bluuebunny/crossref_metadata_2025_split huggingface dataset:
2023 roadmap for materials for quantum technologies
Authors: Becher Christoph , Gao Weibo , Kar Swastik , Marciniak Christian D , Monz Thomas , Bartholomew John G , Goldner Philippe , Loh Huanqian , Marcellina Elizabeth , Goh Kuan Eng Johnson , Koh Teck Seng , Weber Bent , Mu Zhao , Tsai Jeng-Yuan , Yan Qimin , Huber-Loyola Tobias , Höfling Sven , Gyger Samuel , Steinhauer Stephan , Zwiller Val 
Published: November 2022

AbstractQuantum technologies are poised to move the foundational principles of quantum physics to the forefront of applications. This roadmap identifies some of the key challenges and provides insights on material innovations underlying a range of exciting quantum technology frontiers. Over the past decades, hardware platforms enabling different quantum technologies have reached varying levels of maturity. This has allowed for first proof-of-principle demonstrations of quantum supremacy, for example quantum computers surpassing their classical counterparts, quantum communication with reliable security guaranteed by laws of quantum mechanics, and quantum sensors uniting the advantages of high sensitivity, high spatial resolution, and small footprints. In all cases, however, advancing these technologies to the next level of applications in relevant environments requires further development and innovations in the underlying materials. From a wealth of hardware platforms, we select representative and promising material systems in currently investigated quantum technologies. These include both the inherent quantum bit systems and materials playing supportive or enabling roles, and cover trapped ions, neutral atom arrays, rare earth ion systems, donors in silicon, color centers and defects in wide-band gap materials, two-dimensional materials and superconducting materials for single-photon detectors. Advancing these materials frontiers will require innovations from a diverse community of scientific expertise, and hence this roadmap will be of interest to a broad spectrum of disciplines.
VSTH: a user-friendly web server for structure-based virtual screening on Tianhe-2
Authors: Mo Qing , Xu Zexin , Yan Hui , Chen Pin , Lu Yutong 
Published: November 2022

AbstractSummaryVSTH is a user-friendly web server with the complete workflow for virtual screening. By self-customized visualization software, users can interactively prepare protein files, set docking sites as well as view binding conformers in a target protein in a few clicks. We provide serval purchasable ligand libraries for selection. And, we integrate six open-source docking programs as computing engine, or as conformational sampling tools for DLIGAND2. Users can select various docking methods simultaneously and personalize computing parameters. After docking processing, user can filter docking conformations by ranked scores, or cluster-based molecular similarity to find highly populated clusters of low-energy conformations.Availability and implementationThe VSTH web server is free and open to all users at https://matgen.nscc-gz.cn/VirtualScreening.htmlSupplementary informationSupplementary data are available at Bioinformatics online.
htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets
Authors: Sahadevan Sudeep , Sekaran Thileepan , Ashaf Nadia , Fritz Marko , Hentze Matthias W , Huber Wolfgang , Schwarzl Thomas 
Published: November 2022

Abstract

Summary
Transcriptome-wide detection of binding sites of RNA-binding proteins is achieved using Individual-nucleotide crosslinking and immunoprecipitation (iCLIP) and its derivative enhanced CLIP (eCLIP) sequencing methods. Here, we introduce htseq-clip, a python package developed for preprocessing, extracting and summarizing crosslink site counts from i/eCLIP experimental data. The package delivers crosslink site count matrices along with other metrics, which can be directly used for filtering and downstream analyses such as the identification of differential binding sites.

