bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic segmentation of MRI images for brain radiotherapy planning using deep ensemble learning
Authors: Yoganathan SA , Torfeh Tarraf , Paloor Satheesh , Hammoud Rabih , Al-Hammadi Noora , Zhang Rui 
Published: January 2025

Abstract

Background
and Purpose
: This study aimed to develop and evaluate an efficient method to automatically segment T1- and T2-weighted brain magnetic resonance imaging (MRI) images. We specifically compared the segmentation performance of individual convolutional neural network (CNN) models against an ensemble approach to advance the accuracy of MRI-guided radiotherapy (RT) planning. Materials and Methods. The evaluation was conducted on a private clinical dataset and a publicly available dataset (HaN-Seg). Anonymized MRI data from 55 brain cancer patients, including T1-weighted, T1-weighted with contrast, and T2-weighted images, were used in the clinical dataset. We employed an EDL strategy that integrated five independently trained 2D neural networks, each tailored for precise segmentation of tumors and organs at risk (OARs) in the MRI scans. Class probabilities were obtained by averaging the final layer activations (Softmax outputs) from the five networks using a weighted-average method, which were then converted into discrete labels. Segmentation performance was evaluated using the Dice similarity coefficient (DSC) and Hausdorff distance at 95% (HD95). The EDL model was also tested on the HaN-Seg public dataset for comparison. Results. The EDL model demonstrated superior segmentation performance on both the clinical and public datasets. For the clinical dataset, the ensemble approach achieved an average DSC of 0.7 ± 0.2 and HD95 of 4.5 ± 2.5 mm across all segmentations, significantly outperforming individual networks which yielded DSC values ≤0.6 and HD95 values ≥14 mm. Similar improvements were observed in the HaN-Seg public dataset. Conclusions. Our study shows that the EDL model consistently outperforms individual CNN networks in both clinical and public datasets, demonstrating the potential of ensemble learning to enhance segmentation accuracy. These findings underscore the value of the EDL approach for clinical applications, particularly in MRI-guided RT planning.
Turning International Law against Indigenous Peoples
Authors: Becker Lorca Arnulf , Álvez Marín Amaya 
Published: January 2025

Abstract
This chapter examines how international law shaped the fortunes of the Indigenous peoples of Latin America. Arnulf Becker and Amaya Álvez argue that international law was part and parcel of the project of completing the colonization or elimination of the Indigenous peoples of the Americas after Independence. International law doctrines such as uti posseditis, celebrated by Alejandro Álvarez as a Latin American innovation, allowed the early republics to claim sovereignty over Indigenous land that they did not yet possess or govern in any real sense, but over which they aimed to gain dominion. Becker and Álvez highlight critical moments in the nineteenth and twentieth centuries in which international law was used to strip Indigenous peoples of land and autonomy and exclude them from the international order.
Latin American and Caribbean Contributions to Human Rights Law
Authors: Jensen Steven L B , Sikkink Kathryn 
Published: January 2025

Abstract
This chapter explores the role of the Latin American and Caribbean states as early protagonists of the international protection of human rights. It focuses on their contributions in two “defining” periods for international human rights law: the 1940s and the 1960s. It illustrates their contributions as a constitutive part of a global history of human rights because their influence was so far-reaching. In the decades following the periods discussed in this chapter, Latin American and Caribbean countries would have complicated and conflictual engagements with the international and regional human rights system. By contrast, the two decades in focus show the region’s formative influences on international human rights and provide a valid precursor to a larger story about Latin America and the Caribbean.
Contributions of Latin America to International Law
Authors: Grossman Guiloff Claudio 
Published: January 2025

Abstract
In this chapter, Claudio Grossman, one of the group of lawyers who helped shape litigation before the inter-American system into what it is today, provides an in-depth analysis of the evolution of the law of reparations in the region from the Calvo doctrine in the late 1800s to the advancement of the concept of integral reparations by the Inter-American Commission and Court. He also extends the analysis to other institutions in dialogue with the Inter-American human rights system, showing its impact outside the region. The chapter closes with concern for how the rise in populist politics may impact this doctrine in the near future.
Community of Practice and the Ius Constitutionale Commune en América Latina
Authors: Céspedes-Báez Lina M , Prieto-Rios Enrique , Mazariegos-Rodas Mónica 
Published: January 2025

