bluuebunny/crossref_metadata_2025_split huggingface dataset:
The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish
Authors: Moore Billy , Herrera Marcela , Gairin Emma , Li Chengze , Miura Saori , Jolly Jeffrey , Mercader Manon , Izumiyama Michael , Kawai Erina , Ravasi Timothy , Laudet Vincent , Ryu Taewoo 
Published: January 2023

Abstract
Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.
The EU and the invasion of Ukraine: a collective responsibility to act?
Authors: Maurer Heidi , Whitman Richard G , Wright Nicholas 
Published: January 2023

Abstract
Russia's February 2022 invasion of Ukraine has upended Europe's security order, with many observers calling it a turning point for the European Union. This article contends, however, that the EU's response has been less a turning point and more of an epiphany, providing a reality check for the EU and its member states about how far European foreign policy cooperation has evolved in recent decades. It suggests that an understanding of the EU's response to Russia's invasion of Ukraine requires consideration of the member states' foreign policy co-operation, which has intensified over the past half-century, and its underpinning norm which we term a ‘collective European responsibility to act’. In emphasizing this norm, we identify core ideas about the functioning of collective European foreign policy. We re-examine three key preoccupations of the EU foreign policy-making practice and assessment through the lens of the collective European responsibility to act and show how it enables a different and novel re-reading of the added value of EU foreign policy cooperation. The EU's response to Russia's invasion of Ukraine thus serves as a timely focusing event that demands a rethink of the premises that have underpinned our analysis and understanding of collective European foreign policy-making over decades.
Galectin-4 increases the ability of M2 macrophages to enhance antiviral CD4+ T-cell responses
Authors: Lee In-Gu , Joo Yong-Hyun , Jeon Hoyeon , Jeong Raehyuk , Kim Eui Ho , Chung Hyunwoo , Eyun Seong-il , Kim Jeongkyu , Seo Young-Jin , Hong So-Hee 
Published: January 2023

Abstract
Galectin-4 (Gal-4) is a β-galactoside–binding protein belonging to the galectin family. Although Gal-4 is known to be involved in several physiologic processes of the gastrointestinal tract, its immunomodulatory roles remain unclear. In this study, we investigated whether Gal-4 influences the function of M1 and M2 macrophages. Gal-4 treatment drove more robust changes in the gene expression of M2 macrophages compared to M1 macrophages. Antiviral immune response–related genes were significantly upregulated in Gal-4–treated M2 macrophages. Gal-4 significantly enhanced the immunostimulatory activity of M2 macrophages upon Toll-like receptor 7 stimulation or infection with lymphocytic choriomeningitis virus (LCMV). Moreover, the antibody production against LCMV infection and the antiviral CD4+ T-cell responses, but not the antiviral CD8+ T-cell responses, were greatly increased by Gal-4–treated M2 macrophages in vivo. The present results indicate that Gal-4 enhances the ability of M2 macrophages to promote antiviral CD4+ T-cell responses. Thus, Gal-4 could be used to boost antiviral immune responses.
RIG-I immunotherapy overcomes radioresistance in p53-positive malignant melanoma
Authors: Lambing Silke , Tan Yu Pan , Vasileiadou Paraskevi , Holdenrieder Stefan , Müller Patrick , Hagen Christian , Garbe Stephan , Behrendt Rayk , Schlee Martin , van den Boorn Jasper G , Bartok Eva , Renn Marcel , Hartmann Gunther 
Published: January 2023

Abstract
Radiotherapy induces DNA damage, resulting in cell cycle arrest and activation of cell-intrinsic death pathways. However, the radioresistance of some tumour entities such as malignant melanoma limits its clinical application. The innate immune sensing receptor retinoic acid-inducible gene I (RIG-I) is ubiquitously expressed and upon activation triggers an immunogenic form of cell death in a variety of tumour cell types including melanoma. To date, the potential of RIG-I ligands to overcome radioresistance of tumour cells has not been investigated. Here, we demonstrate that RIG-I activation enhanced the extent and immunogenicity of irradiation-induced tumour cell death in human and murine melanoma cells in vitro and improved survival in the murine B16 melanoma model in vivo. Transcriptome analysis pointed to a central role for p53, which was confirmed using p53–/– B16 cells. In vivo, the additional effect of RIG-I in combination with irradiation on tumour growth was absent in mice carrying p53–/– B16 tumours, while the antitumoural response to RIG-I stimulation alone was maintained. Our results identify p53 as a pivotal checkpoint that is triggered by RIG-I resulting in enhanced irradiation-induced tumour cell death. Thus, the combined administration of RIG-I ligands and radiotherapy is a promising approach to treating radioresistant tumours with a functional p53 pathway, such as melanoma.
Differential trends in rising endometrial cancer incidence by age, race, and ethnicity
Authors: Liu Lihua , Habeshian Talar S , Zhang Juanjuan , Peeri Noah C , Du Mengmeng , De Vivo Immaculata , Setiawan Veronica Wendy 
Published: January 2023