Availability and implementation
The Python package htseq-clip is available via pypi (python package index), bioconda and the Galaxy Tool Shed under the open source MIT License. The code is hosted at https://github.com/EMBL-Hentze-group/htseq-clip and documentation is available under https://htseq-clip.readthedocs.io/en/latest.
Neutrophil extracellular traps contribute to myofibroblast differentiation and scar hyperplasia through the Toll-like receptor 9/nuclear factor Kappa-B/interleukin-6 pathway
Authors: Shao Yiming , Guo Zaiwen , Yang Yunxi , Liu Lu , Huang Jiamin , Chen Yi , Li Linbin , Sun Bingwei 
Published: November 2022

Abstract

Background
Inflammation is an important factor in pathological scarring. The role of neutrophils, one of the most important inflammatory cells, in scar hyperplasia remains unclear. The purpose of this article is to study the correlation between neutrophil extracellular traps (NETs) and scar hyperplasia and identify a new target for inhibiting scar hyperplasia.

Methods
Neutrophils were isolated from human peripheral blood by magnetic-bead sorting. NETs in plasma and scars were detected by enzyme-linked immunosorbent assays (ELISAs), immunofluorescence and flow cytometry. Immunohistochemistry was used to assess neutrophil (CD66B) infiltration in hypertrophic scars. To observe the entry of NETs into fibroblasts we used immunofluorescence and flow cytometry.

Results
We found that peripheral blood neutrophils in patients with hypertrophic scars were more likely to form NETs (p &lt; 0.05). Hypertrophic scars showed greater infiltration with neutrophils and NETs (p &lt; 0.05). NETs activate fibroblasts in vitro to promote their differentiation and migration. Inhibition of NETs with cytochalasin in wounds reduced the hyperplasia of scars in mice. We induced neutrophils to generate NETs with different stimuli in vitro and detected the proteins carried by NETs. We did not find an increase in the expression of common scarring factors [interleukin (IL)-17 and transforming growth factor-β (TGF-β), p &gt; 0.05]. However, inhibiting the production of NETs or degrading DNA reduced the differentiation of fibroblasts into myofibroblasts. In vitro, NETs were found to be mediated by Toll-like receptor 9 (TLR-9) in fibroblasts and further phosphorylated nuclear factor Kappa-B (NF-κB). We found that IL-6, which is downstream of NF-κB, was increased in fibroblasts. Additionally, IL-6 uses autocrine and paracrine signaling to promote differentiation and secretion.

Conclusions
Our experiments found that NETs activate fibroblasts through the TLR-9/NF-κB/IL-6 pathway, thereby providing a new target for regulating hypertrophic scars.
Hsa_circ_0094606 promotes malignant progression of prostate cancer by inducing M2 polarization of macrophages through PRMT1-mediated arginine methylation of ILF3
Authors: Zhang Yuwei , Wang Ke , Yang Delin , Liu Fengping , Xu Xinyu , Feng Yangkun , Wang Yang , Zhu Sha , Gu Chaoqun , Sheng Jiayi , Hu Lei , Xu Bin , Lu Yong-Jie , Feng Ninghan 
Published: November 2022

Abstract
Circular RNA (circRNA), a type of noncoding RNAs, has been demonstrated to act vital roles in tumorigenesis and cancer deterioration. Although tumor-associated macrophages are involved in tumor malignancy, the interactions between circRNAs and tumor-associated macrophages in prostate cancer (PCa) remain unclear. In the present study, we found that hsa_circ_0094606 (subsequently named circ_0094606) could promote proliferation, epithelial-mesenchymal transition (EMT) as well as migration of PCa cells through cell viability and migration assays and the determination of EMT markers. Mass spectrometry analysis after RNA pull-down experiment identified that circ_0094606 bound to protein arginine methyltransferase 1 (PRMT1) in PCa cells, and further functional assays revealed that circ_0094606 promoted the malignant progression of PCa by binding to PRMT1. Moreover, co-immunoprecipitation (Co-IP), glutathione-S-transferase (GST) pull-down and immunofluorescence showed that PRMT1 mediated arginine methylation of ILF3 to stabilize the protein. Bioinformatics analysis combined with data from RNA-binding protein immunoprecipitation and RNA pull-down suggested that ILF3 could stabilize IL-8 mRNA, which promoted the M2 polarization in coculture study. Finally, in vivo experiments showed that circ_0094606 subserve PCa growth and promoted the M2 polarization of macrophages through the PRMT1/ILF3/IL-8 regulation pathway, supporting circ_0094606 as a potential novel effective target for PCa treatment.
“She is as feminine as my mother, as my sister, as my biologically female friends”: On the promise and limits of transgender visibility in fashion media
Authors: Zhang Erique 
Published: November 2022