Abstract
This chapter discusses a key area of Latin American doctrinal development regarding human rights: whether human rights sit at the international or constitutional level or, increasingly, at both levels. In recent years, a group of scholars has argued that the practice of human rights and constitutional rights in the region has given rise to an ius contitutionale in Latin America (ICCAL), or “a transformative constitutional project” that “seeks to achieve and promote human rights, democracy, and the rule of law and analyze how the region has embraced and implemented these constitutional normative values.” Lina M. Céspedes-Báez, Enrique Prieto-Rios, and Mónica Mazariegos-Rodas take on the many critics of the ICCAL theory, showing how the “communities of practice” in Latin America have strategically appropriated and mobilized transformative constitutionalism’s narratives and ways of interpreting the law to grant agency and guarantee the human rights of subalterns in the region.
Maritime Delimitation in Latin America
Authors: Teresa Infante Caffi María 
Published: January 2025

Abstract
In this chapter, professor Maria Teresa Infante reviews the practice of maritime delimitation among Latin American states since the mid-twentieth century, when maritime law underwent dramatic changes. Judge Infante walks the reader through a tour of the different fora and diverse sources of law that states have turned to for maritime delimitation, as well as an exploration of the different factors, including geographical and geostrategic elements (or legal geography), that shape decision-making in this realm. She highlights several regional features, including reliance on the International Court of Justice and bilateral treaty-making. Professor Infante argues that delimitation practice has been by the contingencies of each case, such that there is no distinctive Latin American practice in this realm.
Transfeminine Joking on Argentina’s Bailando por un sueño
Authors: Tobin Jeffrey 
Published: January 2025

Abstract
As Argentines debated marriage equality and gender identity in the 2010s, two travesti (transfeminine) comedians achieved fame as contestants on Argentina’s version of Strictly Come Dancing. Florencia de la V started her career as the butt of jokes about her transfemininity, but she was able to use her earnestness as a dancer to separate her embodiment of femininity from her verbal comedy. Florencia also starred in a revue that made fun of why homophobic, straight-identified men are attracted to travestis. Lizy Tagliani used campy dancing to suspend judgment regarding her transfemininity. Also, by deploying her travesti body to impersonate famous ciswomen, Lizy called attention to the artificiality of cisgenderism. In her own way, each travesti used dancing to advance trans rights in Argentina. A coda considers whether a “new inclusivity” in Argentina has the perverse effect of discriminating against ciswomen despite the artists’ good intentions.
Connecting the dots: Low-grade appendiceal mucinous neoplasms and serrated polyps in the appendix
Authors: Mahadik Juhi Devendra , Assarzadegan Naziheh 
Published: January 2025

Abstract

Objective
This study aimed to examine the relationship between low-grade appendiceal mucinous neoplasms (LAMNs) and serrated polyps (SPs) of the appendix, both characterized by KRAS mutations and overlapping morphologic features.

Methods
We analyzed 27 cases of LAMN and 24 cases of SP from archival records, reviewed pathology, and performed molecular analysis on select cases. Four cases initially diagnosed as LAMN were excluded for not meeting diagnostic criteria, and 1 SP case was reclassified as LAMN.

Results
Microscopic evaluation revealed serrated architecture in 8 (29.6%) of 27 LAMNs: 4 hyperplastic polyp-like, 2 sessile serrated lesion-like (SSL), and 1 traditional serrated adenoma-like (TSA). One case exhibited both SSL- and TSA-like areas. Among SPs, 3 (12.5%) of 24 cases showed morphologic overlap with LAMN due to cytoplasmic mucin, flattened mucosa, and conventional adenoma-like features; all were grossly visible. KRAS was the most common mutation in LAMNs with serrated architecture (4/4, 100%), 1 classic LAMN, and 1 SP with dysplasia and associated signet-ring cell carcinoma.

