bluuebunny/crossref_metadata_2025_split huggingface dataset:
Out of and in East Asia: phylogeny, biogeography and diversification of Thalictroideae (Ranunculaceae) in the Northern Hemisphere
Authors: Ling Yuan-Yuan , Peng Huan-Wen , Lian Lian , Erst Andrey S , Xiang Kun-Li , Wang Wei 
Published: August 2024

Abstract

Background and Aims
Understanding the biogeographical patterns and processes underlying the distribution of diversity within the Northern Hemisphere has fascinated botanists and biogeographers for over a century. However, as a well-known centre of species diversity in the Northern Hemisphere, whether East Asia acted as a source and/or a sink of plant diversity of the Northern Hemisphere remains unclear. Here, we used Thalictroideae, a subfamily widely distributed in the Northern Hemisphere with the majority of species in East Asia, to investigate the role of East Asia in shaping the biogeographical patterns of the Northern Hemisphere and to test whether East Asia acted as a museum or a cradle for herbaceous taxa.

Methods
Based on six plastid and one nuclear DNA regions, we generated the most comprehensive phylogeny for Thalictroideae, including 217 taxa (~66 % species) from all ten of the currently recognized genera. Within this phylogenetic framework, we then estimated divergence times, ancestral ranges and diversification rates.

Key Results
The monophyletic Thalictroideae contains three major clades. All genera with more than one species are strongly supported as monophyletic except for Isopyrum, which is nested in Enemion. The most recent common ancestor of Thalictroideae occurred in East Asia in the late Eocene (~36 Mya). From the Miocene onwards, ≥46 dispersal events were inferred to be responsible for the current distribution of this subfamily. East Asian Thalictroideae lineages experienced a rapid accumulation at ~10 Mya.

Conclusions
The biogeographical patterns of Thalictroideae support the ‘out of and in East Asia’ hypothesis, i.e. East Asia is both a source and a sink of biodiversity of the Northern Hemisphere. The global cooling after the middle Miocene Climatic Optimum, combined with the exposed land bridges owing to sea-level decline, might jointly have caused the bidirectional plant exchanges between East Asia and other Northern Hemisphere regions. East Asia serves as evolutionary museums and cradles for the diversity of Thalictroideae and probably for other herbaceous lineages.
Centromere drive may propel the evolution of chromosome and genome size in plants
Authors: Plačková Klára , Bureš Petr , Lysak Martin A , Zedek František 
Published: August 2024

Abstract

Background
Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages.

Methods
We analysed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein–Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades.

Results
Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades.

Conclusions
Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potentially also influencing the process of post-polyploid diploidization. We propose a model which in a single framework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution.
Towards automated animal density estimation with acoustic spatial capture-recapture
Authors: Wang Yuheng , Ye Juan , Li Xiaohui , Borchers David L 
Published: August 2024

ABSTRACT
Passive acoustic monitoring can be an effective way of monitoring wildlife populations that are acoustically active but difficult to survey visually, but identifying target species calls in recordings is non-trivial. Machine learning (ML) techniques can do detection quickly but may miss calls and produce false positives, i.e., misidentify calls from other sources as being from the target species. While abundance estimation methods can address the former issue effectively, methods to deal with false positives are under-investigated. We propose an acoustic spatial capture-recapture (ASCR) method that deals with false positives by treating species identity as a latent variable. Individual-level outputs from ML techniques are treated as random variables whose distributions depend on the latent identity. This gives rise to a mixture model likelihood that we maximize to estimate call density. We compare our method to existing methods by applying it to an ASCR survey of frogs and simulated acoustic surveys of gibbons based on real gibbon acoustic data. Estimates from our method are closer to ASCR applied to the dataset without false positives than those from a widely used false positive “correction factor” method. Simulations show our method to have bias close to zero and accurate coverage probabilities and to perform substantially better than ASCR without accounting for false positives.
Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach
Authors: Sarol M Janina , Hong Gibong , Guerra Evan , Kilicoglu Halil 
Published: August 2024

