bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neoliberalism: A Very Short Introduction
Authors: Steger Manfred B. , Roy Ravi K. 
Published: January 2021

Abstract
Neoliberalism: A Very Short Introduction explores the considerable variations of neoliberalism around the world. It also discusses the origins, evolution, and core ideas of neoliberalism. Neoliberalism emerged as the world's dominant economic paradigm in the 1990s. The global financial crash of 2008 and the subsequent emergence of more nationalist ideologies have challenged both neoliberal assumptions and related financial systems—a development most spectacularly reflected in 2016's pro-Brexit referendum in the UK and the Trump election victory in the same year. This new edition asks whether changing versions of neoliberalism might succeed in drowning out the calls for a return to territorial sovereignty and national greatness.
Adverse Childhood Experiences and Rate of Memory Decline From Mid to Later Life: Evidence From the English Longitudinal Study of Ageing
Authors: O’Shea Brendan Q , Demakakos Panayotes , Cadar Dorina , Kobayashi Lindsay C 
Published: January 2021

Abstract
Evidence on the role of early-life adversity in later-life memory decline is conflicting. We investigated the relationships between adverse childhood experiences (ACEs) and memory performance and rate of decline over a 10-year follow-up among middle-aged and older adults in England. Data were from biennial interviews with 5,223 participants aged 54 years or older in the population-representative English Longitudinal Study of Ageing from 2006/2007 to 2016/2017. We examined self-reports of 9 ACEs prior to age 16 years that related to abuse, household dysfunction, and separation from family. Memory was assessed at each time point as immediate and delayed recall of 10 words. Using linear mixed-effects models with person-specific random intercepts and slopes and adjusted for baseline age, participants’ baseline age squared, sex, ethnicity, and childhood socioeconomic factors, we observed that most individual and cumulative ACE exposures had null to weakly negative associations with memory function and rate of decline over the 10-year follow-up. Having lived in residential or foster care was associated with lower baseline memory (adjusted β = −0.124 standard deviation units; 95% confidence interval: −0.273, −0.025) but not memory decline. Our findings suggest potential long-term impacts of residential or foster care on memory and highlight the need for accurate and detailed exposure measures when studying ACEs in relation to later-life cognitive outcomes.
Market Segmentation and Shirley Jackson’s Domestic Humor
Authors: Mangrum Benjamin 
Published: January 2021

Abstract
Shirley Jackson’s essays in popular women’s magazines negotiate the gendered tensions and commercial contradictions of postwar print culture. This essay shows how the women in Jackson’s essays are figures of the fraught convergence of women’s public affiliation and the restrained politics of gender critique. These female figures are also representative of broader issues in US print culture after the Second World War. In particular, Jackson’s essays represent how a certain strain of feminist writing—sometimes known as “domestic humor”—was absorbed within the market forces of print capitalism. To explain this absorption, I draw on mid-century theories of market segmentation.
Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E
Authors: Suzuki Manami , Takita Teisuke , Kuwata Kohei , Nakatani Kota , Li Tongyang , Katano Yuta , Kojima Kenji , Mizutani Kimihiko , Mikami Bunzo , Yatsunami Rie , Nakamura Satoshi , Yasukawa Kiyoshi 
Published: January 2021

ABSTRACT
The mechanism of thermostabilization of GH10 xylanase, XynR, from Bacillus sp. strain TAR-1 by the mutation of S92 to E was investigated. Thermodynamic analysis revealed that thermostabilization was driven by the decrease in entropy change of activation for thermal inactivation. Crystallographic analysis suggested that this mutation suppressed the fluctuation of the amino acid residues at position 92-95.
Accurate prediction of inter-protein residue–residue contacts for homo-oligomeric protein complexes
Authors: Yan Yumeng , Huang Sheng-You 
Published: January 2021

