bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ocean‐Wide Conservation Genomics of Blue Whales Suggest New Northern Hemisphere Subspecies
Authors: Wolf Magnus , de Jong Menno J. , Janke Axel 
Published: December 2024

ABSTRACTThe blue whale is an endangered and globally distributed species of baleen whale with multiple described subspecies, including the morphologically and genetically distinct pygmy blue whale. North Atlantic and North Pacific populations, however, are currently regarded as a single subspecies despite being separated by continental land masses and acoustic call differences. To determine the degree of isolation among the Northern Hemisphere populations, 14 North Pacific and 6 Western Australian blue whale nuclear and mitochondrial genomes were sequenced and analysed together with 11 publicly available North Atlantic blue whale genomes. Population genomic analyses revealed distinctly differentiated clusters and limited genetic exchange among all three populations, indicating a high degree of isolation between the Northern Hemisphere populations. Nevertheless, the genomic and mitogenomic distances between all blue whale populations, including the Western Australian pygmy blue whale, are low when compared to other inter‐subspecies distances in cetaceans. Given that the Western Australian pygmy blue whale is an already recognised subspecies and further supported by previously reported acoustic differences, a proposal is made to treat the two Northern Hemisphere populations as separate subspecies, namely Balaenoptera musculus musculus (North Atlantic blue whale) and Balaenoptera musculus sulfureus (North Pacific blue whale). Furthermore, a first molecular viability assessment of all three populations not only found a generally high genomic diversity among blue whales but also a lack of alleles at low frequency, non‐neutral evolution and increased effects of inbreeding. This suggests a substantial anthropogenic impact on the genotypes of blue whales and calls for careful monitoring in future conservation plans.
Environmental Stress and Resource Availability Affect the Maintenance of Genetic Variation in a Dominant Marsh Plant (Spartina alterniflora)
Authors: Zerebecki Robyn A. , Hughes A. Randall 
Published: December 2024

ABSTRACTChanges in genetic variation, and particularly documented declines in genetic diversity, influence not only evolutionary potential but also current ecological function. Given this context, it is essential to understand what abiotic and biotic factors promote or disrupt the maintenance of genetic variation in natural populations. To address this knowledge gap in the context of salt marsh plants, we established a three‐year field experiment, testing the independent and interactive effects of nutrient availability and physical stress on the maintenance of plant (Spartina alterniflora) genotypic diversity. We found that in environments with high physical stress (i.e., low marsh elevations), diversity declined over time. However, the addition of nutrients promoted the maintenance of Spartina genotypic diversity across the physical stress gradient. We also observed changes in genotypic composition and genetic divergence across environmental stress treatments, indicating variation among Spartina genotypes in their response to these factors. Our results suggest that tidal inundation acts a selective gradient within coastal marshes, altering genotypic diversity and composition across the landscape. Moreover, our work highlights that the effects of increasing inundation due to continued sea‐level rise on the maintenance of diversity may be modulated by concomitant changes in nutrient inputs, with cascading effects on marsh structure and function.
Recent Range Expansion and Genomic Admixture in a Kleptoparasitic Spider, Argyrodes lanyuensis: A Case of Adaptive Introgression on Small, Isolated Islands of the Taiwan–Philippine Transition Zone?
Authors: Responte Mae A. , Wu Cheng‐Yu , Elias Noraya U. , Brown Rafe M. , Dai Chia‐Yen , Su Yong‐Chao 
Published: December 2024

ABSTRACTAdaptive introgression involves the acquisition of advantageous genetic variants through hybridisation, which are subsequently favoured by natural selection due to their association with beneficial traits. Here, we analysed speciation patterns of the kleptoparasitic spider, Argyrodes lanyuensis, through genomic analyses and tested for possible genetic evidence of adaptive introgression at the Taiwan–Philippines transition zone. Our study used highly polymorphic SNPs to demonstrate that speciation occurred when the Hualien (on Taiwan Island + Green Island) and Orchid Island + Philippine lineages separated during the early to mid‐Pleistocene. The best colonisation model suggested by approximate Bayesian computation and random forests and biogeographical analyses supported an inference of a bottleneck during speciation, an interpretation reinforced by observation of lower FST values and reduced genetic diversity of the Orchid Island + Philippines lineage. We also found the highest support for the occurrence of introgression on the youngest island (Green Island) of the Taiwan–Philippines transition zone based on the ABBA‐BABA test. Our study highlights the inference of two noteworthy species (Hualien + Green Island and Orchid Island + Philippines) based on our species delimitation tests, with gene flow between Green Island and Orchid Island that indicates introgression. The potential adaptive alleles in Green Island population, which are under balancing selection, provide initial evidence of possible rare case of adaptive introgression. This could represent an evolutionary response to a newly formed niche (or novel geographical context) lying between the tropical climate of the Philippines and the subtropical climate of Hualien, Taiwan.
Increasing Rubisco as a simple means to enhance photosynthesis and productivity now without lowering nitrogen use efficiency
Authors: Salesse‐Smith Coralie E. , Wang Yu , Long Stephen P. 
Published: December 2024

