bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulating Weapons: An Aristotelian Account
Authors: Lang Anthony F. 
Published: December 2023

AbstractRegulating war has long been a concern of the international community. From the Hague Conventions to the Geneva Conventions and the multiple treaties and related institutions that have emerged in the twentieth and twenty-first centuries, efforts to mitigate the horrors of war have focused on regulating weapons, defining combatants, and ensuring access to the battlefield for humanitarians. But regulation and legal codes alone cannot be the end point of an engaged ethical response to new weapons developments. This short essay reviews some of the existing ethical works on lethal autonomous weapon systems (LAWS), highlighting how rule- and consequence-based accounts fail to provide adequate guidance for how to deal with them. I propose a virtue-based account, which I link up with an Aristotelian framework, for how the international community might better address these weapons systems.
How best can we name the channels seen in the setting of deficient ventricular septation?
Authors: Anderson Robert H. , Spicer Diane E. , McMahon Colin J. , Kumar R. Krishna , Tretter Justin T. 
Published: December 2023

AbstractSurgical repair of channels between the ventricles is enhanced when the surgeon knows precisely where to place a patch, or baffle, so as to restore septal integrity. The paediatric cardiologist should provide the necessary information. Communication will be enhanced if the same words are used to account for the structures in question. Currently, however, the same term, namely “ventricular septal defect,” is used to account for markedly different areas within the heart. Closure of perimembranous defects found in hearts with concordant or discordant ventriculo-arterial connections restores the integrity of the ventricular septum, at the same time separating the systemic and pulmonary blood streams. When both arterial trunks arise from the right ventricle, in contrast, the surgeon when placing a baffle so as to separate the blood streams, does not close the channel most frequently described as the “ventricular septal defect.” In this review, we show that the perimembranous lesions as found in hearts with concordant or discordant ventriculo-arterial connections are the right ventricular entrances to the areas subtended beneath the hinges of the leaflets of the aortic or pulmonary valves. When both arterial trunks arise from the right ventricle, and the channel between the ventricles is directly subaortic, then the channel termed the “ventricular septal defect” is the left ventricular entrance to the comparable space subtended beneath the aortic root. We argue that recognition of these fundamental anatomical differences enhances the appreciation of the underlying morphology of the various lesions that reflect transfer, during cardiac development, of the aortic root from the morphologically right to the morphologically left ventricle.
Virtual reality evidence on the impact of physicians' open versus defensive communication on patients
Authors: Daniels Lotte , Marneffe Wim , Bielen Samantha 
Published: December 2023

AbstractUsing virtual reality (VR) in an experimental setting, we analyse how communicating more openly about a medical incident influences patients' feelings and behavioural intentions. Using VR headsets, participants were immersed in an actual hospital room where they were told by a physician that a medical incident had occurred. In a given scenario, half of the participants were confronted by a physician who communicated openly about the medical incident, while the other half were confronted with the exact same scenario except that the physician employed a very defensive communication strategy. The employed technology allowed us to keep everything else in the environment constant. Participants exposed to open disclosure were significantly more likely to take further steps (such as contacting a lawyer to discuss options and filing a complaint against the hospital) and express more feelings of blame against the physician. At the same time, these participants rated the physician's communication skills and general impression more highly than those who were confronted with a defensive physician. Nevertheless, communicating openly about the medical incident does not affect trust in the physician and his competence, perceived incident severity and likelihood of changing physician and filing suit.
Pacific‐Driven Salinity Variability in the Timor Passage Since 1777
Authors: Patterson Elizabeth W. , Cole Julia E. , Dyez Kelsey A. , Vetter Lael , Lough Janice 
Published: December 2023

AbstractSalinity in the Indonesian seas integrates regional oceanographic and atmospheric processes, such as Indonesian Throughflow (ITF) and monsoon rainfall. Here we present a multicentury (1777–1983) δ18O coral record from Nightcliff Reef, located in the Timor Passage off the coast of northern Australia, which we use to infer local salinity change. We show that Australian monsoon rainfall and ITF influence salinity at the study site. These reconstructed salinity changes in the Timor Passage correlate with changes in Pacific sea surface temperature (SST) modes, including the El Niño Southern Oscillation (ENSO) and the Interdecadal Pacific Oscillation (IPO). While environmental stress creates challenging conditions for coral growth, this record particularly tracks the central Pacific signature of ENSO‐driven interannual variability, in agreement with reconstructions of rainfall across northern Australia. The strength of interannual variance in the record follows fluctuations in other local ENSO‐sensitive rainfall reconstructions, demonstrating a strong regional ENSO signature. However, this regional pattern differs from variance in composite ENSO reconstructions, suggesting that the multi‐site nature of these reconstructions may create biases. Salinity variability on decadal and longer time scales occurs throughout the record. Some of these oscillations are consistent with other ITF‐sensitive coral records. Our new salinity record adds a strongly Pacific‐sensitive record to the existing suite of regional paleoclimate reconstructions. Relationships among these records highlight the complexity of salinity in the Indonesian seas and the controls on its variability.
Response of Siliceous Marine Organisms to the Permian‐Triassic Climate Crisis Based on New Findings From Central Spitsbergen, Svalbard
Authors: Foster W. J. , Asatryan G. , Rauzi S. , Botting J. P. , Buchwald S. Z. , Lazarus D. B. , Isson T. , Renaudie J. , Kiessling W. 
Published: December 2023