Conclusions
Serrated polyps and LAMNs likely represent a biological continuum, sharing key features such as KRAS mutations and morphologic overlap. Our findings underscore the need for careful molecular and histopathologic evaluation in diagnosing these neoplasms.
AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody–antigen interaction prediction
Authors: Zhang Kaiwen , Tao Yuhao , Wang Fei 
Published: January 2025

Abstract
Antibodies play a key role in medical diagnostics and therapeutics. Accurately predicting antibody–antigen binding is essential for developing effective treatments. Traditional protein–protein interaction prediction methods often fall short because they do not account for the unique structural and dynamic properties of antibodies and antigens. In this study, we present AntiBinder, a novel predictive model specifically designed to address these challenges. AntiBinder integrates the unique structural and sequence characteristics of antibodies and antigens into its framework and employs a bidirectional cross-attention mechanism to automatically learn the intrinsic mechanisms of antigen–antibody binding, eliminating the need for manual feature engineering. Our comprehensive experiments, which include predicting interactions between known antigens and new antibodies, predicting the binding of previously unseen antigens, and predicting cross-species antigen–antibody interactions, demonstrate that AntiBinder outperforms existing state-of-the-art methods. Notably, AntiBinder excels in predicting interactions with unseen antigens and maintains a reasonable level of predictive capability in challenging cross-species prediction tasks. AntiBinder’s ability to model complex antigen–antibody interactions highlights its potential applications in biomedical research and therapeutic development, including the design of vaccines and antibody therapies for rapidly emerging infectious diseases.
Land use influences the faecal glucocorticoid metabolites of multiple species across trophic levels
Authors: Chiu-Werner Antje , Fanson Kerry V , Cameron Elissa , Jones Menna 
Published: January 2025

Abstract
Human landscape modification is amongst the greatest drivers of biodiversity loss. Measuring faecal glucocorticoid metabolites (FGM) in wildlife is of great value to measure the impact of human activities on local biodiversity because FGM offer a non-invasive way of measuring an animal’s response to changes in its environment in the form of adrenocortical activity. Here, we measure the concentration of FGM in three native Australian mammal species belonging to different trophic levels: the Tasmanian devil (Sarcophilus harrisii) and the spotted-tailed quoll (Dasyurus maculatus), both carnivores, and an omnivore that is primarily an arboreal folivore, the brushtail possum (Trichosurus vulpecula), and compare the FGM concentrations across three major land uses: agricultural, plantation and National Parks. We find that land use influences the FGM concentration in all three species and that general patterns emerge in FGM concentrations across multiple species and trophic levels in relation to land use. Specifically, plantation landscapes are associated with the lowest median and range of variation of FGM concentration in all species with several plausible explanations depending on the species. Our results suggest that measuring FGM in multiple species can offer a time- and cost-efficient snapshot of how different animals experience the same environment, potentially simplifying FGM interpretation. This study is the first to apply a community approach to understand how multiple species of different trophic levels respond collectively, and separately, to different land use types.
Runoff and accumulation of microplastics derived from polymer-coated fertilizer in Japanese paddy fields
Authors: Katsumi Naoya , Kusube Takasei 
Published: January 2025

