bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthodontic treatment and root resorption: an overview of systematic reviews
Authors: Yassir Yassir A , McIntyre Grant T , Bearn David R 
Published: September 2020

SummaryBackgroundRoot resorption can be considered the most unfortunate complication of orthodontic treatment.ObjectiveTo evaluate the available evidence regarding orthodontically induced inflammatory root resorption (OIIRR).Search methodsA comprehensive literature search was conducted for the systematic reviews investigating OIIRR published up to 24 May 2020. This was accomplished using electronic databases: MEDLINE via OVID, EMBASE, AMED (Allied and Complementary Medicine Database), PubMed, and Web of Science. Any ongoing systematic reviews were searched using Prospero and a grey literature search was undertaken using Google Scholar and OpenGrey (www.opengrey.eu/). No language restriction was applied.Selection criteriaOnly studies investigating OIIRR were included.Data collection and analysisScreening, quality assessment [using the AMSTAR 2 tool (A Measurement Tool to Assess Systematic Reviews)], and data extraction were performed by two authors independently. Information was categorized and narratively synthesized for the key findings from moderate and high-quality reviews.ResultsA total of 2033 potentially eligible studies were identified. After excluding the non-relevant studies, 28 systematic reviews were included. Of which, 20 systematic reviews (71.5%) were of moderate and high-quality level of evidence. The incidence and severity of OIIRR increase with the fixed appliance, especially with heavy force, intrusion, torqueing movements, increased treatment duration, and treatment with extractions or with long apical displacement (particularly for maxillary incisors). There was insufficient evidence regarding most other treatment- and patient-related factors on OIIRR. Following all precautionary measures, pausing treatment and regular monitoring benefits patients with OIIRR.Conclusions and implicationsThere is a limited number of high-quality studies in terms of OIIRR. The influence of fixed appliance on root resorption was noted; however, the cause and effect relationship between OIIRR and orthodontic biomechanics has not been confirmed. Avoiding heavy, continuous forces and a greater amount of apical displacement over a long duration of treatment is recommended. Precautionary measures should be carefully considered when treating patients with a high risk of OIIRR.RegistrationCRD42020166629.
Animals and the prehistoric origins of economic development
Authors: Riahi Ideen A 
Published: September 2020

Abstract
This paper revisits the macro-level relationship between human genetic variation (genetic distance and diversity) and economic development. If other continents were biogeographically more similar to Eurasia, their populations’ capacities to ward off the adverse effects of European colonization would have been much higher and, thus, their economies considerably more prosperous today. At the continental scale, genetic differences between people do not matter for comparative development.
The one hundred year journey of the genus Brucella (Meyer and Shaw 1920)
Authors: Moreno Edgardo 
Published: September 2020

ABSTRACT
The genus Brucella, described by Meyer and Shaw in 1920, comprises bacterial pathogens of veterinary and public health relevance. For 36 years, the genus came to include three species that caused brucellosis in livestock and humans. In the second half of the 20th century, bacteriologists discovered five new species and several ʻatypicalʼ strains in domestic animals and wildlife. In 1990, the Brucella species were recognized as part of the Class Alphaproteobacteria, clustering with pathogens and endosymbionts of animals and plants such as Bartonella, Agrobacterium and Ochrobactrum; all bacteria that live in close association with eukaryotic cells. Comparisons with Alphaproteobacteria contributed to identify virulence factors and to establish evolutionary relationships. Brucella members have two circular chromosomes, are devoid of plasmids, and display close genetic relatedness. A proposal, asserting that all brucellae belong to a single species with several subspecies debated for over 70 years, was ultimately rejected in 2006 by the subcommittee of taxonomy, based on scientific, practical, and biosafety considerations. Following this, the nomenclature of having multiples Brucella species prevailed and defined according to their molecular characteristics, host preference, and virulence. The 100-year history of the genus corresponds to the chronicle of scientific efforts and the struggle for understanding brucellosis.
Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers
Authors: Li Xiangchen , Cheng Jian , Liu Xiaonan , Guo Xiaoxian , Liu Yuqian , Fan Wenjing , Lu Lina , Ma Yanhe , Liu Tao , Tao Shiheng , Jiang Huifeng 
Published: September 2020

