bluuebunny/crossref_metadata_2025_split huggingface dataset:
A retrospective and regional approach assessing the genomic diversity ofSalmonellaDublin
Authors: De Sousa Violante Madeleine , Podeur Gaëtan , Michel Valérie , Guillier Laurent , Radomski Nicolas , Lailler Renaud , Le Hello Simon , Weill François-Xavier , Mistou Michel-Yves , Mallet Ludovic 
Published: July 2022

AbstractFrom a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis processes of regional S. Dublin outbreaks events between 2015 and 2017. Samples were clustered and assessed for correlation against metadata including isolation date, isolation matrices, geographical origin and epidemiological hypotheses. Significant findings can be drawn from this work. We found that the geographical distance was a major factor explaining genetic groups in the early stages of the cheese production processes (animals, farms) while down-the-line transformation steps were more likely to host genomic diversity. This supports the hypothesis of a generalised local persistence of strains from animal to finished products, with occasional migration. We also observed that the bacterial surveillance is representative of diversity, while targeted investigations without genomics evidence often included unrelated isolates. Combining both approaches in phylogeography methods allows a better representation of the dynamics, of outbreaks.
On the use of current and forward-looking data in monetary policy: a behavioural macroeconomic approach
Authors: De Grauwe Paul , Ji Yuemei 
Published: July 2022

AbstractWe analyse the question of whether the use of forward-looking data in monetary policy is to be preferred over the use of current data. We use a behavioural macroeconomic model that generates periods of tranquillity alternating with crisis periods characterized by fat tails in the distribution of output gap. We find that in a strict inflation targeting (SIT) regime, the use of forward-looking data leads to a lower quality of monetary policymaking than in a dual mandate monetary policy regime, because the first regime creates more extreme movements in output and inflation than the second one. We also find that nowcasting tends to improve the quality of monetary policy, especially in a SIT regime. Finally, we provide a case study of monetary policies in the USA and the eurozone during 2000–20.
Benchmarking active learning strategies for materials optimization and discovery
Authors: Wang Alex , Liang Haotong , McDannald Austin , Takeuchi Ichiro , Kusne Aaron Gilad 
Published: July 2022

Abstract
Autonomous physical science is revolutionizing materials science. In these systems, machine learning (ML) controls experiment design, execution and analysis in a closed loop. Active learning, the ML field of optimal experiment design, selects each subsequent experiment to maximize knowledge toward the user goal. Autonomous system performance can be further improved with the implementation of scientific ML, also known as inductive bias-engineered artificial intelligence, which folds prior knowledge of physical laws (e.g. Gibbs phase rule) into the algorithm. As the number, diversity and uses for active learning strategies grow, there is an associated growing necessity for real-world reference datasets to benchmark strategies. We present a reference dataset and demonstrate its use to benchmark active learning strategies in the form of various acquisition functions. Active learning strategies are used to rapidly identify materials with optimal physical properties within a compositional phase diagram mapping a ternary materials system. The data are from an actual Fe-Co-Ni thin-film library and include previously acquired experimental data for materials compositions, X-ray diffraction patterns and two functional properties of magnetic coercivity and the Kerr rotation. Popular active learning methods along with a recent scientific active learning method are benchmarked for their materials optimization performance. Among the acquisition functions benchmarked, Expected Improvement demonstrated the best overall performance. We discuss the relationship between algorithm performance, materials search space complexity and the incorporation of prior knowledge, and we encourage benchmarking more and novel active learning schemes.
Two transporters mobilize magnesium from vacuolar stores to enable plant acclimation to magnesium deficiency
Authors: Tang Ren-Jie , Yang Yang , Yan Yu-Wei , Mao Dan-Dan , Yuan Hong-Mei , Wang Chao , Zhao Fu-Geng , Luan Sheng 
Published: July 2022

