bluuebunny/crossref_metadata_2025_split huggingface dataset:
On unit free assessment of the extent of multilateral distributional variation
Authors: Anderson Gordon , Linton Oliver , Pittau Maria Grazia , Whang Yoon-Jae , Zelli Roberto 
Published: February 2021

SummaryMultilateral comparison of outcomes drawn from multiple groups pervade the social sciences and measurement of their variability, usually involving functions of respective group location and scale parameters, is of intrinsic interest. However, such approaches frequently mask more fundamental differences that more comprehensive examination of relative group distributional structures reveal. Indeed, in categorical data contexts, location- and scale-based techniques are no longer feasible without artificial and questionable cardinalisation of categories. Here, Gini’s transvariation measure is extended and employed in providing quantitative and visual multilateral comparison tools in discrete, continuous, categorical, univariate, or multivariate settings which are particularly useful in paradigms where cardinal measure is absent. Two applications, one analysing Eurozone cohesion in terms of the convergence or divergence of constituent nations income distributions, the other, drawn from a study of ageing, health, and income inequality in China, exemplify their use in a continuous and categorical data environment.
Immunopathogenesis of genitalChlamydiainfection: insights from mouse models
Authors: Dockterman Jacob , Coers Jörn 
Published: February 2021

ABSTRACTChlamydiae are pathogenic intracellular bacteria that cause a wide variety of diseases throughout the globe, affecting the eye, lung, coronary arteries and female genital tract. Rather than by direct cellular toxicity, Chlamydia infection generally causes pathology by inducing fibrosis and scarring that is largely mediated by host inflammation. While a robust immune response is required for clearance of the infection, certain elements of that immune response may also damage infected tissue, leading to, in the case of female genital infection, disease sequelae such as pelvic inflammatory disease, infertility and ectopic pregnancy. It has become increasingly clear that the components of the immune system that destroy bacteria and those that cause pathology only partially overlap. In the ongoing quest for a vaccine that prevents Chlamydia-induced disease, it is important to target mechanisms that can achieve protective immunity while preventing mechanisms that damage tissue. This review focuses on mouse models of genital Chlamydia infection and synthesizes recent studies to generate a comprehensive model for immunity in the murine female genital tract, clarifying the respective contributions of various branches of innate and adaptive immunity to both host protection and pathogenic genital scarring.
Gene tagging via CRISPR-mediated homology-directed repair in cassava
Authors: Veley Kira M , Okwuonu Ihuoma , Jensen Greg , Yoder Marisa , Taylor Nigel J , Meyers Blake C , Bart Rebecca S 
Published: February 2021

Abstract
Research on a few model plant–pathogen systems has benefitted from years of tool and resource development. This is not the case for the vast majority of economically and nutritionally important plants, creating a crop improvement bottleneck. Cassava bacterial blight (CBB), caused by Xanthomonas axonopodis pv. manihotis (Xam), is an important disease in all regions where cassava (Manihot esculenta Crantz) is grown. Here, we describe the development of cassava that can be used to visualize one of the initial steps of CBB infection in vivo. Using CRISPR-mediated homology-directed repair (HDR), we generated plants containing scarless insertion of GFP at the 3’ end of CBB susceptibility (S) gene MeSWEET10a. Activation of MeSWEET10a-GFP by the transcription activator-like (TAL) effector TAL20 was subsequently visualized at transcriptional and translational levels. To our knowledge, this is the first such demonstration of HDR via gene editing in cassava.
A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila
Authors: Jia Yongyi , Zheng Jianbo , Liu Shili , Li Fei , Chi Meili , Cheng Shun , Gu Zhimi 
Published: February 2021

