bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drug–Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information
Authors: Li Yanfei , Sun Chang , Wei Jin-Mao , Liu Jian 
Published: September 2022

Abstract

Motivation
Large-scale heterogeneous data provide diverse perspectives for predicting drug–protein interactions (DPIs). However, the available information on molecular interactions and clinical associations related to drugs or proteins is incomplete because there may be unproven interactions and associations. This incomplete information in the available data is presented in the form of non-interaction and non-correlation, which may mislead the prediction model. Existing methods fuse incomplete and complete information without considering their integrity, so the negative effects of incomplete information still exist.

Results
We develop a network-based DPI prediction method named BRWCP, which uses the complete information network to correct the prediction results acquired by the incomplete information network. By integrating relevant heterogeneous information that may be incomplete, the feature similarities of drugs and proteins are obtained. Combining the feature similarities and known DPIs, an incomplete information-based drug–protein heterogeneous network is constructed. Then, a bidirectional random walk with pruning algorithm is adopted in this heterogeneous network to predict potential DPIs. Next, the predicted DPIs are combined with the chemical fingerprint similarity of drugs and amino acid sequence similarity of proteins to construct the complete information network. The bidirectional random walk with pruning algorithm is applied in the new network to obtain the final prediction results until it converges. Experimental results show that BRWCP is superior to several state-of-the-art DPI prediction methods, and case studies further confirm its ability to tap potential DPIs.

Availability and implementation
The code and data used in BRWCP are available at https://github.com/lyfdomain/BRWCP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Race and Men’s Imprisonment in the United States: Religious Conservatism, Political Conservatism and Racial Threat
Authors: Levchak Philip J , Heimer Karen , Lang Joseph B , Lauritsen Janet L 
Published: September 2022

AbstractBlack men are overrepresented in United States prisons and the number of Black men incarcerated increased dramatically during America’s “prison boom.” Yet, existing research on male imprisonment rates in the United States has focused on explaining overall rates and has not statistically modeled rates disaggregated by race over time. This study uses seemingly unrelated regression techniques to analyze annual rates of Black and non-Black men incarcerated in state prisons during the period of greatest increase in United States imprisonment rates. The findings show that increasing evangelical religious conservativism is associated with higher Black imprisonment rates and, importantly, this effect is “amplified” when state legislatures are more politically conservative. We also find that as Black populations increase, the punitive effect of religious conservatism is moderated or attenuated, and this holds for the incarceration of Black as well as non-Black men. In addition, consistent with a racial threat perspective, growth in Black populations in states is linked with increases in Black as well as non-Black male imprisonment rates. Together these effects emphasize the importance of examining imprisonment rates disaggregated by race and highlight the joint and conditional effects of religious conservatism, political conservatism, and racial threat for understanding imprisonment in the United States.
Professional Encounters with ‘the Other’: Widening Accessibility of Social Work Practices in Urban Neighbourhoods
Authors: Ponzoni Elena , de Ruyter Doret 
Published: September 2022

AbstractSocial work professionals in urban contexts struggle to serve different groups equally. Critical social work literature advocates critical reflexivity in social work practices. Focusing on existing support practices, it encourages scrutinising the implicit ways social work practices can maintain and reproduce power imbalances and othering structures. However, it has not examined the tensions connected with phases in which the first contact between clients and professionals occurs and clients’ engagement in social work programmes begins. Stimulated by an empirical research into parenting-support in a city in the Netherlands, this article examines theoretically the notion of ‘encounter practices’ through which professionals reach out to people considered in need of support but not asking for help. We disentangle how encounter practices can be interpreted through different understandings of professional engagement, emerging from either critical or affirmative traditions of social work. The encounter context poses specific challenges for critical reflexivity, but it also offers the possibility of exploring one’s social positioning in relation to others through informal micro-interactions preceding the instalment of professional relations between professionals and parents. Drawing on insights from urban studies, we distinguish ‘fleeting’, ‘convivial’ and ‘engaged encounters’ as different levels of encounter that allow unsettling othering structures in outreach practices.
Why are you just watching?: polyvalent Korean spectatorship and critical Western spectatorship in Squid Game
Authors: Dunn Jennifer C , Young Stephanie L 
Published: September 2022