Abstract
Polymer-coated fertilizers, widely used in rice cultivation in Japan, contribute to reactive nitrogen management and agricultural productivity but are a source of microplastics in the environment. Here, we investigated microplastics derived from polymer-coated fertilizer (microcapsule) runoff in Japanese paddy fields at 38 sites to quantitatively assess the behavior of microcapsules in paddy fields and to estimate the total amount of runoff and accumulation in Japan. We also examined the factors causing variations in the amount of runoff among paddy fields. Between 61% and 100% of microcapsule runoff during the irrigation period occurred between puddling and rice transplanting, with concentrations ranging from 2–482 mg/m2 in paddy fields. Water management practices and wind direction and speed explained the difference in runoff between plots. The total amount of microcapsules discharged from Japanese paddy fields during the irrigation season was estimated to be between 17 and 6,291 t (median 1,157 t) from the loads obtained in this study. According to fertilizer statistics and our results, total microcapsule accumulation on agricultural land in Japan was estimated to be 75,623 t. These results suggest that paddy fields in Japan will remain a long-term source of marine microplastics.
DNA metabarcoding captures temporal and vertical dynamics of mesozooplankton communities
Authors: Novotny Andreas , Rodrigues Caterina , Jacquemot Loïc , Clemente-Carvalho Rute B G , Piercey Rebecca S , Morien Evan , Galbraith Moira , Kellogg Colleen T E , Lemay Matthew A , Hunt Brian P V 
Published: January 2025

Abstract
In this study, we evaluated how well DNA metabarcoding of environmental samples captures changes in marine mesozooplankton community composition to optimize the use of sequencing data for studying seasonal dynamics. Although DNA metabarcoding is increasingly used to monitor the distribution of marine communities, there is a lack of standardized methods, and it remains uncertain to what extent the DNA data reflects patterns of community dynamics observed by other methods. Zooplankton net samples were collected every second week throughout 2017 in the northern Salish Sea, British Columbia. We compared metabarcoding of two genetic markers (18S targeting eukaryotes and cytochrome oxidase I targeting invertebrates) with microscopic assessments of the zooplankton collected. We also evaluated how data transformation using relative abundance, presence/absence, and the eDNA-index, affects the linearity between the morphological and genetic methods. Despite low taxonomic agreement between DNA metabarcoding and microscopy, we found most biomass dominating genera to be well represented. Using the eDNA-index, we found a generally good congruence between the seasonal cycles observed with microscopy and DNA, and that discrete water samples analyzed with DNA metabarcoding can provide information on the vertical distributions of mesozooplankton genera. We conclude by presenting guidelines for future studies that aim to use DNA to study marine zooplankton community dynamics.
Global convergence of SGD on two layer neural nets
Authors: Gopalani Pulkit , Mukherjee Anirbit 
Published: January 2025

Abstract
In this note, we consider appropriately regularized $\ell _{2}-$empirical risk of depth $2$ nets with any number of gates and show bounds on how the empirical loss evolves for Stochastic Gradient Descent (SGD) iterates on it—for arbitrary data and if the activation is adequately smooth and bounded like sigmoid and tanh. This, in turn, leads to a proof of global convergence of SGD for a special class of initializations. We also prove an exponentially fast convergence rate for continuous time SGD that also applies to smooth unbounded activations like SoftPlus. Our key idea is to show the existence of Frobenius norm regularized loss functions on constant-sized neural nets that are ‘Villani functions’ and thus be able to build on recent progress with analyzing SGD on such objectives. Most critically, the amount of regularization required for our analysis is independent of the size of the net.
Gut-resident Tregs (GTregs) play a pivotal role in maintaining bone health under post-menopausal osteoporotic conditions
Authors: Bhardwaj Asha , Sapra Leena , Madan Divya , Ahuja Vineet , Sharma Hanuman Prasad , Velpandian Thirumurthy , Mishra Pradyumna K , Srivastava Rupesh K 
Published: January 2025

