bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coarse to superfine: can hyperspectral soil organic carbon models predict higher-resolution information?
Authors: Kabiri Shayan , O’Rourke Sharon M. 
Published: July 2024

Introduction: Modeling and mapping of soil organic carbon concentration and distribution at the pedon scale is a current knowledge gap that can be addressed by laboratory-based hyperspectral imaging and chemometric analysis of soil cores. Despite the advancements in soil organic carbon models based on hyperspectral images, it is not clear how these models will perform upon input with images at higher resolutions than those of their training sets. This study aims to measure the generalizability of a soil organic carbon model based on a test set with higher resolution hyperspectral images than that of its training set.Methods: Organic carbon contents were measured at 10 cm intervals on eight soil cores for use as the training set and at 1 cm intervals on a single core for use as the test set. Three regression models, namely, multilayer perceptron, partial least-squares, and support vector regressions, were trained and tested with the median of each hyperspectral image for each of these intervals as the training and test predictors. Permutation importance analysis was performed to explain the models.Results: The results show that although all three models had the same validation R2 of 0.92 for cross-validation on the 10 cm data, multilayer perceptron regression allowed the best generalization with a test R2 of 0.96 compared to the partial least-squares regression (0.81) and support vector regression (0.86). It was demonstrated that the multilayer perceptron model is more robust to soil surface anomalies and that it predicts soil organic carbon on the test set by learning the spectral features related to soil organic matter chromophore activity in the 950–1,150 nm region along with clay mineralogy derived from peaks at 1,400, 1,900, 2,200, 2,250, and 2,350 nm.Conclusions: This study shows that while the regression models based on hyperspectral images perform well at the 10-cm-resolution cross validation, multilayer perceptron regression shows superior generalization and robustness for a higher 1-cm-resolution test set without much loss of prediction power.
Integrative analysis of the ovarian metabolome and transcriptome of the Yaoshan chicken and its improved hybrids
Authors: Miao Xiaomeng , Wu Tian , Pan Hongyuan , Zhang Yalan , Liu Jia , Fan Ying , Du Lin , Gong Yu , Li Liang , Huang Tengda , Ning Zhonghua 
Published: July 2024

Introduction: Laying performance is a key factor affecting production efficiency in poultry, but its molecular mechanism is still indistinct. In this study, Yaoshan chickens, a local breed in Guizhou, China, and merchant chickens (GYR) with higher egg yield after the three-line cross improvement hybridization of Yaoshan chickens were used as animal samples.Methods: To explore the regulatory mechanism of the diversities in laying performance, RNA-seq and ultra-performance liquid chromatographytandem mass spectrometry (UPLC—MS/MS) were used to describe the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens.Results: At the transcriptional level, 288 differentially expressed genes were upregulated in Yaoshan chickens and 353 differentially expressed genes were upregulated in GYR chickens. In addition, GSEA showed that ECM-receptor interactions and the TGF-β signaling pathway were restrained, resulting in increased egg production in GYR chickens. Furthermore, the upregulation of thiamine and carnitine was identified by metabolomic analysis to facilitate the laying performance of hens. Finally, comprehensive analyses of the transcriptome and metabolome found that thiamine and carnitine were negatively correlated with ECM-receptor interactions and the TGF-β signaling pathway, which jointly regulate the laying performance of Yaoshan chickens and GYR chickens.Discussion: Taken together, our research delineates differences in the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens during the peak egg production period and provides new hypotheses and clues for further research on poultry egg production performance and the improvement of economic benefits.
Timing of maternal vaccination against COVID-19 for effective protection of neonates: cohort study
Authors: Nowakowska Aleksandra , Lee Seung Mi , Kim Minjee , Chun Jungmin , Kim Sehyun , Kim Byung Chul , In Hyun Ju , Lee Eunji , Lee Chanyeong , Lee Hyeondong , Jang Yuyeon , Cho Hansam , Kim Jinha , Lee Jeesun , Lee Hee-Jung , Lee Yoo-Kyoung , Park Joong Shin , Kim Young Bong 
Published: July 2024