Abstract
Magnesium (Mg) is an essential metal for chlorophyll biosynthesis and other metabolic processes in plant cells. Mg is largely stored in the vacuole of various cell types and remobilized to meet cytoplasmic demand. However, the transport proteins responsible for mobilizing vacuolar Mg2+ remain unknown. Here, we identified two Arabidopsis (Arabidopsis thaliana) Mg2+ transporters (MAGNESIUM TRANSPORTER 1 and 2; MGT1 and MGT2) that facilitate Mg2+ mobilization from the vacuole, especially when external Mg supply is limited. In addition to a high degree of sequence similarity, MGT1 and MGT2 exhibited overlapping expression patterns in Arabidopsis tissues, implying functional redundancy. Indeed, the mgt1 mgt2 double mutant, but not mgt1 and mgt2 single mutants, showed exaggerated growth defects as compared to the wild type under low-Mg conditions, in accord with higher expression levels of Mg-starvation gene markers in the double mutant. However, overall Mg level was also higher in mgt1 mgt2, suggesting a defect in Mg2+ remobilization in response to Mg deficiency. Consistently, MGT1 and MGT2 localized to the tonoplast and rescued the yeast (Saccharomyces cerevisiae) mnr2Δ (manganese resistance 2) mutant strain lacking the vacuolar Mg2+ efflux transporter. In addition, disruption of MGT1 and MGT2 suppressed high-Mg sensitivity of calcineurin B-like 2 and 3 (cbl2 cbl3), a mutant defective in vacuolar Mg2+ sequestration, suggesting that vacuolar Mg2+ influx and efflux processes are antagonistic in a physiological context. We further crossed mgt1 mgt2 with mgt6, which lacks a plasma membrane MGT member involved in Mg2+ uptake, and found that the triple mutant was more sensitive to low-Mg conditions than either mgt1 mgt2 or mgt6. Hence, Mg2+ uptake (via MGT6) and vacuolar remobilization (through MGT1 and MGT2) work synergistically to achieve Mg2+ homeostasis in plants, especially under low-Mg supply in the environment.
Seven steps to enhance Open Science practices in animal science
Authors: Muñoz-Tamayo Rafael , Nielsen Birte L , Gagaoua Mohammed , Gondret Florence , Krause E Tobias , Morgavi Diego P , Olsson I Anna S , Pastell Matti , Taghipoor Masoomeh , Tedeschi Luis , Veissier Isabelle , Nawroth Christian 
Published: July 2022

Abstract
The Open Science movement aims at ensuring accessibility, reproducibility, and transparency of research. The adoption of Open Science practices in animal science, however, is still at an early stage. To move ahead as a field, we here provide seven practical steps to embrace Open Science in animal science. We hope that this paper contributes to the shift in research practices of animal scientists towards open, reproducible, and transparent science, enabling the field to gain additional public trust and deal with future challenges to guarantee reliable research. Although the paper targets primarily animal science researchers, the steps discussed here are also applicable to other research domains.
It was good while it lasted: politics is at the heart of public health but are we willing to engage?
Authors: McKee Martin 
Published: July 2022

Abstract
This paper, written to mark the 50th anniversary of the Faculty of Public Health, reflects on the challenges to governance in a United Kingdom outside the European Union. Drawing on Virchow’s call to address the political determinants of health, it describes a situation in which the current government consistently displays disregard for the institutions of state, and the principles on which they are based, such as honesty and the rule of law. It argues that this is a departure from the past and that it undermines the trust that is essential for effective public health policies that attract public support. It ends with a challenge to the public health establishment in the United Kingdom to decide whether they will challenge the decline in public standards, and thus promote structures that can consider and prioritize health or continue to pick up the pieces of political failings.
On 2-Representation Infinite Algebras Arising From Dimer Models
Authors: Nakajima Yusuke 
Published: July 2022

AbstractThe Jacobian algebra arising from a consistent dimer model is a bimodule 3-Calabi–Yau algebra, and its center is a 3-dimensional Gorenstein toric singularity. A perfect matching (PM) of a dimer model gives the degree, making the Jacobian algebra $\mathbb{Z}$-graded. It is known that if the degree zero part of such an algebra is finite dimensional, then it is a 2-representation infinite algebra that is a generalization of a representation infinite hereditary algebra. Internal PMs, which correspond to toric exceptional divisors on a crepant resolution of a 3-dimensional Gorenstein toric singularity, characterize the property that the degree zero part of the Jacobian algebra is finite dimensional. Combining this characterization with the theorems due to Amiot–Iyama–Reiten, we show that the stable category of graded maximal Cohen–Macaulay modules admits a tilting object for any 3-dimensional Gorenstein toric isolated singularity. We then show that all internal PMs corresponding to the same toric exceptional divisor are transformed into each other using the mutations of PMs, and this induces derived equivalences of 2-representation infinite algebras.
On Contact Surgery and Knot Floer Invariants
Authors: Matkovič Irena 
Published: July 2022

Abstract
We establish some general relations between Heegaard-Floer-based contact invariants. In particular, we observe that if the contact invariant of large negative, respectively positive, contact surgeries along a Legendrian knot does not vanish, then the Legendrian invariant, respectively the Legendrian inverse limit invariant, of that knot is non-zero. We use sutured Floer homology and the limit constructions due to Golla and Etnyre, Vela-Vick and Zarev.
Basic calcium phosphate crystals induce the expression of extracellular matrix remodelling enzymes in tenocytes
Authors: Chhana Ashika , Pool Bregina , Callon Karen E , Naot Dorit , Gao Ryan , Coleman Brendan , Cornish Jillian , McCarthy Geraldine M , Dalbeth Nicola 
Published: July 2022

