bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level phased genome assembly of “Antonovka” identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1
Authors: Švara Anže , Sun Honghe , Fei Zhangjun , Khan Awais 
Published: November 2023

Abstract
Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab-resistance loci Vhc1 in “Honeycrisp” and Rvi17 in “Antonovka,” were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Previously published chromosome-scale phased assembly of Honeycrisp and a newly assembled phased genome of Antonovka 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with 8 available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87–95 and 81–95%, respectively. Among these homologs, 2 candidate genes in Antonovka and Honeycrisp haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1 and identifies candidate genes for further resistance characterization.
Toxoplasma gondii IgG Serointensity Is Positively Associated With Frailty
Authors: Mohyuddin Hira , Laffon Blanca , Teixeira João P , Costa Solange , Teixeira-Gomes Armanda , Pásaro Eduardo , Constantine Niel , Dagdag Aline , Ortmeyer Heidi K , Tizenberg Boris , Afram Liubov , Yen Poyu , Marano Christopher , Lowry Christopher A , Hoisington Andrew J , RachBeisel Jill A , Valdiglesias Vanessa , Lema-Arranz Carlota , Fernández-Bertólez Natalia , Maseda Ana , Millán-Calenti José C , Kovacs Elizabeth J , Gostner Johanna M , Fuchs Dietmar , Brenner Lisa A , Lorenzo-López Laura , Postolache Teodor T 
Published: November 2023

Abstract

Background
Persistent inflammation related to aging (“inflammaging”) is exacerbated by chronic infections and contributes to frailty in older adults. We hypothesized associations between Toxoplasma gondii (T. gondii), a common parasite causing an oligosymptomatic unremitting infection, and frailty, and secondarily between T. gondii and previously reported markers of immune activation in frailty.

Methods
We analyzed available demographic, social, and clinical data in Spanish and Portuguese older adults [N = 601; age: mean (SD) 77.3 (8.0); 61% women]. Plasma T. gondii immunoglobulin G (IgG) serointensity was measured with an enzyme-linked immunosorbent assay. The Fried criteria were used to define frailty status. Validated translations of Mini-Mental State Examination, Geriatric Depression Scale, and the Charlson Comorbidity Index were used to evaluate confounders. Previously analyzed biomarkers that were significantly associated with frailty in both prior reports and the current study, and also related to T. gondii serointensity, were further accounted for in multivariable logistic models with frailty as outcome.

Results
In T. gondii-seropositives, there was a significant positive association between T. gondii IgG serointensity and frailty, accounting for age (p = .0002), and resisting adjustment for multiple successive confounders. Among biomarkers linked with frailty, kynurenine/tryptophan and soluble tumor necrosis factor receptor II were positively associated with T. gondii serointensity in seropositives (p &lt; .05). Associations with other biomarkers were not significant.

Conclusions
This first reported association between T. gondii and frailty is limited by a cross-sectional design and warrants replication. While certain biomarkers of inflammaging were associated with both T. gondii IgG serointensity and frailty, they did not fully mediate the T. gondii–frailty association.
An illiberal power? EU bordering practices and the liberal international order
Authors: Fassi Enrico , Ceccorulli Michela , Lucarelli Sonia 
Published: November 2023

Abstract
The relevance of bordering practices and dynamics for the European Union has significantly increased in recent years, ranging from Brexit to the open-border policies towards Ukrainians fleeing Russia's military aggression, through the crises in the Schengen area due to migration and COVID–19. In its attempts to respond to these challenges, the EU has been widely criticized in particular for its approach to migration; it has been alluded to as being cynical, negligent and even ‘illiberal’. The aim of this article is to analyse whether and in which sense this allegation is correct, providing clear normative criteria. Drawing from political theory, we identify three different understandings of ‘just’ migration governance, all compatible with a liberal approach, and use them as benchmarks to evaluate the EU's stance. Focusing on selected EU bordering practices—physical, administrative and external bordering—we detect a general trend towards re-bordering, meaning processes through which the control of borders is enhanced and their exclusionary meaning is increased. Most of all, the article shows that EU policies have been leaning towards one specific understanding of liberalism to the detriment of the others, which poses significant challenges to the EU's credentials as a pillar of the liberal international order (LIO).
A Systematic Review on the Increasing Incidence of Inflammatory Bowel Disease in Southeast Asia: Looking Beyond the Urbanization Phenomenon
Authors: Chew Deborah Chia Hsin , Khoo Xin-Hui , Lee Tiong See , Chin Kok-Yong , Raja Ali Raja Affendi , Muhammad Nawawi Khairul Najmi , Wan Ibrahim Nik Razima , Hilmi Ida 
Published: November 2023