AbstractProtein–protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein–protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein–protein interactions. Recently, deep learning has led to a breakthrough in intra-protein contact prediction, achieving an unusual high accuracy in recent Critical Assessment of protein Structure Prediction (CASP) structure prediction challenges. However, due to the limited number of known homologous protein–protein interactions and the challenge to generate joint multiple sequence alignments of two interacting proteins, the advances in inter-protein contact prediction remain limited. Here, we have proposed a deep learning model to predict inter-protein residue–residue contacts across homo-oligomeric protein interfaces, named as DeepHomo. Unlike previous deep learning approaches, we integrated intra-protein distance map and inter-protein docking pattern, in addition to evolutionary coupling, sequence conservation, and physico-chemical information of monomers. DeepHomo was extensively tested on both experimentally determined structures and realistic CASP-Critical Assessment of Predicted Interaction (CAPRI) targets. It was shown that DeepHomo achieved a high precision of &gt;60% for the top predicted contact and outperformed state-of-the-art direct-coupling analysis and machine learning-based approaches. Integrating predicted inter-chain contacts into protein–protein docking significantly improved the docking accuracy on the benchmark dataset of realistic homo-dimeric targets from CASP-CAPRI experiments. DeepHomo is available at http://huanglab.phys.hust.edu.cn/DeepHomo/
Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance
Authors: Huang Dan , Wang Xiansong , Liu Yingzhi , Huang Ziheng , Hu Xiaoxu , Hu Wei , Li Qing , Chan Hung , Zou Yidan , Ho Idy H T , Wang Yan , Cheng Alfred S L , Kang Wei , To Ka F , Wang Maggie H T , Wong Sunny H , Yu Jun , Gin Tony , Zhang Qingpeng , Li Zheng , Shen Jianxiong , Zhang Lin , Chan Matthew T V , Liu Xiaodong , Wu William K K 
Published: January 2021

AbstractTumor suppressor genes (TSGs) exhibit distinct evolutionary features. We speculated that TSG promoters could have evolved specific features that facilitate their tumor-suppressing functions. We found that the promoter CpG dinucleotide frequencies of TSGs are significantly higher than that of non-cancer genes across vertebrate genomes, and positively correlated with gene expression across tissue types. The promoter CpG dinucleotide frequencies of all genes gradually increase with gene age, for which young TSGs have been subject to a stronger evolutionary pressure. Transcription-related features, namely chromatin accessibility, methylation and ZNF263-, SP1-, E2F4- and SP2-binding elements, are associated with gene expression. Moreover, higher promoter CpG dinucleotide frequencies and chromatin accessibility are positively associated with the ability of TSGs to resist downregulation during tumorigenesis. These results were successfully validated with independent datasets. In conclusion, TSGs evolved specific promoter features that optimized cancer resistance through achieving high expression in normal tissues and resistance to downregulation during tumorigenesis.
essHi-C: essential component analysis of Hi-C matrices
Authors: Franzini Stefano , Di Stefano Marco , Micheletti Cristian 
Published: January 2021

Abstract

Motivation
Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C assays reflects in an inherent stochastic background of the interactions matrices, which inevitably convolve the features of interest with largely non-specific ones.

Results
Here, we introduce and discuss essHi-C, a method to isolate the specific or essential component of Hi-C matrices from the non-specific portion of the spectrum compatible with random matrices. Systematic comparisons show that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth of topologically associating domains identification, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices.

Availability and implementation
The essHi-C software package is available at https://github.com/stefanofranzini/essHIC.

Supplementary information
Supplementary data are available at Bioinformatics online.
eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition
Authors: Wang Hao , Liang Pengfei , Zheng Lei , Long ChunShen , Li HanShuang , Zuo Yongchun 
Published: January 2021

Abstract

Motivation
Hematopoietic stem cells (HSCs) give rise to all blood cells and play a vital role throughout the whole lifespan through their pluripotency and self-renewal properties. Accurately identifying the stages of early HSCs is extremely important, as it may open up new prospects for extracorporeal blood research. Existing experimental techniques for identifying the early stages of HSCs development are time-consuming and expensive. Machine learning has shown its excellence in massive single-cell data processing and it is desirable to develop related computational models as good complements to experimental techniques.

