bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feed plants, ethnoveterinary medicine, and biocultural values: insights on the Luchuan pig from Hakka communities in China
Authors: Liufu Yongqing , Zhou Jilong , Fu Qiongyao , Shao Min , Xie Yaozhang , Luo Binsheng 
Published: September 2023

Abstract
Background
The Luchuan pig is an indigenous breed from Luchuan County, China, with cultural and genetic significance. However, traditional knowledge and conservation status have not been systematically documented.

Methods
Using ethnobiological methods, we surveyed 72 Luchuan pig farmers in 7 townships during 2021–2023. Semi-structured interviews and participant observation were conducted to document traditional knowledge and management practices.

Results
The locals reported 51 plant species used as pig feed, with 30 wild species. Growth-stage-specific feeding and seasonal adjustment practices were documented. We recorded 62 ethnoveterinary plant uses, mainly for treating pigs' heat stress and skin conditions. Luchuan pigs play central roles in local Hakka customs, rituals, and cuisine. Additonally, the new ecological farming models minimize the environmental impacts to the local community. However, there are still some challenges remained for conserving and promoting Luchuan pigs.

Conclusions
The Luchuan Hakka people possess rich traditional knowledge and management experience in raising Luchuan pigs. Our study provides extensive documentation of traditional knowledge and recommends integrating cultural and genetic aspects for sustaining this biocultural heritage. Findings can inform initiatives supporting local breed conservation globally.
Causal associations of Sjögren’s syndrome with cancers: a two-sample Mendelian randomization study
Authors: Jia Yiwei , Yao Peizhuo , Li Jia , Wei Xinyu , Liu Xuanyu , Wu Huizi , Wang Weiwei , Feng Cong , Li Chaofan , Zhang Yu , Cai Yifan , Zhang Shuqun , Ma Xingcong 
Published: September 2023

Abstract
Background
Several observational studies have explored the associations between Sjögren’s syndrome (SS) and certain cancers. Nevertheless, the causal relationships remain unclear. Mendelian randomization (MR) method was used to investigate the causality between SS and different types of cancers.

Methods
We conducted the two-sample Mendelian randomization with the public genome-wide association studies (GWASs) summary statistics in European population to evaluate the causality between SS and nine types of cancers. The sample size varies from 1080 to 372,373. The inverse variance weighted (IVW) method was used to estimate the causal effects. A Bonferroni-corrected threshold of P < 0.0031 was considered significant, and P value between 0.0031 and 0.05 was considered to be suggestive of an association. Sensitivity analysis was performed to validate the causality. Moreover, additional analysis was used to assess the associations between SS and well-accepted risk factors of cancers.

Results
After correcting the heterogeneity and horizontal pleiotropy, the results indicated that patients with SS were significantly associated with an increased risk of lymphomas (odds ratio [OR] = 1.0010, 95% confidence interval [CI]: 1.0005–1.0015, P = 0.0002) and reduced risks of prostate cancer (OR = 0.9972, 95% CI: 0.9960–0.9985, P = 2.45 × 10−5) and endometrial cancer (OR = 0.9414, 95% CI: 0.9158–0.9676, P = 1.65 × 10−5). Suggestive associations were found in liver and bile duct cancer (OR = 0.9999, 95% CI: 0.9997–1.0000, P = 0.0291) and cancer of urinary tract (OR = 0.9996, 95% CI: 0.9992–1.0000, P = 0.0281). No causal effect of SS on other cancer types was detected. Additional MR analysis indicated that causal effects between SS and cancers were not mediated by the well-accepted risk factors of cancers. No evidence of the causal relationship was observed for cancers on SS.

Conclusions
SS had significant causal relationships with lymphomas, prostate cancer, and endometrial cancer, and suggestive evidence of association was found in liver and bile duct cancer and cancer of urinary tract, indicating that SS may play a vital role in the incidence of these malignancies.
Appendiceal mucocele as an exceptional cause of ileocecocolic intussusception in adults: a case report
Authors: Zabeirou Aliou , Efared Boubacar , James Didier Lassey , Younssa Hama , Adama Saidou , Moussa Younoussa , Rachid Sani 
Published: September 2023

Abstract
Background
Intussusception is a rare condition in adults, accounting for 5% of intestinal intussusception and being responsible for approximately 1% of all adult bowel obstructions. Neoplastic origin is the most common etiology of intestinal intussusception in adults, unlike pediatric intussusception, which is usually idiopathic. Intussusception due to the appendiceal mucocele is exceptional, and only a few cases have been reported in the medical literature.

