bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved DNA sequence features underlie pervasive RNA polymerase pausing
Authors: Gajos Martyna , Jasnovidova Olga , van Bömmel Alena , Freier Susanne , Vingron Martin , Mayer Andreas 
Published: March 2021

Abstract
Pausing of transcribing RNA polymerase is regulated and creates opportunities to control gene expression. Research in metazoans has so far mainly focused on RNA polymerase II (Pol II) promoter-proximal pausing leaving the pervasive nature of pausing and its regulatory potential in mammalian cells unclear. Here, we developed a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data and a new native elongating transcript sequencing approach, termed nested NET-seq, that strongly reduces artifactual peaks commonly misinterpreted as pausing sites. Leveraging PDA and nested NET-seq reveal widespread genome-wide Pol II pausing at single-nucleotide resolution in human cells. Notably, the majority of Pol II pauses occur outside of promoter-proximal gene regions primarily along the gene-body of transcribed genes. Sequence analysis combined with machine learning modeling reveals DNA sequence properties underlying widespread transcriptional pausing including a new pause motif. Interestingly, key sequence determinants of RNA polymerase pausing are conserved between human cells and bacteria. These studies indicate pervasive sequence-induced transcriptional pausing in human cells and the knowledge of exact pause locations implies potential functional roles in gene expression.
Rational design of high-quality 2D/3D perovskite heterostructure crystals for record-performance polarization-sensitive photodetection
Authors: Zhang Xinyuan , Li Lina , Ji Chengmin , Liu Xitao , Li Qing , Zhang Kun , Peng Yu , Hong Maochun , Luo Junhua 
Published: March 2021

Abstract
Polarization-sensitive photodetection is central to optics applications and has been successfully demonstrated in photodetectors of two-dimensional (2D) materials, such as layered hybrid perovskites; however, achieving high polarization sensitivity in such a photodetector remains extremely challenging. Here, for the first time, we demonstrate a high-performance polarization-sensitive photodetector using single-crystalline 2D/3D perovskite heterostructure, namely, (4-AMP)(MA)2Pb3Br10/MAPbBr3 (MA = methylammonium; 4-AMP = 4-(aminomethyl)piperidinium), which exhibits ultrahigh polarization sensitivity up to 17.6 under self-driven mode. To our knowledge, such a high polarization selectivity has surpassed all of the reported perovskite-based devices, and is comparable to, or even better than, the traditional inorganic heterostructure-based photodetectors. Further studies reveal that the built-in electric field formed at the junction can spatially separate the photogenerated electrons and holes, reducing their recombination rate and thus enhancing the performance for polarization-sensitive photodetection. This work provides a new source of polarization-sensitive materials and insights into designing novel optoelectronic devices.
Hepatitis C Virus Relapse After Ultrashort Direct-Acting Antiviral Therapy Associates With Expression of Genes Involved With Natural Killer-Cell and CD8+ T-Cell Function
Authors: Orr Cody , Masur Henry , Kottilil Shyam , Meissner Eric G 
Published: March 2021

Abstract
To identify immunologic correlates of hepatitis C virus (HCV) relapse after direct-acting antiviral (DAA) therapy, we quantified select immune transcripts in whole blood from noncirrhotic HCV subjects treated with 4–6 weeks of DAAs. We identified specific markers of natural killer-cell and CD8+ T-cell function (GZMB, PRF1, NKp46) with higher expression in subjects who relapsed. These findings suggest a role for host immunity in HCV eradication with ultrashort DAA therapy.
We quantified whole blood immune transcripts in noncirrhotic HCV subjects treated with shortcourse antiviral therapy. Markers of natural killer-cell and CD8+ T-cell function had higher expression in virologic relapsers, suggesting a role for host immunity in HCV eradication.
Management in education systems
Authors: Hwa Yue-Yi , Leaver Clare 
Published: March 2021

Abstract There is increasing interest in measuring management in schools. This paper discusses a popular measurement tool: the World Management Survey (WMS) for schools. Drawing on WMS data, secondary sources, and the recent literature on school management, we take stock of the WMS and make recommendations for its use in future research and policy. We conclude that the WMS remains a highly useful tool for its stated purpose—the standardized measurement of (a subset of) management practices within schools—and make two sets of recommendations. First, we encourage those seeking to benchmark management practices in schools to take a systems perspective by extending the WMS approach upwards into the education bureaucracy. Second, when measuring practices within schools, we recommend that researchers consider: how best to assess alignment across practices in the operations domain; the challenge of measuring student learning for monitoring and target-setting; and the context specificity of people management.
Do Anti-Elitist Parties Use Their Parliamentary Tools Differently?
Authors: Otjes Simon , Louwerse Tom 
Published: March 2021