Abstract
Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type antibiotics biosynthetic gene clusters (BGCs) in different antibiotics producing strains remained an enigma. In this study, we investigated the distribution and evolution of the fusidane BGCs in 1,284 fungal genomes. We identified 12 helvolic acid BGCs, 4 fusidic acid BGCs, and 1 cephalosporin P1 BGC in Pezizomycotina fungi. Phylogenetic analyses indicated six horizontal gene transfer (HGT) events in the evolutionary trajectory of the BGCs, including 1) three transfers across Eurotiomycetes and Sordariomycetes classes; 2) one transfer between genera under Sordariomycetes class; and 3) two transfers within Aspergillus genus under Eurotiomycetes classes. Finally, we proposed that the ancestor of fusidane BGCs would be originated from the Zoopagomycota by ancient HGT events according to the phylogenetic trees of key enzymes in fusidane BGCs (OSC and P450 genes). Our results extensively clarify the evolutionary trajectory of fusidane BGCs by HGT among distantly related fungi and provide new insights into the evolutionary mechanisms of metabolic pathways in fungi.
Clinical implication of tumour spread through air spaces in pathological stage I lung adenocarcinoma treated with lobectomy
Authors: Yi Eunjue , Lee Jeong Hyeon , Jung Younggi , Chung Jae Ho , Lee Youngseok , Lee Sungho 
Published: September 2020

Abstract

OBJECTIVES
The aim of this study was to evaluate the clinical implication of tumour spread through air spaces (STAS) as a prognostic factor in pathological stage I lung adenocarcinoma treated with lobectomy and to identify related parameters.

METHODS
Medical records of patients who underwent pulmonary lobectomy for stage I (American Joint Committee on Cancers eighth edition) lung adenocarcinomas between 2012 and February 2018 at our institutions were reviewed retrospectively. Patients with minimally invasive adenocarcinomas and tumours ≥3 cm in size were excluded. Included patients were classified into STAS (+) and STAS (−) groups. Clinical implications of STAS and recurrence in patients were investigated.

RESULTS
A total of 109 patients was analysed: 41 (37.6%) in the STAS (+) and 68 (62.4%) in the STAS (−) group. STAS was associated with larger consolidation diameter on chest tomography (≥1.5 cm; P = 0.006) or a higher invasive ratio (≥85%; P = 0.012) and presence of a micropapillary pattern in multivariable analysis (P = 0.003) The recurrence-free survival curve showed statistical difference (P = 0.008) with 3-year survival rates of 73.0% (9 patients) and 96.8% (2 patients) in the STAS (+) and STAS (−) group, respectively. However, no statistical significance was observed in the lung cancer-related survival curve (P = 0.648). The presence of STAS was an independent risk factor for recurrence in multivariable analysis (hazard ratio = 5.9, P = 0.031).

CONCLUSIONS
The presence of STAS could be an important risk factor for recurrence in patients with early-stage invasive lung adenocarcinoma treated with pulmonary lobectomy.
Finite element convergence for the time-dependent Joule heating problem with mixed boundary conditions
Authors: Jensen Max , Målqvist Axel , Persson Anna 
Published: September 2020

Abstract
We prove strong convergence for a large class of finite element methods for the time-dependent Joule heating problem in three spatial dimensions with mixed boundary conditions on Lipschitz domains. We consider conforming subspaces for the spatial discretization and the backward Euler scheme for the temporal discretization. Furthermore, we prove uniqueness and higher regularity of the solution on creased domains and additional regularity in the interior of the domain. Due to a variational formulation with a cut-off functional, the convergence analysis does not require a discrete maximum principle, permitting approximation spaces suitable for adaptive mesh refinement, responding to the difference in regularity within the domain.
Guillain-Barré Syndrome After High-Dose Influenza Vaccine Administration in the United States, 2018–2019 Season
Authors: Perez-Vilar Silvia , Hu Mao , Weintraub Eric , Arya Deepa , Lufkin Bradley , Myers Tanya , Woo Emily Jane , Lo An-Chi , Chu Steve , Swarr Madeline , Liao Jiemin , Wernecke Michael , MaCurdy Tom , Kelman Jeffrey , Anderson Steven , Duffy Jonathan , Forshee Richard A 
Published: September 2020

Abstract

Background
The Vaccine Safety Datalink (VSD) identified a statistical signal for an increased risk of Guillain-Barré syndrome (GBS) in days 1–42 after 2018–2019 high-dose influenza vaccine (IIV3-HD) administration. We evaluated the signal using Medicare.