AbstractAs transgender media representation continues to gain traction, trans scholars and activists have contended with the double-edged sword of visibility: while trans visibility has the potential to familiarize cisgender audience with trans experiences, it also risks reinforcing normative ideas about gender expression. Taking fashion media as a case study, I look at trans representation between 2013 and 2020 in the print editions of U.S.-based fashion publications Vogue, Harper’s Bazaar, and Women’s Wear Daily. I argue that trans representation in fashion magazines produces competing discourses about trans identity as simultaneously conforming to gender norms and subverting the gender binary. Further, fashion magazines employ a neoliberal logic of visibility and self-empowerment, positioning trans individuals—particularly trans women of color—as exceptional figures and role models. Finally, I find a recent shift towards a social justice framework as trans activists of color are given greater voice in the pages of fashion magazines.
Governing digital platform power for industrial development: towards an entrepreneurial-regulatory state
Authors: Andreoni Antonio , Roberts Simon 
Published: November 2022

Abstract
Data and digital platforms have simultaneously upended entrenched positions in some industries, opening-up greater and disruptive competition, while driving overall higher levels of concentration through the growing power of multi-sided digital platforms. The coexistence of rivalry and collusion – a key feature of Cowling’s monopoly capitalism – persists and takes new forms in the digital economy. Taking into account the heterogenous nature of platforms, this paper analyses the relationships between large digital platforms and the development of industrial capabilities, especially in middle-income countries and the implications for industrial and competition policies. We advance an analytical-policy framework connecting the different dimensions and sources of platform power responsible for value capture and extraction, and the different platform capability-functions responsible for value creation. Building on this recasting of Hymer’s ‘efficiency contradiction’ and Cowling theory of monopoly capitalism, we advance an integrated industrial-competition policy approach to overcome it and propose a conception of an ‘entrepreneurial-regulatory state’. Complementary industrial and competition policies are required to foster optimal rivalry, being a rivalry which rewards the development of dynamic capabilities and enables contestation by different business models.
Impact of nutrients on the function of the chlamydial Rsb partner switching mechanism
Authors: Kuwabara Shiomi , Landers Evan R , Fisher Derek J 
Published: November 2022

Abstract
The obligate intracellular bacterial pathogen Chlamydia trachomatis is a leading cause of sexually transmitted infections and infectious blindness. Chlamydia undergo a biphasic developmental cycle alternating between the infectious elementary body (EB) and the replicative reticulate body (RB). The molecular mechanisms governing RB growth and RB-EB differentiation are unclear. We hypothesize that the bacterium senses host cell and bacterial energy levels and metabolites to ensure that development and growth coincide with nutrient availability. We predict that a partner switching mechanism (PSM) plays a key role in the sensing and response process acting as a molecular throttle sensitive to metabolite levels. Using purified wild type and mutant PSM proteins, we discovered that metal type impacts enzyme activity and the substrate specificity of RsbU and that RsbW prefers ATP over GTP as a phosphate donor. Immunoblotting analysis of RsbV1/V2 demonstrated the presence of both proteins beyond 20 hours post infection and we observed that an RsbV1-null strain has a developmental delay and exhibits differential growth attenuation in response to glucose levels. Collectively, our data support that the PSM regulates growth in response to metabolites and further defines biochemical features governing PSM-component interactions which could help in the development of novel PSM-targeted therapeutics.
Inequalities in Retirement Life Span in the United States
Authors: Shi Jiaxin , Dudel Christian , Monden Christiaan , van Raalte Alyson 
Published: November 2022

