bluuebunny/crossref_metadata_2025_split huggingface dataset:
Androgen receptor pathway inhibitors and taxanes in metastatic prostate cancer: an outcome-adaptive randomized platform trial
Authors: De Laere Bram , Crippa Alessio , Discacciati Andrea , Larsson Berit , Persson Maria , Johansson Susanne , D’hondt Sanne , Bergström Rebecka , Chellappa Venkatesh , Mayrhofer Markus , Banijamali Mahsan , Kotsalaynen Anastasijia , Schelstraete Céline , Vanwelkenhuyzen Jan Pieter , Hjälm-Eriksson Marie , Pettersson Linn , Ullén Anders , Lumen Nicolaas , Enblad Gunilla , Thellenberg Karlsson Camilla , Jänes Elin , Sandzén Johan , Schatteman Peter , Nyre Vigmostad Maria , Olsson Martha , Ghysel Christophe , Sautois Brieuc , De Roock Wendy , Van Bruwaene Siska , Anden Mats , Verbiene Ingrida , De Maeseneer Daan , Everaert Els , Darras Jochen , Aksnessether Bjørg Y. , Luyten Daisy , Strijbos Michiel , Mortezavi Ashkan , Oldenburg Jan , Ost Piet , Eklund Martin , Grönberg Henrik , Lindberg Johan 
Published: August 2024

AbstractProBio is the first outcome-adaptive platform trial in prostate cancer utilizing a Bayesian framework to evaluate efficacy within predefined biomarker signatures across systemic treatments. Prospective circulating tumor DNA and germline DNA analysis was performed in patients with metastatic castration-resistant prostate cancer before randomization to androgen receptor pathway inhibitors (ARPIs), taxanes or a physician’s choice control arm. The primary endpoint was the time to no longer clinically benefitting (NLCB). Secondary endpoints included overall survival and (serious) adverse events. Upon reaching the time to NLCB, patients could be re-randomized. The primary endpoint was met after 218 randomizations. ARPIs demonstrated ~50% longer time to NLCB compared to taxanes (median, 11.1 versus 6.9 months) and the physician’s choice arm (median, 11.1 versus 7.4 months) in the biomarker-unselected or ‘all’ patient population. ARPIs demonstrated longer overall survival (median, 38.7 versus 21.7 and 21.8 months for taxanes and physician’s choice, respectively). Biomarker signature findings suggest that the largest increase in time to NLCB was observed in AR (single-nucleotide variant/genomic structural rearrangement)-negative and TP53 wild-type patients and TMPRSS2–ERG fusion-positive patients, whereas no difference between ARPIs and taxanes was observed in TP53-altered patients. In summary, ARPIs outperform taxanes and physician’s choice treatment in patients with metastatic castration-resistant prostate cancer with detectable circulating tumor DNA. ClinicalTrials.gov registration: NCT03903835.
The involvement of cyclotides in the heavy metal tolerance of Viola spp.
Authors: Sychta Klaudia , Słomka Aneta , Shariatgorji Reza , Andrén Per E. , Samardakiewicz Sławomir , Göransson Ulf , Slazak Blazej 
Published: August 2024