SummaryGlobal demand for food may rise by 60% mid‐century. A central challenge is to meet this need using less land in a changing climate. Nearly all crop carbon is assimilated through Rubisco, which is catalytically slow, reactive with oxygen, and a major component of leaf nitrogen. Developing more efficient forms of Rubisco, or engineering CO2 concentrating mechanisms into C3 crops to competitively repress oxygenation, are major endeavors, which could hugely increase photosynthetic productivity (≥ 60%). New technologies are bringing this closer, but improvements remain in the discovery phase and have not been reduced to practice. A simpler shorter‐term strategy that could fill this time gap, but with smaller productivity increases (c. 10%) is to increase leaf Rubisco content. This has been demonstrated in initial field trials, improving the productivity of C3 and C4 crops. Combining three‐dimensional leaf canopies with metabolic models infers that a 20% increase in Rubisco increases canopy photosynthesis by 14% in sugarcane (C4) and 9% in soybean (C3). This is consistent with observed productivity increases in rice, maize, sorghum and sugarcane. Upregulation of Rubisco is calculated not to require more nitrogen per unit yield and although achieved transgenically to date, might be achieved using gene editing to produce transgene‐free gain of function mutations or using breeding.
Evolution of sympatric host‐specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems
Authors: Rojas‐Barrera Idalia C. , Flores‐Núñez Victor M. , Haueisen Janine , Alizadeh Alireza , Salimi Fatemeh , Stukenbrock Eva H. 
Published: December 2024

Summary

The barley disease Septoria Speckled Leaf Blotch, caused by the fungus Zymoseptoria passerinii, last appeared in North America in the early 2000s. Although rare in crops, field sampling of wild grasses in the Middle East revealed the disease persistence in wild barley.

Identification of Z. passerinii in various wild barley species prompted us to examine genomic signatures of host specialization and trace the emergence of the domesticated‐barley‐infecting lineage. Furthermore, we applied virulence assays and confocal laser microscopy to evaluate whether the disease development differs between wild and domesticated barley.

Wild‐ and domesticated‐host‐infecting populations have diverged, and phylogenetic relationships support the evolution of sympatric host‐specialized lineages in wild hosts. Cross‐virulence assays showed that Z. passerinii from domesticated hosts infect domesticated barley and its wild ancestor, Hordeum spontaneum. However, wild isolates from Iran did not infect domesticated barley. Wild and domesticated pathosystems have similar disease timing and progression, suggesting its persistence does not depend on a shorter period of incubation.

The study supports that a wide range of hosts can foster the evolution of host‐specialized lineages in sympatry and provide novel insights into the evolution of understudied fungal pathogens on wild hosts.
First ABO‐Incompatible Pediatric Kidney Transplant in South Africa—A Case Report
Authors: Coetzee Ashton , Nourse Peter , Abdo Theresa , Pienaar Taryn , Siyothula Thozama , Du Toit Tinus , Thomson Dave , Barday Zunaid A. , Ndamase Bongiswa , McCulloch Mignon I. 
Published: December 2024