Abstract
Populist parties have become an important factor in opposition politics all over Europe. While we know a lot about the behaviour of populist parties in the electoral arena and even in the governmental arena, we know surprisingly little about their behaviour in parliament. This article studies the behaviour of populist opposition parties in parliament. We hypothesise that it is the anti-elitism of populism that is the ‘active’ element that shapes their parliamentary behaviour. Anti-elitist parties are more likely to be ‘responsive’ parties, using parliament as a bully pulpit to amplify citizens’ objections to policy and less likely to be ‘responsible’ parties, using the legislature as a place to find support for policy alternatives. We hypothesise anti-elitist parties to use parliamentary scrutiny tools more often than other parties. We make use of recently collected cross-national data on parliamentary behaviour in seven European democracies to test this hypothesis. Our results indicate that parties that have been characterised as anti-elitist tend to vote more against legislation, but they do not ask more parliamentary questions.
Altered chromatin architecture and gene expression during polyploidization and domestication of soybean
Authors: Wang Longfei , Jia Guanghong , Jiang Xinyu , Cao Shuai , Chen Z Jeffrey , Song Qingxin 
Published: March 2021

Abstract
Polyploidy or whole-genome duplication (WGD) is widespread in plants and is a key driver of evolution and speciation, accompanied by rapid and dynamic changes in genomic structure and gene expression. The 3D structure of the genome is intricately linked to gene expression, but its role in transcription regulation following polyploidy and domestication remains unclear. Here, we generated high-resolution (∼2 kb) Hi-C maps for cultivated soybean (Glycine max), wild soybean (Glycine soja), and common bean (Phaseolus vulgaris). We found polyploidization in soybean may induce architecture changes of topologically associating domains and subsequent diploidization led to chromatin topology alteration around chromosome-rearrangement sites. Compared with single-copy and small-scale duplicated genes, WGD genes displayed more long-range chromosomal interactions and were coupled with higher levels of gene expression and chromatin accessibilities but void of DNA methylation. Interestingly, chromatin loop reorganization was involved in expression divergence of the genes during soybean domestication. Genes with chromatin loops were under stronger artificial selection than genes without loops. These findings provide insights into the roles of dynamic chromatin structures on gene expression during polyploidization, diploidization, and domestication of soybean.
3D-printed gelatin methacrylate (GelMA)/silanated silica scaffold assisted by two-stage cooling system for hard tissue regeneration
Authors: Choi Eunjeong , Kim Dongyun , Kang Donggu , Yang Gi Hoon , Jung Bongsu , Yeo MyungGu , Park Min-Jeong , An SangHyun , Lee KyoungHo , Kim Jun Sik , Kim Jong Chul , Jeong Woonhyeok , Yoo Hye Hyun , Jeon Hojun 
Published: March 2021

Abstract
Among many biomaterials, gelatin methacrylate (GelMA), a photocurable protein, has been widely used in 3D bioprinting process owing to its excellent cellular responses, biocompatibility and biodegradability. However, GelMA still shows a low processability due to the severe temperature dependence of viscosity. To overcome this obstacle, we propose a two-stage temperature control system to effectively control the viscosity of GelMA. To optimize the process conditions, we evaluated the temperature of the cooling system (jacket and stage). Using the established system, three GelMA scaffolds were fabricated in which different concentrations (0, 3 and 10 wt%) of silanated silica particles were embedded. To evaluate the performances of the prepared scaffolds suitable for hard tissue regeneration, we analyzed the physical (viscoelasticity, surface roughness, compressive modulus and wettability) and biological (human mesenchymal stem cells growth, western blotting and osteogenic differentiation) properties. Consequently, the composite scaffold with greater silica contents (10 wt%) showed enhanced physical and biological performances including mechanical strength, cell initial attachment, cell proliferation and osteogenic differentiation compared with those of the controls. Our results indicate that the GelMA/silanated silica composite scaffold can be potentially used for hard tissue regeneration.
An effective method to generate controllable levels of ROS for the enhancement of HUVEC proliferation using a chlorin e6-immobilized PET film as a photo-functional biomaterial
Authors: Hong Seung Hee , Koo Min-Ah , Lee Mi Hee , Seon Gyeung Mi , Park Ye Jin , Jeong HaKyeong , Kim Dohyun , Park Jong-Chul 
Published: March 2021