AbstractSiliceous marine ecosystems play a critical role in shaping the Earth's climate system by influencing rates of organic carbon burial and marine authigenic clay formation (i.e., reverse weathering). The ecological demise of silicifying organisms associated with the Permian‐Triassic mass extinction is postulated to have elevated marine authigenic clay formation rates, resulting in a prolonged greenhouse climate during the Early Triassic. Yet, our understanding of the response of siliceous marine organisms during this critical interval is poor. Whilst radiolarians experienced the strongest diversity loss in their evolutionary history and perhaps also the greatest population decline of silica‐secreting organisms during this event, only a small number of Griesbachian (post‐extinction) localities that record siliceous organisms are known. Here, we report newly discovered latest Changhsingian to early Griesbachian (Clarkina meishanensis ‐ Hindeodus parvus Zone) radiolarians and siliceous sponge spicules from Svalbard. This fauna documents the survival of a low‐diversity radiolarian assemblage alongside stem‐group hexactinellid sponges making this the first described account of post‐extinction silica‐secreting organisms from the Permian/Triassic boundary in a shallow marine shelf environment and a mid‐northern paleolatitudinal setting. Our findings indicate that latitudinal diversity gradients for silica‐secreting organisms following the mass extinction were significantly altered, and that silica productivity was restricted to high latitude and deep water thermal refugia. This result has potential to further shape our understanding of changes in marine dissolved silica levels and in turn rates of reverse weathering, with implications for our understanding of carbon cycle dynamics during this interval.
IgSF11 deficiency alleviates osteoarthritis in mice by suppressing early subchondral bone changes
Authors: Kim Gyeong Min , Kim Jihee , Lee June-Yong , Park Min-Chan , Lee Soo Young 
Published: December 2023

AbstractOsteoarthritis (OA) is a degenerative joint disease. While it is classically characterized by articular cartilage destruction, OA affects all tissues in the joints and is thus also accompanied by local inflammation, subchondral bone changes, and persistent pain. However, our understanding of the underlying subchondral bone dynamics during OA progression is poor. Here, we demonstrate the contribution of immunoglobulin superfamily 11 (IgSF11) to OA subchondral bone remodeling by using a murine model. In particular, IgSF11 was quickly expressed by differentiating osteoclasts and upregulated in subchondral bone soon after destabilization-of-the-medial-meniscus (DMM)-induced OA. In mice, IgSF11 deficiency not only suppressed subchondral bone changes in OA but also blocked cartilage destruction. The IgSF11-expressing cells in OA subchondral bone were found to be involved in osteoclast maturation and bone resorption and colocalized with receptor-activator of nuclear-factor κ-B (RANK), the key osteoclast differentiation factor. Thus, our study shows that blocking early subchondral bone changes in OA can ameliorate articular cartilage destruction in OA.
Processing stimulus dynamics by the NF-κB network in single cells
Authors: Son Minjun , Wang Andrew G. , Keisham Bijentimala , Tay Savaş 
Published: December 2023

AbstractCells at the site of an infection experience numerous biochemical signals that vary in amplitude, space, and time. Despite the diversity of dynamic signals produced by pathogens and sentinel cells, information-processing pathways converge on a limited number of central signaling nodes to ultimately control cellular responses. In particular, the NF-κB pathway responds to dozens of signals from pathogens and self, and plays a vital role in processing proinflammatory inputs. Studies addressing the influence of stimulus dynamics on NF-κB signaling are rare due to technical limitations with live-cell measurements. However, recent advances in microfluidics, automation, and image analysis have enabled investigations that yield high temporal resolution at the single-cell level. Here, we summarize the recent research which measures and models the NF-κB response to pulsatile and fluctuating stimulus concentrations, as well as different combinations and sequences of signaling molecules. Collectively, these studies show that the NF-κB network integrates external inflammatory signals and translates these into downstream transcriptional responses.
Molecular mechanisms of cellular metabolic homeostasis in stem cells
Authors: Li Xiaoyu , Jiang Ou , Wang Songlin 
Published: December 2023