Results
In this study, we presented a novel predictor called eHSCPr specifically for predicting the early stages of HSCs development. To reveal the distinct genes at each developmental stage of HSCs, we compared F-score with three state-of-art differential gene selection methods (limma, DESeq2, edgeR) and evaluated their performance. F-score captured the more critical surface markers of endothelial cells and hematopoietic cells, and the area under receiver operating characteristic curve (ROC) value was 0.987. Based on SVM, the 10-fold cross-validation accuracy of eHSCpr in the independent dataset and the training dataset reached 94.84% and 94.19%, respectively. Importantly, we performed transcription analysis on the F-score gene set, which indeed further enriched the signal markers of HSCs development stages. eHSCPr can be a powerful tool for predicting early stages of HSCs development, facilitating hypothesis-driven experimental design and providing crucial clues for the in vitro blood regeneration studies.

Availability and implementation
http://bioinfor.imu.edu.cn/ehscpr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators
Authors: Yao Qiuming , Ferragina Paolo , Reshef Yakir , Lettre Guillaume , Bauer Daniel E , Pinello Luca 
Published: January 2021

Abstract

Motivation
Genome-wide association studies (GWASs) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging. These genetic variants can overlap the binding sites of transcription factors (TFs) and therefore could alter gene expression. However, we currently lack a systematic understanding on how this mechanism contributes to phenotype.

Results
We present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predictive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Given trait-associated non-coding variants, Motif-Raptor can recover relevant cell types and critical TFs to drive hypotheses regarding their mechanism of action. We tested Motif-Raptor on complex traits such as rheumatoid arthritis and red blood cell count and demonstrated its ability to prioritize relevant cell types, potential regulatory TFs and non-coding SNPs which have been previously characterized and validated.

Availability and implementation
Motif-Raptor is freely available as a Python package at: https://github.com/pinellolab/MotifRaptor.

Supplementary information
Supplementary data are available at Bioinformatics online.
RAD: a web application to identify region associated differentially expressed genes
Authors: Guo Yixin , Xue Ziwei , Yuan Ruihong , Li Jingyi Jessica , Pastor William A. , Liu Wanlu 
Published: January 2021

Abstract

Summary
With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually less focused, largely due to the lack of reliable tools to link these regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes (DEGs). With DEGs and genomic regions of interest (gROI) as input, RAD maps the up- and down-regulated genes associated with any gROI and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance.

Availability and implementation
RAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available at https://labw.org/rad as online web service.

Supplementary information
Supplementary data are available at Bioinformatics online.
Exact maximal reduction of stochastic reaction networks by species lumping
Authors: Cardelli Luca , Perez-Verona Isabel Cristina , Tribastone Mirco , Tschaikowski Max , Vandin Andrea , Waizmann Tabea 
Published: January 2021

Abstrtact

Motivation
Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortunately, in all but simplest models the resulting discrete state-space representation hinders analytical tractability and makes numerical simulations expensive. Reduction methods can lower complexity by computing model projections that preserve dynamics of interest to the user.

Results
We present an exact lumping method for stochastic reaction networks with mass-action kinetics. It hinges on an equivalence relation between the species, resulting in a reduced network where the dynamics of each macro-species is stochastically equivalent to the sum of the original species in each equivalence class, for any choice of the initial state of the system. Furthermore, by an appropriate encoding of kinetic parameters as additional species, the method can establish equivalences that do not depend on specific values of the parameters. The method is supported by an efficient algorithm to compute the largest species equivalence, thus the maximal lumping. The effectiveness and scalability of our lumping technique, as well as the physical interpretability of resulting reductions, is demonstrated in several models of signaling pathways and epidemic processes on complex networks.

