bluuebunny/crossref_metadata_2025_split huggingface dataset:
[Ti]-YNU-5: a large-pore titanosilicate as an efficient catalyst for selective oxidations
Authors: Zhang Shengxiang , Asanuma Kai , Inagaki Satoshi , Kubota Yoshihiro 
Published: July 2024

Abstract
A novel large-pore titanosilicate with YFI topology, [Ti]-YNU-5, was prepared via post-synthetic isomorphous substitution of Ti for Al in the YFI framework. It exhibited the enhanced catalytic performances in the liquid-phase epoxidation of bulky alkenes and the oxidation of phenol with hydrogen peroxide. Hydrophobicity was found to be an important factor.
Electrochemical synthesis of heterocyclic compounds via carbon–heteroatom bond formation: direct and indirect electrolysis
Authors: Okumura Yasuyuki , Sato Eisuke , Mitsudo Koichi , Suga Seiji 
Published: July 2024

Abstract
Electrochemical organic synthesis has attracted attention as an environmentally friendly method for constructing heterocyclic compounds via carbon–heteroatom bond formation. Herein, we describe the representative examples of electrochemical reactions to produce heterocycles and discuss them according to whether they involve direct or indirect electrolysis.
Geopolitical Kingmakers: South Korea and the Philippines as Linchpins amid the China–US Competition
Authors: Cook Richard J , Ohle Maximilian , Han Zhaoying 
Published: July 2024

Abstract
South Korea and the Philippines hold pivotal geopolitical positions amidst escalating tensions between the USA and China. Both Seoul and Manila find themselves ensnared in the expanding rivalry between these great powers, subjecting them to numerous strategic challenges amid the prevailing regional status quo of instability. Despite their efforts to maintain a delicate balance, often characterized as hedging behavior, the space available for such maneuvering is diminishing, compelling them toward perilous geopolitical alignments. Therefore, this paper seeks to address the following questions: How does the shrinking space to hedge influence the alignment strategies of South Korea and the Philippines? How do their alignment choices impact the geopolitical dynamics of the China–US strategic competition? It argues that as this space contracts, they possess the capability to significantly influence the regional balance of power through their alignment, which we frame as the kingmaker’s role and the power of the weak paradox. Seoul, navigating the complex dynamics of the Korean Peninsula, must carefully weigh its commitments to both Washington and Beijing, particularly in light of ongoing developments with North Korea. Meanwhile, Manila, in the aftermath of the Duterte administration’s alignment oscillations, has sought to establish a clearer strategic direction largely influenced by tensions in the South China Sea. Both are now increasingly tacking hard toward Washington for security assurances and have acknowledged economic security anxieties concerning their links with Beijing. Furthermore, they are placing greater emphasis on upholding the rules-based international order amid growing global uncertainties.
Tensions and duality in developing a circular fashion economy in Kenya
Authors: England Lauren , Ikpe Eka , Comunian Roberta 
Published: July 2024

Abstract
This paper critically considers the circular economy in the Kenyan fashion industry context, addressing structural and geographical hierarchies and inequalities in the conceptualisation of the circular economy and its associated practices in fashion. From the perspective of fashion designers, it highlights specific geopolitical and geo-economic tensions between local cultural foundations of ‘circular’ fashion and the impact of global market forces. Focusing on dynamics relating to second-hand clothing imports and Export Processing Zones (EPZs) for garment manufacturing, we present findings from qualitative research with Kenyan fashion designers (2019–2023) demonstrating how they both inhibit circular economy development in fashion and provide opportunities for innovations through creative adaptation practices.
Time and place affect the acoustic structure of frog advertisement calls
Authors: James Logan S , Ryan Michael J 
Published: July 2024

