bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lesser kestrels of the same colony do not overwinter together
Authors: García-Macía Jorge , Chaouni Munir , Morollón Sara , Bustamante Javier , López-Ricaurte Lina , Martínez-Dalmau Juan , Rodríguez-Moreno Beatriz , Urios Vicente 
Published: July 2023

Abstract
Migratory connectivity describes the linkage between breeding and nonbreeding sites, having major ecological implications in birds: 1 season influence the success of an individual or a population in the following season. Most studies on migratory connectivity have used large-scale approaches, often considering regional populations, but fine-scale studies are also necessary to understand colony connectivity. The lesser kestrel Falco naumanni, an insectivorous migratory raptor which form colonies during the breeding period, was considered to have strong connectivity based on regional populations. However, no small-scale studies on migratory connectivity have been conducted. Therefore, we GPS (Global Positioning System)-tracked 40 adult lesser kestrels from 15 different Spanish breeding colonies, estimating the overlap index between home ranges and the distance between their centroids. It was found that lesser kestrels from the same breeding colony placed their nonbreeding areas at 347 ± 281 km (mean ± standard deviation) away from each other (range = 23–990), and their home ranges overlapped by 38.4 ± 23.6%. No differences between intra-colony and inter-colony metrics were found, which suggests that lesser kestrels from the same breeding cluster do not overwinter together, but they spread out and mixed independently of the colony belonging throughout the nonbreeding range of the species. Ultimately, this study highlights the importance of performing connectivity studies using fine-scale approaches.
Inflammatory myofibroblastic tumors: recent progress and future of targeted therapy
Authors: Nakano Kenji 
Published: July 2023

AbstractAn inflammatory myofibroblastic tumor is a rare component of bone and soft-tissue sarcomas that has distinct pathological features as a lymphoplasmacytic inflammatory infiltrate. As is the case for other non-small round cell sarcomas, surgical resection remains the standard treatment strategy for inflammatory myofibroblastic tumors, but recurrence is possible. Concerning systemic therapy, the available data for conventional chemotherapy (such as those of doxorubicin-based regimens) are limited, and case reports of anti-inflammatory inflammatory myofibroblastic tumor treatments describe some degree of symptom relief and efficacy against tumor progression. However, as more information about cancer genomics accumulates, the potential for molecularly targeted therapies for inflammatory myofibroblastic tumors has become more promising. Approximately half of inflammatory myofibroblastic tumors harbor anaplastic lymphoma kinase (ALK) fusion genes, and the other half could have potentially targetable fusion genes or mutations such as ROS1, NTRK and RET; case reports demonstrating the clinical efficacy of treatments targeted to inflammatory myofibroblastic tumor have been published, as have several prospective clinical trials. Few drugs are approved for the treatment of inflammatory myofibroblastic tumor, and most of them were approved for tumor-agnostic indications. Drugs that could be used for pediatric indications and dosing in inflammatory myofibroblastic tumor have also not been established. To provide effective targeted therapy for rare diseases such as inflammatory myofibroblastic tumor, it is necessary to obtain clinical evidence by designing and performing clinical trials and to find a path toward regulatory approval.
Evictionism, Libertarianism, and Duties of the Fetus
Authors: Dominiak Łukasz , Wysocki Igor 
Published: July 2023

Abstract
In “Evictionism and Libertarianism,” published in this journal, Walter Block defends the view that, although the fetus is a human being with all the rights to its body, it may nonetheless be evicted from the woman’s body as a trespasser, provided the pregnancy is unwanted. We argue that this view is untenable: the statement that the unwanted fetus is a trespasser does not follow from the premises that the fetus uninvitedly resides in the woman’s body and that the woman is a full self-owner. For this statement to follow, one more statement would have to be true; namely, the woman would have to hold her self-ownership rights specifically against the fetus, and for this to be the case, the fetus would have to have a correlative duty to the woman to abstain from interfering with her body. This statement, however, is false.
Consistent and fast inference in compartmental models of epidemics using Poisson Approximate Likelihoods
Authors: Whitehouse Michael , Whiteley Nick , Rimella Lorenzo 
Published: July 2023

AbstractAddressing the challenge of scaling-up epidemiological inference to complex and heterogeneous models, we introduce Poisson approximate likelihood (PAL) methods. In contrast to the popular ordinary differential equation (ODE) approach to compartmental modelling, in which a large population limit is used to motivate a deterministic model, PALs are derived from approximate filtering equations for finite-population, stochastic compartmental models, and the large population limit drives consistency of maximum PAL estimators. Our theoretical results appear to be the first likelihood-based parameter estimation consistency results which apply to a broad class of partially observed stochastic compartmental models and address the large population limit. PALs are simple to implement, involving only elementary arithmetic operations and no tuning parameters, and fast to evaluate, requiring no simulation from the model and having computational cost independent of population size. Through examples we demonstrate how PALs can be used to: fit an age-structured model of influenza, taking advantage of automatic differentiation in Stan; compare over-dispersion mechanisms in a model of rotavirus by embedding PALs within sequential Monte Carlo; and evaluate the role of unit-specific parameters in a meta-population model of measles.
Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes
Authors: Jang Min-Jeong , Hong Woo-Jong , Park Young-Soo , Jung Ki-Hong , Kim Seungill 
Published: July 2023

