bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-based classification of Pedobacter polysacchareus sp. nov., isolated from Antarctic soil producing exopolysaccharide
Authors: Wang Wenjing , Mu Hongmei , Ren Xingtao , Ouyang Qingqing , Li Jing 
Published: April 2023

Abstract
A psychrotolerant bacterial strain, designated ZS13-49T, with strong extracellular polysaccharide synthesis ability was isolated from soil collected in Antarctica and subjected to polyphasic taxonomic and comparative genomics. Chemotaxonomic features, including fatty acids, and polar lipid profiles, support the assignment of strain ZS13-49T to the genus Pedobacter. 16S rRNA gene phylogeny demonstrates that strain ZS13-49T forms a well-supported separate branch as a sister clade to Pedobacter gandavensis LMG 31462T and is clearly separated from Pedobacter steynii DSM 19110T and Pedobacter caeni DSM 16990T. Phylogenetic analysis showed strain ZS13-49T shared the highest 16S rRNA gene sequence similarity (99.9%) with P. gandavensis LMG 31462T. However, the digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) value and average amino identity (AAI) value between strain ZS13-49T and P. gandavensis LMG 31462T were 26.5%, 83.3%, and 87.5%, respectively. Phylogenomic tree and a comparative genomic analysis indicated distinct characteristics to distinguish strain ZS13-49T from the closely related species. The complete genome sequence of strain ZS13-49T consists of 5 830 353 bp with 40.61% G + C content. Genomic features of strain ZS13-49T adapted to Antarctic environment were also revealed. Based on the phenotypic, chemotaxonomic, and genomic data, strain ZS13-49T could be assigned to a novel species within the genus Pedobacter for which the name Pedobacter polysacchareus sp. nov. is proposed. The type strain is ZS13-49T ( = CCTCC AB 2019394T = KCTC 72824T).
Pathogen vacuole membrane contact sites – close encounters of the fifth kind
Authors: Vormittag Simone , Ende Rachel J , Derré Isabelle , Hilbi Hubert 
Published: April 2023

AbstractVesicular trafficking and membrane fusion are well-characterized, versatile, and sophisticated means of ‘long range’ intracellular protein and lipid delivery. Membrane contact sites (MCS) have been studied in far less detail, but are crucial for ‘short range’ (10–30 nm) communication between organelles, as well as between pathogen vacuoles and organelles. MCS are specialized in the non-vesicular trafficking of small molecules such as calcium and lipids. Pivotal MCS components important for lipid transfer are the VAP receptor/tether protein, oxysterol binding proteins (OSBPs), the ceramide transport protein CERT, the phosphoinositide phosphatase Sac1, and the lipid phosphatidylinositol 4-phosphate (PtdIns(4)P). In this review, we discuss how these MCS components are subverted by bacterial pathogens and their secreted effector proteins to promote intracellular survival and replication.
Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch
Authors: Galindo Luis Javier , Prokina Kristina , Torruella Guifré , López-García Purificación , Moreira David 
Published: April 2023

Abstract
Ophirinina is a recently described suborder of jakobid protists (Excavata) with only one described species to date, Ophirina amphinema. Despite the acquisition and analysis of massive transcriptomic and mitogenomic sequence data from O. amphinema, its phylogenetic position among excavates remained inconclusive, branching as sister group either to all Jakobida or to all Discoba. From a morphological perspective, it has not only several typical jakobid features but also unusual traits for this group, including the morphology of mitochondrial cristae (sac-shaped to flattened-curved cristae) and the presence of two flagellar vanes. In this study, we have isolated, morphologically characterized, and sequenced genome and transcriptome data of two new Ophirinina species: Ophirina chinija sp. nov. and Agogonia voluta gen. et sp. nov. Ophirina chinija differs from O. amphinema in having rounded cell ends, subapically emerging flagella and a posterior cell protrusion. The much more distantly related A. voluta has several unique ultrastructural characteristics, including sac-shaped mitochondrial cristae and a complex “B” fiber. Phylogenomic analyses with a large conserved-marker dataset supported the monophyly of Ophirina and Agogonia within the Ophirinina and, more importantly, resolved the conflicting position of ophirinids as the sister clade to all other jakobids. The characterization of the mitochondrial genomes showed that Agogonia differs from all known gene-rich jakobid mitogenomes by the presence of two group II introns and their corresponding maturase protein genes. A phylogenetic analysis of the diversity of known maturases confirmed that the Agogonia proteins are highly divergent from each other and define distant families among the prokaryotic and eukaryotic maturases. This opens the intriguing possibility that, compared to other jakobids, Ophirinina may have retained additional mitochondrial elements that may help to understand the early diversification of eukaryotes and the evolution of mitochondria.
Slip model with supershear rupture velocity and stress drop for an M4.5 aftershock of the 2019 Ridgecrest, California, earthquake sequence
Authors: Fletcher Jon B , Erdem Jemile E , Baker Lawrence M 
Published: April 2023