AbstractThe Violaceae family is rich in metal-tolerant species and species producing cyclic peptides (cyclotides) that are linked to the resistance to biotic factors. Plants that inhabit areas polluted with heavy metals have developed various mechanisms of tolerance. To test the role of cyclotides in protection against abiotic factors, including heavy metals, cell suspension cultures of Viola species/genotypes (V. lutea ssp. westfalica, V. tricolor, V. arvensis, and V. uliginosa), representing different levels of tolerance to heavy metals (from the most tolerant-MET to the least tolerant populations/species-NMET), were used. The relative abundances of the cyclotides in the control, untreated cell suspensions of all the selected species/genotypes, and cells treated with Zn or Pb (200 µM or 2000 µM) for 24 h or 72 h were determined via MALDI-MS. Transmission electron microscopy with X-ray microanalysis was used to detect putative co-localization of the cyclotides with Zn or Pb in the cells of V. tricolor treated with the highest concentration of heavy metals for 72 h. Cyclotide biosynthesis was dependent on the type of heavy metal and its concentration, time of treatment, plant species, and population type (MET vs. NMET). It was positively correlated with the level of tolerance of particular Viola species. The increased production of cyclotides was observed in the cells of metallophyte species, mostly in Zn-treated cells. The nonmetallophyte—V. uliginosa presented a decrease in the production of cyclotides independent of the dose and duration of the metal treatment. Cyclotides co-localized with Pb more evidently than with Zn, suggesting that cyclotides have heavy metal affinity. V. lutea ssp. westfalica transcriptome mining yielded 100 cyclotide sequences, 16 known and 84 novel named viwe 1–84. These findings support the hypothesis that cyclotides are involved in certain mechanisms of plant tolerance to heavy metals.
Genomic architecture and population structure of Boreogadus saida from Canadian waters
Authors: Bringloe Trevor T. , Bourret Audrey , Cote David , Marie-Julie Roux , Herbig Jennifer , Robert Dominique , Geoffroy Maxime , Parent Geneviève J. 
Published: August 2024

AbstractThe polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4–16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.
A satellite imagery-driven framework for rapid resource allocation in flood scenarios to enhance loss and damage fund effectiveness
Authors: Eudaric Jeremy , Kreibich Heidi , Camero Andrés , Rafiezadeh Shahi Kasra , Martinis Sandro , Zhu Xiao Xiang 
Published: August 2024

AbstractThe impact of climate change and urbanization has increased the risk of flooding. During the UN Climate Change Conference 28 (COP 28), an agreement was reached to establish “The Loss and Damage Fund” to assist low-income countries impacted by climate change. However, allocating the resources required for post-flood reconstruction and reimbursement is challenging due to the limited availability of data and the absence of a comprehensive tool. Here, we propose a novel resource allocation framework based on remote sensing and geospatial data near the flood peak, such as buildings and population. The quantification of resource distribution utilizes an exposure index for each municipality, which interacts with various drivers, including flood hazard drivers, buildings exposure, and population exposure. The proposed framework asses the flood extension using pre- and post-flood Sentinel-1 Synthetic Aperture Radar (SAR) data. To demonstrate the effectiveness of this framework, an analysis was conducted on the flood that occurred in the Thessaly region of Greece in September 2023. The study revealed that the municipality of Palamas has the highest need for resource allocation, with an exposure index rating of 5/8. Any government can use this framework for rapid decision-making and to expedite post-flood recovery.
Impact of various microplastics on the morphological characteristics and nutrition of the young generation of beech (Fagus sylvatica L.)
Authors: Lasota Jarosław , Błońska Ewa , Kempf Marta , Kempf Piotr , Tabor Sylwester 
Published: August 2024

AbstractMicroplastics have the capacity to accumulate in soil due to their high resistance to degradation, consequently altering soil properties and influencing plant growth. This study focused on assessing the impact of various types and doses of microplastics on beech seedling growth. In our experiment, we used polypropylene and styrene granules with diameter of 4.0 mm in quantities of 2.5% and 7%. The hypothesis was that microplastics significantly affect seedlings' nutritional status and growth characteristics. The research analysed seedlings' nutrition, root morphological features, above-ground growth, and enzymatic activity in the substrate. Results confirmed the importance of microplastics in shaping the nutritional status of young beech trees. Microplastic type significantly impacted N/P and Ca/Mg stoichiometry, while microplastic quantity influenced Ca/Al and Ca+K+Mg/Al stoichiometry. Notably, only in the case of root diameter were significantly thicker roots noted in the control variant, whereas microplastics played a role in shaping the leaves' characteristics of the species studied. The leaf area was significantly larger in the control variant compared to the variant with polypropylene in the amount of 2.5% and styrene in the amount of 7%. Additionally, the study indicates a significant impact of microplastics on enzyme activity. In the case of CB and SP, the activity was twice as high in the control variant compared to the variants with microplastics. In the case of BG, the activity in the control variant was higher in relation to the variants used in the experiment. Research on the impact of microplastics on the growth of beech seedlings is crucial for enhancing our understanding of the effects of environmental pollution on forest ecosystems. Such studies are integral in shaping forestry management practices and fostering a broader public understanding of the ecological implications of plastic pollution.
Performance evaluation of a hyphenated laser spectroscopy system with conventional methods for microplastic analysis
Authors: Vasudeva M. , Adarsh U. K. , Warrier Anish Kumar , George Sajan D. , Unnikrishnan V. K. 
Published: August 2024