Abstract
The dark sleeper, Odontobutis potamophila, is a commercially valuable fish that widely distributed in China and Southeast Asia countries. The phenomenon of sexual dimorphism in growth is conspicuous, which the males grow substantially larger and faster than the females. However, the high-quality genome resources for gaining insight into sex-determining mechanisms to develop sex-control breeding are still lacking. Here, a chromosomal-level genome assembly of O. potamophila was generated from a combination of Illumina reads, 10× Genomics sequencing, and Hi-C chromatin interaction sequencing. The assembled genome was 1,134.62 Mb with a contig N50 of 22.25 Mb and a scaffold N50 of 24.85 Mb, representing 94.4% completeness (Benchmarking Universal Single-Copy Orthologs). Using Hi-C data, 96.49% of the total contig bases were anchored to the 22 chromosomes, with a contig N50 of 22.25 Mb and a scaffold N50 of 47.68 Mb. Approximately 54.18% of the genome were identified as repetitive elements, and 23,923 protein-coding genes were annotated in the genome. The assembled genome can be used as a valuable resource for molecular breeding and functional studies of O. potamophila in the future.
The Heterochromatin Block That Functions as a Rod Cell Microlens in Owl Monkeys Formed within a 15-Myr Time Span
Authors: Tanabe Hideyuki , Kusakabe Ken Takeshi , Imai Hiroyuki , Yokota Shin-Ichi , Kuraishi Takeshi , Hattori Shosaku , Kai Chieko , Koga Akihiko 
Published: February 2021

Abstract
In rod cells of many nocturnal mammals, heterochromatin localizes to the central region of the nucleus and serves as a lens to send light efficiently to the photoreceptor region. The genus Aotus (owl monkeys) is commonly considered to have undergone a shift from diurnal to nocturnal lifestyle. We recently demonstrated that rod cells of the Aotus species Aotus azarae possess a heterochromatin block at the center of its nucleus. The purpose of the present study was to estimate the time span in which the formation of the heterochromatin block took place. We performed three-dimensional hybridization analysis of the rod cell of another species, Aotus lemurinus. This analysis revealed the presence of a heterochromatin block that consisted of the same DNA components as those in A. azarae. These results indicate that the formation was complete at or before the separation of the two species. Based on the commonly accepted evolutionary history of New World monkeys and specifically of owl monkeys, the time span for the entire formation process was estimated to be 15 Myr at most.
A mouse model of BBS identifies developmental and homeostatic effects of BBS5 mutation and identifies novel pituitary abnormalities
Authors: Bentley-Ford Melissa R , Engle Staci E , Clearman Kelsey R , Haycraft Courtney J , Andersen Reagan S , Croyle Mandy J , Rains Addison B , Berbari Nicolas F , Yoder Bradley K 
Published: February 2021

Abstract
Primary cilia are critical sensory and signaling compartments present on most mammalian cell types. These specialized structures require a unique signaling protein composition relative to the rest of the cell to carry out their functions. Defects in ciliary structure and signaling result in a broad group of disorders collectively known as ciliopathies. One ciliopathy, Bardet–Biedl syndrome (BBS; OMIM 209900), presents with diverse clinical features, many of which are attributed to defects in ciliary signaling during both embryonic development and postnatal life. For example, patients exhibit obesity, polydactyly, hypogonadism, developmental delay and skeletal abnormalities along with sensory and cognitive deficits, but for many of these phenotypes it is uncertain, which are developmental in origin. A subset of BBS proteins assembles into the core BBSome complex, which is responsible for mediating transport of membrane proteins into and out of the cilium, establishing it as a sensory and signaling hub. Here, we describe two new mouse models for BBS resulting from a targeted LacZ gene trap allele (Bbs5−/−) that is a predicted congenital null mutation and conditional (Bbs5flox/flox) allele of Bbs5. Bbs5−/− mice develop a complex phenotype consisting of increased pre-weaning lethality craniofacial and skeletal defects, ventriculomegaly, infertility and pituitary anomalies. Utilizing the conditional allele, we show that the male fertility defects, ventriculomegaly and pituitary abnormalities are only present when Bbs5 is disrupted prior to postnatal day 7, indicating a developmental origin. In contrast, mutation of Bbs5 results in obesity, independent of the age of Bbs5 loss.
Application of a multibeam echosounder to document changes in animal movement and behaviour around a tidal turbine structure
Authors: Williamson Benjamin J , Blondel Philippe , Williamson Laura D , Scott Beth E 
Published: February 2021