IntroductionAlthough the safety and effectiveness of COVID-19 vaccination during pregnancy have been proven, there is still little data explaining neonatal outcomes of maternal pre-pregnancy vaccination.MethodsHere, we investigated the impact of vaccination and SARS-CoV-2 infection on maternal-neonate immune response in a cohort study involving 141 pregnant individuals, and defined the importance of maternal COVID-19 vaccination timing for its effectiveness.Results and discussionOur data indicate that vertically transferred maternal hybrid immunity provides significantly better antiviral protection for a neonate than either maternal post-infection or post-vaccination immunity alone. Higher neutralization potency among mothers immunized before pregnancy and their newborns highlights the promising role of pre-pregnancy vaccination in neonatal protection. A comparison of neutralizing antibody titers calculated for each dyad suggests that infection and pre-/during-pregnancy vaccination all support transplacental transfer, providing the offspring with strong passive immunity against SARS-CoV-2. Analysis of neutralizing antibody levels in maternal sera collected during pregnancy and later during delivery shows that immunization may exert a positive effect on maternal protection.
Gastric cancer fibroblasts affect the effect of immunotherapy and patient prognosis by inducing micro-vascular production
Authors: Xia Yan , Wang Xiaolu , Lin Jie , Li Yuan , Dong Lidan , Liang Xue , Wang Huai-Yu , Ding Xia , Wang Qi 
Published: July 2024

IntroductionImmunotherapy is critical for treating many cancers, and its therapeutic success is linked to the tumor microenvironment. Although anti-angiogenic drugs are used to treat gastric cancer (GC), their efficacy remains limited. Cancer-associated fibroblast (CAF)-targeted therapies complement immunotherapy; however, the lack of CAF-specific markers poses a challenge. Therefore, we developed a CAF angiogenesis prognostic score (CAPS) system to evaluate prognosis and immunotherapy response in patients with GC, aiming to improve patient stratification and treatment efficacy.MethodsWe assessed patient-derived GC CAFs for promoting angiogenesis using EdU, cell cycle, apoptosis, wound healing, and angiogenesis analysis.ResultsWe then identified CAF-angiogenesis-associated differentially-expressed genes, leading to the development of CAPS, which included THBS1, SPARC, EDNRA, and VCAN. We used RT-qPCR to conduct gene-level validation, and eight GEO datasets and the HPA database to validate the CAPS system at the gene and protein levels. Six independent GEO datasets were utilized for validation. Overall survival time was shorter in the high- than the low-CAPS group. Immune microenvironment and immunotherapy response analysis showed that the high-CAPS group had a greater tendency toward immune escape and reduced immunotherapy efficacy than the low-CAPS group.DiscussionCAPS is closely associated with GC prognosis and immunotherapy outcomes. It is therefore an independent predictor of GC prognosis and immunotherapy efficacy.
Lactococcus lactis subsp. cremoris YRC3780 modifies function of mesenteric lymph node dendritic cells to modulate the balance of T cell differentiation inducing regulatory T cells
Authors: Nakagawa Ryogo , Gu Wenting , Mizobuchi Hibine , Kodera Shuhei , Takano Tomohiro , Wang Yimei , Fujioka Ikumi , Uchida Kenji , Nakajima-Adachi Haruyo , Hachimura Satoshi 
Published: July 2024

IntroductionThe intestinal immune system plays a pivotal role in the induction of immune responses against food. In the case of T cell response, dendritic cells (DCs) are especially important. However, the regulation of immune responses to food by intestinal DCs has been poorly described. In this study, we analyzed the effect of Lactococcus lactis subsp. cremoris YRC3780, a lactic acid bacterial strain isolated from kefir, a traditional fermented milk product, on the immune responses induced by antigen presentation by intestinal DCs to T cells as well as the mechanism of action of these immunomodulatory effects. It has been shown that L. cremoris YRC3780 ameliorates the symptoms of pollinosis in both animal and human studies.MethodsCD11c+ cells from mesenteric lymph nodes (MLNs) of BALB/c mice were cultured as MLN DCs with L. cremoris YRC3780 and expression of genes inducing regulatory T cells (Tregs) was examined by qPCR. In addition, MLN DCs were cocultured with CD4+ T cells from DO11.10 transgenic mice expressing an ovalbumin (OVA)-specific TCR and the OVA antigen peptide and L. cremoris YRC3780. Induction of Tregs was examined by flow cytometry, gene expression was analyzed by DNA microarray and qPCR, and the production of cytokines was measured by ELISA. MLN DCs from TLR2-deficient mice and components of L. cremoris YRC3780 were used to examine the recognition of YRC3780 by MLN DCs.ResultsL. cremoris YRC3780 enhanced the expression of genes involved in Treg induction in MLN DCs and induced Foxp3+CD4+T cells in an MLN DC and CD4+ T-cell co-culture system. The effect on MLN DCs was likely mediated by receptors other than TLR2. Together with microarray analyses of CD4+ T cell gene expression and cytokine ELISA, it was demonstrated that L. cremoris YRC3780 promoted the induction of Th1 and Tregs, and regulated the balance of Th1/Th2 and Treg/Th17 cells involving multiple genes via the antigen-presentation of MLN DCs.DiscussionOur findings provide insights into the modulation of intestinal immune responses mediated by DCs and the antiallergic effects of lactic acid bacteria.
Novel predictors of intravenous immunoglobulin resistance in patients with Kawasaki disease: a retrospective study
Authors: Yi Cong , Zhou Yu-Neng , Guo Jun , Chen Jia , She Xiang 
Published: July 2024