Abstract
Although the narrative of Squid Game critiques socioeconomic structures, the characters, genre, filming techniques, and aesthetics, ironically, situate audiences as passive spectators. In this article, we discuss the ways Squid Game constructs a polyvalent Korean spectatorship and a critical Western spectatorship within the survival game genre. We argue the series hails spectators to consent to the same oppressive socioeconomic structures the show seemingly critiques. Additionally, we consider potentials of rhetorical witnessing for activating audiences and extending spectatorship theory.
Zonulin, as a marker of intestinal permeability, is elevated in IgA nephropathy and IgA vasculitis with nephritis
Authors: Li Qianqian , Yuan Xiaohan , Shi Sufang , Liu Lijun , Lv Jicheng , Zhu Li , Zhang Hong 
Published: September 2022

ABSTRACT

Background
Immunoglobulin A nephropathy (IgAN) and IgA vasculitis with nephritis (IgAV-N) are considered related diseases and share some similar clinicopathologic phenotypes. Elevated circulating galactose-deficient IgA1 (Gd-IgA1)-containing immune complexes and mucosal immunity were associated with the pathogenesis of IgAN and IgAV-N. Recently, studies have identified that the zonulin level, as a modulator of intestinal permeability, is significantly elevated in several inflammatory and autoimmune-related diseases. However, whether zonulin also plays a role in IgAN and IgAV-N is not clear.

Methods
A total of 73 IgAV-N patients, 68 IgAN patients and 54 healthy controls were assessed for circulating zonulin and Gd-IgA1 levels by enzyme-linked immunosorbent assay. The diagnostic efficiency of the combination of zonulin with Gd-IgA1 was evaluated by the area under the receiver operating characteristic curve (AUC) and integrated discrimination improvement (IDI) analysis.

Results
Compared with healthy controls, we found that both IgAV-N and IgAN patients had elevated zonulin and Gd-IgA1 levels (P &lt; .001). Additionally, patients with IgAV-N presented with even higher circulating zonulin levels than patients with IgAN (P = .020). The addition of zonulin to Gd-IgA1 showed better predictive performance than Gd-IgA1 alone in the diagnosis of both IgAN and IgAV-N, as illustrated by a significantly increased AUC (IgAN: 0.805 versus 0.708, P = .0021; IgAV-N: 0.886 versus 0.673, P &lt; .001) and significant IDI (IgAN: IDI 0.136, P &lt; .001; IgAV-N: IDI 0.281, P &lt; .001).

Conclusion
Elevated circulating zonulin levels were detected in both patients with IgAV-N and those with IgAN. Combined detection of circulating zonulin and Gd-IgA1 is recommended as a noninvasive diagnostic biomarker for IgAV-N and IgAN.
DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands
Authors: Alemany Iris , Pérez-Cembranos Ana , Pérez-Mellado Valentín , Castro José Aurelio , Picornell Antònia , Ramon Cori , Jurado-Rivera José A 
Published: September 2022

Abstract
Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species
Authors: Liska Orsolya , Bohár Balázs , Hidas András , Korcsmáros Tamás , Papp Balázs , Fazekas Dávid , Ari Eszter 
Published: September 2022

Abstract
Analysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor–target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription factor–target gene interactions (∼12 million), nucleotide sequences and genomic locations of transcription factor binding sites (∼9 million) for human and six model organisms: mouse, rat, zebrafish, fruit fly, worm and yeast by integrating 10 resources. TFLink provides user-friendly access to data on transcription factor–target gene interactions, interactive network visualizations and transcription factor binding sites, with cross-links to several other databases. Besides containing accurate information on transcription factors, with a clear labelling of the type/volume of the experiments (small-scale or high-throughput), the source database and the original publications, TFLink also provides a wealth of standardized regulatory data available for download in multiple formats. The database offers easy access to high-quality data for wet-lab researchers, supplies data for gene set enrichment analyses and facilitates systems biology and comparative gene regulation studies.
Database URL https://tflink.net/
Re-intervention percutaneous balloon mitral valvuloplasty in a patient with left atrial appendage thrombus: a case report
Authors: Parikh Rujuta , Singh Gaurav , Mishra Ashish , Sharma Kamal 
Published: September 2022

Abstract

Background
Percutaneous balloon mitral valvuloplasty (PBMV) using an Accura balloon is an effective method for management of rheumatic mitral stenosis.