Methods
We conducted early- and end-of-season claims-based self-controlled risk interval analyses among Medicare beneficiaries ages ≥65 years, using days 8–21 and 1–42 postvaccination as risk windows and days 43–84 as control window. The VSD conducted chart-confirmed analyses.

Results
Among 7 453 690 IIV3-HD vaccinations, we did not detect a statistically significant increased GBS risk for either the 8- to 21-day (odds ratio [OR], 1.85; 95% confidence interval [CI], 0.99–3.44) or 1- to 42-day (OR, 1.31; 95% CI, 0.78–2.18) risk windows. The findings from the end-of-season analyses were fully consistent with the early-season analyses for both the 8- to 21-day (OR, 1.64; 95% CI, 0.92–2.91) and 1- to 42-day (OR, 1.12; 95% CI, 0.70–1.79) risk windows. The VSD’s chart-confirmed analysis, involving 646 996 IIV3-HD vaccinations, with 1 case each in the risk and control windows, yielded a relative risk of 1.00 (95% CI, 0.06–15.99).

Conclusions
The Medicare analyses did not exclude an association between IIV3-HD and GBS, but it determined that, if such a risk existed, it was similar in magnitude to prior seasons. Chart-confirmed VSD results did not confirm an increased risk of GBS.
The novel macrolide resistance genes mef(F) and msr(G) are located on a plasmid in Macrococcus canis and a transposon in Macrococcus caseolyticus
Authors: Fernandez Javier Eduardo , Perreten Vincent , Schwendener Sybille 
Published: September 2020

Abstract

Objectives
To analyse macrolide resistance in a Macrococcus canis strain isolated from a dog with an ear infection, and determine whether the resistance mechanism is also present in other bacteria, and associated with mobile genetic elements.

Methods
The whole genome of M. canis Epi0082 was sequenced using PacBio and Illumina technologies. Novel macrolide resistance determinants were identified through bioinformatic analysis, and functionality was demonstrated by expression in Staphylococcus aureus. Mobile genetic elements containing the novel genes were analysed in silico for strain Epi0082 as well as in other bacterial strains deposited in GenBank.

Results
M. canis Epi0082 contained a 3212 bp operon with the novel macrolide resistance genes mef(F) and msr(G) encoding a efflux protein and an ABC-F ribosomal protection protein, respectively. Cloning in S. aureus confirmed that both genes individually confer resistance to the 14- and 15-membered ring macrolides erythromycin and azithromycin, but not the 16-membered ring macrolide tylosin. A reduced susceptibility to the streptogramin B pristinamycin IA was additionally observed when msr(G) was expressed in S. aureus under erythromycin induction. Epi0082 carried the mef(F)–msr(G) operon together with the chloramphenicol resistance gene fexB in a novel 39 302 bp plasmid pMiCAN82a. The mef(F)–msr(G) operon was also found in macrolide-resistant Macrococcus caseolyticus strains in the GenBank database, but was situated in the chromosome as part of a novel 13 820 bp or 13 894 bp transposon Tn6776.

Conclusions
The identification of mef(F) and msr(G) on different mobile genetic elements in Macrococcus species indicates that these genes hold potential for further dissemination of resistance to the clinically important macrolides in the bacterial population.
Each patient is a research biorepository: informatics-enabled research on surplus clinical specimens via the living BioBank
Authors: Alekseyenko Alexander V , Hamidi Bashir , Faith Trevor D , Crandall Keith A , Powers Jennifer G , Metts Christopher L , Madory James E , Carroll Steven L , Obeid Jihad S , Lenert Leslie A 
Published: September 2020