ObjectiveThe aim of this study was to investigate the predictive value of systemic immune inflammation index (SII), systemic inflammatory response index (SIRI), and pan-immune inflammation value (PIV) in predicting intravenous immunoglobulin (IVIG) resistance in children diagnosed with Kawasaki disease (KD).MethodsThe clinical data of pediatric patients diagnosed with Kawasaki disease and admitted to our hospital between January 2006 and December 2022 were retrospectively analyzed.ResultsIn total, 771 children diagnosed with KD were included in this study, 86 (11.2%) of whom were diagnosed with IVIG resistance. The correlation between SII, SIRI, PIV and IVIG resistance was evaluated using univariate testing, binary logistic regression analysis, and receiver operating characteristic (ROC) curve analysis. Our study found that the SII, SIRI, and PIV were independent risk factors (p=0.001, p&lt;0.001, and p=0.02, respectively). The area under the ROC curve (AUC) values of the SII, SIRI, and PIV were 0.626 (95% confidence interval (CI): 0.553–0.698, p&lt;0.001), 0.571 (95% CI: 0.500–0.642, p=0.032), and 0.568 (95% CI: 0.495–0.641, p=0.040), respectively, and the cutoff values were 2209.66, 3.77, and 1387.825, respectively.ConclusionThe SII, SIRI, and PIV have potential value in predicting IVIG resistance in patients with KD.
Puppies as the primary causal animal for human rabies cases: three-year prospective study of human rabies in the Philippines
Authors: Saito Nobuo , Inton Karren L. , Mauhay Jaira D. , Solante Rontgene M. , Guzman Ferdinand D. , Yamada Kentaro , Kamiya Yasuhiko , Saito-Obata Mariko , Quiambao Beatriz P. , Yahiro Takaaki , Kimitsuki Kazunori , Nishizono Akira 
Published: July 2024

IntroductionWhile rabies remains a global concern, detailed studies on human rabies, particularly regarding causal animals and the reasons for not receiving postexposure prophylaxis (PEP), are lacking.MethodsWe conducted a 3-year prospective study (October 2019–September 2022) at the Philippines’ largest rabies referral center. We interviewed patients with suspected rabies and their families. We used LN34 qRT-PCR and rapid fluorescent focus inhibition test on saliva samples. We also compared our findings with two retrospective studies at the same hospital.ResultsWe enrolled 151 patients, including 131 with potential rabies exposure. Similar to retrospective studies, the participants were predominantly males (75.5%), adults (76.8%), low-income individuals (91.4%), and rural dwellers (62.3%). The causal animals were mainly dogs (97.0%), with similar incubation periods, clinical symptoms, and a high proportion not receiving vaccines or immunoglobulins (93.2%). Most causal animals were owned by either the patients’ households or their neighbors (60.2%), with a significant proportion being puppies (58.8%). Most patients had knowledge of rabies; however, reasons for not seeking PEP included misconceptions about minor bites not causing rabies (51.3%), beliefs in traditional healers (33.9%), and economic constraints (22.6%). Despite completing the WHO regimen, two PEP failures were observed. LN34 qRT-PCR detected 98 positive cases (sensitivity, 64.9%; 95% CI 56.7–72.5). These strains belong to the Southeast Asia 4 subclade.DiscussionIn conclusion, this study highlights the role of puppies as primary causal animals and the presence of misconceptions that preclude patients from acquiring PEP.
Repeating late-phase pseudo-progression in a patient with non-small cell lung cancer treated with long-term nivolumab monotherapy; a case report
Authors: Ebisuda Rikako , Furuya Naoki , Inoue Takeo , Kaneko Shotaro , Numata Yu , Shinozaki Yusuke , Mineshita Masamichi 
Published: July 2024

