bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-specific minimizers via polar sets
Authors: Zheng Hongyu , Kingsford Carl , Marçais Guillaume 
Published: May 2021

Abstract

Motivation
Minimizers are efficient methods to sample k-mers from genomic sequences that unconditionally preserve sufficiently long matches between sequences. Well-established methods to construct efficient minimizers focus on sampling fewer k-mers on a random sequence and use universal hitting sets (sets of k-mers that appear frequently enough) to upper bound the sketch size. In contrast, the problem of sequence-specific minimizers, which is to construct efficient minimizers to sample fewer k-mers on a specific sequence such as the reference genome, is less studied. Currently, the theoretical understanding of this problem is lacking, and existing methods do not specialize well to sketch specific sequences.

Results
We propose the concept of polar sets, complementary to the existing idea of universal hitting sets. Polar sets are k-mer sets that are spread out enough on the reference, and provably specialize well to specific sequences. Link energy measures how well spread out a polar set is, and with it, the sketch size can be bounded from above and below in a theoretically sound way. This allows for direct optimization of sketch size. We propose efficient heuristics to construct polar sets, and via experiments on the human reference genome, show their practical superiority in designing efficient sequence-specific minimizers.

Availability and implementation
A reference implementation and code for analyses under an open-source license are at https://github.com/kingsford-group/polarset.

Supplementary information
Supplementary data are available at Bioinformatics online.
Heterogeneous subpopulations of adventitial progenitor cells regulate vascular homeostasis and pathological vascular remodelling
Authors: Jolly Austin J , Lu Sizhao , Strand Keith A , Dubner Allison M , Mutryn Marie F , Nemenoff Raphael A , Majesky Mark W , Moulton Karen S , Weiser-Evans Mary C M 
Published: May 2021

AbstractCardiovascular diseases are characterized by chronic vascular dysfunction and provoke pathological remodelling events, such as neointima formation, atherosclerotic lesion development, and adventitial fibrosis. While lineage-tracing studies have shown that phenotypically modulated smooth muscle cells (SMCs) are the major cellular component of neointimal lesions, the cellular origins and microenvironmental signalling mechanisms that underlie remodelling along the adventitial vascular layer are not fully understood. However, a growing body of evidence supports a unique population of adventitial lineage-restricted progenitor cells expressing the stem cell marker, stem cell antigen-1 (Sca1; AdvSca1 cells) as important effectors of adventitial remodelling and suggests that they are at least partially responsible for subsequent pathological changes that occur in the media and intima. AdvSca1 cells are being studied in murine models of atherosclerosis, perivascular fibrosis, and neointima formation in response to acute vascular injury. Depending on the experimental conditions, AdvSca1 cells exhibit the capacity to differentiate into SMCs, endothelial cells, chondrocytes, adipocytes, and pro-remodelling cells, such as myofibroblasts and macrophages. These data indicate that AdvSca1 cells may be a targetable cell population to influence the outcomes of pathologic vascular remodelling. Important questions remain regarding the origins of AdvSca1 cells and the essential signalling mechanisms and microenvironmental factors that regulate both maintenance of their stem-like, progenitor phenotype and their differentiation into lineage-specified cell types. Adding complexity to the story, recent data indicate that the collective population of adventitial progenitor cells is likely composed of several smaller, lineage-restricted subpopulations, which are not fully defined by their transcriptomic profile and differentiation capabilities. The aim of this review is to outline the heterogeneity of Sca1+ adventitial progenitor cells, summarize their role in vascular homeostasis and remodelling, and comment on their translational relevance in humans.
The crustal structure of the Kerimbas Basin across the offshore branch of the East African Rift System
Authors: Vormann Maren , Jokat Wilfried 
Published: May 2021