Abstract
Acoustic communication signals are important for species recognition and mate attraction across numerous taxa. For instance, most of the thousands of species of frogs have a species-specific advertisement call that females use to localize and discriminate among potential mates. Thus, the acoustic structure of the advertisement call is critical for reproductive success. The acoustic structure of calls will generally diverge over evolutionary time and can be influenced by the calls of sympatric species. While many studies have shown the influence of geography on contemporary call variation in populations of frogs, no study has compared the acoustic structure of frog calls across many species to ask whether we can detect an influence of divergence time and overall geographic overlap on the differences in acoustic structure of species-typical calls that we observe now. To this end, we compared acoustic features of the calls of 225 species of frogs within 4 families. Furthermore, we used a behavioral assay from 1 species of frog to determine which acoustic features to prioritize in our large-scale analyses. We found evidence that both phylogeny (time) and geography (place) relate to advertisement call acoustics albeit with large variation in these relationships across the 4 families in the analysis. Overall, these results suggest that, despite the many ecological and evolutionary forces that influence call structure, the broad forces of time and place can shape aspects of advertisement call acoustics.
Improving biomedical entity linking for complex entity mentions with LLM-based text simplification
Authors: Borchert Florian , Llorca Ignacio , Schapranow Matthieu-P 
Published: July 2024

Abstract
Large amounts of important medical information are captured in free-text documents in biomedical research and within healthcare systems, which can be made accessible through natural language processing (NLP). A key component in most biomedical NLP pipelines is entity linking, i.e. grounding textual mentions of named entities to a reference of medical concepts, usually derived from a terminology system, such as the Systematized Nomenclature of Medicine Clinical Terms. However, complex entity mentions, spanning multiple tokens, are notoriously hard to normalize due to the difficulty of finding appropriate candidate concepts. In this work, we propose an approach to preprocess such mentions for candidate generation, building upon recent advances in text simplification with generative large language models. We evaluate the feasibility of our method in the context of the entity linking track of the BioCreative VIII SympTEMIST shared task. We find that instructing the latest Generative Pre-trained Transformer model with a few-shot prompt for text simplification results in mention spans that are easier to normalize. Thus, we can improve recall during candidate generation by 2.9 percentage points compared to our baseline system, which achieved the best score in the original shared task evaluation. Furthermore, we show that this improvement in recall can be fully translated into top-1 accuracy through careful initialization of a subsequent reranking model. Our best system achieves an accuracy of 63.6% on the SympTEMIST test set. The proposed approach has been integrated into the open-source xMEN toolkit, which is available online via https://github.com/hpi-dhc/xmen.
Can temporomandibular joint osteoarthritis be diagnosed on MRI proton density-weighted images with diagnostic support from the latest deep learning classification models?
Authors: Nozawa Michihito , Fukuda Motoki , Kotaki Shinya , Araragi Marino , Akiyama Hironori , Ariji Yoshiko 
Published: July 2024

Abstract

Objectives
This study aimed to clarify the performance of MRI-based deep learning classification models in diagnosing temporomandibular joint osteoarthritis (TMJ-OA) and to compare the developed diagnostic assistance with human observers.

Methods
The subjects were 118 patients who underwent MRI for examination of TMJ disorders. One hundred condyles with TMJ-OA and 100 condyles without TMJ-OA were enrolled. Deep learning was performed with 4 networks (ResNet18, EfficientNet b4, Inception v3, and GoogLeNet) using 5-fold cross validation. Receiver operating characteristics (ROC) curves were drawn for each model and diagnostic metrics were determined. The performances of the 4 network models were compared using Kruskal-Wallis tests and post hoc Scheffe tests, and ROCs between the best model and human were compared using chi-square tests, with P &lt; .05 considered significant.

Results
ResNet18 had areas under the curves (AUCs) of 0.91-0.93 and accuracy of 0.85-0.88, which were the highest among the 4 networks. There were significant differences in AUC and accuracy between ResNet and GoogLeNet (P = .0264 and.0418, respectively). The kappa values of the models were large, 0.95 for ResNet and 0.93 for EfficientNet. The experts achieved similar AUC and accuracy values to the ResNet metrics, 0.94 and 0.85, and 0.84 and 0.84, respectively, but with a lower kappa of 0.67. Those of the dental residents showed lower values. There were significant differences in AUCs between ResNet and residents (P &lt; .0001) and between experts and residents (P &lt; .0001).