Case presentation
We report the case of a 25-year-old black African male patient with no medical history. He presented to the emergency department for abdominal pain, nausea, and bilious vomiting. The abdominal examination revealed typical signs of acute bowel obstruction. Enhanced abdominopelvic computed tomography showed an invagination of the last ileal loop, cecum, and ascending colon into the lumen of the transverse colon, with a rounded image with hypodense content and some calcifications compatible with an appendiceal mucocele. An emergency exploratory laparoscopy was performed and confirmed the ileocecocolic intussusception. Right hemicolectomy and ileocolic anastomosis were performed. The patient recovery postoperatively was uneventful, and he was discharged 4 days later. Histological examination of the surgical specimen confirmed the diagnosis of mucinous cystadenoma.

Conclusion
The symptoms of bowel intussusception with the appendiceal mucocele as the lead point in adults are similar to any other bowel intussusception. Differential diagnosis is often carried out thanks to the injected abdominal computed tomography scan.
rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation
Authors: Baquer Gerard , Sementé Lluc , Ràfols Pere , Martín-Saiz Lucía , Bookmeyer Christoph , Fernández José A. , Correig Xavier , García-Altares María 
Published: September 2023

AbstractMatrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) spatially resolves the chemical composition of tissues. Lipids are of particular interest, as they influence important biological processes in health and disease. However, the identification of lipids in MALDI-MSI remains a challenge due to the lack of chromatographic separation or untargeted tandem mass spectrometry. Recent studies have proposed the use of MALDI in-source fragmentation to infer structural information and aid identification. Here we present rMSIfragment, an open-source R package that exploits known adducts and fragmentation pathways to confidently annotate lipids in MALDI-MSI. The annotations are ranked using a novel score that demonstrates an area under the curve of 0.7 in ROC analyses using HPLC–MS and Target-Decoy validations. rMSIfragment applies to multiple MALDI-MSI sample types and experimental setups. Finally, we demonstrate that overlooking in-source fragments increases the number of incorrect annotations. Annotation workflows should consider in-source fragmentation tools such as rMSIfragment to increase annotation confidence and reduce the number of false positives.
A 14-year series of leaf phenological data collected for European beech (Fagus sylvatica L.) and silver fir (Abies alba Mill.) from their geographic range margins in south-eastern France
Authors: Jean Frederic , Davi Hendrik , Oddou-Muratorio Sylvie , Fady Bruno , Scotti Ivan , Scotti-Saintagne Caroline , Ruffault Julien , Journe Valentin , Clastre Philippe , Marloie Olivier , Brunetto William , Correard Marianne , Gilg Olivier , Pringarbe Mehdi , Rei Franck , Thevenet Jean , Turion Norbert , Pichot Christian 
Published: September 2023

Key messagePhenology is of increasing interest to climate change science and adaptation ecology. Here, we provide bud development, leafing, and leaf senescence data, collected on 772 European beech and silver fir trees between 2006 and 2019 on Mont Ventoux, France. Dataset access is at https://doi.org/10.15454/TRFMZN. Associated metadata are available at https://metadata-afs.nancy.inra.fr/geonetwork/srv/fre/catalog.search#/metadata/a33c8375-9a90-4bc3-a0d7-19317160b68f.
Paedoksan ameliorates allergic disease through inhibition of the phosphorylation of STAT6 in DNCB-induced atopic dermatitis like mice
Authors: Lee Sang Heon , Oh Youngse , Bong Sim-Kyu , Lee Jin Woo , Park No-June , Kim Young-Joo , Park Hyun Bong , Kim Yong Kee , Kim Seung Hyun , Kim Su-Nam 
Published: September 2023