SUMMARY
The Davie Fracture Zone (DFZ) evolved during the Jurassic and Cretaceous breakup and subsequent drift of Gondwana off East Africa. This old weak zone has been reactivated during the evolution of the East African Rift System. Recent faulting of Cenozoic sediments in the Kerimbas Basin off northern Mozambique shows that they are affected by the neotectonics. The question is if and how the crustal fabric in our research area has been modified by the rifting process. We present two seismic refraction profiles acquired offshore northern Mozambique to investigate its regional crustal structure and tectonic history. The profiles show a continent–ocean transition zone that widens from around 40 km at 13°S to more than 100 km at 11°S. In the west the transitional crust is up to 12 km thick. To the east, around 150 km off the Mozambique coast lies oceanic crust whose thickness varies from 4.9 to 6.5 km along the northern line and from 6.5 to 7.5 km along the southern one. The latter presents an unusual high-velocity lower crustal body (7.0–7.2 km s−1), about 40 km wide and 3.8 km thick, underlying the oceanic crust. The body may consist of underplated melt with the same source as the nearby Paisley Seamount, which has not yet reached its isostatic equilibrium. Despite well documented recent seismicity along the margin, neither of the profiles reveal significant crustal modifications or reduced crustal seismic velocities that might be related to ongoing extensional tectonics as part of of the East African Rift System. Neither profile reveals seismic evidence for the presence of a major fracture zone or sheared continental margin parallel to the margin. Instead, the profiles’ broad continent–ocean transitions are consistent with their formation during an early Jurassic stage of plate divergence oblique to the margin. Later, after 157 Ma, the azimuth of relative plate motion between East and West Gondwana changed to be parallel to the margin, and parts of the continent–ocean transitions may have been locally reactivated in a strike-slip sense. However, details on the plate movements during the directional change of the seafloor spreading between 157 and 144 Ma are not available. The oceanic crust formed by the initial divergent oblique extension became faulted/modified by the strike-slip movements between both plates. Instead of a narrow deformation zone, the DFZ is charcaterized by a broad, diffuse zone of transtensional deformation.
Change-points in antibiotic consumption in the community, European Union/European Economic Area, 1997–2017
Authors: Bruyndonckx Robin , Hoxha Ana , Quinten Chantal , Ayele Girma Minalu , Coenen Samuel , Versporten Ann , Adriaenssens Niels , Muller Arno , Heuer Ole , Monnet Dominique L , Goossens Herman , Molenberghs Geert , Weist Klaus , Hens Niel ,   the ESAC-Net study group, Strauss Reinhild , Vandael Eline , Sabtcheva Stefana , Payerl-Pal Marina , Kyriakidou Isavella , Vlček Jiří , Sönksen Ute Wolff , Linask Elviira , Sarvikivi Emmi , Cavalié Philippe , Gröschner Karin , Kontopidou Flora , Matuz Mária , Aspelund Gudrunw , Oza Gudrun , Fortinguerra Filomena , Seilis Andis , Kuklytė Jolanta , Bruch Marcel , Zarb Peter , Natsch Stephanie , Blix Hege Salvesen , Olczak-Pieńkowska Anna , Silva Ana , Iosif Ionel , Tesař Tomáš , Čižman Milan , Herreras Mayte Alonso , Bergfeldt Vendela , Müller-Pebody Berit 
Published: May 2021

Abstract

Objectives
Surveillance of antibiotic consumption in the community is of utmost importance to inform and evaluate control strategies. Data on two decades of antibiotic consumption in the community were collected from 30 EU/European Economic Area (EEA) countries. This article reviews temporal trends and the presence of abrupt changes in subgroups of relevance in antimicrobial stewardship.

Methods
For the period 1997–2017, data on yearly antibiotic consumption in the community, aggregated at the level of the active substance, were collected using the WHO ATC classification and expressed in DDD (ATC/DDD index 2019) per 1000 inhabitants per day. We applied a range of non-linear mixed models to assess the presence of changes in the consumption of antibacterials for systemic use (ATC group J01) and eight antibiotic subgroups.

Results
For the majority of the studied groups, a country-specific change-point model provided the best fit. Depending on the antibiotic group/subgroup and on the country, change-points were spread out between 2000 and 2013.

Conclusions
Due to the heterogeneity in antibiotic consumption in the community across EU/EEA countries, a country-specific change-point model provided the better fit. Given the limitations of this model, our recommendation for the included countries is to carefully interpret the country-specific results presented in this article and to use the tutorial included in this series to conduct their own change-point analysis when evaluating the impact of changes in regulations, public awareness campaigns, and other national interventions to improve antibiotic consumption in the community.
Bacterial quorum sensing facilitates Xanthomonas campesteris pv. campestris invasion of host tissue to maximize disease symptoms
Authors: Samal Biswajit , Chatterjee Subhadeep 
Published: May 2021