AbstractObjectivesBasic calcium phosphate (BCP) crystals contribute to several syndromes associated with tendon disease, including acute calcific tendinitis and Milwaukee shoulder syndrome. Interactions between BCP crystals and tenocytes (tendon cells) may contribute to these clinical syndromes. This study aimed to determine the direct effects of BCP crystals on tenocyte function and viability.MethodsIn vitro assays were used to assess changes in human tenocytes cultured with BCP crystals. Real-time PCR was used to determine changes in the expression of tendon-related genes and extracellular matrix remodelling enzymes (MMPs; a disintegrin and metalloproteases, ADAMTS; and tissue inhibitor of metalloproteinases, TIMPs). ELISA was used to measure protein concentrations in tenocyte supernatants. MTT and alamarBlue™ assays were used to determine changes in cell viability.ResultsBCP crystals upregulated tenocyte gene expression of MMP-1, MMP-3, ADAMTS-4 and TIMP-1 after 24 h. Time-course experiments showed expression peaked at 8 h for TIMP-1 and 48 h for MMP-1 and ADAMTS-4. Cyclooxygenase (COX)-1 gene expression was upregulated after 48 h. Tenocytes did not alter expression of scleraxis and tendon collagens, and expression of pro-inflammatory cytokines was not induced with BCP crystals. BCP crystals increased tenocyte release of prostaglandin E2 (PGE2) and MMP-1 protein after 24 h. However, neither COX-1 inhibition nor COX-2 inhibition led to consistent change in BCP crystal-induced tenocyte gene expression of extracellular matrix remodelling enzymes. BCP crystals had no effect on tenocyte viability.ConclusionBCP crystals induce extracellular matrix remodelling enzymes, but not inflammatory cytokines, in tenocytes.
Serum cholesterol loading capacity of macrophages is regulated by seropositivity and C-reactive protein in rheumatoid arthritis patients
Authors: Karpouzas George A , Papotti Bianca , Ormseth Sarah R , Palumbo Marcella , Hernandez Elizabeth  , Marchi Cinzia , Zimetti Francesca , Budoff Matthew J , Ronda Nicoletta 
Published: July 2022

AbstractObjectiveExcessive cholesterol accumulation in macrophages is the pivotal step underlying atherosclerotic plaque formation. We here explore factors in the serum of patients with RA, and mechanisms through which they interact with and influence cholesterol loading capacity (CLC) of macrophages.MethodsIn a cross-sectional observational cohort of 104 patients with RA, CLC was measured as intracellular cholesterol content in human THP-1–derived macrophages after incubation with patient serum. Low-density lipoprotein (LDL) oxidation was measured in terms of oxidized phospholipids on apoB100-containing particles (oxPL-apoB100). Antibodies against oxidized LDL (anti-oxLDL), proprotein convertase subtilisin/Kexin type-9 (PCSK9) and high-sensitivity CRP were also quantified. All analyses adjusted for atherosclerotic cardiovascular disease (ASCVD) risk score, obesity, total LDL, statin use, age at diagnosis, and anti-oxLDL IgM.ResultsOxPL-apoB100, anti-oxLDL IgG and PCSK9 were positively associated with CLC (all P &lt; 0.020). OxPL-apoB100 directly influenced CLC only in dual RF- and ACPA-positive patients [unstandardized b (95% bootstrap CI)=2.08 (0.38, 3.79)]. An indirect effect of oxPL-apoB100 on CLC through anti-oxLDL IgG increased, along with level of CRP [index of moderated mediation = 0.55 (0.05–1.17)]. CRP also moderated yet another indirect effect of oxPL-apoB100 on CLC through upregulation of PCSK9, but only among dual-seropositive patients [conditional indirect effect = 0.64 (0.13–1.30)].ConclusionOxidized LDL can directly influence CLC in dual-seropositive RA patients. Two additional and independent pathways—via anti-oxLDL IgG and PCSK9—may mediate the effects of oxPL-apoB100 on CLC, depending on CRP and seropositivity status. If externally validated, these findings may have clinical implications for cardiovascular risk prevention.
Non-State Actors of Protection and the Sliding Scale of Protection for Refugee Women
Authors: Querton Christel 
Published: July 2022

Abstract
The article argues that although the gradual recognition of non-State actors as agents of persecution was hailed as a success in ensuring better protection for refugee women at risk of harm from their community or family, the associated development of non-state actors as agents of protection has had a detrimental impact on the protection of refugee women in Europe and more globally. More specifically, the article identifies various everyday practices of reliance on male family members and undefined social networks as actors of protection. These co-constructing practices are exercised by different entities involved in refugee status determination processes, including governments, national and regional courts, and regional and international asylum agencies. Although the trend has gone largely unnoticed, it has resulted in a sliding scale of protection for refugee women. The article argues that endorsing non-State actors of protection, such as male family members and undefined social networks, amounts to a requirement that women seeking asylum take action to avoid being persecuted by placing themselves under the protection of those private actors. This is contrary to international refugee law doctrine, fails to consider the possibility of new forms of harm and is, in itself, a breach of women’s human rights.
Temperature-Dependent Evolutionary Speed Shapes the Evolution of Biodiversity Patterns Across Tetrapod Radiations
Authors: Skeels A , Bach W , Hagen O , Jetz W , Pellissier L 
Published: July 2022

AbstractBiodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 myr of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modeled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modeling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time. [Biogeography; diversification; machine learning; macroevolution; molecular evolution; simulation.]
Landlordism on Trial: Rent Tribunals and Resistance in Post-War London, 1946–64
Authors: Cartwright Alistair 
Published: July 2022

Abstract
Rent Tribunals were first established in England and Wales in 1946 as a means of regulating rents among furnished lets in the private rented sector, before their authority was extended to cover unfurnished dwellings in 1949. This article shows how rent tribunals created an informal space of justice that provided a forum for tenants’ voices. Tenants used rent tribunals to dramatize their everyday complaints, articulate their sense of entitlement to better housing, and organize collectively to exert pressure on landlords and administrative machinery. The tribunals in turn reconfigured the state’s relationship to the space of the home and echoed representational tropes circulating in popular culture. But in putting landlordism on trial, rent tribunals, and those who participated in them, also came up against the limits of traditional constructions of property ownership and the home. The expansion of homeownership intersected and in some cases fused with increasingly racialized notions of belonging, domesticity, and national identity. Through an examination of these novel regulatory forums, the article highlights both the centrality of working-class agency and the contradictory nature of the welfare state.
Validation of a Novel Statistical Method to Identify Aberrant Patient Logging: A Multi-Institutional Study
Authors: Min Elana A. , Lie Desiree , Barry Carey , Moloney-Johns Amanda , Hibbard Susan T. , Ritsema Tamara S. , D’Aquila Mitzi , Honda Trenton 
Published: July 2022

Introduction:
Student patient encounter logging informs the quality of supervised clinical practice experiences (SCPEs). Yet, it is unknown whether logs accurately reflect patient encounters, and the faculty resources necessary to review for potential aberrant logging are significant. The purpose of this study was to identify a statistical method to identify aberrant logging.

Methods:
A multi-institutional (n = 6) study examined a statistical method for identifying potentially aberrant logging behavior. An automated statistical Mahalanobis Distance (MD) measurement was used to categorize student logs as aberrant if they were identified as probable multivariate outliers. This approach was validated using a gold standard for aberrant logging behavior with manual review by 4 experienced faculty (“faculty consensus”) and then comparing interrater agreement between faculty and MD-based categorization. In secondary analyses, we compared the relative accuracy of MD-based categorization to individual faculty categorizing data from their own program (“own program” categorization).

Results:
323 student logging records from 6 physician assistant (PA) programs were included. Compared to “faculty consensus” (the gold standard), MD-based categorization was highly sensitive (0.846, 95% CI: 0.650, 1.000) and specific (0.766, 95% CI: 0.645, 0.887). Additionally, there was no significant difference in sensitivity, specificity, positive predictive value, or negative predictive value between MD-based categorization and “own program” categorization.

Discussion:
The MD-based method of identifying aberrant and nonaberrant student logging compared favorably to the more traditional, faculty-intensive approach of reviewing individual student logging records. This supports MD-based screening as a less labor-intensive alternative to individual faculty review to identify aberrant logging. Identification of aberrant logging may facilitate early intervention with students to improve clinical exposure logging during their SCPEs.
Moral Injury, Nurse Well-being, and Resilience Among Nurses Practicing During the COVID-19 Pandemic
Authors: Fitzpatrick Joyce J. , Pignatiello Grant , Kim Minjin , Jun Jin , O'Mathúna Dónal P. , Duah Henry O. , Taibl Jessica , Tucker Sharon 
Published: July 2022

OBJECTIVE
The aim of this study was to determine relationships between moral injury (MI), well-being, and resilience among staff nurses and nurse leaders practicing during the COVID-19 (coronavirus disease 2019) pandemic.

BACKGROUND
Attention to MI among health professionals, including nurses, increased in 2021, particularly related to the pandemic. Few studies examined MI, well-being, and resilience; even fewer provided implications for leadership/management.

METHODS
The sample included 676 RNs practicing in Ohio. The electronic survey included assessments of MI, well-being, and resilience distributed via the Ohio Nurses Association and the schools of nursing alumni Listservs.

RESULTS
There was a significant association between MI and negative well-being and negative association between MI and resilience. Differences were observed between staff nurses and leaders.

CONCLUSIONS
This is the first study relating MI, resilience, and well-bring among nurses and nurse leaders during the pandemic. There is a need for additional research to further our understanding about nurses' health and well-being during the pandemic and beyond.