter cell function. In contrast to their important physiological roles, PADs and citrullinated proteins are also involved in several female-specific diseases including autoimmune disorders and reproductive cancers. Herein, we review current knowledge regarding PAD expression and function and highlight the role of protein citrullination in both normal female reproductive tissues and associated diseases.
Job Stress during the COVID-19 Pandemic amongst Social Workers: A Comparison between Chinese Mainland and Macao
Authors: Tang Ning , Sun Fei , Zhang Donghang , Leung Charles , Gao Xiang 
Published: September 2022

AbstractThe COVID-19 pandemic may have resulted in front line social workers experiencing job stress, burnout and other psychological distress. Little is known about the work-related stress experienced by Chinese social workers during the pandemic. This study focused on the job stress of social workers from Mainland and Macao. The research aims of this study included: (1) testing whether there is a difference in job stress between social workers from Mainland and Macao during the pandemic and (2) identifying mediating factors that helped explain such regional differences. An online survey collected data from 292 social workers in Mainland China and 108 from Macao in 2020. Mainland participants reported significantly higher job stress than Macao participants. Regional differences in job stress amongst Mainland and Macao social workers were partially attributed to their age and professional role identity. More attention needs to be paid to social workers in Mainland China as they experience higher job stress than their counterparts from Macao. Future research is needed to examine other factors (e.g. job demand and financial compensation) that may contribute to such regional differences.
Suicide Risk amongst University Students of Social Work in Spain
Authors: Reina-Aguilar Pastora , Díaz-Jiménez Rosa María , Caravaca-Sánchez Francisco 
Published: September 2022

AbstractSuicide is a phenomenon existing amongst university students worldwide, generally associated with mental health problems. Although the evidence has revealed a greater psychosocial vulnerability amongst Social Work students, there are few studies that address this reality. This work, thus, has focused on detecting the risk of suicide amongst undergraduate Social Work students at Spanish universities. A total of 511 students (89 per cent female) at eighteen Spanish universities completed an online questionnaire assessing both support and risk factors for suicide. A total of 28.8 per cent reported suicidal ideation, 15.3 per cent planned suicide and 24.9 per cent presented suicide risk. Logistic regression analysis showed that this risk was, understandably, associated with higher depressive symptomatology, lower perceived social support and lower life satisfaction. The results obtained indicate the prevalence of the risk of suicide ideation, planning and the imminent risk of suicide amongst Social Work students at Spanish universities, and this study’s findings have specific implications for the university Social Work community, and for governmental, academic and university bodies in general.
Providers Have a Responsibility to Discuss Options for Infant Feeding With Pregnant People With Human Immunodeficiency Virus in High-Income Countries
Authors: McKinney Jennifer , Mirani Gayatri , Levison Judy 
Published: September 2022

Abstract
Guidelines in high-income countries generally recommend against breastfeeding for a pregnant person with HIV due to the historical risk of transmission to the infant and generally acceptable, safe, and sustainable access to formula. Maternal antiretroviral therapy and infant prophylaxis have been shown to significantly decrease the risk of transmission during breastfeeding. In addition, formula may not be acceptable to patients for a variety of cultural, social, or personal reasons, and its sustainability is called into question in the setting of the current nationwide formula shortage. Providers caring for pregnant people with HIV have a responsibility to discuss infant feeding with their patients, and help them weigh the risks and benefits within the limits of the current body of evidence. We outline a process, including a written agreement, that can be used to discuss infant feeding with all patients and help them make the best decision for their family.
Efficient link prediction model for real-world complex networks using matrix-forest metric with local similarity features
Authors: Gul Haji , Al-Obeidat Feras , Amin Adnan , Tahir Muhammad , Huang Kaizhu 
Published: September 2022

Abstract
Link prediction in a complex network is a difficult and challenging issue to address. Link prediction tries to better predict relationships, interactions and friendships based on historical knowledge of the complex network graph. Many link prediction techniques exist, including the common neighbour, Adamic-Adar, Katz and Jaccard coefficient, which use node information, local and global routes, and previous knowledge of a complex network to predict the links. These methods are extensively used in various applications because of their interpretability and convenience of use, irrespective of the fact that the majority of these methods were designed for a specific field. This study offers a unique link prediction approach based on the matrix-forest metric and vertex local structural information in a real-world complex network. We empirically examined the proposed link prediction method over 13 real-world network datasets obtained from various sources. Extensive experiments were performed that demonstrated the superior efficacy of the proposed link prediction method compared to other methods and outperformed the existing state-of-the-art in terms of prediction accuracy.
Estimating the number of communities in the stochastic block model with outliers
Authors: Xiao Jingsong , Ye Fei , Ma Weidong , Yang Ying 
Published: September 2022