AbstractMicroplastics are one of the concerning environmental pollutants because of their ubiquity. Their capability to adsorb other environmental pollutants increases the risk even further. Existing identification approaches for microplastic characterization for polymer class and their surface-adsorbed heavy metal detection require the utilization of multiple resources and expertise. The article discusses the applicability of a custom-made hyphenated Laser Induced Breakdown Spectroscopy (LIBS)—Raman spectroscopic system in characterizing microplastics by comparing the analytical performance with conventional methods such as Attenuated Total Reflectance- Fourier Transform Infrared (ATR-FTIR) spectroscopy, confocal Raman spectroscopy, and Scanning Electron Microscopy–Energy Dispersive X-ray Spectroscopy (SEM–EDS). Raman analysis identified polyethylene (PE), polypropylene (PP), and polyethylene terephthalate (PET) plastics, which is confirmed by confocal Raman and FTIR study of the same. LIBS study of microplastics detected heavy metals such as Al, Ni, Co, and Zn, along with Ca and Mg trace elements. The cross-examination with EDS validates these trace elements' presence on the microplastics' surface. The results of the reported LIBS-Raman analysis and its validity evaluated using conventional gold-standard methods show the applicability of the proposed methodology in characterizing microplastics from environmental resources with less or no sample preparation in short time.
Ionization by XFEL radiation produces distinct structure in liquid water
Authors: Stransky Michal , Lane Thomas J. , Gorel Alexander , Boutet Sébastien , Schlichting Ilme , Mancuso Adrian P. , Jurek Zoltan , Ziaja Beata 
Published: August 2024

AbstractIn the warm dense matter (WDM) regime, where condensed, gas, and plasma phases coexist, matter frequently exhibits unusual properties that cannot be described by contemporary theory. Experiments reporting phenomena in WDM are therefore of interest to advance our physical understanding of this regime, which is found in dwarf stars, giant planets, and fusion ignition experiments. Using 7.1 keV X-ray free electron laser radiation (nominally 5×105 J/cm2), we produced and probed transient WDM in liquid water. Wide-angle X-ray scattering (WAXS) from the probe reveals a new ~9 Å structure that forms within 75 fs. By 100 fs, the WAXS peak corresponding to this new structure is of comparable magnitude to the ambient water peak, which is attenuated. Simulations suggest that the experiment probes a superposition of two regimes. In the first, fluences expected at the focus severely ionize the water, which becomes effectively transparent to the probe. In the second, out-of-focus pump radiation produces O1+ and O2+ ions, which rearrange due to Coulombic repulsion over 10 s of fs. Our simulations account for a decrease in ambient water signal and an increase in low-angle X-ray scattering but not the experimentally observed 9 Å feature, presenting a new challenge for theory.
GEMTELLIGENCE: Accelerating gemstone classification with deep learning
Authors: Bendinelli Tommaso , Biggio Luca , Nyfeler Daniel , Ghosh Abhigyan , Tollan Peter , Kirschmann Moritz Alexander , Fink Olga 
Published: August 2024

AbstractThe value of luxury goods, particularly investment-grade gemstones, is influenced by their origin and authenticity, often resulting in differences worth millions of dollars. Traditional methods for determining gemstone origin and detecting treatments involve subjective visual inspections and a range of advanced analytical techniques. However, these approaches can be time-consuming, prone to inconsistencies, and lack automation. Here, we propose GEMTELLIGENCE, a novel deep learning approach enabling streamlined and consistent origin determination of gemstone origin and detection of treatments. GEMTELLIGENCE leverages convolutional and attention-based neural networks that combine the multi-modal heterogeneous data collected from multiple instruments. The algorithm attains predictive performance comparable to expensive laser-ablation inductively-coupled-plasma mass-spectrometry analysis and expert visual examination, while using input data from relatively inexpensive analytical methods. Our methodology represents an advancement in gemstone analysis, greatly enhancing automation and robustness throughout the analytical process pipeline.
Immunotherapies targeting the oncogenic fusion gene CLDN18-ARHGAP in gastric cancer
Authors: Wang Yue , Wang Hanbing , Shi Tao , Song Xueru , Zhang Xin , Zhang Yue , Wang Xuan , Che Keying , Luo Yuting , Yu Lixia , Liu Baorui , Wei Jia 
Published: August 2024