Availability and implementation
The algorithms for species equivalence have been implemented in the software tool ERODE, freely available for download from https://www.erode.eu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Transanal total mesorectal excision and low anterior resection syndrome
Authors: van der Heijden J A G , Qaderi S M , Verhoeven R , Custers J A E , Klarenbeek B R , Maaskant-Braat A J G , de Wilt J H W ,   the PLCRC group, Beets G L , Belt E J Th , Berbée M , Beverdam F H , Blankenburgh R , Coene P P L O , de Groot J W B , de Hingh I H J T , de Vos A I , de Wilt J H W , Dekker J W T , Erdkamp F L G , Haringhuizen A W , Helgason H H , Hendriks M P , Hoekstra R , Ijzermans J N M , Jansen J , Kloppenberg F W H , Los M , Meijerink M R , Mekenkamp L J M , Nieboer P , Peeters K C M J , Peters N A J B , Polée M B , Verdaasdonk E G G , Quarles van Ufford-Mannesse P , Rietbroek R C , Schiphorst A H W , Schouten van der Velden A , Schrauwen R W M , Sie M P S , Simkens L , Sommeijer D W , Sonneveld D J A , Spierings L E A , Stockmann H B A C , Talsma K , ten Tije A J , Terheggen F , Tjin-A-Ton M L R , Valkenburg-van Iersel L B J , van Cruijsen H , van der Velden A M T , van Dodewaard-de Jong J M , van Lent A U G , van Voorthuizen T , Vermaas M , Vles W J , Vogelaar J F J , Zimmerman D D E , van Grevenstein H W M U , Vink G R 
Published: January 2021

Abstract

Background
Bowel dysfunction after rectal cancer surgery is common, with some experiencing low anterior resection syndrome (LARS) is common after rectal cancer surgery. This study examined if transanal total mesorectal excision (TaTME) has a similar risk of LARS and altered quality of life (QoL) as patients who undergo low anterior resection (LAR).

Methods
Patients who underwent TaTME or traditionally approached total mesorectal excision in a prospective colorectal cancer cohort study (2014–2019) were propensity score matched in a 1 : 1 ratio. LARS and QoL scores were assessed before and after surgery with a primary endpoint of major LARS at 12 months analysed for possible association between factors by logistic regression.

Results
Of 61 TaTME and 317 LAR patients eligible, 55 from each group were propensity score matched. Higher LARS scores (30.6 versus 25.4, P = 0.010) and more major LARS (65 versus 42 per cent, P = 0.013; OR 2.64, 95 per cent c.i. 1.22 to 5.71) were reported after TaTME. Additionally, QoL score differences (body image, bowel frequency, and embarrassment) were worse in the TaTME group.

Conclusions
TaTME may be associated with more severe bowel dysfunction than traditional approaches to rectal cancer.
Purchasing Power and Self-Determination: Social Worker Perspectives
Authors: Bailey Charlotte , Plath Debbie , Sharma Alankaar 
Published: January 2021

Abstract
The international policy trend towards personalised budgets, which is designed to offer people with disabilities purchasing power to choose services that suit them, is exemplified in the Australian National Disability Insurance Scheme (NDIS). This article examines how the ‘purchasing power’ afforded to service users through individualised budgets impacts on social work practice and the choice and self-determination of NDIS service users. Social workers’ views were sought on the alignment between the NDIS principles of choice and control and social work principles of participation and self-determination and how their social work practice has changed in order to facilitate client access to supports through NDIS budgets and meaningful participation in decision-making. A survey was completed by forty-five social workers, and in-depth semi-structured interviews were conducted with five of these participants. The findings identify how social workers have responded to the shortfalls of the NDIS by the following: interpreting information for clients; assisting service users to navigate complex service provision systems; supporting clients through goal setting, decision-making and implementation of action plans; and adopting case management approaches. The incorporation of social work services into the NDIS service model is proposed in order to facilitate meaningful choice and self-determination associated with purchasing power.
Debt Managers’ Reaction to Sovereign Risk in the Euro Area: Evidence and Policy Implications
Authors: Arnold Ivo J M 
Published: January 2021

