bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics
Authors: Roberts Jackson R , Bernstein Justin M , Austin Christopher C , Hains Taylor , Mata Joshua , Kieras Michael , Pirro Stacy , Ruane Sara 
Published: May 2024

Abstract
We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.
Archives, Transitional Justice and the Spectre of Politics
Authors: Lühe Ulrike 
Published: May 2024

Abstract
This review essay considers The Prisons Memory Archive. A Case Study in Filmed Memory of Conflict edited by Jolene Mairs Dyer, Conor McCafferty and Cahal McLaughlin (2022) and Archives and Human Rights edited by Jens Boel, Perrine Canavaggio and Antonio González Quintana (2021). Both books are discussed in terms of their key themes, approaches and contributions before discussing their specific contributions to understanding the interaction of transitional, domestic and international politics and archival practice.
Combining statistical dialog management and intent recognition for enhanced response selection
Authors: Griol David , Callejas Zoraida 
Published: May 2024

Abstract
Conversational interfaces are becoming ubiquitous in an increasing number of application domains as Artificial Intelligence, Natural Language Processing and Machine Learning methods associated with the recognition, understanding and generation of natural language advance by leaps and bounds. However, designing the dialog model of these systems is still a very demanding task requiring a great deal of effort given the number of information sources to be considered related to the analysis of user utterances, interaction context, information repositories, etc. In this paper, we present a general framework for increasing the quality of the system responses by combining a statistical dialog management technique and a deep learning-based intention recognizer that allow replacing the system responses initially selected by the statistical dialog model with other presumably better candidates. This approach is portable to different task-oriented domains, a diversity of methodologies for dialog management and intention estimation techniques. We have evaluated our two-step proposal using two conversational systems, assessed several intention recognition methodologies and used the developed modules to dynamically select the system responses. The results of the evaluation show that the proposed framework achieves satisfactory results by making it possible to reduce the number of non-coherent dialog responses by replacing them by more coherent alternatives.
The application of artificial neural networks to forecast financial time series
Authors: González-Cortés D , Onieva E , Pastor I , Wu J 
Published: May 2024

Abstract
The amount of information that is produced on a daily basis in the financial markets is vast and complex; consequently, the development of systems that simplify decision-making is an essential endeavor. In this article, several intelligent systems are proposed and tested to predict the closing price of the IBEX 35 index using more than ten years of historical data and five distinct architectures for neural networks. A multi-layer perceptron was the first step, followed by a simple recurrent neural network, a gated recurrent unit network and two long-short-term memory (LSTM) networks. The results of the analyses performed on these models have demonstrated a powerful capacity for prediction. Additionally, the findings of this research point to the fact that the application of intelligent systems can simplify the decision-making process in financial markets, which is a substantial advantage. Furthermore, by comparing the predicted outcome errors between the models, the LSTM presents the lowest error with a higher computational time in the training phase. The LSTM was able to accurately forecast the closing price of the day as well as the price for the following one and two days in advance. In conclusion, the empirical results demonstrated that these models could accurately predict financial data for trading purposes and that the application of intelligent systems, such as the LSTM network, represents a promising advancement in financial technology.
A Multicountry Model of the Term Structures of Interest Rates with a GVAR
Authors: Candelon Bertrand , Moura Rubens 
Published: May 2024

Abstract
Extant multicountry affine term structure models (ATSMs) handle global financial interdependence at the cost of increasing model dimensionality. To address this challenge, we propose a novel no-arbitrage ATSM with risk factor dynamics following a global vector-autoregressive (GVAR). Compared to referenced benchmarks, the GVAR − ATSM offers a more parsimonious representation, enables a faster estimation process, produces more precise model estimates, yields more plausible term premia dynamics, and improves bond yield out-of-sample forecasting. Furthermore, our empirical findings reveal the significant impact of China’s economic stances on Latin American yield curve dynamics, underscoring its importance as a global economic player.
Bayesian inference of atomic column positions in scanning transmission electron microscopy images
Authors: Nomura Yuki , Anada Satoshi , Kobayashi Shunsuke 
Published: May 2024

