bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partially Linear Models under Data Combination
Authors: D’Haultfœuille X , Gaillac C , Maurel A 
Published: March 2024

Abstract
We study partially linear models when the outcome of interest and some of the covariates are observed in two different datasets that cannot be linked. This type of data combination problem arises very frequently in empirical microeconomics. Using recent tools from optimal transport theory, we derive a constructive characterization of the sharp identified set. We then build on this result and develop a novel inference method that exploits the specific geometric properties of the identified set. Our method exhibits good performances in finite samples, while remaining very tractable. We apply our approach to study intergenerational income mobility over the period 1850–1930 in the U.S. Our method allows us to relax the exclusion restrictions used in earlier work, while delivering confidence regions that are informative.
Secreted in Xylem 6 (SIX6) Mediates Fusarium oxysporum f. sp. fragariae Race 1 Avirulence on FW1-Resistant Strawberry Cultivars
Authors: Dilla-Ermita Christine Jade , Goldman Polly , Anchieta Amy , Feldmann Mitchell J. , Pincot Dominique D. A. , Famula Randi A. , Vachev Mishi , Cole Glenn S. , Knapp Steven J. , Klosterman Steven J. , Henry Peter M. 
Published: March 2024

Fusarium oxysporum f. sp. fragariae ( Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof race 2 is virulent on FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between a gene at the FW1 locus and an avirulence gene ( AvrFW1) in Fof race 1. To identify a candidate AvrFW1, we compared genomes of 24 Fof race 1 and three Fof race 2 isolates. We found one candidate gene that was present in race 1, was absent in race 2, was highly expressed in planta, and was homologous to a known effector, secreted in xylem 6 ( SIX6). We knocked out SIX6 in two Fof race 1 isolates by homologous recombination. All SIX6 knockout transformants (Δ SIX6) gained virulence on FW1/fw1 cultivars, whereas ectopic transformants and the wildtype isolates remained avirulent. Δ SIX6 isolates were quantitatively less virulent on FW1/fw1 cultivars Fronteras and San Andreas than fw1/fw1 cultivars. Seedlings from an FW1/fw1 × fw1/fw1 population were genotyped for FW1 and tested for susceptibility to a SIX6 knockout isolate. Results suggested that additional minor-effect quantitative resistance genes could be present at the FW1 locus. This work demonstrates that SIX6 acts as an avirulence factor interacting with a resistance gene at the FW1 locus. The identification of AvrFW1 enables surveillance for Fof race 2 and provides insight into the mechanisms of FW1-mediated resistance. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Decoding the Arsenal: Protist Effectors and Their Impact on Photosynthetic Hosts
Authors: Mukhopadhyay Soham , Garvetto Andrea , Neuhauser Sigrid , Pérez-López Edel 
Published: March 2024

Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes, and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, which makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionizing the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools like AlphaFold2 enable structure-based function prediction of effector candidates with divergent protein sequences. In turn, this allows us to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Cardiac lipotoxicity and fibrosis underlie impaired contractility in a mouse model of metabolic dysfunction‐associated steatotic liver disease
Authors: Badmus Olufunto O. , da Silva Alexandre A. , Li Xuan , Taylor Lucy C. , Greer Jennifer R. , Wasson Andrew R. , McGowan Karis E. , Patel Parth R. , Stec David E. 
Published: March 2024