Abstract
When sovereign spreads increase, debt managers in the euro area face a funding dilemma. They can either issue more short-term debt, thereby increasing roll-over risk, or issue long-term debt at higher borrowing costs. The latter choice may threaten debt sustainability. Using a sample of monthly data for 10 countries in the euro area, we measure how the share of short-term debt issuance reacts to bond yields, term spreads, default spreads, and money market spreads. We find that sovereign risk is a significant variable in debt reaction functions: higher default spreads increase the reliance on short-term funding, making the euro area more prone to funding crises in individual member states. As a solution to this problem, we discuss a proposal for an interest stabilization mechanism. By providing conditional interest subsidies to distressed countries, such a mechanism can maintain market access and avoid bad bond market equilibria. It will reduce the incentive of debt managers to shorten the maturity structure of public debt and thereby make the euro area less fragile (JEL codes: E43, F45, and H63).
Immuno-metabolic interfaces in cardiac disease and failure
Authors: Bertero Edoardo , Dudek Jan , Cochain Clement , Delgobo Murilo , Ramos Gustavo , Gerull Brenda , Higuchi Takahiro , Vaeth Martin , Zernecke Alma , Frantz Stefan , Hofmann Ulrich , Maack Christoph 
Published: January 2021

Abstract
The interplay between the cardiovascular system, metabolism, and inflammation plays a central role in the pathophysiology of a wide spectrum of cardiovascular diseases, including heart failure. Here, we provide an overview of the fundamental aspects of the interrelation between inflammation and metabolism, ranging from the role of metabolism in immune cell function to the processes how inflammation modulates systemic and cardiac metabolism. Furthermore, we discuss how disruption of this immuno-metabolic interface is involved in the development and progression of cardiovascular disease, with a special focus on heart failure. Finally, we present new technologies and therapeutic approaches that have recently emerged and hold promise for the future of cardiovascular medicine.
Profile shape variation and sexual dimorphism amongst middle-aged Northern Europeans
Authors: Kanavakis Georgios , Silvola Anna-Sofia , Halazonetis Demetrios , Lähdesmäki Raija , Pirttiniemi Pertti 
Published: January 2021

Summary

Aim
To explore profile shape variation in a large population of middle-aged individuals and investigate features of sexual dimorphism.

Materials and methods
Facial profile photographs of 1776 individuals (964 females and 812 males; 46 years old), members of the Northern Finland Birth Cohort 1966 (NFBC1966), were uploaded and digitized with Viewbox software. Profile shape was defined with 47 landmarks (4 fixed and 43 sliding semi-landmarks). Digitized images were reoriented and scaled with Procrustes Superimposition, and shape variation was determined with a Principal Component Analysis.

Results
More than 90 per cent of profile shape variation was explained by Principal Components (PC) 1–9. PC1, explaining the largest amount of variation (33.1 per cent) described changes in facial convexity, slope of the forehead, lip, and chin protuberance. PC2 (23.1 per cent variation) was more related to vertical changes of the lower facial third and PC3 (11 per cent variation) primarily described changes in lip protrusion and nasal projection. Shape analysis showed a significant difference between the average female and the average male profile shape (P &lt; 0.001); however, this was not evident upon visual observation. The shape variable most associated with sex was PC3 (η 2 = 0.245; P &lt; 0.001), which described changes in lip prominence and in projection of the dorsal nasal surface. An additional discriminant analysis showed that profile shape predicted sex in 76 per cent of males and 79.6 per cent of females.

Conclusions
There is significant sexual dimorphism in facial profile among middle-aged adults. Profile shape variation was associated to changes in lip protrusion, nasal protuberance, and chin projection.