Abstract
Biomedical relation extraction from scientific publications is a key task in biomedical natural language processing (NLP) and can facilitate the creation of large knowledge bases, enable more efficient knowledge discovery, and accelerate evidence synthesis. In this paper, building upon our previous effort in the BioCreative VIII BioRED Track, we propose an enhanced end-to-end pipeline approach for biomedical relation extraction (RE) and novelty detection (ND) that effectively leverages existing datasets and integrates state-of-the-art deep learning methods. Our pipeline consists of four tasks performed sequentially: named entity recognition (NER), entity linking (EL), RE, and ND. We trained models using the BioRED benchmark corpus that was the basis of the shared task. We explored several methods for each task and combinations thereof: for NER, we compared a BERT-based sequence labeling model that uses the BIO scheme with a span classification model. For EL, we trained a convolutional neural network model for diseases and chemicals and used an existing tool, PubTator 3.0, for mapping other entity types. For RE and ND, we adapted the BERT-based, sentence-bound PURE model to bidirectional and document-level extraction. We also performed extensive hyperparameter tuning to improve model performance. We obtained our best performance using BERT-based models for NER, RE, and ND, and the hybrid approach for EL. Our enhanced and optimized pipeline showed substantial improvement compared to our shared task submission, NER: 93.53 (+3.09), EL: 83.87 (+9.73), RE: 46.18 (+15.67), and ND: 38.86 (+14.9). While the performances of the NER and EL models are reasonably high, RE and ND tasks remain challenging at the document level. Further enhancements to the dataset could enable more accurate and useful models for practical use. We provide our models and code at https://github.com/janinaj/e2eBioMedRE/.
Database URL: https://github.com/janinaj/e2eBioMedRE/
MACSFeD—a database of mosquito acoustic communication and swarming features
Authors: Loh YuMin M , Su Matthew P , Haruni Kayla G , Kamikouchi Azusa 
Published: August 2024

Abstract
Acoustic communication plays an important role during the courtship of many mosquito species. Male mosquitoes show strong attraction to female wing beat frequencies, mediated via spectral matching between female wing beat frequency and male ear mechanical tuning frequency. Such acoustic communication typically occurs within swarms, male-dominated aggregations with species-specific properties. Despite hundreds of relevant publications being available, the lack of a central platform hosting all associated data hinders research efforts and limits cross-species comparisons. Here, we introduce MACSFeD (Mosquito Acoustic Communication and Swarming Features Database), an interactive platform for the exploration of our comprehensive database containing 251 unique reports focusing on different aspects of mosquito acoustic communication, including hearing function, wing beat frequency and phonotaxis, as well as male swarming parameters. MACSFeD serves as an easily accessible, efficient, and robust data visualization tool for mosquito acoustic communication research. We envision that further in-depth studies could arise following the use of this new platform.
Database URL: https://minmatt.shinyapps.io/MACSFeD/
Homeowners’ financial vulnerability over the house price cycle
Authors: Tarne Ruben 
Published: August 2024

Abstract
This paper investigates the financial vulnerability dynamics of indebted homeowners over the housing cycle using an agent-based housing market model, calibrated with UK microdata. The findings suggest that financial vulnerability is primarily driven by house purchases and dissaving due to a wealth effect on consumption. The former is more important during house price upswings, while the latter becomes significant at high price levels. Additionally, current vulnerability is path-dependent on previous purchases at high prices, as these purchases, due to a wealth effect, result in temporarily elevated consumption and consequently reduced financial buffers.
The Hox-based positional memory in muscle stem cells
Authors: Okino Ryosuke , Goda Yuki , Ono Yusuke 
Published: August 2024

Abstract
The skeletal muscle is a contractile tissue distributed throughout the body with various anatomical sizes, shapes and functions. In pathological conditions, such as muscular dystrophy, age-related sarcopenia and cancer cachexia, skeletal muscles are not uniformly affected throughout the body. This region-specific vulnerability cannot be fully explained by known physiological classifications, including muscle fiber types. Accumulating evidence indicates that the expression patterns of topographic homeobox (Hox) genes provide a molecular signature of positional memory, reflecting the anatomical locations and embryonic history of muscles and their associated muscle stem cells in adult mice and humans. Hox-based positional memory is not merely a remnant of embryonic development but is expected to be an intrinsic determinant controlling muscle function because recent studies have shown that aberrant Hox genes affect muscle stem cells. In this review, we discuss the concept of Hox-based positional memory, which may offer a new perspective on the region-specific pathophysiology of muscle disorders.
The Utility of Second-Look US to Evaluate Abnormal Molecular Breast Imaging Findings: A Retrospective Study
Authors: Teichgraeber Davis C , Bassett Roland L , Whitman Gary J 
Published: August 2024

Abstract

Objective
The purpose of this study was to evaluate the utility of US for identifying and characterizing lesions detected on molecular breast imaging (MBI).

Methods
A retrospective single-institution review was performed of patients with MBI studies with subsequent US for abnormal MBI findings between January 1, 2015, and September 30, 2021. Medical records, imaging, and histopathology were reviewed. The reference standard was histopathology and/or imaging follow-up. Associations among MBI findings, the presence of an US correlate, and histopathology were evaluated by Fisher exact tests.