AbstractThe leading cause of death among patients with metabolic dysfunction‐associated steatotic liver disease (MASLD) is cardiovascular disease. A significant percentage of MASLD patients develop heart failure driven by functional and structural alterations in the heart. Previously, we observed cardiac dysfunction in hepatocyte‐specific peroxisome proliferator‐activated receptor alpha knockout (PparaHepKO), a mouse model that exhibits hepatic steatosis independent of obesity and insulin resistance. The goal of the present study was to determine mechanisms that underlie hepatic steatosis‐induced cardiac dysfunction in PparaHepKO mice. Experiments were performed in 30‐week‐old PparaHepKO and littermate control mice fed regular chow. We observed decreased cardiomyocyte contractility (0.17 ± 0.02 vs. 0.24 ± 0.02 μm, p < 0.05), increased cardiac triglyceride content (0.96 ± 0.13 vs. 0.68 ± 0.06 mM, p < 0.05), collagen type 1 (4.65 ± 0.25 vs. 0.31 ± 0.01 AU, p < 0.001), and collagen type 3 deposition (1.32 ± 0.46 vs. 0.05 ± 0.03 AU, p < 0.05). These changes were associated with increased apoptosis as indicated by terminal deoxynucleotidyl transferase dUTP nick end labeling staining (30.9 ± 4.7 vs. 13.1 ± 0.8%, p < 0.006) and western blots showing increased cleaved caspase‐3 (0.27 ± 0.006 vs. 0.08 ± 0.01 AU, p < 0.003) and pro‐caspase‐3 (5.4 ± 1.5 vs. 0.5 ± 0.3 AU, p < 0.02), B‐cell lymphoma protein 2‐associated X (0.68 ± 0.07 vs. 0.04 ± 0.04 AU, p < 0.001), and reduced B‐cell lymphoma protein 2 (0.29 ± 0.01 vs. 1.47 ± 0.54 AU, p < 0.05). We further observed elevated circulating natriuretic peptides and exercise intolerance in PparaHepKO mice when compared to controls. Our data demonstrated that lipotoxicity, and fibrosis underlie cardiac dysfunction in MASLD.
NGS of brush cytology samples improves the detection of high-grade dysplasia and cholangiocarcinoma in patients with primary sclerosing cholangitis: A retrospective and prospective study
Authors: Boyd Sonja , Mustamäki Taru , Sjöblom Nelli , Nordin Arno , Tenca Andrea , Jokelainen Kalle , Rantapero Tommi , Liuksiala Thomas , Lahtinen Laura , Kuopio Teijo , Kytölä Soili , Mäkisalo Heikki , Färkkilä Martti , Arola Johanna 
Published: March 2024

Background:
Biliary dysplasia, a precursor of cholangiocarcinoma (CCA), is a common complication of primary sclerosing cholangitis. Patients with high-grade dysplasia (HGD) or early CCA who have received oncological treatment are candidates for liver transplantation. The preoperative diagnosis of CCA or HGD is challenging, and the sensitivity of biliary brush cytology (BC) is limited.

Methods:
By using next-generation sequencing (NGS), we retrospectively analyzed archived tissue samples (n=62) obtained from explanted liver tissue and CCA samples to identify oncogenic mutations that occur during primary sclerosing cholangitis carcinogenesis. BC samples were prospectively collected from patients with primary sclerosing cholangitis (n=97) referred for endoscopic retrograde cholangiography to measure the diagnostic utility of NGS combined with BC compared with traditional cytology alone.

Results:
Mutations in KRAS, GNAS, FLT3, RNF43, TP53, ATRX, and SMAD4 were detected in archived CCA or HGD samples. KRAS, GNAS, TP53, CDKN2A, FBXW7, BRAF, and ATM mutations were detected in prospectively collected brush samples from patients with histologically verified CCA or HGD. One patient with low-grade dysplasia in the explanted liver had KRAS and GNAS mutations in brush sample. No mutations were observed in brush samples or archived tissues in liver transplantation cases without biliary neoplasia. While KRAS mutations are common in biliary neoplasms, they were also observed in patients without biliary neoplasia during surveillance.

Conclusions:
In summary, NGS of BC samples increased the sensitivity of detecting biliary neoplasia compared with traditional cytology. Performing NGS on BC samples may help diagnose HGD or early CCA, benefiting the timing of liver transplantation.
A real-time augmented reality system integrated with artificial intelligence for skin tumor surgery: experimental study and case series
Authors: Huang Kai , Liao Jun , He Jishuai , Lai Sicen , Peng Yihao , Deng Qian , Wang Han , Liu Yuancheng , Peng Lanyuan , Bai Ziqi , Yu Nianzhou , Li Yixin , Jiang Zixi , Su Juan , Li Jinmao , Tang Yan , Chen Mingliang , Lu Lixia , Chen Xiang , Yao Jianhua , Zhao Shuang 
Published: March 2024

Background:
Skin tumors affect many people worldwide, and surgery is the first treatment choice. Achieving precise preoperative planning and navigation of intraoperative sampling remains a problem and is excessively reliant on the experience of surgeons, especially for Mohs surgery for malignant tumors.