AbstractReactive oxygen species (ROS) are byproducts of cellular metabolism; they play a significant role as secondary messengers in cell signaling. In cells, high concentrations of ROS induce apoptosis, senescence, and contact inhibition, while low concentrations of ROS result in angiogenesis, proliferation, and cytoskeleton remodeling. Thus, controlling ROS generation is an important factor in cell biology. We designed a chlorin e6 (Ce6)-immobilized polyethylene terephthalate (PET) film (Ce6-PET) to produce extracellular ROS under red-light irradiation. The application of Ce6-PET films can regulate the generation of ROS by altering the intensity of light-emitting diode sources. We confirmed that the Ce6-PET film could effectively promote cell growth under irradiation at 500 μW/cm2 for 30 min in human umbilical vein endothelial cells. We also found that the Ce6-PET film is more efficient in generating ROS than a Ce6-incorporated polyurethane film under the same conditions. Ce6-PET fabrication shows promise for improving the localized delivery of extracellular ROS and regulating ROS formation through the optimization of irradiation intensity.
Therapeutic effects of EGF-modified curcumin/chitosan nano-spray on wound healing
Authors: Li Yue , Leng QingQing , Pang XianLun , Shi Huan , Liu YanLin , Xiao SuSu , Zhao Ling , Zhou Ping , Fu ShaoZhi 
Published: March 2021

Abstract
Dermal injury, including trauma, surgical incisions, and burns, remain the most prevalent socio-economical health care issue in the clinic. Nanomedicine represents a reliable administration strategy that can promote the healing of skin lesions, but the lack of effective drug delivery methods can limit its effectiveness. In this study, we developed a novel nano-drug delivery system to treat skin defects through spraying. We prepared curcumin-loaded chitosan nanoparticles modified with epidermal growth factor (EGF) to develop an aqueous EGF-modified spray (EGF@CCN) for the treatment of dermal wounds. In vitro assays showed that the EGF@CCN displayed low cytotoxicity, and that curcumin was continuously and slowly released from the EGF@CCN. In vivo efficacy on wound healing was then evaluated using full-thickness dermal defect models in Wistar rats, showing that the EGF@CCN had significant advantages in promoting wound healing. On day 12 post-operation, skin defects in the rats of the EGF@CCN group were almost completely restored. These effects were related to the activity of curcumin and EGF on skin healing, and the high compatibility of the nano formulation. We therefore conclude that the prepared nano-scaled EGF@CCN spray represents a promising strategy for the treatment of dermal wounds.
Older rationales and other challenges in handling causes of death in historical individual-level databases: the case of Copenhagen, 1880–1881
Authors: Revuelta-Eugercios Barbara , Castenbrandt Helene , Løkke Anne 
Published: March 2021

Summary
Large-scale historical databases featuring individual-level causes of death offer the potential for longitudinal studies of health and illnesses. There is, however, a risk that the transformation of the primary sources into ‘data’ may strip them of the very qualities required for proper medical historical analysis. Based on a pilot study of all 11,100 deaths registered in Copenhagen in 1880–1881, we identify, analyse and discuss the challenges of transcribing and coding cause of death sources into a database. The results will guide us in building Link-Lives, a database featuring close to all nine million Danish deaths from 1787 to 1968. The main challenge is how to accommodate different older medical rationales in one classification system. Our key finding is multi-coding with more than one version of the ICD system (e.g. ICD-1893 and ICD-10) can be used as a novel method to systematically handle historical causes of death over time.
Improved Whole-Genome Sequence of Phytophthora capsici Generated by Long-Read Sequencing
Authors: Shi Jinxia , Ye Wenwu , Ma Dongfang , Yin Junliang , Zhang Zhichao , Wang Yuanchao , Qiao Yongli 
Published: March 2021

The soilborne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N50 scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole-genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
The Use of Detached Leaf Inoculation for Selecting Cercospora kikuchii Resistance in Soybean Genotypes
Authors: Kashiwa Takeshi , Lavilla Miguel Angel , Paleo Antonio Diaz , Ivancovich Antonio Juan Gerardo , Yamanaka Naoki 
Published: March 2021

Cercospora leaf blight (CLB) causes extensive losses in soybean production in worldwide, including major soybean-producing countries such as Argentina. Cercospora kikuchii, C. cf. sigesbeckiae, C. cf. flagellaris, and C. cf. nicotianae are identified as pathogens of CLB. Soybean resistance against CLB is still unknown. Also, chemical control for CLB is losing effectiveness because of fungicide resistance of pathogens such as C. kikuchii. We urgently need to breed a CLB-resistant cultivar. Unfortunately, efficient methods for the screening of a resistant soybean genotype have not yet been established. In this study, we designed a new, high-throughput inoculation method for identifying resistance against one of the CLB pathogens, C. kikuchii. We used liquid-cultured mycelia of the pathogen C. kikuchii on detached soybean leaves. Lesions on soybean leaflets appeared 9 days postinoculation by this method. We used this method to select four C. kikuchii-resistant genotypes from 80 genotypes in the World Soybean Core Collection. The high-throughput screening method developed in this study can contribute to the research about C. kikuchii resistance by facilitating identification of resistant varieties. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Manifestation of Sexual Minority Identity in First‐Year Medical Students
Authors: Smith Theodore , Flinders David , O'Loughlin Valerie 
Published: March 2021