Abstract
Quorum sensing (QS) helps the Xanthomonas group of phytopathogens to infect several crop plants. The vascular phytopathogen Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot disease on Brassicaceae leaves, where a typical v-shaped lesion spans both vascular and mesophyll regions with progressive leaf chlorosis. Recently, the role of QS has been elucidated during Xcc early infection stages. However, a detailed insight into the possible role of QS-regulated bacterial invasion in host chlorophagy during late infection stages remains elusive. In this study, using QS-responsive whole-cell bioreporters of Xcc, we present a detailed chronology of QS-facilitated Xcc colonization in the mesophyll region of cabbage (Brassica oleracea) leaves. We report that QS-enabled localization of Xcc to parenchymal chloroplasts triggers leaf chlorosis and promotion of systemic infection. Our results indicate that the QS response in the Xanthomonas group of vascular phytopathogens maximizes their population fitness across host tissues to trigger stage-specific host chlorophagy and establish a systemic infection.
Uniform affinity-tuning of N-methyl-aminoacyl-tRNAs to EF-Tu enhances their multiple incorporation
Authors: Iwane Yoshihiko , Kimura Hiroyuki , Katoh Takayuki , Suga Hiroaki 
Published: May 2021

Abstract
In ribosomal translation, the accommodation of aminoacyl-tRNAs into the ribosome is mediated by elongation factor thermo unstable (EF-Tu). The structures of proteinogenic aminoacyl-tRNAs (pAA-tRNAs) are fine-tuned to have uniform binding affinities to EF-Tu in order that all proteinogenic amino acids can be incorporated into the nascent peptide chain with similar efficiencies. Although genetic code reprogramming has enabled the incorporation of non-proteinogenic amino acids (npAAs) into the nascent peptide chain, the incorporation of some npAAs, such as N-methyl-amino acids (MeAAs), is less efficient, especially when MeAAs frequently and/or consecutively appear in a peptide sequence. Such poor incorporation efficiencies can be attributed to inadequate affinities of MeAA-tRNAs to EF-Tu. Taking advantage of flexizymes, here we have experimentally verified that the affinities of MeAA-tRNAs to EF-Tu are indeed weaker than those of pAA-tRNAs. Since the T-stem of tRNA plays a major role in interacting with EF-Tu, we have engineered the T-stem sequence to tune the affinity of MeAA-tRNAs to EF-Tu. The uniform affinity-tuning of the individual pairs has successfully enhanced the incorporation of MeAAs, achieving the incorporation of nine distinct MeAAs into both linear and thioether-macrocyclic peptide scaffolds.
Women empowerment indicators and uptake of child health services in sub-Saharan Africa: a multilevel analysis using cross-sectional data from 26 countries
Authors: Seidu Abdul-Aziz , Ahinkorah Bright Opoku , Ameyaw Edward Kwabena , Budu Eugene , Yaya Sanni 
Published: May 2021

Abstract

Background
The sustainable development goal 3, target 2, seeks to reduce under-five mortality to as low as 25 deaths per 1000 live births by 2030. As such, seeking child health services has become a priority concern for all countries, particularly those in sub-Saharan Africa (SSA). Evidence suggests that empowered women are more likely to seek child health services. Hence, this study examined the association between women empowerment indicators and uptake of child health services in SSA.

Methods
The study used data from the Demographic and Health Surveys of 26 SSA countries, which were conducted between 2010 and 2019. Two different samples were considered in the study: a total of 12 961 children within the vaccination age of 12–23, and 9489 children under age 5 with diarrhoea symptoms in the last 2 weeks before the survey. Women empowerment indicators comprised disagreement with reasons to justify wife beating, decision-making power and knowledge level, while child health services constituted complete vaccination uptake and seeking diarrhoea treatment. Frequencies, percentages and multivariable, multilevel binary logistic regression models were employed.

Results
The study shows that women with high decision-making power [adjusted odds ratio (AOR) = 1.20, 95% confidence interval (CI) = 1.07, 1.35] had higher odds of seeking treatment for childhood diarrhoea compared to those with low decision-making power. It was also observed that among children aged 12–23 months [AOR = 1.28, 95% CI = 1.14, 1.43], mothers had higher odds of seeking diarrhoea treatment for them compared to those who were aged less than 12 months. Children whose mothers had medium decision-making power [AOR = 1.30, 95% CI = 1.19, 1.41] were more likely to seek complete immunization for their children compared to those with low decision-making power. Also, those with medium [AOR = 1.19, 95% CI = 1.07, 1.31] and high knowledge [AOR = 1.25, 95% CI = 1.10, 1.42] had higher odds of completing immunization for their children compared to those with low knowledge. Women with medium acceptance had lower odds [AOR = 0.76, 95% CI = 0.67, 0.83] of completing immunization for their children compared with those with low acceptance of wife beating.