Abstract
The stochastic block model (SBM) is a popular model for community detecting problems. Many community detecting approaches have been proposed, and most of them assume that the number of communities is given previously. However, in practice, the number of communities is often unknown. Plenty of approaches were proposed to estimate the number of communities, but most of them were computationally intensive. Moreover, when outliers exist, there are no approaches to consistently estimate the number of communities. In this article, we propose a fast method based on the eigenvalues of the regularized and normalized adjacency matrix to estimate the number of communities under the SBM with outliers. We show that our method can consistently estimate the number of communities when outliers exist. Moreover, we extend our method to the degree-corrected SBM. We show that our approach is comparable to the other existing approaches in simulations. We also illustrate our approach on four real-world networks.
Effects of high-absorption curcumin for the prevention of hypertensive heart disease: a double-blind, placebo-controlled, randomized clinical study
Authors: Funamoto Masafumi , Sunagawa Yoichi , Katanasaka Yasufumi , Kato Toru , Funada Junichi , Ajiro Yoichi , Komiyama Maki , Akao Masaharu , Yasoda Akihiro , Yamakage Hajime , Satoh-Asahara Noriko , Wada Hiromichi , Ikeda Yasumasa , Morimoto Tatsuya , Hasegawa Koji 
Published: September 2022

Abstract

Aims
Hypertension is a strong risk factor for heart failure with preserved ejection fraction. Curcumin has p300-specific histone acetyltransferase inhibitory activity, suppresses cardiomyocyte hypertrophy and fibrosis, and significantly reduces myocardial brain natriuretic peptide (BNP) expression without altering blood pressure in a rat model of hypertensive heart disease. This double-blind, placebo-controlled, randomized study, for the first time, aimed to examine the efficacy of a high-absorption curcumin for the prevention of hypertensive heart disease in humans.

Methods and results
Patients exhibiting initial signs of hypertensive heart disease with left ventricular ejection fraction ≥60% and stable blood pressure &lt;140/90 mmHg orally took a double-blinded capsule (either a 90 mg curcumin capsule or placebo) twice daily for 24 weeks. The primary endpoint was per cent changes in left ventricular diastolic function (E/E′) from baseline to 6 months after administration. The secondary endpoint was the per cent change in plasma BNP levels. The E/E′ ratio per cent change from baseline to 6 months after administration was similar between the placebo (n = 69) and the curcumin (n = 73) groups. The per cent change in plasma BNP levels was significantly lower in the curcumin group than in the placebo group. In patients &lt;65 years, BNP per cent changes were significantly lower in the curcumin group than in the placebo group, but similar between groups in ≥65 years (&lt;65 vs. ≥65 years: P for interaction = 0.011).

Conclusions
A high-absorption curcumin agent did not affect the E/E′ ratio, rather it significantly inhibited the increase in plasma BNP levels in patients with initial signs of hypertensive heart disease.
A Raise for Grandma: Pensions and Household Expenditure*
Authors: Párraga Rodríguez Susana 
Published: September 2022

Abstract
This paper analyses the causal effect of changes in public pensions on household spending. The identification exploits the introduction of a new welfare system in Spain during the 1980s and 1990s, and uses a novel narrative series of legislated pension changes as an instrument for pension income. Despite public pensions having a limited impact in the aggregate, I find a high, though less than unity, marginal propensity to consume for pensioners due to permanent income shocks at the household level. Moreover, large spending responses for pensioners with the highest income and wealth mean that liquidity considerations can be disregarded as a key source of marginal propensity to consume heterogeneity. Instead, a strong precautionary savings motive can explain the excess smoothness of consumption, and costly adjustments explain the skewed spending response for durables.
Investor Sentiment, Sovereign Debt Mispricing, and Economic Outcomes
Authors: Al-Amine Ramzy , Willems Tim 
Published: September 2022

Abstract
We find that countries able to borrow at spreads that seem low given fundamentals (e.g., because investors are bullish regarding the country’s future) are more likely to develop medium-term difficulties. We establish this by regressing spreads on fundamentals. Subsequently deploying first-stage residuals in a second-stage regression suggests that an optimistic sentiment reduces growth in the medium term while increasing odds of fiscal crises. Incorporating information from our mispricing estimate reduces the root-mean-square error of out-of-sample growth forecasts by 15%. This supports theories of sentiment affecting the business cycle and suggests that countries should not solely rely on spreads when setting fiscal policy.
What is known in pre-, peri-, and post-procedural anticoagulation in micro-axial flow pump protected percutaneous coronary intervention?
Authors: Leick Jürgen , Grottke Oliver , Oezkur Mehmet , Mangner Norman , Sanna Tommaso , Al Rashid Fadi , Vandenbriele Christophe 
Published: September 2022