Abstract
Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.
CasDinG is a 5′-3′ dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity
Authors: Domgaard Hannah , Cahoon Christian , Armbrust Matthew J , Redman Olivine , Jolley Alivia , Thomas Aaron , Jackson Ryan N 
Published: July 2023

Abstract
CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5′-3′ DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5′-GNAWN-3′ on the 5′-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.
G-quadruplexes in the evolution of hepatitis B virus
Authors: Brázda Václav , Dobrovolná Michaela , Bohálová Natália , Mergny Jean-Louis 
Published: July 2023

Abstract
Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of ‘genetic camouflage’ to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.
Integration of gene expression and DNA methylation data across different experiments
Authors: Itai Yonatan , Rappoport Nimrod , Shamir Ron 
Published: July 2023

AbstractIntegrative analysis of multi-omic datasets has proven to be extremely valuable in cancer research and precision medicine. However, obtaining multimodal data from the same samples is often difficult. Integrating multiple datasets of different omics remains a challenge, with only a few available algorithms developed to solve it. Here, we present INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples. To enable integration, INTEND learns a predictive model between the two omics by training on multi-omic data measured on the same set of samples. In comprehensive testing on 11 TCGA (The Cancer Genome Atlas) cancer datasets spanning 4329 patients, INTEND achieves significantly superior results compared with four state-of-the-art integration algorithms. We also demonstrate INTEND’s ability to uncover connections between DNA methylation and the regulation of gene expression in the joint analysis of two lung adenocarcinoma single-omic datasets from different sources. INTEND’s data-driven approach makes it a valuable multi-omic data integration tool. The code for INTEND is available at https://github.com/Shamir-Lab/INTEND.
Fulminant Hepatic Failure as the Initial Presentation of Hodgkin Lymphoma in 4 Patients With Human Immunodeficiency Virus
Authors: Cook Mary , Williams Matthew , Law Jennie Y , Riedel David J 
Published: July 2023

Abstract
In the era of antiretroviral therapy (ART), Hodgkin Lymphoma (HL) is a common non-AIDS-defining cancer with increasing incidence in people with human immunodeficiency virus (PWH). Through review of these cases, we identify clinical patterns such as declining CD4 count despite ART, hyperbilirubinemia and recurrent fever, which preceded diagnosis. Identifying these important signs and symptoms may lead to earlier diagnosis and initiation of therapy. Fulminant hepatic failure limits the ability to give standard of care chemotherapy, likely jeopardizing outcomes in this patient population. Alternative bridging therapies should be considered until hepatic function improves.
Unexpected Loa loa Finding in an Asymptomatic Patient From The Gambia: A Case Report
Authors: Treviño Begoña , Zarzuela Francesc , Oliveira-Souto Inés , Maturana Carles Rubio , Serre-Delcor Núria , Aznar Maria L , Pou Diana , Goterris Lidia , Salvador Fernando , Bosch-Nicolau Pau , Rubio José M , Ruiz Edurne , Molina Israel , Sulleiro Elena 
Published: July 2023

Abstract
A 17-year-old asymptomatic male from The Gambia presented for a routine health examination after migration to Spain. Laboratory diagnosis confirmed the presence of Loa loa microfilariae. This unusual finding emphasizes the importance of screening in newly arrived migrants and the need of an extended anamnesis including migratory route and previous travels.
A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus
Authors: Dougherty Laura , Borejsza-Wysocka Ewa , Miaule Alexandre , Wang Ping , Zheng Desen , Jansen Michael , Brown Susan , Piñeros Miguel , Dardick Christopher , Xu Kenong 
Published: July 2023

Abstract
Plant architecture is 1 of the most important factors that determines crop yield potential and productivity. In apple (Malus domestica), genetic improvement of tree architecture has been challenging due to a long juvenile phase and growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is 1 of the 4 paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis (Arabidopsis thaliana). The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T&gt;C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that colocalizes with Region III, 1 of the 5 conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Overexpressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.
Sequence variations affect the 5′ splice site selection of plant introns
Authors: Cheng Wenzhen , Hong Conghao , Zeng Fang , Liu Nan , Gao Hongbo 
Published: July 2023