BackgroundImmune check point inhibitors (ICIs) are standard treatment for patients with non-small cell lung cancer (NSCLC). Nearly a decade has passed since nivolumab was approved by the FDA for NSCLC patients. However, long-term outcomes and clinical features remain unclear for individual cases. Pseudo-progression is a well-known paradoxical radiological response pattern under ICI treatment which occurs when tumor index lesions regress after apparent initial progression. We herein report a unique case of NSCLC with repeating pseudo-progression in late phase treated with nivolumab monotherapy for 8.5 years.Case presentationA 56-year-old male diagnosed with Non-sq NSCLC clinical stage IVA, at the left upper lobe primary lesion. The primary lesion was PD-L1 negative with no oncogenic driver mutations. He had multiple pulmonary metastases and a left adrenal gland metastasis, and subsequently, received nivolumab as third-line therapy. After initiation of nivolumab, the lung lesion and adrenal metastasis shrank rapidly; however, the patient experienced three late-phase pseudo-progressions in the mediastinal lymph node (LN). This patient is still receiving nivolumab with no symptoms and PS 0. Acquired resistance should be judged carefully in patients with LN-only oligo-progression to avoid unnecessary local therapies and the misjudgment of treatment.
ECM1 and ANXA1 in urinary extracellular vesicles serve as biomarkers for breast cancer
Authors: Huang Hai , Wan Jingyu , Ao Xudong , Qu Shuang , Jia Meng , Zhao Keyu , Liang Junqing , Zen Ke , Liang Hongwei 
Published: July 2024

ObjectiveAlthough urinary extracellular vesicles (uEVs) have been extensively studied in various cancers, their involvement in breast cancer (BC) remains largely unexplored. The non-invasive nature of urine as a biofluid and its abundant protein content offer considerable potential for the early detection of breast cancer.MethodsThis study analyzed the proteomic profiles of uEVs from BC patients and healthy controls (HC). The dysregulation of ECM1 and ANXA1 in the uEVs was validated in a larger cohort of 128 BC patients, 25 HC and 25 benign breast nodules (BBN) by chemiluminescence assay (CLIA). The expression levels of ECM1 and ANXA1 were also confirmed in the uEVs of MMTV-PyMT transgenic breast cancer mouse models.ResultsLC-MS/MS analysis identified 571 dysregulated proteins in the uEVs of BC patients. ECM1 and ANXA1 were selected for validation in 128 BC patients, 25 HC and 25 BBN using CLIA, as their fold change showed a significant difference of more than 10 with p-value&lt;0.05. Protein levels of ECM1 and ANXA1 in uEVs were significantly increased in BC patients. In addition, the protein levels of ECM1 and ANXA1 in the uEVs of MMTV-PyMT transgenic mice were observed to increase progressively with the progression of breast cancer.ConclusionWe developed a simple and purification-free assay platform to isolate uEVs and quantitatively detect ECM1 and ANXA1 in uEVs by WGA-coupled magnetic beads and CLIA. Our results suggest that ECM1 and ANXA1 in uEVs could potentially serve as diagnostic biomarkers for breast cancer.
Unveiling the landscape of pathomics in personalized immunotherapy for lung cancer: a bibliometric analysis
Authors: Yuan Lei , Shen Zhiming , Shan Yibo , Zhu Jianwei , Wang Qi , Lu Yi , Shi Hongcan 
Published: July 2024

BackgroundPathomics has emerged as a promising biomarker that could facilitate personalized immunotherapy in lung cancer. It is essential to elucidate the global research trends and emerging prospects in this domain.MethodsThe annual distribution, journals, authors, countries, institutions, and keywords of articles published between 2018 and 2023 were visualized and analyzed using CiteSpace and other bibliometric tools.ResultsA total of 109 relevant articles or reviews were included, demonstrating an overall upward trend; The terms “deep learning”, “tumor microenvironment”, “biomarkers”, “image analysis”, “immunotherapy”, and “survival prediction”, etc. are hot keywords in this field.ConclusionIn future research endeavors, advanced methodologies involving artificial intelligence and pathomics will be deployed for the digital analysis of tumor tissues and the tumor microenvironment in lung cancer patients, leveraging histopathological tissue sections. Through the integration of comprehensive multi-omics data, this strategy aims to enhance the depth of assessment, characterization, and understanding of the tumor microenvironment, thereby elucidating a broader spectrum of tumor features. Consequently, the development of a multimodal fusion model will ensue, enabling precise evaluation of personalized immunotherapy efficacy and prognosis for lung cancer patients, potentially establishing a pivotal frontier in this domain of investigation.
Laparoscopic-assisted sclerotherapy in pediatric retroperitoneal lymphatic malformations
Authors: Shi Hao , Lv Zhibao , Xu Weijue , Liu Jiangbin , Sheng Qingfeng , Ren Xiang , Chen Zhou 
Published: July 2024