SUMMARY
We use records from 24 stations with epicentral distances under 50 km to invert for slip and rupture time of an M4.5 aftershock of the 2019 Ridgecrest, California, earthquake sequence. Slip was determined by inverting source time functions (STFs), which were obtained at each station by decomposing a main shock, in this case an M4.5 aftershock, into a series of subevents using an empirical Green's function (eGf) as a template. The technique is iterative in the time domain with a positivity constraint. The STFs are characterized by a single pulse with durations that were longer in the southeast direction (about 1.0 s) and shorter in the northwest direction (about 0.6 s) suggesting rupture directivity to the northwest. We inverted the STFs for slip using a tomographic algorithm from that uses a high-frequency approximation to ray theory for the forward problem. The tomographic algorithm solves for slip and rupture time on a grid of points, which provides a better strategy for elucidating directivity than a model that uses subfaults. We solve for the strike-slip intensity on a near-vertical plane striking northwest, similar to the M7.1. After nine iterations, the slip model reduces the chi-squared estimate of fit by 68 per cent. Most of the slip is to the northwest, with a narrow well-defined peak in slip about 0.3 km NW of the origin. The peak is fairly symmetrical and about 1.5 km across its base. The model shows significant directivity to the northwest as suggested by the azimuthal variation of the STF pulse widths. Rupture velocity increases from nucleation to the peak in slip, becomes supershear, and then slows to about 3.2 km s−1, but there is little slip beyond 0.8 s contour in the forward direction. It appears that the peak in slip contributed stress to accelerate the rupture to the northwest. Low-level, parabolic-shaped slip patterns are seen to the northwest, which could be where the rupture front is dying out. Similar, but fainter curves facing the southeast suggests some bilateral rupture but the rupture to the northwest was stronger. Static stress drop was calculated using a formula for an elastic half-space giving a maximum of 35 bars at the peak in slip, but smoothing controls the absolute value. The average over a presumed fault plane is about 1.4 bars, much less than the peak. Slip and stress drop are highly heterogeneous.
Revisiting the Framework for Compulsory Licensing of Patents in the European Union – Reflections on the European Commission’s Initiative
Authors: Lamping Matthias , Batista Pedro Henrique D , Correa Juan Ignacio , Hilty Reto M , Kim Daria , Slowinski Peter R , Steinhart Miriam 
Published: April 2023

Abstract
Within the scope of its initiative on ‘Compulsory Licensing in the EU’,8 the European Commission launched a call for evidence on 1 April 2022 and a public consultation on 7 July 2022 with the aim of gathering views from stakeholders. The objective of this initiative is to explore the possibility of revising the framework for compulsory licensing in the EU to make it more ‘adequately prepared and coordinated to tackle future crises’.9 The authors of this position paper welcome the Commission’s attempt to reinvigorate the public discourse on this important subject.
Depending on the issue to be addressed and the extent of the Commission’s willingness to reform, different regulatory approaches are conceivable. Subject to compatibility with the principles of subsidiarity and proportionality, these include:
Rather than making concrete recommendations on the regulatory approach, this paper addresses selected aspects by way of a preliminary, non-exhaustive note on: the proposed reform’s scope and the grounds for a compulsory licence; the requirements of prior negotiation and licensing failure; government use; procedural matters; compulsory licences for patent applications and products; the relation with other regulations and sui generis regimes (i.e. trade secret protection, regulatory data protection and supplementary protection certificates); the concept of adequate remuneration; compulsory licences for European patents with unitary effect; and the exhaustion of products placed on the market under a compulsory licence.
– soft law measures, such as guidelines and recommendations;
– harmonisation of national laws (substantive and/or procedural);10
– judicial cooperation (i.e. mutual recognition of judgments and of decisions in extrajudicial cases);11
– centralisation of granting and/or judicial review competences;
– creation of a supranational compulsory licence;
– or any combination thereof.
Antecedents and consequences of fake news exposure: a two-panel study on how news use and different indicators of fake news exposure affect media trust
Authors: Lee Sangwon , Gil de Zúñiga Homero , Munger Kevin 
Published: April 2023