Materials and methods:
To achieve precise preoperative planning and navigation of intraoperative sampling, we developed a real-time augmented reality (AR) surgical system integrated with artificial intelligence (AI) to enhance three functions: AI-assisted tumor boundary segmentation, surgical margin design, and navigation in intraoperative tissue sampling. Non-randomized controlled trials were conducted on manikin, tumor-simulated rabbits, and human volunteers in Hunan Engineering Research Center of Skin Health and Disease Laboratory to evaluate the surgical system.

Results:
The results showed that the accuracy of the benign and malignant tumor segmentation was 0.9556 and 0.9548, respectively, and the average AR navigation mapping error was 0.644 mm. The proposed surgical system was applied in 106 skin tumor surgeries, including intraoperative navigation of sampling in 16 Mohs surgery cases. Surgeons who have used this system highly recognize it.

Conclusions:
The surgical system highlighted the potential to achieve accurate treatment of skin tumors and to fill the gap in global research on skin tumor surgery systems.
Pulsatile flow increases METTL14-induced m6A modification and attenuates septic cardiomyopathy: an experimental study
Authors: Zhu Shenyu , Wang Kai , Yu Zhexuan , Tang Wei , Zhang Yu , Shinge Shafiu A. , Qiang Yongjia , Liu Hangyu , Zeng Jianfeng , Qiao Kun , Liu Chi , Li Guanhua 
Published: March 2024

Introduction:
Septic cardiomyopathy is a sepsis-mediated cardiovascular complication with severe microcirculatory malperfusion. Emerging evidence has highlighted the protective effects of pulsatile flow in case of microcirculatory disturbance, yet the underlying mechanisms are still elusive. The objective of this study was to investigate the mechanisms of N6-methyladenosine (m6A) modification in the alleviation of septic cardiomyopathy associated with extracorporeal membrane oxygenation (ECMO)-generated pulsatile flow.

Methods:
Rat model with septic cardiomyopathy was established and was supported under ECMO either with pulsatile or non-pulsatile flow. Peripheral perfusion index (PPI) and cardiac function parameters were measured using ultrasonography. Dot blot assay was applied to examine the m6A level, while qRT-PCR, Western blot, immunofluorescence, and immunohistochemistry were used to measure the expressions of related genes. RNA immunoprecipitation assay was performed to validate the interaction between molecules.

Results:
The ECMO-generated pulsatile flow significantly elevates microcirculatory PPI, improves myocardial function, protects the endothelium, and prolongs survival in rat models with septic cardiomyopathy. The pulsatile flow mediates the METTL14-mediated m6A modification to zonula occludens-1 (ZO-1) mRNA (messenger RNA), which stabilizes the ZO-1 mRNA depending on the presence of YTHDF2. The pulsatile flow suppresses the PI3K–Akt signaling pathway, of which the downstream molecule Foxo1, a negative transcription factor of METTL14, binds to the METTL14 promoter and inhibits the METTL14-induced m6A modification.

Conclusion:
The ECMO-generated pulsatile flow increases METTL14-induced m6A modification in ZO-1 and attenuates the progression of septic cardiomyopathy, suggesting that pulsatility might be a new therapeutic strategy in septic cardiomyopathy by alleviating microcirculatory disturbance.
Visual analysis of bone malignancies immunotherapy: A bibliometric analysis from 2010 to 2023
Authors: Shen Kaiyu , Yang Liu , Ke Shuaiyi , Gao Wencang 
Published: March 2024

Background:
Bone malignancies (BM), including osteosarcoma, Ewing’s sarcoma, chondrosarcoma, and chordoma, are characterized by high rates of recurrence and mortality, despite the availability of diverse treatment approaches. Immunotherapy has gained increasing importance in cancer treatment. However, there is a lack of comprehensive studies that utilize bibliometric analysis to explore immunotherapy for BM.