Abstract
The incidence of inflammatory bowel disease (IBD) has been increasing in Southeast Asia (SEA) in tandem with its economic growth and urbanization over the past 2 decades. Specific characteristics of IBD in SEA are similar to East Asia and the West, such as the declining ratio of ulcerative colitis to Crohn’s disease. However, exceptionally low familial aggregation is seen. Smoking is also not a common risk factor in patients with Crohn’s disease. The incidence of perianal disease is higher in SEA than in Australia and is comparable to the West. In a multiracial population, such as Singapore and Malaysia, Indians have the highest incidence and prevalence rates, which are likely to be due to important putative mutations. For instance, a higher frequency of the NOD2 predisposing mutation SNP5 and IBD risk allele IGR2198a and IGR2092a were found in Indians. Although differences in the genetic constitution play an important role in the epidemiology and prognosis of IBD in SEA, the emergence of this disease offers a unique opportunity to identify potential exposomes that contribute to its pathogenesis.
Pregnancy-associated Breast Cancer: Why Breast Imaging During Pregnancy and Lactation Matters
Authors: Pyle Chelsea , Hill Molly , Sharafi Shahrzad , Forton Camelia , Sohaey Roya 
Published: November 2023

Abstract
Pregnancy-associated breast cancer is characterized as breast cancer diagnosed during pregnancy, within the first postpartum year, or during lactation. It usually presents as a palpable mass, although the large majority of palpable masses during pregnancy are benign. Breast cancer is the most common invasive malignancy diagnosed during pregnancy and lactation, and its incidence is increasing as more women delay childbearing. Understanding the appropriate methods for screening and diagnostic workup of breast findings in this population is imperative for radiologists to promptly diagnose pregnancy-associated breast cancer. Use of available imaging modalities should be tailored to patient-specific factors, with US typically the first-line modality due to patient age and decreased sensitivity of mammography in the setting of lactational changes. This article illustrates the spectrum of imaging appearances of pregnancy-associated breast cancer, the appropriate diagnostic imaging workup, and the unique challenges encountered in evaluation of this patient population.
Refining age at legal-size estimation in the Newfoundland & Labrador populations of the snow crab Chionoecetes opilio (Fabricius, 1788) (Decapoda: Brachyura: Oregoniidae)
Authors: Mullowney Darrell , O’Connell Nicole , Kilada Raouf , Rochette Rémy 
Published: November 2023

Abstract
Current knowledge of age at legal size in Newfoundland & Labrador (NL) and other snow-crab stocks is incomplete due to historic estimations not accounting for skip-molting growth delays. Previous work has shown skip-molting incidence to occasionally be very high in males, both in NL and some other major snow-crab stocks. This warrants research to better understand impacts of skip-molting on snow-crab age and growth dynamics, which are central to population assessment and resource management. We simulated the impact of skip-molting on growth dynamics of snow crabs from three regions around NL by coupling a nineteen year time series of molt-type probabilities derived from field trawl surveys to historical data on age-at-instar based on cohort analysis of wild populations that do not consider skip-molting in making age estimations. Trawl surveys and simulations showed that skip-molting is a prominent feature in NL snow crabs, with up to four skip-molts being a reasonable maximum possible estimate for males in portions of the NL snow-crab stock. A complementary analysis examining the ability to age snow crabs using gastric mill band counts showed overall strong agreement with published growth trajectories that were modified to include skip-molting as well as reasonable average age approximations for most crabs, but unexpectedly high variability in age estimates for individuals of a same instar stage and unexpectedly low age estimates for younger crabs. Our study leads to a refinement of age at legal size for NL snow crab from the current nine-year estimate to a range of 9–13 years. Although this range is deemed to capture virtually every crab reaching legal size in NL snow-crab populations, ages higher than 11 years to fishery recruitment (2 skip-molts) are relatively infrequent.
Potential distribution of marsupials (Didelphimorphia: Didelphidae) in Mexico under 2 climate change scenarios
Authors: Ortiz-Acosta Miguel Á , Galindo-González Jorge , Castro-Luna Alejandro A , Mota-Vargas Claudio 
Published: November 2023