Conclusions
This study has demonstrated a strong association between women empowerment indicators and the uptake of child health services. Therefore, efforts should be made to seek policy tools to empower women to help improve the well-being of women and the children they care for.
Cluster analysis reveals three main patterns of beliefs and intention with respect to SARS-CoV-2 vaccination in patients with autoimmune and inflammatory diseases
Authors: Felten Renaud , Dubois Maxime , Ugarte-Gil Manuel F , Chaudier Aurore , Kawka Lou , Bergier Hugo , Costecalde Charlotte , Pijnenburg Luc , Fort Jérémy , Chatelus Emmanuel , Sordet Christelle , Javier Rose-Marie , Gottenberg Jacques-Eric , Sibilia Jean , Fuentes-Silva Yurilis J , Arnaud Laurent 
Published: May 2021

Abstract

Introduction
Given the COVID-19 pandemic, it is crucial to understand the underlying behavioural determinants of SARS-CoV-2 vaccine hesitancy in patients with autoimmune or inflammatory rheumatic diseases (AIIRDs). We aimed to analyse patterns of beliefs and intention regarding SARS-CoV-2 vaccination in AIIRD patients, as a mean of identifying pragmatic actions that could be taken to increase vaccine coverage in this population.

Methods
Data relating to 1258 AIIRD patients were analysed using univariate and multivariate logistic regression models, to identify variables associated independently with willingness to get vaccinated against SARS-CoV-2. Subsets of patients showing similar beliefs and intention about SARS-CoV-2 vaccination were characterized using cluster analysis.

Results
Hierarchical cluster analysis identified three distinct clusters of AIIRD patients. Three predominant patient attitudes to SARS-COV-2 vaccination were identified: voluntary, hesitant and suspicious. While vaccine willingness differed significantly across the three clusters (P &lt; 0.0001), there was no significant difference regarding fear of getting COVID-19 (P = 0.11), the presence of comorbidities (P = 0.23), the use of glucocorticoids (P = 0.21), or immunocompromised status (P = 0.63). However, patients from cluster #2 (hesitant) and #3 (suspicious) were significantly more concerned about vaccination, the use of a new vaccine technology, lack of long-term data in relation to COVID-19 vaccination, and potential financial links with pharmaceutical companies (P &lt; 0.0001 in all) than patients from cluster #1 (voluntary).

Discussion
Importantly, the differences between clusters in terms of patient beliefs and intention was not related to the fear of getting COVID-19 or to any state of frailty, but was related to specific concerns about vaccination. This study may serve as a basis for improved communication and thus help increase COVID-19 vaccine coverage among AIIRD patients.
Practice Implications from the WCET® International Ostomy Guideline 2020
Authors: Chabal Laurent O. , Prentice Jennifer L. , Ayello Elizabeth A. 
Published: May 2021

ABSTRACT
The second edition of the WCET® International Ostomy Guideline (IOG) was launched in December 2020 as an update to the original guideline published in 2014. The purpose of this article is to introduce the 15 recommendations covering four key arenas (education, holistic aspects, and pre- and postoperative care) and summarize key concepts for clinicians to customize for translation into their practice. The article also includes information about the impact of the novel coronavirus 2019 on ostomy care.

GENERAL PURPOSE
To introduce the 15 recommendations of the International Ostomy Guideline (IOG) 2020, covering the four key arenas of education, holistic aspects, and pre- and postoperative care; and to summarize key concepts for clinicians to customize for translation into their practice.

TARGET AUDIENCE
This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care.

LEARNING OBJECTIVES/OUTCOMES
After participating in this educational activity, the participant will:
1. Analyze supporting evidence for the education recommendations in the IOG 2020.
2. Identify a benefit of the International Charter of Ostomate Rights.
3. Distinguish concepts related to pre- and postoperative ostomy-related care.
4. Select a potential barrier to IOG 2020 guideline implementation.
Usability of a Novel Instrument to Measure Damaged Peristomal Skin in Patients with an Ostomy
Authors: Yang Hui , Zhao Xinyue , Yang Qing , Jiang Qinghua 
Published: May 2021

ABSTRACT

OBJECTIVE
To evaluate the usability of a novel instrument (stoma ruler) to measure damaged peristomal skin in patients with an ostomy.