AbstractThe CLDN18-ARHGAP fusion gene is an oncogenic driver newly discovered in gastric cancer. It was detected in 9% (8/87) of gastric cancer patients in our center. An immunogenic peptide specifically targeting CLDN18-ARHGAP fusion gene was generated to induce neoantigen-reactive T cells, which was proved to have specific and robust anti-tumor capacity both in in vitro coculture models and in vivo xenograft gastric cancer models. Apart from the immunogenic potential, CLDN18-ARHGAP fusion gene was also found to contribute to immune suppression by inducing a regulatory T (Treg) cell-enriched microenvironment. Mechanistically, gastric cancer cells with CLDN18-ARHGAP fusion activate PI3K/AKT-mTOR-FAS signaling, which enhances free fatty acid production of gastric cancer cells to favor the survival of Treg cells. Furthermore, PI3K inhibition could effectively reverse Treg cells upregulation to enhance anti-tumor cytotoxicity of neoantigen-reactive T cells in vitro and reduce tumor growth in the xenograft gastric cancer model. Our study identified the CLDN18-ARHGAP fusion gene as a critical source of immunogenic neoepitopes, a key regulator of the tumor immune microenvironment, and immunotherapeutic applications specific to this oncogenic fusion.
Below the surface: Unraveling the intricacies of the nonlinear optical properties of aluminum through bound electrons
Authors: Scalora M. , Hallman K. , Mukhopadhyay S. , Pruett S. , Zappa D. , Comini E. , de Ceglia D. , Vincenti M. A. , Akozbek N. , Trull J. , Cojocaru C. 
Published: August 2024

By uncovering novel aspects of second harmonic generation in aluminum, we show that there are unusual and remarkable consequences of resonant absorption, namely an unexpectedly critical role that bound electrons play for light–matter interactions across the optical spectrum, suggesting that a different basic approach is required to fully explain the physics of surfaces. We tackle an issue that is never under consideration given the generic hostile conditions to the propagation of light under resonant absorption. Unlike most noble metals, aluminum displays Lorentz-like behavior and interband transitions centered near 810 nm, thus splitting the plasmonic range in an atypical manner and setting its linear and nonlinear optical properties apart. Studies of aluminum nanostructures having complex topologies abound, as do reported inconsistencies in the linear spectral response of surface plasmons and harmonic generation. Our experimental observations of second harmonic generation from aluminum nanolayers show that bound electrons are responsible for a unique signature neither predicted nor observed previously: a hole in the second harmonic spectrum. A hydrodynamic-Maxwell theory explains these findings exceptionally well and becomes the basis for renewed studies of surface physics.
First insights into the vertical habitat use of young porbeagles in the north-western Atlantic with implications for bycatch reduction strategies
Authors: Anderson Brooke N. , Bowlby Heather D. , Saul Steven , Kang Yun , Hammerschlag Neil , Natanson Lisa J. , Sulikowski James A. 
Published: August 2024

Context For threatened marine species, data on their vertical habitat use patterns can reveal risk of interactions with fishing gear and can inform bycatch avoidance strategies. Such data are lacking for young porbeagles (Lamna nasus), which are captured as bycatch in north-western Atlantic fisheries. Aims We aimed to examine temporal patterns in diving and characterise vertical habitat use of young porbeagles during summer and autumn. Methods We used data from short-term (28-day), high-resolution (5-min interval) pop-off satellite tags attached to 14 young (young-of-the-year and 1-year-old) porbeagles to model depth use. Key results Occupied depths ranged from the sea surface to 679 m, with ambient water temperatures of −0.2 to 26°C. Diel period and season were factors related to depth use. Conclusions Sharks exhibited a diel activity pattern characterised by more extensive use of the water column during the day while remaining primarily at the surface at night. Depth use differed between seasons, with summer characterised by greater affinity for surface waters (0–10 m) compared to autumn. Implications Young porbeagles are at risk of interaction with active fisheries on the continental shelf, but interactions may be reduced by setting gear deeper at night or during summer.
The revelry of plastic! Quali-quantitative variation of microplastics in freshwater before and after Carnival in south-eastern Brazil
Authors: da Costa Igor David , de Freitas Queiroz Eduardo , Nunes Natalia Neto dos Santos , Costa Leonardo Lopes , Zalmon Ilana Rosental 
Published: August 2024