Abstract
Climate change is one of the main threats to biodiversity in the 21st century. However, the effects that it may have on different mammal species are unknown, making it difficult to implement conservation strategies. In this paper, we used species distribution models (SDM) to assess the effect of global climate change on the potential distribution of the 8 of the 9 marsupial species in Mexico, and analyzed their distribution in the current system of natural protected areas (NPAs). We used presence records for each species and bioclimatic variables from the present and the future (2050 and 2080) with 2 contrasting possible scenarios (representative concentration pathways RCP 4.5 and 8.5). We found that Tlacuatzin canescens would have the most stable potential range under any climate change scenario, while the remaining species (Caluromys derbianus, Chironectes minimus, Didelphis marsupialis, D. virginiana, Philander opossum, Marmosa mexicana, and Metachirus nudicaudatus) would undergo notable range losses in the future, though there would not only be losses—according to our SDMs, for all species there would be some range gain under the different climate scenarios, assuming the vegetation cover remained. The current system of NPAs in Mexico currently protects and under the 2 future scenarios would protect less than 20% of the potential range of marsupials, so a reevaluation of their areas beyond the NPAs is highly recommended for the long-term conservation of this group. Our results provide relevant information on the estimated effects of global climate change on marsupials, allowing us to design more effective methodologies for the protection of this portion of the mammalian fauna in Mexico.
On Becoming an Artist Anew: Refugees’ Arrival in the Field of Cultural Production in Austria
Authors: Parzer Michael 
Published: November 2023

Abstract
This article focuses on how artists who had to flee Syria between 2011 and 2016 have restarted their artistic careers in Austria. Pries’ concept of arrival and Lamont’s symbolic boundary approach offer an analytical framework for examining the process of becoming an artist anew. By drawing on data collected from a 4-year ethnography in various fields of cultural production in Vienna, this article sheds light on the barriers these artists face in their process of arriving. The findings show two superordinate challenges: ‘having to start from zero’ and ‘struggling to be seen and recognized as artist’. A better understanding of the factors that affect refugees’ artistic practices could be particularly beneficial regarding the role of art as a means of social inclusion. Finally, the question arises as to what extent artistic pathways can serve as a lens for studying the experience of arrival in the context of forced migration.
Methodological observations concerning word rankings and z-score refinements
Authors: Ilsemann Hartmut 
Published: November 2023

Abstract
This article evaluates word rankings suggested by Ary L. Goldberger, Albert C. Yang, and C. Peng as a means of establishing the authorship of texts in the light of Delta, developed by John Burrows at about the same time. The tests carried out with high ranking function words and results established with the more modern approaches of Rolling Delta, Rolling Classify, and the General Imposters method give clear evidence that word rankings only return crude and unreliable results that cannot keep up with non-traditional modern methods. Even though the stylistic difference between Marlowe and Shakespeare plays could be stated, word rankings failed to recognize Shakespearean stylistics in The Jew of Malta, Edward II, and Doctor Faustus. It was only through the use of z-scores that a wider vocabulary provided a larger degree of differentiation.
Songs at the Docks: Nicolas-Claude Fabri de Peiresc and Musical Entanglements in Seventeenth-Century Marseille
Authors: Van der Miesen Leendert 
Published: November 2023