Abstract
The ability to analyze human specimens is the pillar of modern-day translational research. To enhance the research availability of relevant clinical specimens, we developed the Living BioBank (LBB) solution, which allows for just-in-time capture and delivery of phenotyped surplus laboratory medicine specimens. The LBB is a system-of-systems integrating research feasibility databases in i2b2, a real-time clinical data warehouse, and an informatics system for institutional research services management (SPARC). LBB delivers deidentified clinical data and laboratory specimens. We further present an extension to our solution, the Living µBiome Bank, that allows the user to request and receive phenotyped specimen microbiome data. We discuss the details of the implementation of the LBB system and the necessary regulatory oversight for this solution. The conducted institutional focus group of translational investigators indicates an overall positive sentiment towards potential scientific results generated with the use of LBB. Reference implementation of LBB is available at https://LivingBioBank.musc.edu.
A Generalized Additive Model Correlating Blacklegged Ticks With White-Tailed Deer Density, Temperature, and Humidity in Maine, USA, 1990–2013
Authors: Elias Susan P , Gardner Allison M , Maasch Kirk A , Birkel Sean D , Anderson Norman T , Rand Peter W , Lubelczyk Charles B , Smith Robert P 
Published: September 2020

AbstractGeographical range expansions of blacklegged tick [Ixodes scapularis Say (Acari: Ixodidae)] populations over time in the United States have been attributed to a mosaic of factors including 20th century reforestation followed by suburbanization, burgeoning populations of the white-tailed deer [Odocoileus virginianus Zimmerman (Artiodactyla: Cervidae)], and, at the northern edge of I. scapularis’ range, climate change. Maine, a high Lyme disease incidence state, has been experiencing warmer and shorter winter seasons, and relatively more so in its northern tier. Maine served as a case study to investigate the interacting impacts of deer and seasonal climatology on the spatial and temporal distribution of I. scapularis. A passive tick surveillance dataset indexed abundance of I. scapularis nymphs for the state, 1990–2013. With Maine’s wildlife management districts as the spatial unit, we used a generalized additive model to assess linear and nonlinear relationships between I. scapularis nymph abundance and predictors. Nymph submission rate increased with increasing deer densities up to ~5 deer/km2 (13 deer/mi2), but beyond this threshold did not vary with deer density. This corroborated the idea of a saturating relationship between I. scapularis and deer density. Nymphs also were associated with warmer minimum winter temperatures, earlier degree-day accumulation, and higher relative humidity. However, nymph abundance only increased with warmer winters and degree-day accumulation where deer density exceeded ~2 deer/km2 (~6/mi2). Anticipated increases in I. scapularis in the northern tier could be partially mitigated through deer herd management.
The Gray Area of Institutional Change: How the Security Council Transforms Its Practices on the Fly
Authors: Pouliot Vincent 
Published: September 2020

Abstract
In world politics, institutional development often takes place in a gray area that combines elements of rational design and organic change in practice. Faced with impracticable secondary rules, diplomats evolve semi-formal practices that allow them to make collectively binding decisions even in the absence of a procedure to do so, effectively building the plane while flying it. Changing practices at the United Nations Security Council offer a particularly significant and fertile case here. The ways in which the body conducts its business have significantly evolved in the post–Cold War era, though in the absence of formal changes to the Charter or the Council's Rules of Procedure. How is such a casual institutional transformation possible in the most politicized global governance body? Building on practitioners’ accounts, the article maps out the four spaces of semi-formality and the attendant practices by which the Council transforms itself. First, Council diplomats value flexibility and allow each other to innovate. Second, they attempt to codify evolving ways of conducting Council business. Third, a set of training practices allows for socialization in ways of doing things. Fourth and finally, diplomats on the Council have limited opportunities to collectively discuss their changing practices. Overall, the article suggests that gray zones are far more pervasive than currently acknowledged in world politics, calling for more scholarly interest in this hybrid mode of institutional change in which design emerges organically and is collectively owned.
PositiveMycobacterium tuberculosisGastric Lavage Cultures from Asymptomatic Children With Normal Chest Radiography
Authors: Donald Peter R , Ronge Lena , Demers Anne-Marie , Thee Stephanie , Schaaf H Simon , Hesseling Anneke C 
Published: September 2020