AbstractVarious allergic diseases such as atopic dermatitis (AD), allergic rhinitis, and asthma are considered incurable conditions that have yet to be fully conquered. Paedoksan (PDS), an herbal preparation consisting of 14 medicines, displays effective anti-inflammatory and anti-allergic properties, yet its underlying molecular mechanism is unknown. This study aims to uncover PDS’s mechanism for treating allergic diseases and suggest its therapeutic potential. Through a network pharmacological prediction, its impact on signal transducer and activator of transcription 6 (STAT6) regulation, a sub-mechanism of interleukin 4 (IL-4), a major inflammatory cytokine involved in degranulation and allergy, was investigated in RBL-2H3 cells and an atopic mouse model. PDS inhibits immunoglobulin E (IgE)-induced degranulation and STAT6 phosphorylation evoked by IL-4 in granulocytes. The downregulation of phospho-STAT6 and thymic stromal lymphopoietin (TSLP) by PDS was confirmed in 2,4-dinitrochlorobenzene (DNCB)-induced mouse skin. The results demonstrate that PDS exhibited remarkable effects on degranulation and STAT6 phosphorylation in RBL-2H3 cells, as well as in an atopic mouse model. Furthermore, the main active components from PDS based on chromatographic analysis showed good accordance with PDS’s effects on RBL-2H3 cells. In summary, these findings collectively suggest that PDS holds the potential to effectively suppress inflammatory and allergic reactions by obstructing the target IL-4 protein and its downstream effects, as elucidated through a network pharmacological analysis.
Chest computed tomography severity score is a reliable predictor of mortality in patients with chronic obstructive pulmonary disease co-infected with COVID-19
Authors: Alipour Khabir Yalda , Alipour Khabir Sevda , Anari Hassan , Mohammadzadeh Bahman , Hoseininia Saeed , Aslani Mohammad Reza 
Published: September 2023

Abstract
Background
Coronavirus disease 2019 (COVID-19) pandemic is considered a global health crisis. The data related to chronic obstructive pulmonary disease (COPD) patients with COVID-19 are incomplete, especially the findings of the chest computed tomography (CT). The aim of the current study was to investigate the severity of the disease of COVID-19 in patients with COPD based on CT severity score and to evaluate its predictive power in the mortality of patients.

Methods
In a retrospective study, demographic, clinical, and CT scan findings of COPD patients with COVID-19 were extracted from March 2020 to February 2022. CT severity score was determined based on the extent and nature of involvement of lungs in CT scan findings. By performing receiver operating characteristics (ROC) and Kaplan–Meier survival analysis were determined the disease severity and survival probability.

Results
The most frequent radiological findings in chest CT scan included ground glass opacities (89.3%), consolidations (51.8%), crazy-paving pattern (46.4%), and septal thickening (35.7%). The mean CT severity score of deceased patients (34.61 ± 18.73) was significantly higher than recovered patients (16.71 ± 14.01, p < 0.001). Based on the ROC and Kaplan–Meier survival curves, it was revealed that CT severity score was a valuable criteria in the diagnosis of mortality in COPD patients with COVID-19.

Conclusion
The findings of this study revealed that the CT severity scoring in COPD patients with COVID-19 was valuable in identifying poor prognosis, although further studies are needed.
Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua
Authors: Mills Molly , Lee Seungjun , Piperata Barbara A. , Garabed Rebecca , Choi Boseung , Lee Jiyoung 
Published: September 2023

Abstract
Background
Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure.

Results
This study investigated the gut microbiome and resistome of infants and young children (ages 4 days-6 years) in rural Nicaragua using Oxford Nanopore Technology’s MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae, particularly Escherichia coli.

Conclusions
This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health.

Graphical Abstract
Identification of molecular signatures and pathways involved in Rett syndrome using a multi-omics approach
Authors: Pascual-Alonso Ainhoa , Xiol Clara , Smirnov Dmitrii , Kopajtich Robert , Prokisch Holger , Armstrong Judith 
Published: September 2023

Abstract
Background
Rett syndrome (RTT) is a neurodevelopmental disorder mainly caused by mutations in the methyl-CpG-binding protein 2 gene (MECP2). MeCP2 is a multi-functional protein involved in many cellular processes, but the mechanisms by which its dysfunction causes disease are not fully understood. The duplication of the MECP2 gene causes a distinct disorder called MECP2 duplication syndrome (MDS), highlighting the importance of tightly regulating its dosage for proper cellular function. Additionally, some patients with mutations in genes other than MECP2 exhibit phenotypic similarities with RTT, indicating that these genes may also play a role in similar cellular functions. The purpose of this study was to characterise the molecular alterations in patients with RTT in order to identify potential biomarkers or therapeutic targets for this disorder.