Abstract
Osteoporosis is a skeletal condition characterized by the deterioration of bone tissue. The immune system plays a crucial role in maintaining bone homeostasis and combating the development of osteoporosis. Immunoporosis is the term used to describe the recent convergence of research on the immune system's role in osteoporosis. The gut harbors the largest component of the immune system and there is growing evidence that intestinal immunity plays a vital role in regulating bone health. Gut-resident regulatory T cells (GTregs) are essential in inhibiting immune responses and preventing various inflammatory manifestations. Our findings show that GTregs are pivotal in the pathophysiology of post-menopausal osteoporosis (PMO). We investigated the potential of GTregs in regulating the development of bone cells in vitro. We observed that GTregs significantly enhance osteoblastogenesis with concomitant inhibition of osteoclastogenesis in a cell-ratio-dependent manner. We further report that the deficiency of short-chain fatty acids (SCFAs) in osteoporotic conditions substantially disrupts the composition of GTregs, leading to a loss of peripherally derived Tregs (pTregs) and an expansion of thymus-derived Tregs (tTregs). Moreover, the administration of probiotics Lactobacillus rhamnosus (UBLR-58) and Bifidobacterium longum (UBBL-64) modulated the GTregs compartment in an SCFA-dependent manner to mitigate inflammatory bone loss in PMO. Notably, SCFAs-primed GTregs were found to be significantly more effective in inhibiting osteoclastogenesis compared to unprimed GTregs. Altogether our results, for the first time, highlight the crucial role of GTregs in the pathophysiology of PMO, with potential clinical implications.
A spatially resolved spectral analysis of giant radio galaxies with MeerKAT
Authors: Charlton K K L , Delhaize J , Thorat K , Heywood I , Jarvis M J , Hardcastle M J , An F , Delvecchio I , Hale C L , Whittam I H , Brüggen M , Marchetti L , Morabito L , Randriamanakoto Z , White S V , Taylor A R 
Published: January 2025

ABSTRACT
In this study we report the spatially resolved, wideband spectral properties of three giant radio galaxies (GRGs) in the COSMOS field: MGTC J095959.63+024608.6, MGTC J100016.84+015133.0, and MGTC J100022.85+031520.4. One of these galaxies, MGTC J100022.85+031520.4, is reported here for the first time, with a projected linear size of 1.29 Mpc at a redshift of 0.1034. Unlike the other two, it is associated with a brightest cluster galaxy (BCG), making it one of the few GRGs known to inhabit cluster environments. We examine the spectral age distributions of the three GRGs using new MeerKAT UHF-band (544–1088 MHz) observations, and L-band (900–1670 MHz) data from the MeerKAT International GHz Tiered Extragalactic Exploration (MIGHTEE) survey. We test two models of spectral ageing, the Jaffe–Perola and Tribble models, using the Broadband Radio Astronomy Tools (brats) software, and find that they agree well with each other. We estimate the Tribble spectral age for MGTC J095959.63+024608.6 as 68 Myr, for MGTC J100016.84+015133.0 as 47 Myr, and for MGTC J100022.85+031520.4 as 67 Myr. We find significant disagreements between these spectral age estimates and the estimates of the dynamical ages of these GRGs, modelled in cluster and group environments. Our results highlight the need for additional processes that are not accounted for in either the dynamic age or the spectral age estimations.
The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency
Authors: Heilbrun Elisheva E , Tseitline Dana , Wasserman Hana , Kirshenbaum Ayala , Cohen Yuval , Gordan Raluca , Adar Sheera 
Published: January 2025

Abstract
Lung cancer sequencing efforts have uncovered mutational signatures that are attributed to exposure to the cigarette smoke carcinogen benzo[a]pyrene. Benzo[a]pyrene metabolizes in cells to benzo[a]pyrene diol epoxide (BPDE) and reacts with guanine nucleotides to form bulky BPDE adducts. These DNA adducts block transcription and replication, compromising cell function and survival, and are repaired in human cells by the nucleotide excision repair pathway. Here, we applied high-resolution genomic assays to measure BPDE-induced damage formation and mutagenesis in human cells. We integrated the new damage and mutagenesis data with previous repair, DNA methylation, RNA expression, DNA replication, and chromatin component measurements in the same cell lines, along with lung cancer mutagenesis data. BPDE damage formation is significantly enhanced by DNA methylation and in accessible chromatin regions, including transcribed and early-replicating regions. Binding of transcription factors is associated primarily with reduced, but also enhanced damage formation, depending on the factor. While DNA methylation does not appear to influence repair efficiency, this repair was significantly elevated in accessible chromatin regions, which accumulated fewer mutations. Thus, when damage and repair drive mutagenesis in opposing directions, the final mutational patterns appear to be dictated by the efficiency of repair rather than the frequency of underlying damages.