How do sexual minority medical students navigate their first year of medical school? How do their sexual identities affect this learning environment and wellness? Two theories about underrepresented individuals offer general perspectives to social experiences. Queer theory establishes that sexual identity is a vital part of the human experiences, while minority stress theory indicates that minorities experience higher levels of stress in situations than their majority counterparts. How can these theories be used to be proactive and supportive of sexual minority students? This qualitative research examines first‐year sexual minority medical students at Indiana University School of Medicine–Bloomington as they experience encounters with peers, instructors and LGBTQA+ specific curriculum. This research was approved by the Indiana University Institutional Review Board (IRB # 1810842950). Each sexual minority medical student volunteer completed 2 interviews about their experiences and were observed during a classroom activity. Thematic analysis of field notes and interview transcripts was performed. Five major themes of identity manifestation were identified and will be discussed in this poster: Advocacy, Representation, Ignorance/Disrespect, Heteronormativity, and Humor. A model for manifestation of LGBTQA+ identity in medical school is also proposed using the tenets of queer and minority stress theories. Understanding the unique experience of sexual minority medical students may provide instructors with more tools to better assist students during a major life transition.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Conformational and Mechanistic Studies of AlkB and AlkBH2 DNA Demethylases
Authors: Karabencheva‐Christova Tatyana , Waheed Sodic , Chaturvedi Shobhit , Ramanan Rajeev , Christov Christo 
Published: March 2021

DNA demethylases play a crucial role in DNA repair mechanisms and have been linked to pathologies. AlkB enzyme and its human homolog AlkBH2 have been very intensively studied both experimentally and computationally. It is well known also that AlkB exhibits broader substrate specificity than AlkBH2. Applying MD and QM/MM methods here we focus on: i) on the differences between the dynamical properties and collective motions between both enzymes: ii) the different impact on the protein environment on the reaction mechanisms in AlkB and AlkBH2. The provided atomistic insight can be used in designing enzyme‐selective inhibitors and demonstrate the power of computational methods to complement experimental studies.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Weekly Internal Ethical Case Discussions in an ICU—Results Based on 9 Years of Experience With a Highly Structured Approach
Authors: Meyer-Zehnder Barbara , Barandun Schäfer Ursi , Wesch Conrad , Reiter-Theil Stella , Pargger Hans 
Published: March 2021

Objectives:
Various ethical challenges are prevalent in ICUs. In order to handle these problems, a highly structured internal ethical case discussion within the multiprofessional team was implemented in 2011 in a Swiss ICU and has been regularly practiced almost weekly until present. To explore the results of all ethical case discussions taking place in a general ICU and to discuss the outcomes of the patients. To identify the conditions facilitating the implementation of regular ethical case discussions.

Design:
Retrospective case series analysis.

Setting:
Mixed academic ICU.

Patients AND INTERVENTION:
All patients who had an ethical case discussion between January 2011 and December 2019 following the approach called Modular, Ethical, Treatment decisions, Allocation of resources at the micro-level, and Process.

MEASUREMENTS AND Main Results:
Weekly ethical case discussions held regularly on a fixed date were found to be practical for the observed ICU. A total of 314 ethical case discussions were realized in 281 patients. Median patient age was 70 years (interquartile range, 62–77 yr); two thirds were men. The results were categorized into the following groups: established therapy continues, complications to be treated (n = 53; 16.9%); therapy continues, patient’s will to be explored further (n = 77; 24.5%); therapy continues, complications to be treated only after evaluation (n = 62; 19.7%); therapy continues with limitations (e.g., do-not-resuscitate order) (n = 98; 31.2%); and change of treatment plan to end-of-life care (n = 17; 5.4%). Of the discussed patients, 115 (40.9%) died in the ICU and 29 (10.3%) after transfer to the normal ward. Seven patients (2.5%) were transferred to a hospice and 55 (19.6%) to another hospital. Sixty-nine (24.6%) were discharged to a rehabilitative facility and six returned home.

Conclusions:
Regular ethical case discussions can be successfully implemented, enabling careful review of the patient’s will and balancing it with the prognosis of the disease. This facilitates a necessary change of the therapeutic goal whenever appropriate.