ABSTRACTBackgroundBlood group incompatibility previously represented an obstacle to living related donor (LRD) options; desensitization modalities have expanded LRD options. ABO‐incompatible kidney transplants have been successful in adults and pediatric liver transplants, but to date not yet in pediatric kidney transplants in South Africa.Case ReportPatient X is a 5 year old male with end‐stage kidney failure due to Posterior Urethral Valves, requiring peritoneal dialysis pre‐transplant. His sister was the only suitable LRD. The recipient was blood group A+; donor was blood group B+; HLA match was 5/10, nil HLA donor specific antibodies and negative CDC and Flow crossmatches. The recipients' anti‐B titer pre‐transplant was a maximum of 1:8. A pre‐emptive desensitization dose of Rituximab (375 mg/m2) was administered 4 weeks before transplant. The anti‐B titer decreased to 1:2 following the Rituximab (CD19% of 0%). Post‐transplant, the Anti‐B titers were monitored for the first 10 days, with a maximum titer of 1:8 (immunoadsorbtion therapy available if > 1:16, or if associated graft dysfunction). Immunosuppressant protocol consisted of Basiliximab, Tacrolimus, Azathioprine, and Prednisone. Post‐transplant, the creatinine improved to 60–70 μmol/L at Week 1. 7 weeks post‐transplant, serum creatinine increased > 10% with an antibody titer of 1:2. Kidney biopsy showed CNI‐related toxicity; renal function improved with reduction in Tacrolimus doses. Kidney function remains stable 1‐year post‐transplant with nil episodes of rejection.ConclusionThis is the first ABO‐incompatible kidney transplant in a pediatric patient in South Africa and represents an important step in expanding the pool of potential living related donors.
The potential lipid biomarker 5‐HETE for acute exacerbation identified by metabolomics in patients with idiopathic pulmonary fibrosis
Authors: Zhao Yichao , Shi Yanchen , Zhang Ji , Zhang Huizhe , Wang Zimu , Wu Shufei , Zhang Mingrui , Liu Mengying , Ye Xu , Gu Huimin , Jiang Cheng , Ye Xiaoling , Zhu Huihui , Li Qi , Huang Xinmei , Cao Mengshu 
Published: December 2024

AbstractBackground and ObjectiveAcute exacerbation (AE) is often the fatal complication of idiopathic pulmonary fibrosis (IPF). Emerging evidence indicates that metabolic reprogramming and dysregulation of lipid metabolism are distinctive characteristics of IPF. However, the lipid metabolic mechanisms that underlie the pathophysiology of AE‐IPF remain elusive.MethodsSerum samples for pilot study were collected from 34 Controls, 37 stable IPF (S‐IPF) cases and 41 AE‐IPF patients. UHPLC–MS/MS was utilized to investigate metabolic variations and identify lipid biomarkers in serum. ELISA, quantitative PCR and western blot were employed to validate the identified biomarkers.ResultsThere were 32 lipid metabolites and 5 lipid metabolism pathways enriched in all IPF patients compared to Controls. In AE‐IPF versus S‐IPF, 19 lipid metabolites and 12 pathways were identified, with 5‐hydroxyeicosatetraenoic Acid (5‐HETE) significantly elevated in AE‐IPF. Both in internal and external validation cohorts, the serum levels of 5‐HETE were significantly elevated in AE‐IPF patients compared to S‐IPF subjects. Consequently, the indicators related to 5‐HETE in lipid metabolic pathway were significantly changed in AE‐IPF patients compared with S‐IPF cases in the lung tissues. The serum level of 5‐HETE was significantly correlated with the disease severity (CT score and PaO2/FiO2 ratio) and survival time. Importantly, the receiver operating characteristic (ROC) curve, Kaplan–Meier analysis and Multivariate Cox regression analysis demonstrated that 5‐HETE represents a promising lipid biomarker for the diagnosis and prognosis of AE‐IPF.ConclusionOur study highlights lipid reprogramming as a novel therapeutic approach for IPF, and 5‐HETE may be a potential biomarker of AE‐IPF patients.
Brain MRI findings and thoracic CT findings in a dog with hemiparesis and acutely diminished Von‐Willebrand factor levels through Angiostrongylus vasorum infection
Authors: Krüger Benjamin Thilo , Hamm Vinga Carolina , Wennemuth Jan 
Published: December 2024

AbstractA 2‐year‐old intact male Airedale Terrier was presented with a sudden onset of neurological signs, manifesting as hemiparesis, which were neuroanatomically localized to the brain. Initial bloodwork conducted by the local veterinarian indicated decreased levels of von Willebrand factor, and further examination showed an extended buccal mucosal bleeding time. MRI revealed a substantial hemorrhage within the right parietal lobe, while CT exhibited a mixed pulmonary pattern with unstructured interstitial, peribronchial, and alveolar components, presumably associated with larval migration and pulmonary microhemorrhages. A Baermann fecal test yielded positive results, confirming an Angiostrongylus vasorum infection. Following treatment, the patient exhibited a complete remission of all symptoms and findings.
Diffusion data augmentation for enhancing Norberg hip angle estimation
Authors: Yueh Sheng‐Han , Higgins Fiona , Lin Zoe , Todhunter Rory James , Zhang Youshan 
Published: December 2024