Abstract
Endometrial cancer (EC) incidence is on the rise. Although early-onset endometrial cancer (EOEC; age at diagnosis &lt;50 years) is relatively uncommon, the incidence of EOEC has been reportedly increasing in recent decades. However, the rising EOEC has not been thoroughly described with regard to the racial and ethnic disparities and compared with late-onset EC (age at diagnosis ≥50 years). We used the Cancer in North America (CiNA) Analytic File, 1995-2018, from the North American Association of Central Cancer Registries, which allowed us to examine trends in invasive EC incidence by racial and ethnic groups and by age at diagnosis. We found striking differences for demographic and tumor characteristics as well as racial and ethnic patterns and time trends in EC incidence between EOEC and late-onset EC. The faster increases in EOEC incidence rates, especially among non-White women, mirror similar observations in other cancers, pointing to a possible link with rising obesity epidemic in younger generations.
A splenic pseudocyst following laparoscopic sleeve gastrectomy: a case report
Authors: Alqahtani Awadh , Almayouf Mohammad , Billa Srikar , Alsarraj Omar , Zamil Albandry Bin 
Published: January 2023

Abstract
This is the first report of a patient presenting with a splenic pseudocyst following laparoscopic sleeve gastrectomy (LSG). A 26-year-old male with no chronic medical illnesses who underwent LSG presented with vague abdominal pain. An abdominal contrast-enhanced computed tomography revealed a 15 cm well-circumscribed cyst originating from the spleen. Intraoperatively, the findings were significant for a superficial cyst located at the lower pole of the spleen. A laparoscopic spleen-preserving procedure was conducted, specifically marsupialization and packing with omentum. The postoperative period was uneventful, and the patient was discharged on Day 2 postoperatively. The patient was free from complaints at outpatient follow-up clinics. Follow-up visits at the outpatient clinic were free from complaints. Pathology confirmed a splenic pseudocyst, and cytology was unremarkable. Since dissection during LSG is close to the spleen, infarction could occur, predisposing to pseudocyst formation. Marsupialization is an excellent surgical option when applied to appropriate splenic cyst types.
A computational approach to identify efficient RNA cleaving 10–23 DNAzymes
Authors: Pine Angela C , Brooke Greg N , Marco Antonio 
Published: January 2023

Abstract
DNAzymes are short pieces of DNA with catalytic activity, capable of cleaving RNA. DNAzymes have multiple applications as biosensors and in therapeutics. The high specificity and low toxicity of these molecules make them particularly suitable as therapeutics, and clinical trials have shown that they are effective in patients. However, the development of DNAzymes has been limited due to the lack of specific tools to identify efficient molecules, and users often resort to time-consuming/costly large-scale screens. Here, we propose a computational methodology to identify 10–23 DNAzymes that can be used to triage thousands of potential molecules, specific to a target RNA, to identify those that are predicted to be efficient. The method is based on a logistic regression and can be trained to incorporate additional DNAzyme efficiency data, improving its performance with time. We first trained the method with published data, and then we validated, and further refined it, by testing additional newly synthesized DNAzymes in the laboratory. We found that although binding free energy between the DNAzyme and its RNA target is the primary determinant of efficiency, other factors such as internal structure of the DNAzyme also have an important effect. A program implementing the proposed method is publicly available.
On data normalization and batch-effect correction for tumor subtyping with microRNA data
Authors: Wu Yilin , Yuen Becky Wing-Yan , Wei Yingying , Qin Li-Xuan 
Published: January 2023