Abstract
Introns are noncoding sequences spliced out of pre-mRNAs by the spliceosome to produce mature mRNAs. The 5′ ends of introns mostly begin with GU and have a conserved sequence motif of AG/GUAAGU that could base-pair with the core sequence of U1 snRNA of the spliceosome. Intriguingly, ∼ 1% of introns in various eukaryotic species begin with GC. This occurrence could cause misannotation of genes; however, the underlying splicing mechanism is unclear. We analyzed the sequences around the intron 5′ splice site (ss) in Arabidopsis (Arabidopsis thaliana) and found sequences at the GC intron ss are much more stringent than those of GT introns. Mutational analysis at various positions of the intron 5′ ss revealed that although mutations impair base pairing, different mutations at the same site can have different effects, suggesting that steric hindrance also affects splicing. Moreover, mutations of 5′ ss often activate a hidden ss nearby. Our data suggest that the 5′ ss is selected via a competition between the major ss and the nearby minor ss. This work not only provides insights into the splicing mechanism of intron 5′ ss but also improves the accuracy of gene annotation and the study of the evolution of intron 5′ ss.
Sickle cell disease and coronavirus disease-2019 (COVID-19) infection: a single-center experience
Authors: Devarashetty Sindhu P , Grewal Udhayvir S , Le Blanc Kimberly , Walton Jacqueline , Jones Tabitha , Shi Runhua , Master Samip R , Mansour Richard P , Ramadas Poornima 
Published: July 2023

Abstract

Purpose
Sickle cell disease (SCD) has been found to be associated with an increased risk of hospitalization and death from coronavirus disease-2019 (COVID-19). We sought to study clinical outcomes in patients with SCD and a diagnosis of COVID-19 infection.

Methods
We conducted a retrospective analysis of adult patients (&gt;18 years) with SCD who were diagnosed with COVID-19 infection between 1 March 2020 and 31 March 2021. Data on baseline characteristics and overall outcomes were collected and analyzed using SAS 9.4 for Windows.

Results
A total of 51 patients with SCD were diagnosed with COVID-19 infection in the study period, out of which 39.3% were diagnosed and managed in the outpatient setting/emergency room (ER) and 60.3% in the inpatient setting. Disease-modifying therapy such as hydroxyurea did not impact inpatient vs outpatient/ER management (P &gt; 0.05). Only 5.71% (n = 2) required intensive care unit admission and were mechanically ventilated and 3.9% (2 patients) died of complications of COVID-19 infection.

Conclusion
We identified a lower mortality (3.9%) rate among patients in our cohort in comparison to previous studies and a higher burden of inpatient hospitalizations as compared to outpatient/ER management. Further prospective data are needed to validate these findings.
Key messages What is already known on this topic COVID-19 has been shown to have a disproportionately unfavorable impact on African Americans, including longer hospital stays, higher rates of ventilator dependence, and a higher overall mortality rate. Limited data also suggest that sickle cell disease (SCD) is associated with an increased risk of hospitalization and death from COVID-19. What this study adds Our analysis did not show a higher mortality due to COVID-19 in patients with SCD. However, we identified a high burden of inpatient hospitalizations in this population. COVID-19-related outcomes did not improve with the use of disease-modifying therapies. How this study might affect research, practice, or policy These results will aid in decision making for triage of patients with COVID-19 and SCD and ensure the most appropriate use of healthcare resources. Our analysis underscores the need for more robust data to identify patients at higher risk of severe disease and/or mortality, necessitating inpatient hospitalization and aggressive management.
On the identification of radon areas as defined in art. 103 of Council Directive 2013/59/EURATOM
Authors: Salvi Francesco 
Published: July 2023

Abstract
Radon maps are one of the key tools for implementing a graded approach to reduce exposure due to radon. The Council Directive 2013/59/Euratom indicated how to identify the geographical areas of the country most exposed to indoor radon. Using annual average radon concentrations in 5000 dwellings in the Lazio region, located in central Italy, the expected number of dwellings with annual average radon concentrations above the reference level of 300 Bq per m3 within the 6 km grid squares was estimated. For the purpose of application, radon areas were identified by arbitrarily selecting grid squares with at least 10 expected dwellings per square kilometer above 300 Bq per m3. Since comprehensive measurements surveys must be conducted within the radon areas to identify all dwellings exceeding the reference level for the purpose of reducing radon concentration, quantitative economic considerations are reported.
Strategies for rate and rhythm control of atrial fibrillation in the ED
Authors: Zapata James , Akopian Erik , Yvanovich Anthony 
Published: July 2023

ABSTRACT
Atrial fibrillation (AF) is one of the most common dysrhythmias managed in the ED and accounts for more than half a million visits a year in the United States. More than 6 out of 10 of these visits result in admissions. As the prevalence of AF has continued to increase in recent years, so has the presentation of patients with AF to the ED. For these reasons, clinicians in emergency settings must be knowledgeable of evidence-based rate and rhythm control strategies for stabilizing patients and preventing complications. This article discusses options, indications, contraindications, and safe implementation of rate and rhythm control strategies for ED clinicians. Recent studies have suggested that early rhythm control may benefit newly diagnosed patients, reducing stroke risk, cardiovascular deaths, and disease progression.