BackgroundRetroperitoneal lymphatic malformations (LMs) are rare. Currently, the treatment of retroperitoneal LMs remains challenging. This study aimed to examine the safety and efficacy of laparoscopic-assisted sclerotherapy for retroperitoneal LMs in pediatric patients.MethodsWe retrospectively reviewed patients treated with laparoscopic-assisted sclerotherapy for retroperitoneal LMs in a single tertiary medical center between July 2020 and February 2023. Doxycycline was prepared into a solution with a concentration of 10 mg/ml for use in sclerotherapy. Demographic data, clinical features, details of management, and outcomes were collected and analyzed.ResultsA total of six patients, comprising three males and three females, were identified. The LMs were categorized into four macrocystic and two mixed-cystic types. The mean age and weight were 52.2 months (range, 11–108 months) and 20 kg (range, 12.5–27.5 kg), respectively. Three patients presented with abdominal pain or distension, while the other three patients were asymptomatic. All six patients underwent a total of eight sclerotherapy sessions. Two patients experienced intra-cystic hemorrhage and required a second sclerotherapy session. Only one patient presented with vomiting after sclerotherapy, which resolved spontaneously. Five patients met the complete response criteria, and one patient met the effective criteria. The mean reduction in lesion size was 92.3% (range, 69.9%–99.6%). No further complications or recurrence were recorded during follow-up.ConclusionLaparoscopic-assisted sclerotherapy is a safe and effective approach for treating retroperitoneal LMs. This technique is applicable for both macrocystic and mixed-cystic retroperitoneal LMs.
Knockout of C1q/tumor necrosis factor-related protein-9 aggravates cardiac fibrosis in diabetic mice by regulating YAP-mediated autophagy
Authors: Ruan Shiyan , Li Jun , Lei Shengyun , Zhang Shaomeng , Xu Dan , Zuo Anju , Li Linxi , Guo Yuan 
Published: July 2024

IntroductionDiabetic cardiomyopathy (DCM) is predominantly distinguished by impairment in ventricular function and myocardial fibrosis. Previous studies revealed the cardioprotective properties of C1q/tumor necrosis factor-related protein 9 (CTRP9). However, whether CTRP9 affects diabetic myocardial fibrosis and its underlying mechanisms remains unclear.MethodsWe developed a type 1 diabetes (T1DM) model in CTRP9-KO mice via streptozotocin (STZ) induction to examine cardiac function, histopathology, fibrosis extent, Yes-associated protein (YAP) expression, and the expression of markers for autophagy such LC3-II and p62. Additionally, we analyzed the direct impact of CTRP9 on high glucose (HG)-induced transdifferentiation, autophagic activity, and YAP protein levels in cardiac fibroblasts.ResultsIn diabetic mice, CTRP9 expression was decreased in the heart. The absence of CTRP9 aggravated cardiac dysfunction and fibrosis in mice with diabetes, alongside increased YAP expression and impaired autophagy. In vitro, HG induced the activation of myocardial fibroblasts, which demonstrated elevated cell proliferation, collagen production, and α-smooth muscle actin (α-SMA) expression. CTRP9 countered these adverse effects by restoring autophagy and reducing YAP protein levels in cardiac fibroblasts. Notably, the protective effects of CTRP9 were negated by the inhibition of autophagy with chloroquine (CQ) or by YAP overexpression through plasmid intervention. Notably, the protective effect of CTRP9 was negated by inhibition of autophagy caused by chloroquine (CQ) or plasmid intervention with YAP overexpression.DiscussionOur findings suggest that CTRP9 can enhance cardiac function and mitigate cardiac remodeling in DCM through the regulation of YAP-mediated autophagy. CTRP9 holds promise as a potential candidate for pharmacotherapy in managing diabetic cardiac fibrosis.