AbstractChanges in animal movement and behaviour at fine scales (tens of metres) in immediate proximity to tidal stream turbine structures are largely unknown and have implications for risks of animal collision with turbine blades. This study used upward-facing multibeam echosounder data to detect and track animal movement comprising fish, diving seabirds, and marine mammals. Measurements over spring-neap tidal cycles at a turbine structure (no blades present) are compared to a neighbouring reference area with no structure and comparable conditions, with measurements consecutive in time to maximize comparability.The majority of tracked animals (93.4% around turbine structure and 99.1% without turbine structure) were observed swimming against the flow, with 87.5% and 97.8%, respectively, making ground and showing capability of manoeuvring in tidal stream flow speeds. Track tortuosity increased around the turbine structure compared to the reference site, particularly in the wake and at low flow speeds, indicating animal station-holding or milling behaviour. These data also evidence the benefits of multibeam echosounders to measure animal movement through larger measurement volumes rather than relying on single-beam echosounders to measure animal presence alone, including to avoid large biases overestimating the size of schools swimming against the flow measured by time-in-beam.
Social inequalities and COVID-19 mortality in the city of São Paulo, Brazil
Authors: Ribeiro Karina Braga , Ribeiro Ana Freitas , Veras Maria Amélia de Sousa Mascena , de Castro Marcia Caldas 
Published: February 2021

Abstract

Background
Heterogeneity in COVID-19 morbidity and mortality is often associated with a country's health-services structure and social inequality. This study aimed to characterize social inequalities in COVID-19 mortality in São Paulo, the most populous city in Brazil and Latin America.

Methods
We conducted a population-based study, including COVID-19 deaths among São Paulo residents from March to September 2020. Age-standardized mortality rates and unadjusted rate ratios (RRs) [with corresponding 95% confidence intervals (CIs)] were estimated by race, sex, age group, district of residence, household crowding, educational attainment, income level and percentage of households in subnormal areas in each district. Time trends in mortality were assessed using the Joinpoint model.

Results
Males presented an 84% increase in COVID-19 mortality compared with females (RR = 1.84, 95% CI 1.79–1.90). Higher mortality rates were observed for Blacks (RR = 1.77, 95% CI 1.67–1.88) and mixed (RR = 1.42, 95% CI 1.37–1.47) compared with Whites, whereas lower mortality was noted for Asians (RR = 0.63, 95% CI 0.58–0.68). A positive gradient was found for all socio-economic indicators, i.e. increases in disparities denoted by less education, more household crowding, lower income and a higher concentration of subnormal areas were associated with higher mortality rates. A decrease in mortality over time was observed in all racial groups, but it started earlier among Whites and Asians.

Conclusion
Our results reveal striking social inequalities in COVID-19 mortality in São Paulo, exposing structural inequities in Brazilian society that were not addressed by the governmental response to COVID-19. Without an equitable response, COVID-19 will further exacerbate current social inequalities in São Paulo.
Compactifications of Cluster Varieties and Convexity
Authors: Cheung Man-Wai , Magee Timothy , Nájera Chávez Alfredo 
Published: February 2021

Abstract
Gross–Hacking–Keel–Kontsevich [13] discuss compactifications of cluster varieties from positive subsets in the real tropicalization of the mirror. To be more precise, let ${\mathfrak {D}}$ be the scattering diagram of a cluster variety $V$ (of either type– ${\mathcal {A}}$ or ${\mathcal {X}}$), and let $S$ be a closed subset of $\left (V^\vee \right )^{\textrm {trop}} \left ({\mathbb {R}}\right )$—the ambient space of ${\mathfrak {D}}$. The set $S$ is positive if the theta functions corresponding to the integral points of $S$ and its ${\mathbb {N}}$-dilations define an ${\mathbb {N}}$-graded subalgebra of $\Gamma (V, \mathcal {O}_V){ [x]}$. In particular, a positive set $S$ defines a compactification of $V$ through a Proj construction applied to the corresponding ${\mathbb {N}}$-graded algebra. In this paper, we give a natural convexity notion for subsets of $\left (V^\vee \right )^{\textrm {trop}} \left ({\mathbb {R}}\right )$, called broken line convexity, and show that a set is positive if and only if it is broken line convex. The combinatorial criterion of broken line convexity provides a tractable way to construct positive subsets of $\left (V^\vee \right )^{\textrm {trop}} \left ({\mathbb {R}}\right )$ or to check positivity of a given subset.
Exploiting the Microbiota for the Diagnosis of Anal Precancerous Lesions in Men Who Have Sex With Men
Authors: Ron Raquel , Cabello Alfonso , Gosalbes María José , Sánchez-Conde Matilde , Talavera-Rodríguez Alba , Zamora Javier , Monge-Maillo Begoña , Jiménez Daniel , Martínez-Sanz Javier , López Yolanda , Crespillo Clara , Velasco Tamara , Moreno Santiago , Pérez-Molina José A , Serrano-Villar Sergio 
Published: February 2021