AbstractMany tissues and organ systems have intrinsic regeneration capabilities that are largely driven and maintained by tissue-resident stem cell populations. In recent years, growing evidence has demonstrated that cellular metabolic homeostasis plays a central role in mediating stem cell fate, tissue regeneration, and homeostasis. Thus, a thorough understanding of the mechanisms that regulate metabolic homeostasis in stem cells may contribute to our knowledge on how tissue homeostasis is maintained and provide novel insights for disease management. In this review, we summarize the known relationship between the regulation of metabolic homeostasis and molecular pathways in stem cells. We also discuss potential targets of metabolic homeostasis in disease therapy and describe the current limitations and future directions in the development of these novel therapeutic targets.
TMEM44-AS1 promotes esophageal squamous cell carcinoma progression by regulating the IGF2BP2-GPX4 axis in modulating ferroptosis
Authors: Yang Ruotong , Wan Junhu , Ma Liwei , Zhou Fuyou , Yang Zhengwu , Li Zhuofang , Zhang Mingyuan , Ming Liang 
Published: December 2023

AbstractThe long non-coding RNA (lncRNA) TMEM44-AS1 is a novel lncRNA whose pro-carcinogenic role in gastric cancer and glioma has been demonstrated. However, its function in esophageal squamous cell carcinoma (ESCC) is unknown. In this study, we identified that TMEM44-AS1 was highly expressed in ESCC tissues and cells. Functionally, TMEM44-AS1 promoted ESCC cell proliferation, invasion and metastasis in vitro and in vivo. TMEM44-AS1 inhibited ferroptosis in ESCC cells, and ferroptosis levels were significantly increased after knockdown of TMEM44-AS1. Mechanistically, TMEM44-AS1 was positively correlated with GPX4 expression, and TMEM44-AS1 could bind to the RNA-binding protein IGF2BP2 to enhance the stability of GPX4 mRNA, thereby affecting ferroptosis and regulating the malignant progression of ESCC. In summary, this study reveals the TMEM44-AS1-IGF2BP2-GPX4 axis could influence cancer progression in ESCC. TMEM44-AS1 can be used as a potential treatment target against ESCC.
Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals
Authors: Brunoir T. , Mulligan C. , Sistiaga A. , Vuu K. M. , Shih P. M. , O’Reilly S. S. , Summons R. E. , Gold D. A. 
Published: December 2023

AbstractSteranes preserved in sedimentary rocks serve as molecular fossils, which are thought to record the expansion of eukaryote life through the Neoproterozoic Era ( ~ 1000-541 Ma). Scientists hypothesize that ancient C27 steranes originated from cholesterol, the major sterol produced by living red algae and animals. Similarly, C28 and C29 steranes are thought to be derived from the sterols of prehistoric fungi, green algae, and other microbial eukaryotes. However, recent work on annelid worms–an advanced group of eumetazoan animals–shows that they are also capable of producing C28 and C29 sterols. In this paper, we explore the evolutionary history of the 24-C sterol methyltransferase (smt) gene in animals, which is required to make C28+ sterols. We find evidence that the smt gene was vertically inherited through animals, suggesting early eumetazoans were capable of C28+ sterol synthesis. Our molecular clock of the animal smt gene demonstrates that its diversification coincides with the rise of C28 and C29 steranes in the Neoproterozoic. This study supports the hypothesis that early eumetazoans were capable of making C28+ sterols and that many animal lineages independently abandoned its biosynthesis around the end-Neoproterozoic, coinciding with the rise of abundant eukaryotic prey.
Survey of the infant male urobiome and genomic analysis of Actinotignum spp.
Authors: Reasoner Seth A. , Flores Viktor , Van Horn Gerald , Morales Grace , Peard Leslie M. , Abelson Benjamin , Manuel Carmila , Lee Jessica , Baker Bailey , Williams Timothy , Schmitz Jonathan E. , Clayton Douglass B. , Hadjifrangiskou Maria 
Published: December 2023

AbstractThe urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of enhanced culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Cesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum spp., a bacterial genus that has been associated with urinary tract infections in older male adults. Herein, we isolate and sequence 9 distinct strains of Actinotignum spp. enhancing the genomic knowledge surrounding this genus and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.
A new database of the analysis of the physiological needs in amateur female basketball during official matches
Authors: Batalla-Gavalda Abraham , Montoliu Raul , Beltrán-Garrido Jose Vicente , Corbi Francesc 
Published: December 2023