Methods:
A literature search of English studies on BM and immunotherapy from 2010 to 2023 was conducted in the Web of Science Core Collection database. Bibliometric analysis tools such as VOSviewer, CiteSpace, and R Studio were utilized to examine global trends and research hotspots in this field.

Results:
A total of 719 eligible articles, including 528 original research articles and 191 reviews, were analyzed. The number of publications has shown an increasing trend over the past 14 years, particularly in the last 5 years. The majority of the published articles on this topic originated from China (284 articles), followed by the United States and Japan. The institution with the highest number of publications and citations was the University of Texas MD Anderson Cancer Center (30 articles; 1638 citations). Dean A. Lee (12 articles) and Richard Gorlick (576 citations) were the authors with the highest contribution in terms of article count and citation count, respectively. Among these journals, Frontiers in Oncology had the highest number of articles (39 articles), while the Journal of Clinical Oncology had the highest number of citations (1878 citations). Additionally, there has been a shift in the keywords from “antitumor activity” and “NK cells” to popular topics such as “PD-L1,” “open label,” and “single arm.”

Conclusion:
A better understanding of the current status and prospects of immunotherapy for BM is crucial for the rationale selection of appropriate BM patients for immunotherapy. This study is expected to help clinical physicians and researchers gain comprehensive insights into the developmental trends of BM immunotherapy, providing practical guidance for the application of immunotherapy in BM patients.
Cervical clear cell carcinoma: Case report and literature review
Authors: Su Dongying , Song Xia , Wu Fang , Fan Shufeng , Li Miaoer 
Published: March 2024

Rationale:
Clear cell carcinoma (CCC) is a highly invasive malignant tumor. CCCs of the female reproductive system occur mostly in the endometrium and ovaries and rarely in the cervix. So, it is difficult to diagnose cervical clear cell carcinoma (CCAC) on imaging. This report helps to further deepen our understanding of CCAC.

Patient concerns:
A 39-year-old female patient presented with vaginal discharge with no obvious cause, elevated levels of carcinoembryonic antigen (CEA), CA125, CA153, and squamous cell carcinoma antigen (SCC), and underwent ultrasonography (US) CT and MRI examination in our hospital, which showed a mass in the cervix of the uterus, considered of cervical squamous carcinoma.

Diagnoses:
The cervix biopsy guided by vaginoscope biopsy and immunohistochemistry confirmed CCAC, combined Magnetic Resonance Imaging examination, CCAC with pelvic lymph node metastasis was considered.

Interventions and outcomes:
The patient refused further treatment and was discharged from hospital.

Lessons:
CCAC exhibited no specific symptoms, and is slightly different from cervical squamous carcinoma in image features, mainly relying on immunohistochemistry for diagnosis. The reported case raised awareness of CCAC.
Mature solid teratoma of the uterine cervix: A rare case report and review of the literature
Authors: Li Minhua , Zheng Weiping 
Published: March 2024

Rationale:
Most of the mature teratomas are found in the ovaries. Extragonadal teratomas are extremely rare. To date, there are only a handful of reports of uterine cervical teratomas documented in the English literature.

Patient concerns:
Herein we describe a rare case of a 40-year-old patient who was presented to our hospital for a cervical polypoid mass, which was finally confirmed to be mature solid teratoma in uterine cervix.

Diagnoses:
Histological examination of the polypoid mass was found to consist of ciliated pseudostratified columnar respiratory epithelium, intestinal epithelium and smooth muscle tissue, adipose tissue and mature glial component, epidermis, and skin adnexa. Meanwhile, no history of abortion, dilatation, and curettage was present in this patient, so implantation of fetal tissue was excluded. Therefore, we make a diagnosis of uterine cervical mature teratoma.

Interventions:
Tumorectomy was performed after discovering the cervical polypoid mass.

Outcomes:
The patient had been followed-up for next 3 months after surgery and no recurrence was documented until now.