Abstract
Interest in the use of percutaneous left ventricular assist devices (p-LVADs) for patients undergoing high-risk percutaneous coronary intervention (PCI) is growing rapidly. The Impella™ (Abiomed Inc.) is a catheter-based continuous micro-axial flow pump that preserves haemodynamic support during high-risk PCI. Anticoagulation is required to counteract the activation of the coagulation system by the patient’s procoagulant state and the foreign-body surface of the pump. Excessive anticoagulation and the effect of dual antiplatelet therapy (DAPT) increase the risk of bleeding. Inadequate anticoagulation leads to thrombus formation and device dysfunction. The precarious balance between bleeding and thrombosis in patients with p-LVAD support is often the primary reason that patients’ outcomes are jeopardized. In this chapter, we will discuss anticoagulation strategies and anticoagulant management in the setting of protected PCI. This includes anticoagulant therapy with unfractionated heparin, direct thrombin inhibitors, DAPT, purge blockage prevention by bicarbonate-based purge solution, and monitoring by activated clotting time, partial thromboplastin time, as well as anti-factor Xa levels. Here, we provide a standardized approach to the management of peri-interventional anticoagulation in patients undergoing protected PCI.
Female political representation and the gender health gap: a cross-national analysis of 49 European countries
Authors: Reeves Aaron , Brown Chris , Hanefeld Johanna 
Published: September 2022

Abstract

Background
Does increased female participation in the social and political life of a country improve health? Social participation may improve health because it ensures that the concerns of all people are heard by key decision-makers. More specifically, when women’s social participation increases this may lead to health gains because women are more likely to vote for leaders and lobby for policies that will enhance the health of everyone. This article tries to examine whether female participation is correlated with measures of health inequality.

Methods
We draw on data from the World Health Organization Health Equity Status Report initiative and the Varieties of Democracy project to assess whether health is better and health inequalities are smaller in countries where female political representation is greater.

Results
We find consistent evidence that greater female political representation is associated with lower geographical inequalities in infant mortality, smaller inequalities in self-reported health (for both women and men) and fewer disability-adjusted life-years lost for women and men. Finally, we find that greater female political representation is not only correlated with better health for men and women but is also correlated with a smaller gap between men and women because men seem to experience better health in such contexts.

Conclusions
Greater female political representation is associated with better health for everyone and smaller inequalities.
Phyllosphere bacterial communities in urban green areas throughout Europe relate to urban intensity
Authors: Muyshondt Babette , Wuyts Karen , Van Mensel Anskje , Smets Wenke , Lebeer Sarah , Aleixo Cristiana , Alós Ortí Marta , Casanelles-Abella Joan , Chiron François , Giacomo Puglielli , Laanisto Lauri , Moretti Marco , Niinemets Ülo , Pinho Pedro , Tryjanowski Piotr , Woszczyło Patrycja , Samson Roeland 
Published: September 2022

Abstract
The phyllosphere harbours a diverse and specific bacterial community, which influences plant health and ecosystem functioning. In this study, we investigated the impact of urban green areas connectivity and size on the composition and diversity of phyllosphere bacterial communities. Hereto, we evaluated the diversity and composition of phyllosphere bacterial communities of 233 Platanus x acerifolia and Acer pseudoplatanus trees in 77 urban green areas throughout 6 European cities. The community composition and diversity significantly differed between cities but only to a limited extent between tree species. We could show that urban intensity correlated significantly with the community composition of phyllosphere bacteria. In particular, a significant correlation was found between the relative abundances for 29 out of the 50 most abundant families and the urban intensity: the abundances of classic phyllosphere families, such as Acetobacteraceae, Planctomycetes, and Beijerinkiaceae, decreased with urban intensity (i.e. more abundant in areas with more green, lower air pollution, and lower temperature), while those related to human activities, such as Enterobacteriaceae and Bacillaceae, increased with urban intensity. The results of this study suggest that phyllosphere bacterial communities in European cities are associated with urban intensity and that effect is mediated by several combined stress factors.
Marker-assisted mapping enables forward genetic analysis inAedes aegypti, an arboviral vector with vast recombination deserts
Authors: Chen Chujia , Compton Austin , Nikolouli Katerina , Wang Aihua , Aryan Azadeh , Sharma Atashi , Qi Yumin , Dellinger Camden , Hempel Melanie , Potters Mark , Augustinos Antonios , Severson David W , Bourtzis Kostas , Tu Zhijian 
Published: September 2022

AbstractAedes aegypti is a major vector of arboviruses that cause dengue, chikungunya, yellow fever, and Zika. Although recent success in reverse genetics has facilitated rapid progress in basic and applied research, integration of forward genetics with modern technologies remains challenging in this important species, as up to 47% of its chromosome is refractory to genetic mapping due to extremely low rate of recombination. Here, we report the development of a marker-assisted mapping strategy to readily screen for and genotype only the rare but informative recombinants, drastically increasing both the resolution and signal-to-noise ratio. Using marker-assisted mapping, we mapped a transgene that was inserted in a &gt;100-Mb recombination desert and a sex-linked spontaneous red-eye (re) mutation just outside the region. We subsequently determined, by CRISPR/Cas9-mediated knockout, that cardinal is the causal gene of re, which is the first forward genetic identification of a causal gene in Ae. aegypti. The identification of the causal gene of the sex-linked re mutation provides the molecular foundation for using gene editing to develop versatile and stable genetic sexing methods. To facilitate genome-wide forward genetics in Ae. aegypti, we generated and compiled a number of lines with markers throughout the genome. Thus, by overcoming the challenges presented by the vast recombination deserts and the scarcity of markers, we have shown that effective forward genetic analysis is increasingly feasible in this important arboviral vector species.