AbstractObjectivesThe length of retirement life may be highly unequal due to persistent and significant discrepancies in old-age mortality. This study assesses gender and educational differences in the average retirement life span and the variation in retirement life span, taking into account individual labor force exit and reentry dynamics.MethodsWe used longitudinal data from the Health and Retirement Study from 1996 to 2016, focusing on respondents aged 50 and older (N = 32,228). Multistate life tables were estimated using discrete-time event history models. The average retirement life span, as well as absolute and relative variation in retirement life span, were calculated analytically.ResultsAmong women, we found a persistent educational gradient in average retirement life span over the whole period studied; among men, the relationship between education and retirement expectancy differed across periods. Women and the lower-educated had higher absolute variation in retirement life span than men and the higher-educated—yet these relationships were reversed when examined by relative variation.DiscussionOur multistate approach provides an accurate and comprehensive picture of the retirement life span of older Americans over the past two decades. Such findings should be considered in high-level discussions on Social Security. Potential reforms such as raising the eligibility age or cutting benefits may have unexpected implications for different social groups due to their differential effects on retirement initiation and reentry dynamics.
The thin line between farce and tragedy: My Covid story between Italy and Guatemala
Authors: Gasbarri Lorenzo 
Published: November 2022

Abstract
In my “Covid story,” I would like to present some reflections on the effects of the pandemic on global structural inequalities. Based on my personal experiences in Italy and Guatemala, I chronologically present the differences between the two countries in tackling the pandemic. In particular, I focus on the right to health, including access to hospitals, testing, and vaccinations. I also discuss how the justice system reacted to the pandemic, including the management of prisons and the investigations on the actions of the two governments. Public demonstrations in the streets and violent protests in prisons are the background against which I present the legislative measures adopted to curb the pandemic. Farce and tragedy are intended to depict the distance between public institutions and the people they represent. Between the failures of temporary hospitals in Guatemala and Italy’s draconian regulations to enter the country, the very concept of law and public institutions assumed different connotations.
Optimal site selection for wind power plant using multi-criteria decision-making methods: A case study in eastern Iran
Authors: Seyed Alavi Seyed Mohammad , Maleki Akbar , Khaleghi Ali 
Published: November 2022

Abstract
Sustainable and renewable energy resources will play a significant role in the future of the 21st century. One of the most significant resources of sustainable energy is wind energy. Therefore, detection of the potential locations and selection of the optimal place to find a wind farm are a primary step toward using sustainable energy resources. In this research, the feasibility of establishing wind farms in three provinces in the east and north-east parts of Iran is studied using multiple criteria decision-making methods. Fifty proposed options to build a wind farm are ranked based on 13 effective criteria, including area, distance to power lines, distance to the substation, distance to a road, estimated capacity, distance to the city, altitude, population, population density, annual rainfall, average temperature, average wind speed and relative humidity by applying Shannon entropy weighting technique and using three methods of the simple additive weighting (SAW), technique for order of preference by similarity to ideal solution (TOPSIS) and elimination and choice translating reality (ELECTRE). Shannon entropy weighting technique reveals that the criteria of distance to power transmission lines and relative humidity will have the most and least weights, respectively. The ranking results show that, based on the TOPSIS and ELECTRE methods, Gezi Bojnourd option is the best site and Neishabour Hesar Yazdan case is the worst site. Furthermore, Bashirabad Torbatjam case is the most desirable site in the SAW method. The sensitivity analysis results show that the minimum sensitivity to the criteria weights is recorded in the SAW method. On the contrary, ELECTRE method offers the most sensitivity and variation in ranking.
Triggers of Change in Sexual Behavior Among People With HIV: The Swiss U = U Statement and COVID-19 Compared
Authors: Hamusonde Kalongo , Nicca Dunja , Günthard Huldrych F , Stöckle Marcel , Darling Katharine E A , Calmy Alexandra , Bernasconi Enos , Haerry David , Schmid Patrick , Kouyos Roger D , Rauch Andri , Salazar-Vizcaya Luisa ,   the Swiss HIV Cohort Study, Abela I , Aebi-Popp K , Anagnostopoulos A , Battegay M , Bernasconi E , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H F , Hachfeld A , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Jackson-Perry D , Kahlert C R , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Kusejko K , Labhardt N , Leuzinger K , de Tejada B Martinez , Marzolini C , Metzner K J , Müller N , Nemeth J , Nicca D , Notter J , Paioni P , Pantaleo G , Perreau M , Rauch A , Salazar-Vizcaya L , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Wandeler G , Weisser M , Yerly S 
Published: November 2022