Case summary
Herein, we present a case of a 43-year-old female, who had undergone a previous PBMV, who presented with very severe mitral re-stenosis with Type Ia left atrial (LA) clot, in atrial fibrillation and New York Heart Association functional Class III. We used the modified septal puncture and over-the-wire technique, avoiding inadvertent manipulation of the LA clot for PBMV. The mitral valve was successfully dilated from 0.9 to 1.5 cm2, and the patient had an uneventful post-procedure recovery.

Discussion
The presence of LA clot and mitral re-stenosis in a previously intervened valve are considered unfavourable characteristics for a PBMV procedure, and patients are usually advised surgical intervention. These patients are also high-risk candidates for surgery due to late presentation with advanced disease and poor functional capacity. Our patient underwent successful re-intervention with PBMV despite having suboptimal characteristics.
Concrete proof of Murphy’s law: a case report of intracardiac cement embolization
Authors: Krithika Ramaprabhu , Geske Jeffrey B , Villarraga Hector R , Crestanello Juan 
Published: September 2022

Abstract

Background
The literature describing the complications following kyphoplasty is limited. This case report is a reminder that novel therapeutic strategies can be associated with unexpected complications.

Case summary
A 61-year-old woman with rheumatoid arthritis and degenerative lumbar disc disease underwent open posterior instrumented fusion with bilateral open L2 vertebroplasty elsewhere. A month after discharge, she presented to our institution with acute chest pain and dyspnoea. A subsequent gated cardiac computed tomography (CT) angiogram showed three distinct cardiopulmonary emboli. One of the cement fragments had perforated the inferior wall of the right ventricle close to the base of the posterior tricuspid valve leaflet with a moderate circumferential pericardial effusion. Operative extraction of multiple cement emboli as well as repair of the tricuspid valve was pursued. Postoperative echocardiogram showed trivial tricuspid regurgitation after repair. The patient had an uneventful postoperative course and was discharged from the hospital on postoperative Day 5.

Discussion
Cement embolization following kyphoplasty can be associated with serious complications such as vascular injury, hypoxaemia, pulmonary artery obstruction, and cardiac perforation. Clinicians must maintain a high index of suspicion as cement embolism may not always present acutely.
Systematic approach to outcome assessment from coded electronic healthcare records in the DaRe2THINK NHS-embedded randomized trial
Authors: Wang Xiaoxia , Mobley Alastair R , Tica Otilia , Okoth Kelvin , Ghosh Rebecca E , Myles Puja , Williams Tim , Haynes Sandra , Nirantharakumar Krishnarajah , Shukla David , Kotecha Dipak ,   the DaRe2THINK Trial Committees, Beatty Susan , Mehta Samir , Breeze Sophie , Lancaster Karen , Fordyce Stuart , Allen Naomi , Calvert Melanie , Denniston Alastair , Gkoutos George , Jayawardana Sahan , Ball Simon , Baigent Colin , Brocklehurst Peter , Lester Will , McManus Richard , Seri Stefano , Valentine Janet , Camm A John , Haynes Sandra , Moore Dame Julie , Rogers Amy , Stanbury Mary , Flather Marcus , Walker Suzy , Wang Duolao 
Published: September 2022

Abstract

Aims
Improving the efficiency of clinical trials is key to their continued importance in directing evidence-based patient care. Digital innovations, in particular the use of electronic healthcare records (EHRs), allow for large-scale screening and follow up of participants. However, it is critical these developments are accompanied by robust and transparent methods that can support high-quality and high clinical value research.

Methods and results
The DaRe2THINK trial includes a series of novel processes, including nationwide pseudonymized pre screening of the primary-care EHR across England, digital enrolment, remote e-consent, and ‘no-visit’ follow up by linking all primary- and secondary-care health data with patient-reported outcomes. DaRe2THINK is a pragmatic, healthcare-embedded randomized trial testing whether earlier use of direct oral anticoagulants in patients with prior or current atrial fibrillation can prevent thromboembolic events and cognitive decline (www.birmingham.ac.uk/dare2think). This study outlines the systematic approach and methodology employed to define patient information and outcome events. This includes transparency on all medical code lists and phenotypes used in the trial across a variety of national data sources, including Clinical Practice Research Datalink Aurum (primary care), Hospital Episode Statistics (secondary care), and the Office for National Statistics (mortality).