Abstract
Atomic-resolution scanning transmission electron microscopy combined with two-dimensional Gaussian fitting enables the accurate and precise identification of atomic column positions within a few picometers. The measurement performance significantly depends on the signal-to-noise ratio of the atomic columns. In areas with low signal-to-noise ratios, such as near surfaces, the measurement performance was lower than that of the bulk. However, previous studies evaluated the accuracy and precision only in bulk areas, underscoring the need for a method that quantitatively evaluates the accuracy and precision of each atomic column position with various signal-to-noise ratios. This study introduced Bayesian inference to assess the accuracy and precision of determining individual atomic column positions under various signals. We applied this method to simulated and experimental images and demonstrated its effectiveness in identifying statistically significant displacements, particularly near surfaces with signal degradation. The use of vector maps and kernel density estimate plots obtained from Bayesian inference provided a probabilistic understanding of the atom displacement. Therefore, this study highlighted the potential benefits of Bayesian inference in high-resolution imaging to reveal material properties.
Relationships between functional traits and survival mediated by tree size in subtropical forests
Authors: Wang Zhen-Yu , Huang Zhi-Qun 
Published: May 2024

Abstract
An important challenge in ecology is to link functional traits to plant survival for generalizable predictions of plant demographical dynamics. However, whether root and leaf traits are consistently associated with tree survival remains uncertain because of the limited representation of root traits. Moreover, the relationships between plant traits and survival are rarely linear and are likely to vary with tree size. We analyzed demographic data from 17 901 trees of 32 subtropical tree species under 3-year-old monocultures to test whether root and leaf traits have consistent relationships with tree survival and how the relationships between traits and tree survival vary with tree diameter. We discovered that leaf and root traits have inconsistent effects on tree survival. Specifically, while specific leaf area (SLA; an acquisition strategy) showed a marginally significant negative impact on survival, root diameter (RD; a conservative trait within the one-dimensional root economic spectrum) also demonstrated a significant negative effect on survival. Furthermore, we found size-dependent relationships between traits and tree survival. The effect of SLA, leaf phosphorus concentration and specific root length, on survival shifted from negative to positive with increasing tree size. However, species with high leaf thickness and RD were positively linked to survival only for small trees. The results highlight that to accurately predict the relationships between traits and tree survival, it is essential to consider both above- and belowground traits, as well as the size-dependent relationships between traits and tree survival.
A Case of Non-Seminomatous Germ Cell Tumor Complicated by Tumor Thrombus in an Active Duty Soldier
Authors: Grossmann Matthew , Kou Chung-Ting J , Vergonet Breanne , Soderstrom Matthew , Rendo Matthew J , Lee Lauren E 
Published: May 2024

ABSTRACT
Testicular malignancies commonly affect adolescent and young adult males. Although they tend to respond well to cisplatin-based chemotherapy with excellent overall survival, complications such as inferior vena cava tumor thrombus are rare and can be associated with high morbidity and mortality. We present a case of tumor thrombus in a 21-year-old active duty male with a newly diagnosed stage IIIB non-seminomatous germ cell tumor presenting with extensive left lower extremity swelling. Ultrasound with Doppler was notable for significant thrombus of the left common femoral, femoral, and popliteal vein. Computed tomography imaging revealed extensive thrombus of the inferior vena cava, left iliac veins, and left gonadal vein with sparing of the left renal vein. Endovascular thrombectomy was performed with pathologic analysis confirming the presence of malignant cells consistent with tumor thrombus. The patient continued subsequent non-seminomatous germ cell tumor treatment without complications.
Binary mergers in strong gravity background of Kerr black hole
Authors: Camilloni Filippo , Harmark Troels , Grignani Gianluca , Orselli Marta , Pica Daniele 
Published: May 2024