AbstractssThe PHYAFB database is a valuable resource for studying the physiological demands of female amateur basketball players during high-stress official games. It contains heart rate data from ten players aged 18 to 26, collected during ten crucial relegation phase matches, with 348,232 HR samples in CSV and Excel formats for easy access and analysis. The database includes Python source code for initial examination. The primary aim of the PHYAFB database is to provide a useful reference for other teams facing similar situations. Furthermore, the database represents a unique and valuable resource for sports scientists, coaches, and trainers seeking to comprehend the physiological demands of female basketball players during official competitions. Through the analysis of heart rate data, coaches and trainers can identify the intensity and duration of physical activity during games, enabling the development of more effective training programs. Additionally, the database can be used to compare the physiological demands placed on male and female basketball players or to investigate the impact of different game strategies on player performance.
Robotic monitoring of forests: a dataset from the EU habitat 9210* in the Tuscan Apennines (central Italy)
Authors: Pollayil Mathew J. , Angelini Franco , de Simone Leopoldo , Fanfarillo Emanuele , Fiaschi Tiberio , Maccherini Simona , Angiolini Claudia , Garabini Manolo 
Published: December 2023

AbstractEffective monitoring of habitats is crucial for their preservation. As the impact of anthropic activities on natural habitats increases, accurate and up-to-date information on the state of ecosystems has become imperative. This paper presents a new dataset collected from the forests located in the Tuscan Apennines (Italy) using the ANYmal robot. The dataset provides information regarding the structure and composition of the EU priority habitat 9210*. The dataset, which is publicly available through a Zenodo repository, includes photos, videos, and point clouds of the environment. This dataset is a valuable resource for the scientific community working in the field of forest ecology and conservation and has the potential to inform future research and conservation efforts on habitat 9210*. The collaboration between robotic engineers and plant scientists provides a unique perspective on the forest ecosystem and underscores the potential for interdisciplinary work in this field. This dataset constitutes an important contribution to the ongoing effort to monitor and conserve habitats globally, particularly in light of the challenges posed by global changes.
Chromosome-level genome assembly of an agricultural pest Zeugodacus tau (Diptera: Tephritidae)
Authors: Wang Yi-Ting , Cao Li-Jun , Chen Jin-Cui , Song Wei , Ma Wei-Hua , Yang Jing-Fang , Gao Xu-Yuan , Chen Hong-Song , Zhang Yan , Tian Zhen-Ya , Wei Shu-Jun , Zhou Zhong-Shi 
Published: December 2023

AbstractThe fruit fly Zeugodacus tau (Diptera: Tephritidae) is a major pest of melons and other cucurbits in Southeast Asia. In this study, we used Illumina, Nanopore, and Hi-C sequencing technologies to assemble a reference genome of Z. tau at the chromosomal level. The assembled genome was 421.79 Mb and consisted of six chromosomes (one X-chromosome + five autosomes). The contig N50 was 4.23 Mb. We identified 20,922 protein-coding genes, of which 17,251 (82.45%) were functionally annotated. Additionally, we found 247 rRNAs, 435 tRNAs, 67 small nuclear RNAs, and 829 small RNAs in the genome. Repetitive elements accounted for 55.30 Mb (13.15%) of the genome. This high-quality genome assembly is valuable for evolutionary and genetic studies of Z. tau and its relative species.
De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery
Authors: Bočaj Valentina , Pongrac Paula , Fischer Sina , Likar Matevž 
Published: December 2023

AbstractHyperaccumulators are a group of plant species that accumulate high concentrations of one or more metal(loid)s in their above-ground tissues without showing any signs of toxicity. Several hyperaccumulating species belong to the Brassicaceae family, among them the Cd and Zn hyperaccumulator Noccaea praecox. In this paper, we present de novo transcriptome assembled from two naturally occurring N. praecox populations growing in (i) metal-enriched soil and (ii) soil non-contaminated with metals (control site). Total RNA was extracted from the leaves of both populations. We obtained 801,935,101 reads, which were successfully assembled and annotated. The resulting assembly contains 135,323 transcripts, with 103,396 transcripts (76.4%) annotated with at least one function and encoding 53,142 putative proteins. Due to its close relationship with the hyperaccumulating model species N. cearulescens, it will be possible to derive protein functions from sequence comparisons with this species. Comparisons will highlight common and differing pathways of metal acquisition, storage, and detoxification which will allow us to expand our knowledge of these processes.
Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data
Authors: Appasamy Sri Devan , Berrisford John , Gaborova Romana , Nair Sreenath , Anyango Stephen , Grudinin Sergei , Deshpande Mandar , Armstrong David , Pidruchna Ivanna , Ellaway Joseph I. J. , Leines Grisell Díaz , Gupta Deepti , Harrus Deborah , Varadi Mihaly , Velankar Sameer 
Published: December 2023

AbstractMacromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names to over 90% of unique assemblies in the PDB and provided persistent identifiers for each assembly. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of macromolecular complexes. Furthermore, the data standardisation improves the PDB’s FAIR attributes, fostering more effective basic and translational research and scientific education.