Abstract
The discovery of new tumor subtypes has been aided by transcriptomics profiling. However, some new subtypes can be irreproducible due to data artifacts that arise from disparate experimental handling. To deal with these artifacts, methods for data normalization and batch-effect correction have been utilized before performing sample clustering for disease subtyping, despite that these methods were primarily developed for group comparison. It remains to be elucidated whether they are effective for sample clustering. We examined this issue with a re-sampling-based simulation study that leverages a pair of microRNA microarray data sets. Our study showed that (i) normalization generally benefited the discovery of sample clusters and quantile normalization tended to be the best performer, (ii) batch-effect correction was harmful when data artifacts confounded with biological signals, and (iii) their performance can be influenced by the choice of clustering method with the Prediction Around Medoid method based on Pearson correlation being consistently a best performer. Our study provides important insights on the use of data normalization and batch-effect correction in connection with the design of array-to-sample assignment and the choice of clustering method for facilitating accurate and reproducible discovery of tumor subtypes with microRNAs.
Special flow equation and the GKP–Witten relation
Authors: Aoki Sinya , Balog Janos , Onogi Tetsuya , Yokoyama Shuichi 
Published: January 2023

AbstractWe develop a framework for the reconstruction of the bulk theory dual to conformal field theory without any assumption by means of a flow equation. To this end we investigate a minimal extension of the free-flow equation and find that at a special parametrization the conformal transformation for a normalized smeared operator exactly becomes the isometry of anti-de Sitter space (AdS). By employing this special flow equation for O(N) vector models, we explicitly show that the AdS geometry as well as the scalar field satisfying the GKP–Witten relation concurrently emerge in this framework.
Gamma and neutron separation using emission wavelengths in Eu:LiCaI scintillators
Authors: Iida Takashi , Yoshino Masao , Kamada Kei , Sasaki Rei , Yajima Ryuga 
Published: January 2023

Abstract
Scintillators have long been known as radiation detectors and are still used in various applications. Recently, scintillators containing 6Li have been developed as neutron detectors and have attracted attention. 6Li absorbs thermal neutrons and emits α+3H, which is promising as a neutron detector if it can be separated from background gamma rays. We have been developing Eu:LiI–CaI2-based scintillators (Eu:LiCaI) for this purpose. In scintillator detectors, waveform information is generally used to distinguish particles such as neutrons and gamma rays. We propose a new particle identification method using emission wavelength information. In this study, experiments were conducted using Eu:LiCaI crystals, multi-pixel photon counter optical sensors, and long-wavelength cut filters to verify the proposed method. The results of irradiating a 252Cf neutron source and a 60Co gamma-ray source indicate that there is a particle dependence on the output signal ratio with and without filters. This indicates that different types of radiation particles have different emission wavelengths. This is the first demonstration of a wavelength-based particle identification method.
Caution in Transnasal Balloon Dilation of the Eustachian Tube: Middle Ear Penetration of Catheter Tip in a Cadaveric Model
Authors: Treble Alexander , Do Timothy , Sarkis Leba , Newey Allison , Naidoo Soo Yee , Saxby Alexander , Kong Jonathan , Patel Nirmal P. , Jufas Nicholas 
Published: January 2023

Objective
To investigate the degree to which transnasal eustachian tube (ET) dilation balloon catheters are able to be passed through the ET in a cadaver model.

Patients and Interventions
A cadaveric study of 8 cadaver heads (16 ears), which underwent transnasal ET insertion with a 3 × 20-mm balloon catheter with transtympanic endoscopic visualization and grading.

Results
Catheter tip incursion into the protympanum or mesotympanum occurred in all ears. Radiological validation was obtained with correlation to published ET length data.

Conclusion
Middle ear incursion of balloon catheter tips can be demonstrated in a cadaver model and highlights the ongoing need for both caution in novel surgical techniques and evolution in device design.
Late-onset Chronic Kidney Disease Over 2 Decades After Pediatric Liver Transplantation: A Single-center, Retrospective Study
Authors: Umemura Kentaro , Mita Atsuyoshi , Ohno Yasunari , Masuda Yuichi , Yoshizawa Kazuki , Kubota Koji , Notake Tsuyoshi , Hosoda Kiyotaka , Kamachi Atsushi , Goto Takamune , Tomida Hidenori , Yamazaki Shiori , Shimizu Akira , Soejima Yuji 
Published: January 2023

Background.
Although chronic kidney disease (CKD) after liver transplantation (LTx) is a common complication in adults, its long-term significance after pediatric LTx remains unclear. We examined the decades-long transition of renal function and revealed the risk factors for late-onset CKD after pediatric LTx in a single-center retrospective cohort of 117 pediatric LTx recipients who survived >5 y.

Methods.
The estimated glomerular filtration rate (eGFR) and CKD stages were calculated using serum creatinine. Risk factor analysis for late-onset CKD was performed in 41 patients whose eGFR could be evaluated at >20 y after LTx.