Context Pollution by synthetic polymers is even more problematic to the environment when this material is fragmented into small portions, forming microplastics (MPs). Aims We analysed the influence of the Brazilian Carnival on the abundance and richness of MPs in the Paraíba do Sul River (PSR). Specific objectives included classifying MPs by shape, colour and polymer, and quantifying and comparing the abundance and richness of surface-water MPs before, during and after Carnival. Methods Samples were taken from the superficial layer of the water column in 2023, by using manta net. Key results In total, 843 MPs were identified in the surface water of PSR. Higher MP concentrations were observed after the Carnival event than in the other two periods. Blue and black fibres were the predominant MPs. Glitter and sequin occurred only during the Carnival and post-Carnival periods. Polyester, polyamide and polyethylene were the most abundant in all the periods. Conclusions Our findings strongly indicated that Carnival represents a potential short-term source of MP introduction into the PSR basin. Implications A significant 170% increase in MP abundance was observed 10 days after the Carnival, which is an event occurring across multiple locations in the PSR basin.
Acknowledging dispossession
Authors: Martin J. R. , Cruz Priscilla Angela T. 
Published: August 2024

Abstract
This paper illustrates what can be revealed by a linguistic analysis of the discourse strategies deployed in a
bilingual text acknowledging the dispossession of Indigenous peoples in Mindanao (Philippines). The analysis draws on systemic
functional linguistics (SFL) descriptions of English, which model language as a resource for making meaning. It explores the
choices involved from the perspective of critical discourse analysis (CDA), exposing language in the service of power, and
positive discourse analysis (PDA), appreciating language as an instrument of social change. In doing so we exemplify the role of
SFL-informed CDA/PDA in processes of reconciliation, including personal and public acknowledgements and apologies, alongside
considerations of “making peace” with dispossessed Indigenous people through existing, renovated or emerging genres.
Feeling, thinking, acting
Authors: Fryer Daniel Lees 
Published: August 2024

Abstract
This article considers the multi- and intersemiotic expression of empathy and compassion in a campaign organised
by the Vegan Society. It draws upon insights from ecofeminism and the ethics of care as well as systemic functional semiotics as a
way of exploring how instances of attitude (affect, judgment and appreciation) in the campaign’s various texts might be negotiated
and shared, creating potentials for empathetic and compassionate responses. The study finds that parts of the campaign
represent empathy and compassion as exemplars for readers to follow, while other parts of the campaign,
especially social media, provide readers with an opportunity to enact empathy and compassion. The study also
identifies gendered and generational dimensions, and suggests that syndromes or clusters of positive and negative attitude can
form the basis for empathetic and compassionate responses.
Empathic listening as a social semiotic practice within the tradition of Nonviolent Communication
Authors: Thomson Elizabeth A. 
Published: August 2024

Abstract
This article investigates empathic listening as practised in the tradition of Nonviolent Communication (NVC),
noting that this tradition is understood as a designed register of interpersonal connection, “concerned with
progress toward a better world” (Hughes 2018). In the tradition,
empathy is considered “a respectful understanding of what others are experiencing, … we give to others the
time and space they need to express themselves fully and to be understood” (Rosenberg
2015: 91–92). The analysis in this article applies the tools of systemic functional linguistics to demonstrate that
this empathic understanding is achieved by the empathiser supporting the speaker’s exploration of their emotions via a linguistic
pattern of co-created, continuous thematic progression of resonated new information. The article
provides insights into the linguistic machinery powering NVC empathy practice.