Conclusions
Using a deep learning model, high performance was confirmed for MRI diagnosis of TMJ-OA.
Close relationship with the glandular capsule: a highly sensitive diagnostic indicator of major salivary gland metastatic malignancies in ultrasound
Authors: Su Huan-Zhong , Lin Yan-Ting , Huang Shu-Jing , Su Yu-Qing , Liu Qi-Xia , Bai Dong-Yu , Hong Long-Cheng , Zhang Xiao-Dong , Su Yi-Ming 
Published: July 2024

Abstract

Objectives
To investigate the ultrasound (US) characteristics of metastatic malignancies (MM) in the major salivary glands and to assess the diagnostic value of the close relationship with the glandular capsule in identifying MM.

Methods
From January 2016 and April 2022, 122 patients with major salivary gland malignancies, including 20 patients with MM and 102 patients with primary malignancies (PM) confirmed by histopathological examination, were enrolled in this study. Their clinicopathologic and US data were recorded and analysed. The diagnostic performance of the close relationship with the glandular capsule for differentiating MM from PM was analysed.

Results
The mean age of MM were older than that of PM (59.50 ± 14.57 vs. 49.96 ± 15.73, P = .013). Compared with PM patients, MM were associated with a higher prevalence of local pain symptoms (P = .007) and abnormal facial nerve function (P &lt; .001). MM were also more frequently characterized by unclear borders, rough margins, irregular shapes, heterogeneous internal echos, absence of cystic areas, presence of calcifications, close relationship with the glandular capsule, and US-reported positive cervical lymph nodes (all P &lt; .05). The close relationship with the glandular capsule showed to be a good indicator in distinguishing between MM and PM, with an area under the receiver operating characteristic curve of 0.863, a sensitivity of 100%, a specificity of 72.5%, and an accuracy of 92.2%. Positive and negative predictive were calculated at 41.7% and 100%, respectively.

Conclusions
The US finding of a close relationship with the glandular capsule is a highly sensitive diagnostic indicator for MM. Following this finding, US-guided needle biopsy should be recommended to further confirm the diagnosis.
Late dysfunction of a mechanical aortic valve after long-term low molecular weight heparin therapy: a case report
Authors: Mon Aye , Shanmuganathan Selvaraj , Uddin Akhlaque 
Published: July 2024

Abstract

Background
To date, vitamin K anticoagulants are the only recommended long-term therapy for mechanical heart valves. Bleeding episodes, thromboembolic events, and international normalized ratio monitoring are difficult and prevalent complications for these patients. This report reflects the late mechanical aortic valve dysfunction after long-term low molecular weight heparin therapy.

Case summary
A 66-year-old male patient underwent mechanical aortic valve replacement in 2007. He was administered therapeutic doses of enoxaparin for nearly 12 years due to warfarin-related bleeding complications and labile international normalized ratios. However, he experienced multiple cardiovascular and cerebrovascular thromboembolic events, including an anterolateral ST-elevation myocardial infarction with left anterior descending artery thrombus, treated with thrombus aspiration and stenting. The patient was eventually admitted with symptoms and signs of acute heart failure, and echocardiography, fluoroscopy, and a cardiac computed tomography detected mechanical aortic valve prosthesis dysfunction, with an immobile leaflet and pannus. The patient demonstrated no improvement despite switching to unfractionated heparin, and he ultimately underwent redo aortic bioprosthetic valve surgery with a favourable outcome.

Discussion
Low molecular weight heparin is prescribed for patients with aortic mechanical valves who are intolerant to vitamin K antagonists or as bridging in certain situations. Anti-Xa factor monitoring should be considered for long-term prescriptions.
Stroke outcomes in patients with new onset perioperative atrial fibrillation complicating major abdominal surgery compared with patients with new onset non-perioperative atrial fibrillation
Authors: Tas Amine , Fosbøl Emil Loldrup , Vester-Andersen Morten , Burcharth Jakob , Butt Jawad Haider , Køber Lars , Gundlund Anna 
Published: July 2024

Abstract

Background
Major emergency abdominal surgery is associated with postoperative complications and high mortality. Long-term outcomes in patients with perioperative atrial fibrillation (POAF) have recently received increased attention, especially POAF in non-thoracic surgery.

Purpose
This study aimed to compare long-term AF related hospitalization and stroke in patients with POAF in relation to major emergency abdominal surgery and in patients with non-perioperative AF.