Results.
The median age at LTx was 1.3 y, and most primary diagnoses were biliary atresia (77%). The mean pre-LTx and 1, 5, 10, 20, and >20 y post-LTx eGFRs were 180, 135, 131, 121, 106, and 95 mL/min/1.73 m2, respectively, with a median renal follow-up period of 15 y. The eGFR declined by 47% at >20 y after LTx (P < 0.001). CKD was observed in 8%, 19%, and 39% of cases at 10, 20, and >20 y after LTx, respectively. In patients receiving cyclosporine, trough levels were 1.5 times higher in those with CKD up to 10 y after LTx. The multivariate analysis showed that older age at LTx (odds ratio, 1.3 by 1 y; P = 0.008) and episodes of repeated/refractory rejection (odds ratio, 16.2; P = 0.002) were independent risk factors of CKD >20 y after LTx.

Conclusions.
In conclusion, renal function deteriorates slowly yet steadily after pediatric LTx. Long-term careful surveillance is essential after pediatric LTx, especially in repeated/refractory rejection or long-term high trough-level use of cyclosporine cases.
Update on the Financial Well-Being of Surgical Residents in New England
Authors: Esposito Andrew C , Coppersmith Nathan A , White Erin M , Papageorge Marianna V , DiSiena Michael , Hess Donald , LaFemina Jennifer , Larkin Anne C , Miner Thomas J , Nepomnayshy Dmitry , Palesty John , Rosenkranz Kari M , Seymour Neal E , Trevisani Gino , Whiting James , Oliveira Kristin D , Longo Walter E , Yoo Peter S 
Published: January 2023

BACKGROUND:Poor personal financial health has been linked to key components of health including burnout, substance abuse, and worsening personal relationships. Understanding the state of resident financial health is key to improving their overall well-being.STUDY DESIGN:A secondary analysis of a survey of New England general surgery residents was performed to understand their financial well-being. Questions from the National Financial Capability Study were used to compare to an age-matched and regionally matched cohort.RESULTS:Overall, 44% (250 of 570) of surveyed residents responded. Residents more frequently reported spending less than their income each year compared to the control cohort (54% vs 34%, p < 0.01). However, 17% (39 of 234) of residents reported spending more than their income each year. A total of 65% of residents (152 of 234), found it “not at all difficult” to pay monthly bills vs 17% (76 of 445) of the control cohort (p < 0.01). However, 32% (75 of 234) of residents reported it was “somewhat” or “very” difficult to pay monthly bills. Residents more frequently reported they “certainly” or “probably” could “come up with” $2,000 in a month compared to the control cohort (85% vs 62% p < 0.01), but 16% (37 of 234) of residents reported they could not. In this survey, 21% (50 of 234) of residents reported having a personal life insurance policy, 25% (59 of 234) had disability insurance, 6% (15 of 234) had a will, and 27% (63 of 234) had >$300,000 worth of student loans.CONCLUSIONs:Surgical residents have better financial well-being than an age-matched and regionally matched cohort, but there is still a large proportion who suffer from financial difficulties.
Massively parallel single molecule tracking of sequence-dependent DNA mismatch repairin vivo
Authors: Kayikcioglu Tunc , Zarb Jasmin S. , Mohapatra Sonisilpa , Lin Chang-Ting , London James A. , Hansen Kasper D. , Fishel Richard , Ha Taekjip 
Published: January 2023

AbstractWhether due to mutagens or replication errors, DNA mismatches arise spontaneouslyin vivo. Unrepaired mismatches are sources of genetic variation and point mutations which can alter cellular phenotype and cause dysfunction, diseases, and cancer. To understand how diverse mismatches in various sequence contexts are recognized and repaired, we developed a high-throughput sequencing-based approach to track single mismatch repair outcomesin vivoand determined the mismatch repair efficiencies of 5682 distinct singly mispaired sequences inE. coli. We found that CC mismatches are always poorly repaired, whereas local sequence context is a strong determinant of the hypervariable repair efficiency of TT, AG, and CT mismatches. Single molecule FRET analysis of MutS interactions with mismatched DNA showed that well-repaired mismatches have a higher effective rate of sliding clamp formation. The hypervariable repair of TT mismatches can cause selectively enhanced mutability if a failure to repair would result in synonymous codon change or a conservative amino acid change. Sequence-dependent repair efficiency inE. colican explain the patterns of substitution mutations in mismatch repair-deficient tumors, human cells, andC. elegans. Comparison to biophysical and biochemical analyses indicate that DNA physics is the primary determinant of repair efficiency by its impact on the mismatch recognition by MutS.