AbstractThe Norberg angle (NA) plays a crucial role in evaluating hip joint conformation, particularly in canines, by quantifying femoral head subluxation within the hip joint. Therefore, it is an important metric for evaluating hip joint quality and diagnosing canine hip dysplasia, the most prevalent hereditary orthopedic disorder in dogs. While contemporary tools offer automated quantification of the NA, their usage typically entails manual labeling and verification of radiographic images by professional veterinarians. To enhance efficiency and streamline this process, the study aims to develop a tool capable of predicting the NA directly from the image without the need for veterinary intervention. Due to the challenges in acquiring annotated, diverse, high‐quality images, this study introduces diffusion models to expand the training dataset from 219 to 1493 images, encompassing original images. This augmentation enhances the dataset's diversity and scale, thereby improving the accuracy of Norberg angle estimation. The model predicts four key points: the center of left and right femoral heads and the edge of the left and right acetabulum, as well as the radii of the femoral heads and the Norberg angles. By evaluating 18 distinct pretrained ImageNet models, we investigate their performance pre‐ and post‐incorporating augmented data from generated images. The results demonstrate a significant enhancement, with an average 35.3% improvement based on mean absolute percentage error when utilizing generated images from diffusion models. This study showcases the potential of diffusion modeling in advancing canine hip dysplasia diagnosis and underscores the value of incorporating augmented data to elevate model accuracy.
Hepatic parenchymal hypoattenuation in dogs with diabetes mellitus on computed tomography consistent with hepatic steatosis
Authors: Buckley Christy , Fulkerson Caroline. V. , Derre Maxime , Woolcock Andrew , Murakami Masahiro 
Published: December 2024

AbstractHypoattenuation of the liver, consistent with hepatic steatosis or lipidosis, has been reported in veterinary patients. In people, measuring CT hepatic attenuation is diagnostic for hepatic steatosis, and hypoattenuation of the liver is defined as absolute if less than 40 HU or relative if the liver is 10 HU less than the spleen. The purpose of this study is to describe hepatic parenchymal attenuation in dogs with diabetes mellitus with or without diabetic ketosis (DK) or diabetic ketoacidosis (DKA), using the above categorization for absolute and relative hypoattenuation, as with humans. We hypothesized dogs with DK or DKA were more likely to have hypoattenuating livers. Twenty‐seven diabetic dogs were included; fifteen were categorized in Group 1 as without DK or DKA, six in Group 2 as DK, and six in Group 3 as DKA. In Group 3, four of six dogs had absolute and relative hypoattenuating livers. Three of these were visually hypoattenuating to the vasculature, with one having negative attenuation and a histopathologic diagnosis of severe hepatic lipidosis. In Group 2, four of six dogs had relative hypoattenuating livers. In Group 1, only one of 15 dogs had a relatively hypoattenuating liver. Groups 2 and 3 had significantly lower absolute liver attenuation than Group 1. Presumed hepatic steatosis was present on CT and was more common with DK or DKA. These findings may help provide hepatic sampling recommendations and alter patient prognosis. Further research is needed to establish absolute and relative liver attenuation in dogs with correlation to histopathology and patient outcome.
Ultrasonographic features of feline gastrointestinal eosinophilic sclerosing fibroplasia on initial presentation and during follow‐up
Authors: Lopez‐Jimenez Cristobal , Černá Petra , Fukushima Kenjiro , Nakashima Ko , Nakagawa Taisuke , Adam Fiona , Israeliantz Nicolas , Denning Andrew , de la Puerta Anna 
Published: December 2024