Methods and results
We crosslinked data from Danish nationwide registries and identified all patients who underwent major emergency abdominal surgery (2000–2018) and were diagnosed with POAF, and patients who developed AF in a non-perioperative setting. Patients with POAF were matched in a 1:5 ratio on age, sex, year of AF diagnosis, and oral anticoagulation (OAC) status at the beginning of follow-up with patients with non-perioperative AF. From discharge, we examined adjusted hazard ratios (HRs) of stroke using multivariable Cox regression analysis. The study population comprised 1041 (out of 42 021 who underwent major emergency abdominal surgery) patients with POAF and 5205 patients with non-perioperative AF. The median age was 78 years [interquartile range: 71–84] for those initiated on OAC therapy and 78 years [interquartile range: 71–85] for those not initiated on OAC therapy. During the first year of follow up, POAF was associated with similar rates of stroke as non-perioperative AF {patients initiated on OAC: HR 0.96 [95% confidence interval (CI) 0.52–1.77] and patients not initiated on OAC: HR 0.69 (95% CI 0.41–1.15)}.

Conclusion
POAF in relation to major emergency abdominal surgery was associated with similar rates of stroke as non-perioperative AF. These results suggest that POAF not only carry an acute burden but also a long-term burden in patients undergoing major emergency abdominal surgery.
Endogenous Cushing's syndrome and cancer risk
Authors: Rudman Yaron , Fleseriu Maria , Dery Laura , Masri-Iraqi Hiba , Sasson Liat , Shochat Tzipora , Kushnir Shiri , Shimon Ilan , Akirov Amit 
Published: July 2024

Abstract

Objective
Cancer incidence in patients with endogenous Cushing's syndrome (CS) has never been established. Here, we aimed to assess the cancer risk in patients with CS as compared with individually matched controls.

Design
A nationwide retrospective matched cohort study of patients with endogenous CS diagnosed between 2000 and 2023 using the database of Clalit Health Services in Israel.

Methods
Patients with adrenal carcinoma or ectopic CS were excluded. Patients with CS were matched in a 1:5 ratio, with controls individually matched for age, sex, socioeconomic status, and body mass index. The primary outcome was defined as the first diagnosis of any malignancy following a CS diagnosis. Risk of malignancy was calculated using the Cox proportional hazard model, with death as a competing event.

Results
A total of 609 patients with CS and 3018 controls were included [mean age at diagnosis, 48.0 ± 17.2 years; 2371 (65.4%) women]. The median follow-up was 14.7 years (IQR, 9.9–20.2 years). Patients with CS had an increased cancer risk, with a hazard ratio (HR) of 1.78 (95% CI 1.44–2.20) compared with their matched controls. The risk of malignancy was elevated in patients with Cushing's disease (251 cases and 1246 controls; HR 1.65, 95% CI 1.15–2.36) and in patients with adrenal CS (200 cases and 991 controls; HR 2.36, 95% CI 1.70–3.29). The increased cancer risk in patients with CS persists after exclusion of thyroid malignancies.

Conclusion
Endogenous CS is associated with increased malignancy risk. These findings underscore the need for further research to establish recommendations for cancer screening in this population.
Birc5 and Nudc are screened as candidate reference genes for RT-qPCR studies in mouse cementoblast mineralization using time-series RNA-seq data
Authors: Sun Qiao , Li Biao , Li Yicun , Cao Zhengguo , He Hong 
Published: July 2024

Abstract

Background
The robustness and credibility of RT-qPCR results are critically dependent on the selection of suitable reference genes. However, the mineralization of the extracellular matrix can alter the intracellular tension and energy metabolism within cells, potentially impacting the expression of traditional reference genes, namely Actb and Gapdh.

Objective
To methodically identify appropriate reference genes for research focused on mouse cementoblast mineralization.

Materials and methods
Time-series transcriptomic data of mouse cementoblast mineralization were used. To ensure expression stability and medium to high expression levels, three specific criteria were applied to select potential reference genes. The expression stability of these genes was ranked based on the DI index (1/coefficient of variation) to identify the top six potential reference genes. RT-qPCR validation was performed on these top six candidates, comparing their performance against six previously used reference genes (Rpl22, Ppib, Gusb, Rplp0, Actb, and Gapdh). Cq values of these 12 genes were analyzed by RefFinder to get a stability ranking.