Abstract
We assessed changes in sexual behavior among people with human immunodeficiency virus (HIV) over 20 years. Condom use with stable partners steadily declined from over 90% to 29% since the Swiss U = U statement, with similar trajectories between men who have sex with men (MSM) and heterosexuals. Occasional partnership remained higher among MSM compared to heterosexuals even during coronavirus disease 2019 (COVID-19) social distancing.
Synergy of outer membrane disruptor SLAP-S25 with hydrophobic antibiotics against Gram-negative pathogens
Authors: Yang Zhiqiang , Song Meirong , Li Xiaoyu , Zhang Qi , Shen Jianzhong , Zhu Kui 
Published: November 2022

Abstract

Objectives
An effective strategy for combating MDR Gram-negative pathogens can greatly reduce the cost and shorten the antibiotic development progress. Here, we investigated the synergistic activity of outer membrane disruptor SLAP-S25 in combination with hydrophobic antibiotics (LogP &gt; 2, including novobiocin, erythromycin, clindamycin and rifampicin) against MDR Gram-negative pathogens.

Methods
Five representative Gram-negative bacteria were selected as model strains to analyse the synergistic combination of SLAP-S25 and hydrophobic antibiotics. Carbapenem-resistant hypervirulent Klebsiella pneumoniae CRHvKP4 was used to investigate the synergistic mechanism. The in vivo synergistically therapeutic activity of SLAP-S25 and hydrophobic antibiotics was measured in the mouse peritonitis/sepsis model infected with K. pneumoniae CRHvKP4.

Results
SLAP-S25 disrupted the outer membrane by removing LPS from Gram-negative bacteria, facilitating the entry of hydrophobic antibiotics to kill MDR Gram-negative pathogens. Moreover, the combination of SLAP-S25 and rifampicin exhibited promising therapeutic effects in the mouse infection model infected with K. pneumoniae CRHvKP4.

Conclusions
Our findings provide a potential therapeutic strategy to combine SLAP-S25 with hydrophobic antibiotics for combating MDR Gram-negative pathogens.
Epidemic Question Answering: question generation and entailment for Answer Nugget discovery
Authors: Weinzierl Maxwell A , Harabagiu Sanda M 
Published: November 2022

Abstract

Objective
The rapidly growing body of communications during the COVID-19 pandemic posed a challenge to information seekers, who struggled to find answers to their specific and changing information needs. We designed a Question Answering (QA) system capable of answering ad-hoc questions about the COVID-19 disease, its causal virus SARS-CoV-2, and the recommended response to the pandemic.

Materials and Methods
The QA system incorporates, in addition to relevance models, automatic generation of questions from relevant sentences. We relied on entailment between questions for (1) pinpointing answers and (2) selecting novel answers early in the list of its results.

Results
The QA system produced state-of-the-art results when processing questions asked by experts (eg, researchers, scientists, or clinicians) and competitive results when processing questions asked by consumers of health information. Although state-of-the-art models for question generation and question entailment were used, more than half of the answers were missed, due to the limitations of the relevance models employed.

Discussion
Although question entailment enabled by automatic question generation is the cornerstone of our QA system’s architecture, question entailment did not prove to always be reliable or sufficient in ranking the answers. Question entailment should be enhanced with additional inferential capabilities.

Conclusion
The QA system presented in this article produced state-of-the-art results processing expert questions and competitive results processing consumer questions. Improvements should be considered by using better relevance models and enhanced inference methods. Moreover, experts and consumers have different answer expectations, which should be accounted for in future QA development.