Results
The 32 lesions detected on MBI in 25 patients were evaluated by US, and 19 lesions had an US correlate (19/32, 59%). Mass uptake was more likely to have an US correlate (11/13, 85%; P = .02) than nonmass uptake (7/19, 37%), and mass uptake was more likely to be malignant (5/13, 38%; P = .01). Of the 13 lesions without an US correlate, 5 were evaluated and subsequently biopsied by MRI (2 high-risk lesions and 3 benign lesions). Follow-up MBIs demonstrated stability/resolution for 5 lesions in 4 patients at 6 months or longer. Three patients had no further imaging.

Conclusion
Mass lesions identified on MBI were more likely to have an US correlate and were more likely to be malignant than nonmass lesions.
Pulmonary metastases from pancreatic cancer have different clinico-radiological features compared with those from colorectal cancer
Authors: Kawaguchi Takeshi , Takeda Maiko , Yoshikawa Daiki , Taiji Ryosuke , Yamada Aya , Miyata Ryo , Hamaji Masatsugu , Hosono Mitsuharu , Sawabata Noriyoshi 
Published: August 2024

Abstract

Background
Although pulmonary metastasectomy is a commonly-performed procedure, data are lacking on the feasibility and oncological efficacy of removal of pulmonary metastases from pancreatic cancer. In this study, we retrospectively compared features of pulmonary metastases from pancreatic cancer versus colorectal cancer (CRC, patients with CRC being common candidates for pulmonary metastasectomy) and outcomes of removing such metastases, with our aim being to identify specific features of the former.

Methods
Data on removal of 182 pulmonary metastases (29 from pancreatic and 153 from CRC) performed from January 2013 to April 2024 were included in this analysis. Radio-pathological findings were compared between these groups. The study cohort comprised 139 pulmonary metastasectomies in 119 patients (24 with pancreatic cancer and 95 with CRC) in whom R0 resection was achieved and follow-up data were available.

Results
Atypical radiological findings of pulmonary metastases, including polygonal-shape (P &lt; 0.001), spiculae (P &lt; 0.001), air bronchogram (P = 0.012), peripheral ground-glass opacities (P &lt; 0.001), and pleural tags (P &lt; 0.001) were present more frequently in metastases from pancreatic cancer than from CRC. Furthermore, pleural lavage cytology was more frequently positive in pulmonary metastases from pancreatic cancer than in those from CRC (P &lt; 0.001). Disease-free survival was significantly shorter after the removal of metastases from pancreatic than from CRC (P &lt; 0.001).

Conclusions
Some pulmonary metastases from pancreatic cancer have atypical radiological features. Surgical interventions for these may enable diagnosis. The prognosis is significantly poorer after removing metastases from pancreatic cancer than from CRC. The therapeutic significance of our findings requires further investigation.
Clear cell sarcoma in Japan: an analysis of the population-based cancer registry in Japan
Authors: Takemori Toshiyuki , Ogura Koichi , Morizane Chigusa , Satake Tomoyuki , Iwata Shintaro , Toda Yu , Muramatsu Shudai , Kondo Hiroya , Kobayashi Eisuke , Higashi Takahiro , Kawai Akira 
Published: August 2024

Abstract

Background
Clear cell sarcoma is rare, so no reports have previously characterized its national profiles. We examined the nationwide epidemiology and clinical outcomes of patients with clear cell sarcoma based on the National Cancer Registry in Japan.

Methods
Overall, 23 522 patients with soft tissue sarcoma—entered in the National Cancer Registry in 2016–2019 using the International Classification of Diseases for Oncology, Third Edition cancer topography and morphology codes—were enrolled in either the clear cell or the non-clear cell sarcoma group. Data extracted included: demographics (sex and age), tumor details (reason for diagnosis, tumor location, histology and stage), hospital volume and facility type, treatment and prognosis for each patient.

Results
Of 23 522 soft tissue sarcoma patients, 122 were enrolled in the clear cell sarcoma group and 23 400 in the non-clear cell sarcoma group. The incidence of clear cell sarcoma was 0.52% of all soft tissue sarcoma, with an age-adjusted incidence of 0.024/100 000/year. The age at diagnosis was significantly younger, and more tumors were at the localized stage in the clear cell than the non-clear cell sarcoma group. In addition, the overall survival in the clear cell group was worse than in the non-clear cell group (P &lt; 0.001). Of 122 patients with clear cell sarcoma, the localized stage, surgical treatment and treatment without chemotherapy were associated with better overall survival in the univariate analyses.