AbstractMycobacterium tuberculosis culture from gastric lavage from apparently healthy children following tuberculin skin test conversion, despite normal chest radiography (CR), is well known but is a contentious subject. A consensus statement regarding classification of childhood tuberculosis excluded this condition, stating that more data were needed. To assist in this discussion, we reviewed early publications that reported the occurrence of this phenomenon and early anatomical pathology studies that described changes that occur in children following tuberculosis infection. Pathology studies describe frequent cavitation in primary foci in children from whom positive M. tuberculosis cultures might easily arise. These foci were very small in some children who might have normal CR. Positive cultures might also arise from ulcerated mediastinal lymph nodes that are invisible on CR. Young children with recent infection very likely have active primary pulmonary tuberculosis.
Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes
Authors: Ballesteros Jesús A , Setton Emily V W , Santibáñez-López Carlos E , Arango Claudia P , Brenneis Georg , Brix Saskia , Corbett Kevin F , Cano-Sánchez Esperanza , Dandouch Merai , Dilly Geoffrey F , Eleaume Marc P , Gainett Guilherme , Gallut Cyril , McAtee Sean , McIntyre Lauren , Moran Amy L , Moran Randy , López-González Pablo J , Scholtz Gerhard , Williamson Clay , Woods H Arthur , Zehms Jakob T , Wheeler Ward C , Sharma Prashant P 
Published: September 2020

Abstract
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
Modularity in Protein Evolution: Modular Organization and De Novo Domain Evolution in Mollusk Metallothioneins
Authors: Calatayud Sara , Garcia-Risco Mario , Pedrini-Martha Veronika , Eernisse Douglas J , Dallinger Reinhard , Palacios Òscar , Capdevila Mercè , Albalat Ricard 
Published: September 2020

AbstractMetallothioneins (MTs) are proteins devoted to the control of metal homeostasis and detoxification, and therefore, MTs have been crucial for the adaptation of the living beings to variable situations of metal bioavailability. The evolution of MTs is, however, not yet fully understood, and to provide new insights into it, we have investigated the MTs in the diverse classes of Mollusks. We have shown that most molluskan MTs are bimodular proteins that combine six domains—α, β1, β2, β3, γ, and δ—in a lineage-specific manner. We have functionally characterized the Neritimorpha β3β1 and the Patellogastropoda γβ1 MTs, demonstrating the metal-binding capacity of the new γ domain. Our results have revealed a modular organization of mollusk MT, whose evolution has been impacted by duplication, loss, and de novo emergence of domains. MTs represent a paradigmatic example of modular evolution probably driven by the structural and functional requirements of metal binding.
Periphilin self-association underpins epigenetic silencing by the HUSH complex
Authors: Prigozhin Daniil M , Douse Christopher H , Farleigh Laura E , Albecka Anna , Tchasovnikarova Iva A , Timms Richard T , Oda Shun-ichiro , Adolf Frank , Freund Stefan M V , Maslen Sarah , Lehner Paul J , Modis Yorgo 
Published: September 2020

Abstract
Transcription of integrated DNA from viruses or transposable elements is tightly regulated to prevent pathogenesis. The Human Silencing Hub (HUSH), composed of Periphilin, TASOR and MPP8, silences transcriptionally active viral and endogenous transgenes. HUSH recruits effectors that alter the epigenetic landscape and chromatin structure, but how HUSH recognizes target loci and represses their expression remains unclear. We identify the physicochemical properties of Periphilin necessary for HUSH assembly and silencing. A disordered N-terminal domain (NTD) and structured C-terminal domain are essential for silencing. A crystal structure of the Periphilin-TASOR minimal core complex shows Periphilin forms an α-helical homodimer, bound by a single TASOR molecule. The NTD forms insoluble aggregates through an arginine/tyrosine-rich sequence reminiscent of low-complexity regions from self-associating RNA-binding proteins. Residues required for TASOR binding and aggregation were required for HUSH-dependent silencing and genome-wide deposition of repressive mark H3K9me3. The NTD was functionally complemented by low-complexity regions from certain RNA-binding proteins and proteins that form condensates or fibrils. Our work suggests the associative properties of Periphilin promote HUSH aggregation at target loci.