Lessons:
Though teratomas of the uterine cervix are extremely rare, more attention should be paid on this rare but possible tumor for appropriate treatment in these patients.
Identification of serum microRNA alterations associated with long-term exercise-induced motor improvements in patients with Parkinson disease
Authors: Zhang Ziyi , Wu Ziwei , Hu Shenglan , He Miao 
Published: March 2024

Background:
Long-term physical exercise has been shown to benefit patients with Parkinson disease (PD), but there is a lack of evidence regarding the underlying mechanism. A better understanding of how such benefits are induced by exercise might contribute to the development of therapeutic targets for improving the motor function in individuals with PD. The purpose of this study was therefore to investigate the possible association between exercise-induced motor improvements and the changes in serum microRNA (miRNA) levels of PD patients through small RNA sequencing for the first time.

Methods:
Thirteen PD patients completed our 3-month home-and-community-based exercise program, while 6 patients were assigned to the control group. Motor functions were measured, and small RNA sequencing with data analysis was performed on serum miRNAs both before and after the program. The results were further validated by quantitative real-time polymerase chain reaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were then conducted to determine the role of differentially expressed miRNAs.

Results:
The 3-month home-and-community-based exercise program induced significant motor improvements in PD patients in terms of Unified Parkinson’s Disease Rating Scale activities of daily living and Motor Subscale (P < .05), comfortable walking speed (P = .003), fast walking speed (P = .028), Six-Minute Walk Test (P = .004), Berg Balance Scale (P = .039), and Timed Up and Go (P = .002). A total of 11 miRNAs (10 upregulated and one downregulated) were identified to be remarkably differentially expressed after intervention in the exercise group, but not in the control group. The results of miRNA sequencing were further validated by quantitative real-time polymerase chain reaction. It was found that the targets of altered miRNAs were mostly enriched in the mitogen-activated protein kinase, Wnt, and Hippo signaling pathways and the GO annotations mainly included binding, catalytic activity, and transcription regulator activity.

Conclusion:
The exercise-induced motor improvements were possibly associated with changes in circulating miRNA levels in PD patients. These miRNAs, as well as the most enriched pathways and GO terms, may play a critical role in the mechanism of exercise-induced benefits in PD and serve as novel treatment targets for the disease, although further investigations are needed.
Recurrence of locally invasive retroperitoneal dedifferentiated liposarcoma shortly after surgery: A case report and literature review
Authors: Hu Xuelian , Han Bo , Yang Qin , Li Qixuan , Xiao Dongkai , Xu Xiaosong 
Published: March 2024

Rationale:
Retroperitoneal dedifferentiated liposarcoma (RPDDL) is an uncommon malignancy, which often remains undetected for many years due to having adequate space in the retroperitoneal cavity and lacking clinical manifestations in the early stage of the disease. Surgical procedure is usually used as the first choice for treatment. However, it is prone to local recurrence after the operation, resulting in an unfavorable prognosis. Our aim is to draw useful lessons from the new case and provide some experience for management of the disease.

Patient concerns:
We describe a 55-year-old male patient who was admitted for a 3-week history of persistent dull ache of the left waist. A large mass of the left upper abdomen was palpated in physical examination. Moreover, the imaging examination revealed that the diameter of the mass was about 21 cm, and some adjacent vital organs were invaded, which brought great challenges to complete surgical resection.

Diagnosis:
The postoperative pathological results confirmed that the mass was RPDDL with invasion of the surrounding vital structures including pancreas, spleen, left adrenal gland, left kidney, and vasculature with tumor emboli.

Interventions:
Surgical resection of the mass was performed by our multidisciplinary team. The patient received chemotherapy 1 month after surgery.

Outcomes:
The effect of chemotherapy seemed to be unsatisfactory. Local multifocal recurrence of the tumor was considered about 2 months after surgery. Finally, he gave up any treatments and died of the disease.

Lessons:
Regular physical examination and ultrasound screening may detect the disease as early as possible, especially for high-risk group aged 60 to 70, which should be popularized. Incomplete resection, vascular invasion, and interruption of postoperative treatment may lead to an unfavorable prognosis. Therefore, we think that patients with the disease may benefit from complete surgical resection and uninterrupted adjuvant therapy.