Abstract
Despite abundant studies on “fake news,” the long-term consequences have been less explored. In this context, this study examines the dynamic relationship between traditional and social news media use, fake news exposure—measured as perceived fake news exposure and exposure to actual fake news stories, and mainstream media trust. We found interesting patterns across two U.S. panel survey studies. First, we found that exposure to fake news—regardless of how we measured it—decreased people’s trust in the mainstream media. Yet, we also found that while both social media and traditional news use were positively associated with exposure to actual fake news stories, only social media news use was positively associated with perceived fake news exposure. This finding implies that while many people believe that social media is the culprit of fake news exposure, traditional news use may also contribute to people’s exposure to popular fake news stories.
Comparative court-packing
Authors: Kosař David , Šipulová Katarína 
Published: April 2023

Abstract
In the wake of Donald Trump’s presidency, a fierce discussion over expanding the US Supreme Court erupted. However, the expansion of a court’s membership is just one of several court-packing techniques. Moreover, the American debate is peculiar due to the unique features of the US Supreme Court. The aim of this article is to look at court-packing from a comparative perspective, to link the debates on tinkering with courts’ composition on both sides of the Atlantic, and to bring into the conversation a diverse scholarship in the Global North and the Global South. Based on experience from other parts of the world, this article provides a new, broader definition of court-packing that includes not only expansion of the court in question, but also emptying and swapping strategies. It then discusses the typical justifications for and dangers of court-packing and provides a prospective pragmatic mid-level theory that allows us to assess whether a given court-packing plan is legitimate. It argues that the legitimacy of court-packing has two dimensions: one focusing on whether court-packing pursues a legitimate aim (ius ad bellum of court-packing) and a second dimension exploring whether court-packing itself is implemented legitimately (ius in bello of court-packing). This means that even if politicians have a “just cause” for court-packing, their actions are still limited.
Associations of life course obesity with endometrial cancer in the Epidemiology of Endometrial Cancer Consortium (E2C2)
Authors: Harvey Summer V , Wentzensen Nicolas , Bertrand Kimberly , Black Amanda , Brinton Louise A , Chen Chu , Costas Laura , Dal Maso Luigino , De Vivo Immaculata , Du Mengmeng , Garcia-Closas Montserrat , Goodman Marc T , Gorzelitz Jessica , Johnson Lisa , Lacey James V , Liao Linda , Lipworth Loren , Lissowska Jolanta , Miller Anthony B , O'Connell Kelli , O’Mara Tracy A , Ou Xiao , Palmer Julie R , Patel Alpa V , Paytubi Sonia , Pelegrina Beatriz , Petruzella Stacey , Prizment Anna , Rohan Thomas , Sandin Sven , Setiawan Veronica Wendy , Sinha Rashmi , Trabert Britton , Webb Penelope M , Wilkens Lynne R , Xu Wanghong , Yang Hannah P , Zheng Wei , Clarke Megan A 
Published: April 2023

Abstract

Background
Adult obesity is a strong risk factor for endometrial cancer (EC); however, associations of early life obesity with EC are inconclusive. We evaluated associations of young adulthood (18–21 years) and adulthood (at enrolment) body mass index (BMI) and weight change with EC risk in the Epidemiology of Endometrial Cancer Consortium (E2C2).

Methods
We pooled data from nine case-control and 11 cohort studies in E2C2. We performed multivariable logistic regression analyses to estimate odds ratios (OR) and 95% confidence intervals (95% CI) for BMI (kg/m2) in young adulthood and adulthood, with adjustment for BMI in adulthood and young adulthood, respectively. We evaluated categorical changes in weight (5-kg increments) and BMI from young adulthood to adulthood, and stratified analyses by histology, menopausal status, race and ethnicity, hormone replacement therapy (HRT) use and diabetes.