ABSTRACT
Binary-black-hole (BBH) mergers can take place close to a supermassive black hole (SMBH) while being in a bound orbit around the SMBH. In this paper, we study such bound triple systems and show that including the strong gravity effects of describing the SMBH with a Kerr metric can significantly modify the dynamics, as compared to a Newtonian point particle description of the SMBH. We extract the dynamics of the system, using a quadrupole approximation to the tidal forces due to the SMBH. We exhibit how the gyroscope precession is built into this dynamics, and find the secular Hamiltonian by both averaging over the inner and outer orbits, the latter being the orbit of the BBH around the SMBH. We study the long-time-scale dynamics, including the periastron precession and gravitational wave (GW) radiation reaction of the binary system, finding that the strong gravity effects of the SMBH can enhance the von Zeipel–Lidov–Kozai mechanism, resulting in more cycles, higher maximum eccentricity, and thereby a shorter merger time, particularly when the binary is close to, or at, the innermost stable orbit of the SMBH. We end with an analysis of the peak frequency of the GW emission from the binary system, highlighting possible observable signatures in the Einstein Telescope and Laser Interferometer Space Antenna frequency bands.
Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress
Authors: Horvath Attila , Janapala Yoshika , Woodward Katrina , Mahmud Shafi , Cleynen Alice , Gardiner Elizabeth E , Hannan Ross D , Eyras Eduardo , Preiss Thomas , Shirokikh Nikolay E 
Published: May 2024

Abstract
Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach to the mRNA in series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on mRNA and identify them using enhanced translation complex profile sequencing (eTCP-seq) based on rapid in vivo crosslinking. We detect long disome footprints outside regions of non-random elongation stalls and show these are linked to translation initiation and protein biosynthesis rates. We subject footprints of disomes and other translation complexes to artificial intelligence (AI) analysis and construct a new, accurate and self-normalized measure of translation, termed stochastic translation efficiency (STE). We then apply STE to investigate rapid changes to mRNA translation in yeast undergoing glucose depletion. Importantly, we show that, well beyond tagging elongation stalls, footprints of co-localized ribosomes provide rich insight into translational mechanisms, polysome dynamics and topology. STE AI ranks cellular mRNAs by absolute translation rates under given conditions, can assist in identifying its control elements and will facilitate the development of next-generation synthetic biology designs and mRNA-based therapeutics.
Typology of employers offering line manager training for mental health
Authors: Blake H , Hassard J , Dulal-Arthur T , Wishart M , Roper S , Bourke J , Belt V , Bartle C , Pahl N , Leka S , Thomson L 
Published: May 2024

Abstract

Background
Mental ill health has a high economic impact on society and employers. National and international policy advocates line manager (LM) training in mental health as a key intervention, but little is known about employer training provisions.

Aims
To explore the prevalence and characteristics of organizations that offer LM training in mental health.

Methods
Secondary analysis of existing longitudinal anonymised organizational-level survey data derived from computer-assisted telephone interview surveys collected in four waves (2020:1900 firms, 2021:1551, 2022:1904, 2023:1902) in England, before, during and after a global pandemic.

Results
The proportion of organizations offering LM training in mental health increased pre- to post-pandemic (2020:50%, 2023:59%) but 41% do not currently provide it. Logistic regression confirmed that LM training is more likely to be offered by large-sized enterprises, organizations with a larger proportion of employees who are younger (aged 25–49), female, disabled and from ethnic minority communities. Sector patterns were inconsistent, but in 2023, organizations from the ‘Hospitality’ and ‘Business Services’ sectors were more likely to provide LM training than other sectors.

Conclusions
Continued efforts are needed to increase the proportion of employers offering LM training in mental health, particularly small- to medium-sized enterprises, and organizations with predominantly male, White and/or older workforces.
Fertility and pregnancy complications in female orthopaedic surgeons
Authors: Frenkel Rutenberg T , Daglan E , Shadmi N , Iordache S D , Kosashvili Y , Eylon S 
Published: May 2024

Abstract

Background
While the number of female medical graduates continues to increase, only a few pursue an orthopaedic career. This is related to challenges regarding pregnancy and the peripartum period during orthopaedic training.

Aims
To evaluate fertility, pregnancy-related complications and attitudes towards female orthopaedic surgeons in Israel.

Methods
An electronic anonymous 34-question electronic web-based survey was sent to all Israeli female orthopaedic surgeons. Participation was voluntary. Questions were formulated to determine demographics, obstetrics medical history, teratogenic exposure, medical leave and breastfeeding parameters along with attitude towards pregnancy.