Conclusions
The present study is the first to have clarified the epidemiology, clinical features, treatment, prognosis and significant factors affecting the prognosis of patients with clear cell sarcoma in Japan.
Partisan bias in securities enforcement
Authors: Steel Reilly S 
Published: August 2024

Abstract
In this article, I present a partisan theory of agency enforcement and empirically investigate the possibility of partisan bias in the enforcement of the federal securities laws. Leveraging plausibly exogenous shocks to partisan control of the U.S. Securities and Exchange Commission (SEC), I find evidence that a firm’s partisan alignment with the SEC substantially reduces the likelihood of enforcement. For a firm that is ex ante equally likely to be targeted for enforcement or not, my estimates indicate that a typical increase in partisan alignment following a change in party control of the SEC reduces the likelihood of enforcement by over 19%. Partisan alignment also appears to reduce aggregate monetary sanctions, though these estimates are less certain. By contrast, I find little evidence of partisan bias in the initial opening of investigations. These findings suggest there may be meaningful partisan bias in SEC enforcement and have important implications for democratic governance. (JEL D73, K22, K23, K41, K42, P00)
Sampling targets to assess occupational health in occupational health and safety management system audits: a mixed-methods research in Japan
Authors: Inoue Shunsuke , Kajiki Shigeyuki , Shimoda Hayato , Fujita Amane , Mori Koji 
Published: August 2024

Abstract
Background: Occupational health and safety management systems (OHSMS) are the foundation of occupational health and safety activities within an organization. An important element of these systems is audits. However, OHSMS auditors often lack confidence in conducting occupational health audits compared with their proficiency in conducting occupational safety audits. For occupational health to be effectively managed by OHSMS, the sampling competence of auditors engaged in third-party audits should be improved. Therefore, we conducted this study to identify appropriate sampling targets for occupational health related to International Organization for Standardization (ISO) 45001.
Methods: We adopted a mixed methods approach to identify appropriate sampling targets. This involved conducting focus group discussions with experts in occupational health and performing systematic text condensation analysis. The validity of our findings was further reinforced through confirmation by external auditors who specialize in ISO 45001.
Results: In the qualitative phase, 6 occupational health sampling targets were identified, and of these, 5 were subsequently validated in the quantitative phase: (1) Health issues, legal requirements, and occupational health goals identified by the organization; (2) Occupational health risk assessment and control processes; (3) Processes related to occupational health and documented information showing the results of efforts; (4) Organizational roles and functions of occupational health professionals and opportunities for their professional development; and (5) Processes to ensure commitment to occupational health issues and objectives.
Conclusion: To ensure effective and comprehensive occupational health audits, auditors should review these targets. This study will enhance the competence of auditors by identifying appropriate occupational health sampling targets.
Revocability of offer
Authors: Schwenzer Ingeborg , Schroeter Ulrich G 
Published: August 2024

Abstract
This chapter describes Article 16. Article 16 deals with the question whether and under which prerequisites the offeror can revoke its offer after it has already reached the offeree. The provision thereby supplements Article 15(2)’s rule on the ‘withdrawal’ of offers prior to their receipt by the offeree. As in case of the withdrawal of an offer (Article 15(2)), any rule on an offer’s revocation after its receipt has to balance the interest of the offeree of being able to accept a profitable offer and thereby create a contract under the offer’s terms with the offeror’s interest not to remain bound to an offer that, as the offeror has only noticed after its dispatch, is disadvantageous to them. The decisive difference from the constellations addressed in Article 15(2) lies in the opposing interest of the offeree to be able to consider the offer and to have a reasonable time to do so, because this interest obviously carries more weight after the offeree has received the offer. The problem of whether an offer is binding and whether it may be revoked that is the subject of Article 16 was one of the most difficult issues when unifying the law on contract formation, because it was necessary to bridge the gap between dramatically different preconceptions inspired by domestic laws.
Termination of offer by rejection
Authors: Schwenzer Ingeborg , Schroeter Ulrich G 
Published: August 2024

Abstract
This chapter analyses Article 17. The compact wording of Article 17 contains three statements, all of which are of a primarily clarifying nature. It appears self-understood that an offer is being terminated through its rejection by the offeree; Article 17 insofar protects the reasonable expectations of the offeror. In contrast, it is not similarly obvious from a comparative law perspective that the termination only occurs once the rejection reaches the offeror, and not already when it is being dispatched; the point in time referred to in Article 16(1) that was modelled on the Common Law’s ‘mailbox rule’ accordingly does not apply in the present context. Finally, it would not necessarily be clear without Article 17 that a rejection by the offeree also terminates offers that the offeror has designed as irrevocable.
Effect of fundamental breach on passing of risk
Authors: Schwenzer Ingeborg , Schroeter Ulrich G 
Published: August 2024

Abstract
This chapter tackles Article 70, which addresses the situation where the seller has committed a fundamental breach of contract and the goods – for reasons unrelated to that breach – are lost or damaged. In such a case, the risk reverts to the seller and the buyer may continue to exercise its remedies for breach of contract. In other words, the provision prevents the breaching seller from being rescued by coincidental loss of or damage to the goods. The chapter discusses the scope of Article 70 by looking at the fundamental and non-fundamental breach of contract. It also discusses the re-transfer of risk.