Abstract

Background
While the microbiota has been associated with human papillomavirus malignant transformation, it is unclear whether anal bacteria could improve the low specificity of anal cytology for the screening of high-grade intraepithelial squamous neoplasia (HSIL)

Methods
We recruited men who have sex with men undergoing anal cytology and high-resolution anoscopy. We assessed the microbiota composition from fecal samples and cytobrush anal samples using 16S ribosomal DNA sequencing in participants with or without biopsy-proven HSIL (bHSIL). We selected bacterial biomarkers based on their linear discriminant analysis. We assessed their predictive performance using logistic regression and bootstrap resampling.

Results
We included 128 individuals, 47 (36.7%) with bHSIL and 99 (77.3%) with human immunodeficiency virus. We detected 40 potential predictors of bHSIL. Ruminococcaceae NK4A214 group, Alloprevotella genus, Prevotella melanonigenica, and Ruminococcaceae UCG-014 were the most predictive of bHSIL. From 35 false-positive cytologic results, the combination of these 4 biomarkers with the anal cytology reclassified to true-negative 33 individuals (94%) and showed good diagnostic performance (area under the receiver operating characteristic curve, 0.805; 95% confidence interval, .728–.882).

Conclusions
We found anal-associated bacteria indicative of a higher risk of precancerous anal lesions, which combination was highly specific. The microbiota could be developed as a complementary diagnostic tool to overcome the limitations of the current screening strategy for anal cancer.
Global Rotavirus and Pneumococcal Conjugate Vaccine Introductions and the Association With Country Disease Surveillance, 2006–2018
Authors: Peck Megan E , Hampton Lee M , Antoni Sebastian , Ogbuanu Ike , Serhan Fatima , Nakamura Tomoka , Walldorf Jenny A , Cohen Adam L 
Published: February 2021

Abstract

Background
To inform the introduction of pneumococcal conjugate vaccine (PCV) and rotavirus vaccine, the World Health Organization (WHO) established the Global Invasive Bacterial Vaccine-Preventable Disease Surveillance Network (GISN) and the Global Rotavirus Surveillance Network (GRSN) in 2008. We investigated whether participation in these networks or other surveillance was associated with vaccine introduction.

Methods
Between 2006 and 2018, among all WHO member states, we used multivariable models adjusting for economic status to assess (1) the association between surveillance for pneumococcal disease or rotavirus disease, including participation in GISN or GRSN and the introduction of the PCV or the rotavirus vaccine, respectively, and (2) the association between the rotavirus disease burden and the rotavirus vaccine introduction among 56 countries participating in GRSN from 2008 to 2018.

Results
Countries that participated in or conducted surveillance for invasive pneumococcal disease or rotavirus disease were 3.5 (95% confidence interval [CI], 1.7–7.1) and 4.2 (95% CI, 2.1–8.6) times more likely to introduce PCV or rotavirus respectively, compared to those without surveillance. Among countries participating in GRSN, there was insufficient evidence to demonstrate an association between countries with higher rotavirus positivity and vaccine introduction.

Conclusions
Surveillance should be incorporated into advocacy strategies to encourage the introduction of vaccines, with countries benefiting from data from, support for, and coordination of international disease surveillance networks.
Prioritization and management of calls from older people to GP out-of-hours services
Authors: Smith Suzanne , Carragher Lucia 
Published: February 2021

Abstract

Background
Urgent out-of-hours medical care is necessary to ensure people can remain living at home into older age. However, older people experience multiple barriers to using out-of-hours services including poor awareness about the general practitioner (GP) out-of-hours (GPOOH) service and how to access it. In particular, older people are reluctant users of GPOOH services because they expect either their symptoms will not be taken seriously or they will simply be referred to hospital accident and emergency services. The aim of this study was to examine if this expectation was borne out in the manner of GPOOH service provision.