Conclusion
Co-designed by a patient and public involvement team, DaRe2THINK presents an opportunity to transform the approach to randomized trials in the setting of routine healthcare, providing high-quality evidence generation in populations representative of the community at risk.
The Impact of Corporate QE on Liquidity: Evidence from the UK
Authors: Boneva Lena , Elliott David , Kaminska Iryna , Linton Oliver , McLaren Nick , Morley Ben 
Published: September 2022

Abstract
There is substantial uncertainty about the impact of quantitative easing on market liquidity. Identifying the impact is particularly challenging due to the potential for reverse causality, because liquidity considerations might affect quantitative easing purchases. We address this challenge by studying the Bank of England’s 2016–7 Corporate Bond Purchase Scheme. In particular, we use granular offer-level data from the Corporate Bond Purchase Scheme auctions to construct proxy measures for the Bank of England's demand for bonds and auction participants’ supply of bonds, allowing us to control for any reverse causality from liquidity to purchases. We find that Corporate Bond Purchase Scheme purchases improved the liquidity of purchased bonds.
Cardiovascular prevention: sometimes dreams can come true
Authors: Ferrari Roberto , Cimaglia Paolo , Rapezzi Claudio , Tavazzi Luigi , Guardigli Gabriele 
Published: September 2022

Abstract
Cardiovascular disease (CVD) is a chronic condition driven by the complex interaction of different risk factors including genetics, lifestyle, environment, etc. which, differently from other pathologies, can be prevented. Treatment of CVD has been inconceivably successful but now it seems that it has reached a plateau suggesting that prevention is the way forward. However, the COVID-19 pandemic has spotted all the limits of the actual health system regarding territorial and, particularly, of preventive medicine. To this end, recently, the SCORE2 risk prediction algorithms, a contemporary model to estimate 10-years risk of CVD in Europe and the new guidelines on prevention have been released. The present review article describes a dream: how prevention of CVD should be addressed in the future. New concepts and paradigms like early genetically personalized and imaging driven risk factors, cardiac risk cartography, measurements of the exposome, estimation of costs of a delayed outcome vs. healthy lifespan, are all addressed. We highlight the importance of technologies and the concept of being engaged in a ‘healthy’ and not just ‘sick’ system as it is today. The concept of ‘clearing house’ with a ‘healthcare team’ instead of a ‘heart team’ is described. Finally, we articulate the four points necessary for the dream to come true.
New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates?
Authors: Ndashimye Emmanuel , Reyes Paul S , Arts Eric J 
Published: September 2022

Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
Camellia oil trait and DIA quantitative proteomics analyses reveal the impact of harvesting time on the oil content and quality of the late-maturing cultivar C. oleifera ‘Huaxin’
Authors: Wang Jugang , Gao Xiaomin , Liu Min , Li Jianxin , Yang Hong , Wang Zuhua , Yang Lilin 
Published: September 2022

Abstract

Objectives
Harvesting fruits prematurely is a serious problem in many Camellia oleifera ‘Huaxin’ orchards. Systematic views of dynamic alterations in central metabolism associated with the oil content and oil quality of this cultivar at different harvesting dates were investigated.

Materials and Methods
Oil trait analysis was performed in conjunction with data-independent acquisition proteomics analysis using kernels harvested at three time points. Samples were taken from different years and locations to verify oil trait changes, and parallel reaction monitoring (PRM) was performed for some pivotal proteins to validate changes in their abundance.

Results
Samples harvested at 6 d after the recommended harvesting date had the highest contents and best fatty acid composition of Camellia oil. A total of 614 differentially accumulated proteins were detected in three pairwise comparisons. Six days prior to the recommended harvesting date, the maximum expression of ribonucloprotein, helicase ATP-binding domain-containing protein, and glycerol kinase and the highest seed moisture content were observed. The highest mitogen-activated protein kinase 6, very-long-chain 3-oxoacyl-CoA reductase and stearoyl-CoA desaturase expression appeared on the recommended harvesting date. A delayed effect was observed for proteomic and oil trait data. Oil trait and PRM validations indicated that the results were highly reliable.

Conclusions
The current data strongly suggest that in Guizhou Province, ‘Huaxin’ cannot be harvested earlier than the recommended harvesting date; appropriately delaying the harvesting time can improve the ultimate production and quality of Camellia oil.