Results
Twenty-six orthopaedic surgeons complied with the survey, 68% of all registered female orthopaedic surgeons. Participants age was 39.5 (±8.8). The average number of children for a female orthopaedic surgeon was 2.2 (±1.4), with an average of 1.3 (±1.1) deliveries during residency. The average age for a first child was 31.1 (±3.7) years. Four surgeons required fertility treatments and six had abortions. Thirty-eight per cent experienced pregnancy complications. Most surgeons were exposed to radiation and bone cement during pregnancy. The average duration of maternity leave was 19.4 (±9.9) weeks and return to work was associated with cessation of breastfeeding. Seventy-six per cent of surgeons felt that pregnancy had negatively influenced their training, and 12% reported negative attitudes from colleagues and supervisors.

Conclusions
Orthopaedic surgeons in Israel experience a delay in childbirth and higher rates of pregnancy complications. Most feel that their training is harmed by pregnancy. Programme directors should design a personalized support programme for female surgeons during pregnancy and the peripartum period.
Geopolitics and global economic governance
Authors: Hurrell Andrew 
Published: May 2024

Abstract
This article analyses the relationship between geopolitics and global economic governance from an international relations perspective, laying stress on the long-term changes that have taken place in the character and dynamics of modern global international society. First, it unpacks what is involved in talk about the ‘the return of geopolitics’, arguing that the international political system needs to be understood in its own right and according to its distinctive logics and dynamics, separate from those of modern capitalism. The second section shifts the focus from the modern international to the modern global, arguing that the ‘we’ now involved in both geopolitics and global economic governance has changed in fundamental ways and that the diffusion of power and agency and the revolt against Western dominance are far broader than the rise of China. The final section looks at future pathways: the unlikely possibility of the restoration of US hegemony; the case for the primacy of political order over global governance and for refocusing attention on the primary or foundational institutions on which all more elaborate forms of global governance must depend; and the identification of some of the most important institutional pinch-points where geopolitics and global economic governance intersect and need to be managed, including sanctions, security-related trade measures, and industrial strategy.
The microRNA408–plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells
Authors: Yang Yanzhi , Xu Lei , Hao Chen , Wan Miaomiao , Tao Yihan , Zhuang Yan , Su Yanning , Li Lei 
Published: May 2024

Abstract
The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408–PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408–PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops.
The OsMOB1A–OsSTK38 kinase complex phosphorylates CYCLIN C, controlling grain size and weight in rice
Authors: Chen Guoxin , Gao Jiabei , Wu Suting , Chang Yuan , Chen Zhenhua , Sun Jing , Zhang Liying , Wu Jinxia , Sun Xuehui , Quick William Paul , Cui Xuean , Zhang Zhiguo , Lu Tiegang 
Published: May 2024

Abstract
Grain size and weight are crucial yield-related traits in rice (Oryza sativa). Although certain key genes associated with rice grain size and weight have been successfully cloned, the molecular mechanisms underlying grain size and weight regulation remain elusive. Here, we identified a molecular pathway regulating grain size and weight in rice involving the MPS ONE BINDER KINASE ACTIVATOR-LIKE 1A–SERINE/THREONINE-PROTEIN KINASE 38–CYCLIN C (OsMOB1A–OsSTK38–OsCycC) module. OsSTK38 is a nuclear Dbf2-related kinase that positively regulates grain size and weight by coordinating cell proliferation and expansion in the spikelet hull. OsMOB1A interacts with and enhances the autophosphorylation of OsSTK38. Specifically, the critical role of the OsSTK38 S322 site in its kinase activity is highlighted. Furthermore, OsCycC, a component of the Mediator complex, was identified as a substrate of OsSTK38, with enhancement by OsMOB1A. Notably, OsSTK38 phosphorylates the T33 site of OsCycC. The phosphorylation of OsCycC by OsSTK38 influenced its interaction with the transcription factor KNOTTED-LIKE HOMEOBOX OF ARABIDOPSIS THALIANA 7 (OsKNAT7). Genetic analysis confirmed that OsMOB1A, OsSTK38, and OsCycC function in a common pathway to regulate grain size and weight. Taken together, our findings revealed a connection between the Hippo signaling pathway and the cyclin-dependent kinase module in eukaryotes. Moreover, they provide insights into the molecular mechanisms linked to yield-related traits and propose innovative breeding strategies for high-yielding varieties.