Results
A total of 4418 (12.27%) genes met the selection criteria. Among them, Rab5if, Chmp4b, Birc5, Pea15a, Nudc, Supt4a were identified as candidate reference genes. RefFinder analyses revealed that two candidates (Birc5 and Nudc) exhibited superior performance compared to previously used reference genes.

Limitations
RefFinder’s stability ranking does not consider the influence of primer efficiency.

Conclusions and implications
We propose Birc5 and Nudc as candidate reference genes for RT-qPCR studies investigating mouse cementoblast mineralization and cementum repair.
Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region
Authors: Reyes-Herrera Paula H , Delgadillo-Duran Diego A , Flores-Gonzalez Mirella , Mueller Lukas A , Cristancho Marco A , Barrero Luz Stella 
Published: July 2024

Abstract
Potato (Solanum tuberosum) is an essential crop for food security and is ranked as the third most important crop worldwide for human consumption. The Diacol Capiro cultivar holds the dominant position in Colombian cultivation, primarily catering to the food processing industry. This highly heterozygous, autotetraploid cultivar belongs to the Andigenum group and it stands out for its adaptation to a wide variety of environments spanning altitudes from 1,800 to 3,200 meters above sea level. Here, a chromosome-scale assembly, referred to as DC, is presented for this cultivar. The assembly was generated by combining circular consensus sequencing with proximity ligation Hi-C for the scaffolding and represents 2.369 Gb with 48 pseudochromosomes covering 2,091 Gb and an anchor rate of 88.26%. The reference genome metrics, including an N50 of 50.5 Mb, a BUSCO (Benchmarking Universal Single-Copy Orthologue) score of 99.38%, and an Long Terminal Repeat Assembly Index score of 13.53, collectively signal the achieved high assembly quality. A comprehensive annotation yielded a total of 154,114 genes, and the associated BUSCO score of 95.78% for the annotated sequences attests to their completeness. The number of predicted NLR (Nucleotide-Binding and Leucine-Rich-Repeat genes) was 2107 with a large representation of NBARC (for nucleotide binding domain shared by Apaf-1, certain R gene products, and CED-4) containing domains (99.85%). Further comparative analysis of the proposed annotation-based assembly with high-quality known potato genomes, showed a similar genome metrics with differences in total gene numbers related to the ploidy status. The genome assembly and annotation of DC presented in this study represent a valuable asset for comprehending potato genetics. This resource aids in targeted breeding initiatives and contributes to the creation of enhanced, resilient, and more productive potato varieties, particularly beneficial for countries in Latin America.
Genomic and Transcriptomic Insights into the Evolution of C4 Photosynthesis in Grasses
Authors: Lyu Haomin , Yim Won Cheol , Yu Qingyi 
Published: July 2024

Abstract
C4 photosynthesis has independently evolved over 62 times within 19 angiosperm families. The recurrent evolution of C4 photosynthesis appears to contradict the complex anatomical and biochemical modifications required for the transition from C3 to C4 photosynthesis. In this study, we conducted an integrated analysis of genomics and transcriptomics to elucidate the molecular underpinnings of convergent C4 evolution in the grass family. Our genome-wide exploration of C4-related gene families suggests that the expansion of these gene families may have played an important role in facilitating C4 evolution in the grass family. A phylogenomic synteny network analysis uncovered the emergence of C4 genes in various C4 grass lineages from a common ancestral gene pool. Moreover, through a comparison between non-C4 and C4 PEPCs, we pinpointed 14 amino acid sites exhibiting parallel adaptations. These adaptations, occurring post the BEP–PACMAD divergence, shed light on why all C4 origins in grasses are confined to the PACMAD clade. Furthermore, our study revealed that the ancestor of Chloridoideae grasses possessed a more favorable molecular preadaptation for C4 functions compared to the ancestor of Panicoideae grasses. This molecular preadaptation potentially explains why C4 photosynthesis evolved earlier in Chloridoideae than in Panicoideae and why the C3-to-C4 transition occurred once in Chloridoideae but multiple times in Panicoideae. Additionally, we found that C4 genes share similar cis-elements across independent C4 lineages. Notably, NAD-ME subtype grasses may have retained the ancestral regulatory machinery of the C4 NADP-ME gene, while NADP-ME subtype grasses might have undergone unique cis-element modifications.