ABSTRACT
Building on recent musicological research that emphasizes the mobility of songs, this article investigates Marseille as a site of cultural encounter and highlights the musical presence of enslaved galley rowers and translators in the city. It focuses on several descriptions of music-making in southern France by the French antiquarian Nicolas-Claude Fabri de Peiresc and his efforts to find materials on Ottoman and Persian music for the music theorist Marin Mersenne. Utilizing the constant influx of goods and people into the city, Peiresc relied on mercantile networks to obtain transcriptions of songs and music theoretical texts, engaging various informers and translators from the eastern Mediterranean. Focusing on a transcription of a single song that has been lost, the article traces the song’s connections to cultures of collection, cultural translation, and transcription, with singing constituting a central site in which to negotiate and perform otherness.
Unique spectral manifestations around the D3 line observed in the region close to the seismic source of a large solar flare
Authors: Lozitska N I , Yakovkin I I , Lozitsky V G 
Published: November 2023

ABSTRACT
The main goal of our research is to search for super-strong magnetic fields in active processes on the Sun. Our method is based on Stokes V spectro-polarimetry in a wide spectral range from −14 Å to +29 Å relative to the D3 He i line. The object of the study is the area of a seismic source in the large solar flare on 2003 October 28 of the X17.2/4B class. The novelty of our study: we found characteristic spectral manifestations – secondary Stokes V peaks – far from D3 line, at distances of several angstroms. These secondary peaks have the following features: (a) their amplitudes reach 4 per cent – almost an order of magnitude more than previously detected in other flares, (b) in the general picture, the sign of the circular polarization changes when passing through the D3 centre, and (c) narrower spectral peculiarities were found at distances of +4.0, +6.3, and +8.5 Å, where the polarization sign also changes sharply. This unusual feature likely results from significant factors in the area of the seismic source, including substantial descending plasma velocities which exceed 400 km s−1 and, perhaps, super-strong magnetic fields.
Wait-and-scan management in sporadic Koos grade 4 vestibular schwannomas: A longitudinal volumetric study
Authors: Schouten Sammy M , Cornelissen Stefan , Langenhuizen Patrick P H J , Jansen Thijs T G , Mulder Jef J S , Derks Jolanda , Verheul Jeroen B , Kunst Henricus P M 
Published: November 2023

Abstract

Background
Volumetric natural history studies specifically on large vestibular schwannomas (VSs), commonly classified as Koos grade 4, are lacking. The aim of the current study is to present the volumetric tumor evolution in sporadic Koos grade 4 VSs and possible predictors for tumor growth.

Methods
Volumetric tumor measurements and tumor evolution patterns from serial MRI studies were analyzed from selected consecutive patients with Koos grade 4 VS undergoing initial wait-and-scan management between January 2001 and July 2020. The significant volumetric threshold was defined as a change in volume of ≥10%.

Results
Among 215 tumors with a median size (IQR) of 2.7 cm3 (1.8–4.2), 147 tumors (68%) demonstrated growth and 75 tumors (35%) demonstrated shrinkage during follow-up. Growth-free survival rates (95% CI) at 1, 2, 5, and 10 years were 55% (48–61), 36% (29–42), 29% (23–36), and 28% (21–34), respectively and did not significantly differ in tumors&gt; 20 mm (Chi-square = .40; P-value = .53). Four tumor evolution patterns (% of total) were observed: continued growth (60); initial growth then shrinkage (7); continued shrinkage (27); and stability (5). Good hearing (adjusted HR 2.21, 95% CI 1.48–3.30; P &lt; .001) and peritumoral edema (adjusted HR 2.22, 95% CI 1.18–4.13; P = .01) at diagnosis were significantly associated with an increased likelihood of growth.