Results
We included 14 859 cases and 40 859 controls. Obesity in adulthood (OR = 2.85, 95% CI = 2.47–3.29) and young adulthood (OR = 1.26, 95% CI = 1.06–1.50) were positively associated with EC risk. Weight gain and BMI gain were positively associated with EC; weight loss was inversely associated with EC. Young adulthood obesity was more strongly associated with EC among cases diagnosed with endometrioid histology, those who were pre/perimenopausal, non-Hispanic White and non-Hispanic Black, among never HRT users and non-diabetics.

Conclusions
Young adulthood obesity is associated with EC risk, even after accounting for BMI in adulthood. Weight gain is also associated with EC risk, whereas weight loss is inversely associated. Achieving and maintaining a healthy weight over the life course is important for EC prevention efforts.
Drug-related problems as reason for emergency department visit: 3 years of the FARM-URG registry
Authors: Ruiz-Ramos Jesús ,   GRUPO REDFASTER-SEFH, Ruiz-Ramos Jesús , Perrín Rosario Santolaya , Martín Mª Ángeles García , Serrano Paloma Sempere , Riera Margarita Prats , Valls Montal Camil·la , Gutiérrez María del Mar García , Diaz Ana Such , Pinto Ana de Lorenzo , Hernanz Beatriz Calderón , Ramos Nuria Gala , Díez Montserrat Alonso , Sánchez Manuel Bonete , Palomares Ana Gines , Fernández Nerea , Ruiz Bárbara Úbeda , Pardo Ana Arancón , Cabet Macarena García-Trevijano , Pérez Álvaro Parea , Iglesias Manuel Busto , Borrego Ana Juanes , Clemente Yolanda Castellanos , del Mar García Gutiérrez María , Campaña Juan Manuel Real , Fernández Beatriz Somoza , Pérez Marina Fages , Altuna Ana Ayestarán , Banzo Josana Fierro , Candel Gregorio Romero , Ruiz-Morón Ana Fernández , García María Muñoz , Duat Antonia Balet , Martínez Raquel López , Alcon Emili Vallve , Fontelles Gemma Garreta , García Marta Maialen Mediavilla , Blanch Cristina Toro , Pérez Anna Fayet , Benito Anna Dordá , Rodríguez Marta , Albir Mª Jose Company , Rubio Celia Aparicio , Torres María Cuenca , Requejo Carmen Caballero , Grande Ana Suárez-Lledó , Casanova Javier Martínez , Vidal Jaime Barceló , Alarcón Alicia Rodríguez , Navarro Mª Rosario Ortíz , Blanco Cristina Calzón , Clavero Gemma Morla , Rodríguez Javier Ramos 
Published: April 2023

Abstract

Objectives
Drug-related problems (DRPs) are a well-known cause of emergency department (ED) visits. The objective of the FARM-URG project was to assess the prevalence of DRPs using an annual cross-sectional registry. Herein we report results of the first 3 years, indicating the prevalence of DRPs, drugs involved, and patient characteristics.

Methods
A point-prevalence multicenter study was conducted across EDs of hospitals in Spain. A specified day and hour was assigned to collect data from all adult patients attending the ED due to DRPs during three consecutive years. Medical records were retrospectively reviewed, with data recorded in REDCap.

Key findings
Overall, 4752 patients were evaluated at 32 centres, of which 366 (7.7%) visited the ED due to DRPs, with a prevalence ranging from 0 to 16.7%. Antithrombotic drugs accounted for the highest number of DRPs, responsible for 96 (26.8%) episodes. Falls (n = 29; 8.0%) were the most frequent DRPs, followed by haemorrhage (n = 26; 7.12%). Furthermore, 198 (54.2%) reported DRPs were unrelated to medication errors, 80 (21.2%) were overdose errors, and 40 (11.0%) were attributed to poor treatment adherence. Of 366 DRPs-related visits, 54 (14.8%) were due to inappropriately prescribed drugs according to the STOPP-START criteria. Overall, 86 (23.5%) patients revisited the ED within 30 days of discharge, with 34 (9.4%) returning to the ED for new DRPs.