Objective
The objective was to establish the urgency categorization and management of calls to GPOOH , for community dwelling older people in Ireland.

Methods
An 8-week sample of 770 calls, for people over 65 years, to a GPOOH service in Ireland, was analysed using Excel and Nvivo software.

Results
Urgency categorization of older people shows 40% of calls categorized as urgent. Recognition of the severity of symptoms, prompting calls to the GPOOH service, is also reflected in a quarter of callers receiving a home visit by the GP and referral of a third of calls to emergency services. The findings also show widespread reliance on another person to negotiate the GPOOH system, with a third party making 70% of calls on behalf of the older person seeking care.

Conclusion
Older people are in urgent need of medical services when they contact GPOOH service, which plays an effective and patient-centred gatekeeping role, particularly directing the oldest old to the appropriate level of care outside GP office hours. The promotion of GPOOH services should be enhanced to ensure older people understand their role in supporting community living.
Authorship and Creation
Authors: Irmak Nurbay 
Published: February 2021

Abstract
Artworks have authors. According to Christy Mag Uidhir, this simple assumption has significant consequences for the ontology of artworks. One such consequence is that artworks cannot be identified with abstract entities: if there are works of art, they are concrete entities. Therefore, one cannot create an abstract work of art. Mag Uidhir presents a novel challenge against abstract creationism, the view that certain kinds of art objects are abstract artifacts. This article has two aims. First, it provides a defense of abstract creationism against Mag Uidhir’s arguments. Second, it argues that creation, even in the case of concrete artifacts, is never purely causal: to create an artifact is to bring about the conditions on which the created object ontologically depends. I conclude that a properly developed account of creation provides a better understanding of the question of how one comes to create an artifact, be it abstract or concrete.
Evaluation of a thrice weekly administration of teicoplanin in the outpatient setting: a retrospective observational multicentre study
Authors: Asumang John , Heard Katie L , Troise Oliver , Fahmy Sandra , Mughal Nabeela , Moore Luke S P , Hughes Stephen 
Published: February 2021

Abstract

Introduction
The glycopeptide teicoplanin is commonly utilized to facilitate outpatient parenteral antimicrobial therapy (OPAT). Licensed for once daily maintenance dosing, teicoplanin’s long half-life allows for less frequent dosing (e.g. thrice weekly) following successful loading. This service evaluation reviews the safety and effectiveness of a novel thrice weekly teicoplanin dosing regimen.

Methods
A retrospective, observational study was conducted at Chelsea and Westminster Hospital (March 2018 to July 2020), evaluating trough serum teicoplanin concentrations for patients receiving &gt;5 days of teicoplanin in the OPAT setting. Teicoplanin dosing and administration (once daily versus thrice weekly), clinical outcomes and therapeutic levels were analysed for all patients. The project was registered with clinical governance locally.

Results
A total of 82 patients treated with teicoplanin in the OPAT service were included; 53/82 receiving thrice weekly and 29/82 receiving once daily dosing. Mean teicoplanin trough levels were similar in both groups (26.2 mg/L and 25.8 mg/L in once daily and thrice weekly groups, P = 0.8895). High clinical success rates were recorded in both groups (25/29 [86.2%] versus 50/53 [94.3%]). No correlation with clinical outcomes and initial teicoplanin serum levels was identified. Normal renal function (&gt;90 mL/min) was associated with lower teicoplanin serum concentrations (mean [±SD] 21.4 mg/L [±10.1] versus 29.7 mg/L [±14], P = 0.0178) in the thrice weekly dosed group but not with the once daily dosed group (mean [±SD] 28.2 mg/L [±9.4] versus 23.7 mg/L [±9.9], P = 0.2201).

Conclusions
This study supports thrice weekly teicoplanin as a convenient and effective OPAT for administration in the OPAT setting. Therapeutic drug monitoring is advised to adjust for intra-patient variability.