Conclusions
Koos grade 4 VSs show a wide variety in size and growth. Due to variable growth patterns, an initial wait-and-scan strategy with short scan intervals may be an acceptable option in selected tumors, if no significant clinical symptoms of mass effect that warrant treatment are present.
Circulating Tumor Cells Prediction in Hormone Receptor Positive HER2-Negative Advanced Breast Cancer: A Retrospective Analysis of the MONARCH 2 Trial
Authors: Gerratana Lorenzo , Kocherginsky Masha , Davis Andrew A , D’Amico Paolo , Reduzzi Carolina , Puglisi Fabio , Cristofanilli Massimo 
Published: November 2023

Abstract

Background
The MONARCH 2 trial (NCT02107703) showed the efficacy of abemaciclib, a cyclin-dependent kinase 4 & 6 inhibitor (CDK4/6i), in combination with fulvestrant for hormone receptor-positive, HER2-negative metastatic breast cancer (MBC). The aim of this analysis was to explore the prediction of circulating tumor cells (CTCs) stratification using machine learning for hypothesis generation of biomarker-driven clinical trials.

Patients and Methods
Predicted CTCs were computed in the MONARCH 2 trial through a K nearest neighbor (KNN) classifier trained on a dataset comprising 2436 patients with MBC. Patients were categorized into predicted Stage IVaggressive (pStage IVaggressive, ≥5 predicted CTCs) or predicted Stage IVindolent (pStage IVindolent, &lt;5 predicted CTCs). Prognosis was tested in terms of progression-free-survival (PFS) and overall survival (OS) through Cox regression.

Results
Patients classified as predicted pStage IVaggressive and predicted pStage Stage IVindolent were, respectively, 183 (28%) and 461 (72%). After multivariable Cox regression, predicted CTCs were confirmed as independently associated with prognosis in terms of OS, together with ECOG performance status, liver involvement, bone-only disease, and treatment arm. Patients in the pStage Stage IVindolent subgroup treated with abemaciclib experienced the best prognosis both in terms of PFS and OS. The treatment effect of abemaciclib on OS was then explored through subgroup analysis, showing a consistent benefit across all subgroups.

Conclusion
This study is the first analysis of CTCs modeling for stage IV disease stratification. These results show the need to expand biomarker profiling in combination with CTCs stratification for improved biomarker-driven drug development.
Transcription factor SlWRKY50 enhances cold tolerance in tomato by activating the jasmonic acid signaling
Authors: Wang Lihui , Chen Hui , Chen Guoyu , Luo Guangbao , Shen Xinyan , Ouyang Bo , Bie Zhilong 
Published: November 2023

Abstract
Tomato (Solanum lycopersicum) is a cold-sensitive crop but frequently experiences low-temperature stimuli. However, tomato responses to cold stress are still poorly understood. Our previous studies have shown that using wild tomato (Solanum habrochaites) as rootstock can significantly enhance the cold resistance of grafted seedlings, in which a high concentration of jasmonic acids (JAs) in scions exerts an important role, but the mechanism of JA accumulation remains unclear. Herein, we discovered that tomato SlWRKY50, a Group II WRKY transcription factor that is cold inducible, responds to cold stimuli and plays a key role in JA biosynthesis. SlWRKY50 directly bound to the promoter of tomato allene oxide synthase gene (SlAOS), and overexpressing SlWRKY50 improved tomato chilling resistance, which led to higher levels of Fv/Fm, antioxidative enzymes, SlAOS expression, and JA accumulation. SlWRKY50-silenced plants, however, exhibited an opposite trend. Moreover, diethyldithiocarbamate acid (a JA biosynthesis inhibitor) foliar treatment drastically reduced the cold tolerance of SlWRKY50-overexpression plants to wild-type levels. Importantly, SlMYC2, the key regulator of the JA signaling pathway, can control SlWRKY50 expression. Overall, our research indicates that SlWRKY50 promotes cold tolerance by controlling JA biosynthesis and that JA signaling mediates SlWRKY50 expression via transcriptional activation by SlMYC2. Thus, this contributes to the genetic knowledge necessary for developing cold-resistant tomato varieties.