Conclusions
DRPs are frequently responsible for ED visits and are associated with a considerable percentage of post-discharge visits. The goal of the FARM-URG project is to periodically gather data to design and implement preventive measures.
The Normativity of Global Ordering Practices
Authors: Schmidt Dennis R , Williams John 
Published: April 2023

AbstractThis article integrates normative theoretical analysis into accounts of international order by connecting the study of international practice to debates about the nature and moral purpose of states’ social association. Combining English School and social practice theory with insights from scholarship on colonialism, race, and empire, we conceptualize international order as a dynamic, contested, but often stable and durable, set of patterns of practice and show how they set ethical reference points and privilege certain claims over others in relation to legitimate agency and morally appropriate conduct. To allow for a grounded normative analysis of global ordering practices, we connect actors’ capacity to exercise creative normative agency to debates about legitimate membership and morally appropriate conduct in international society. We highlight the normative significance of historical context for the study of international practices and illustrate our theoretical arguments with examples from various ordering practices, including international law, war, diplomacy, and economic practice, where actors frequently draw on foundational values to construct normative claims about inclusion and exclusion. At the same time, agents’ creative capacity to alter existing and create new rights and obligations has transformed our thinking, acting, and arguing about the nature and moral purpose of world order.
Characterization and optimization of bioluminescent bacterial cells immobilization process in calcium alginate hydrogel tablets
Authors: Harpaz Dorin , Zoabi Kosai , Eltzov Evgeni 
Published: April 2023

Abstract

Aims
Whole-cell biosensors are increasingly utilized in various applications. These platforms integrate cells with a signal measurement device. One of the main challenges in the development of such platforms is the immobilization matrix that is used to keep the cells stable, which also affects the portability of the device. In this study, a portable and simple immobilization of bioluminescent bacterial cells in calcium alginate hydrogel was examined.

Methods and results
The effects of several physical parameters were investigated (e.g. calcium alginate solution volume, drying, incubation time, mixing procedure, bacterial concentration, and tablet location within the cylinder). An alginate solution volume of 3 ml was preferred as well as the addition of 400 μl solution after the 15 min of compressing step and before the polymerization step. Also, a stirring mixing mode is favored over vortexing due to the creation of better homogenized tablets, as well as a bacterial concentration of 0.15 OD600nm that produced a high light response while maintaining a lower variance. Lastly, the findings showed a significantly higher response [induction factor (IF)] in the tablets using the optimized immobilization protocol (IF = 8.814) than the old one (IF = 1.979).

Conclusions
To conclude, bacterial cells immobilization in calcium alginate tablets provides improved sensitivity and storability.
Community- and data-driven homelessness prevention and service delivery: optimizing for equity
Authors: Kube Amanda R , Das Sanmay , Fowler Patrick J 
Published: April 2023

Abstract

Objective
The study tests a community- and data-driven approach to homelessness prevention. Federal policies call for efficient and equitable local responses to homelessness. However, the overwhelming demand for limited homeless assistance is challenging without empirically supported decision-making tools and raises questions of whom to serve with scarce resources.

Materials and Methods
System-wide administrative records capture the delivery of an array of homeless services (prevention, shelter, short-term housing, supportive housing) and whether households reenter the system within 2 years. Counterfactual machine learning identifies which service most likely prevents reentry for each household. Based on community input, predictions are aggregated for subpopulations of interest (race/ethnicity, gender, families, youth, and health conditions) to generate transparent prioritization rules for whom to serve first. Simulations of households entering the system during the study period evaluate whether reallocating services based on prioritization rules compared with services-as-usual.

Results
Homelessness prevention benefited households who could access it, while differential effects exist for homeless households that partially align with community interests. Households with comorbid health conditions avoid homelessness most when provided longer-term supportive housing, and families with children fare best in short-term rentals. No additional differential effects existed for intersectional subgroups. Prioritization rules reduce community-wide homelessness in simulations. Moreover, prioritization mitigated observed reentry disparities for female and unaccompanied youth without excluding Black and families with children.

Discussion
Leveraging administrative records with machine learning supplements local decision-making and enables ongoing evaluation of data- and equity-driven homeless services.

Conclusions
Community- and data-driven prioritization rules more equitably target scarce homeless resources.