AbstractThe aim of this study is to describe the ultrasonographic features of feline gastrointestinal eosinophilic sclerosing fibroplasia (FGESF) before histological diagnosis and during follow‐up after surgical excision and/or medical treatment. This multicentric retrospective case series study includes medical records of cats diagnosed histologically, which had an ultrasound before diagnosis and a minimum of one follow‐up ultrasound at least 4 weeks after treatment. Thirty cats were included in the study. The average age was 4.9 years (IQR 3.3–9.3 years). In 25 cases, the mass affected the gastrointestinal system, most commonly the proximal duodenum (36%: 9/25). Three masses originated from the lymph nodes, and two were mesenteric. The most common clinical signs were chronic vomiting, weight loss, and anorexia/reduced appetite. In 25 of 30 (83%) FGESF gastrointestinal cases, ultrasonographically, the lesions generally presented as focal, circumferential, eccentric masses with loss of layering, heterogeneous echogenicity, and hyperechoic areas. Hyperechogenicities in the peritoneum were observed in 63% of the cases, and enlarged lymph nodes (88%) were common. On final follow‐up, 55% of the patients had complete resolution of the main lesion, peritoneal changes, and lymphadenopathies ultrasonographically. The disease recurred in 11 of 30 (37%), and progression was reported in 10 of 30 (33%) cases during the follow‐up. Initially, 9 of these 10 were diagnosed via nonexcisional biopsy (endoscopic biopsy, Trucut biopsy, surgical incisional biopsy) and treated medically; only one patient had had surgical resection of the mass. Clinical signs at the time of recurrence or progression were inconsistent. Feline gastrointestinal eosinophilic sclerosing fibroplasia shows ultrasonographic features similar to neoplasia but commonly demonstrates hyperechoic areas. Data were assessed for normality and then assessed with appropriate parametric or nonparametric tests accordingly. Progression of the disease at any time during the follow‐up was more common in cats treated medically than those treated surgically (P = .02). Clinical signs may or may not be present at the time of ultrasonographic recurrence or progression.
Algebraically overtwisted tight 3‐manifolds from +1$+1$ surgeries
Authors: Li Youlin , Zhou Zhengyi 
Published: December 2024

AbstractWe execute Avdek's algorithm to find many algebraically overtwisted and tight 3‐manifolds by contact surgeries. In particular, we show that a contact surgery on the standard contact 3‐sphere along any Legendrian positive torus knot with the maximal Thurston–Bennequin invariant yields an algebraically overtwisted and tight 3‐manifold, where is a positive integer.
Asymptotic dimension for covers with controlled growth
Authors: Hume David , Mackay John M. , Tessera Romain 
Published: December 2024

AbstractWe prove various obstructions to the existence of regular maps (or coarse embeddings) between commonly studied spaces. For instance, there is no regular map (or coarse embedding) for , or whenever is a bounded degree graph with subexponential growth, where is the 3‐regular tree. We also resolve Question 5.2 (Groups Geom. Dyn. 6 (2012), no. 4, 639–658), proving that there is no regular map whenever is a bounded degree graph with at most polynomial growth, and no quasi‐isometric embedding whenever has subexponential growth. Finally, we show that there is no regular map where is the free group on two generators. To prove these results, we introduce and study generalisations of asymptotic dimension that allow unbounded covers with controlled growth.
Multi‐indice B$B$‐series
Authors: Bruned Yvain , Ebrahimi‐Fard Kurusch , Hou Yingtong 
Published: December 2024

AbstractWe propose a novel way to study numerical methods for ordinary differential equations in one dimension via the notion of multi‐indice. The main idea is to replace rooted trees in Butcher's ‐series by multi‐indices. The latter were introduced recently in the context of describing solutions of singular stochastic partial differential equations. The combinatorial shift away from rooted trees allows for a compressed description of numerical schemes. Furthermore, such multi‐indices ‐series uniquely characterize the Taylor expansion of 1‐dimensional local and affine equivariant maps.
Sharp bounds for the number of rational points on algebraic curves and dimension growth, over all global fields
Authors: Binyamini Gal , Cluckers Raf , Kato Fumiharu 
Published: December 2024

AbstractLet be an algebraic curve over a number field , and denote by the degree of over . We prove that the number of ‐rational points of height at most in is bounded by where are absolute constants. We also prove analogous results for global fields in positive characteristic, and, for higher dimensional varieties. The quadratic dependence on in the bound as well as the exponent of are optimal; the novel aspect is the quadratic dependence on which answers a question raised by Salberger. We derive new results on Heath‐Brown and Serre's dimension growth conjecture for global fields, which generalize in particular the results by the first two authors and Novikov from the case . The proofs however are of a completely different nature, replacing the real analytic approach previously used by the ‐adic determinant method. The optimal dependence on is achieved by a key improvement in the treatment of high multiplicity points on mod reductions of algebraic curves.