METHODS
A wound ostomy and continence nurse used both the stoma ruler and a linear ruler to assess DET (discoloration, erosion, tissue overgrowth) scores and the height of protrusion above the skin of 10 patients with ileostomies and took photographs. The photographs were presented to five ostomy care nurses for reliability testing. The difference between the two methods was determined using paired Wilcoxon signed ranks test.

PRIMARY OUTCOME MEASURE
Interrater reliability of the linear versus stoma ruler.

RESULTS
The interrater reliabilities of the stoma ruler versus the linear ruler for the domain-area DET score were 0.95 (95% confidence interval, 0.89–0.99) and 0.68 (95% confidence interval, 0.42–0.89), respectively. Only nurse 5 reported a significant difference between the two rulers (z = −2.24, P = .03).

CONCLUSIONS
In busy clinical settings, the stoma ruler is easy for ostomy care nurses to use to obtain accurate DET scores and the height of stoma protrusion above the skin. Observing the position of damaged skin using the clock marks on the stoma ruler enhance clinical description and reduce assessment variation among professionals.
Subjective Tools for Burn Scar Assessment: An Integrative Review
Authors: da Costa Pollyana Thays Lameira , Echevarría-Guanilo Maria Elena , Gonçalves Natália , Girondi Juliana Balbinot Reis , Gonçalves Adriana da Costa 
Published: May 2021

ABSTRACT

OBJECTIVE
To review the clinical and scientific literature on the subjective ways of assessing burn scars and describe their main characteristics.

DATA SOURCES
The Latin American, Caribbean Health Sciences Literature, Nursing Database, PubMed, CINAHL, and Scopus and Web of Science databases were used to search for studies published between 2014 and 2018 using descriptors in Portuguese, Spanish, and English.

STUDY SELECTION
After establishing the research question and the location and definition of the studies, as well as accounting for differences among databases and application of filters based on inclusion and exclusion criteria, 886 references remained.

DATA EXTRACTION
Investigators reviewed the titles and abstracts of the sample and selected 188 relevant studies for full review.

DATA SYNTHESIS
Twenty-six subjective forms of assessment were found; most research concerned the Patient and Observer Scar Assessment Scale and the Vancouver Scar Scale.

CONCLUSIONS
The Patient and Observer Scar Assessment Scale and the Vancouver Scar Scale are the most common scales for assessing burn scars and have similar evaluation points such as vascularization, pliability, pigmentation, and height, which are the main parameters that contribute to the general assessment and severity of a scar. There is a need to improve instructions for application of the scales to facilitate better understanding and improve agreement among evaluators.
1. DIFFERENCE BETWEEN TOTAL CHOLESTEROL-HDL RATIO AND GENSINI SCORE IN ACUTE CORONARY SYNDROME PATIENTS AT PROF. DR. R. D. KANDOU HOSPITAL
Authors: Faisal William , Wantania Frans , Panda Agnes Lucia 
Published: May 2021

Background:
Coronary artery disease is one of the most common diseases that endanger human health globally, its incidence has increased over the years and causes acute coronary syndrome disease. Research has found that the ratio of total cholesterol-HDL is a strong independent predictor of cardiovascular disease risk.

Objective:
To determine the difference between total cholesterol-HDL ratio and Gensini Score in patients with acute coronary syndrome.

Method:
Retrospective analytic study by looking at medical records patients with acute coronary syndrome who underwent cardiac catheterization at Prof. Dr. R. D. Kandou hospital from June-August 2020. Ages classified into non-elderly (18–59 years) and elderly (≥60 years). Inclusion criteria were patients who had a cardiac catheterization and had total cholesterol and HDL test results. The variable assessed was cholesterol total-HDL ratio with Gensini Score. The ratio of total cholesterol-HDL divided into below and above 4. Statistical analysis used independent t-test with a significance of p <0.05.

Result:
Of the 63 patients with acute coronary syndrome who underwent cardiac catheterization 54 (86%) male, 9 (14%) female, non-elderly 36 (57%), elderly 27 (43%), patients with cholesterol-HDL ratio <4 23 (36%) and > 4 40 (64%). There is no difference between cholesterol total-HDL ratio below and above 4 and Gensini Score (44.47 ± 29.55 vs. 46.53 ± 31.85, p = 0.802). The average Gensini Score of patients with cholesterol-HDL ratio below 4 is lower than above 4

Conclusion:
There is no significant difference between cholesterol total-HDL ratio below and above 4 and Gensini Score.