Methods
We used a combination of transcriptomics (RNAseq) and proteomics (TMT mass spectrometry) to characterise the expression patterns in fibroblast cell lines from 22 patients with RTT and detected mutation in MECP2, 15 patients with MDS, 12 patients with RTT-like phenotypes and 13 healthy controls. Transcriptomics and proteomics data were used to identify differentially expressed genes at both RNA and protein levels, which were further inspected via enrichment and upstream regulator analyses and compared to find shared features in patients with RTT.

Results
We identified molecular alterations in cellular functions and pathways that may contribute to the disease phenotype in patients with RTT, such as deregulated cytoskeletal components, vesicular transport elements, ribosomal subunits and mRNA processing machinery. We also compared RTT expression profiles with those of MDS seeking changes in opposite directions that could lead to the identification of MeCP2 direct targets. Some of the deregulated transcripts and proteins were consistently affected in patients with RTT-like phenotypes, revealing potentially relevant molecular processes in patients with overlapping traits and different genetic aetiology.

Conclusions
The integration of data in a multi-omics analysis has helped to interpret the molecular consequences of MECP2 dysfunction, contributing to the characterisation of the molecular landscape in patients with RTT. The comparison with MDS provides knowledge of MeCP2 direct targets, whilst the correlation with RTT-like phenotypes highlights processes potentially contributing to the pathomechanism leading these disorders.
Language-dependent cue weighting in distinctive feature: evidence from the perception of Mandarin high vowels by native English speakers
Authors: Zhu Wenhui , Lee Sun-Hee , Zhang Xinting 
Published: September 2023

AbstractThis study investigates the perception of the three Mandarin high vowels /i, u, y/ after dental, retroflex, and palatal fricatives and affricates (/s/-/ʦ/-/ʦʰ/; /ʂ/-/tʂ/-/tʂʰ/, and /ʨ/, /ʨʰ/, /ɕ/) by native English speakers. The results of the perceptual identification and categorization experiments show that among the three target vowels, the high front rounded vowel /y/ presents the greatest challenge for native English speakers. They have a significantly higher tendency to confuse /y/ with the Mandarin high-back rounded vowel /u/ compared to the Mandarin high-front unrounded vowel /i/, as they perceptually classified /y/ and /u/ into the same English vowel category /u/. The findings of the study suggest that native English speakers adopt a perceptual strategy that differs from that of native Japanese and Korean speakers, relying heavier on the feature of roundness as opposed to backness in perceiving the Mandarin /y/. This study contributes to the perceptual cue weighting field by examining the weighting of phonetic cues (i.e., distinctive features) in Mandarin high vowels by native English speakers. These results hold pedagogical significance as they highlight the importance of targeted perception training for learners of different language backgrounds to enhance both their recognition and reproduction of second language sounds.
Predicting volatility of bitcoin returns with ARCH, GARCH and EGARCH models
Authors: Yıldırım Hakan , Bekun Festus Victor 
Published: September 2023

AbstractThe ınvestment decisions of institutional and individual investors in financial markets are largely influenced by market uncertainty and volatility of the investment instruments. Thus, the prediction of the uncertainty and volatilities of the prices and returns of the investment instruments becomes imperative for successful investment. In this study we seek to identify the best fit model that can predict the volatility of return of Bitcoin, which is in high demand as an investment tool in recent times. Using the opening data of weekly Bitcoin prices for the period of 11.24.2013–03.22.2020, their logarithmic returns were calculated. The stationarity properties of the Bitcoin return series was tested by applying the ADF unit root test and the series were found to be stationary. After reaching the average equation model as ARMA (2.2), it was tested whether there was an ARCH effect in the ARMA (2,2) model. As a result of the applied ARCH-LM test, it is reached that the residuals of the average equation model selected have ARCH effect. Volatility of Bitcoin return series after detection of ARCH effect has been tried to predict with conditional variance models such as ARCH (1), ARCH (2), ARCH (3), GARCH (1,1), GARCH (1,2), GARCH (1,3), GARCH (2,1), GARCH (2,2), EGARCH (1,1) and EGARCH (1,2). While the obtained findings indicate that the best model is in the direction of GARCH (1,1) according to Akaike info criterion, it was found that GARCH (1,1) model does not have ARCH effect as a result of the applied ARCH-LM test. Thus, our empirical findings highlight an ample guide on appropriate modeling of price information in the Bitcoin market.
Prognostic Factors in High-Grade Osteosarcoma of theExtremities or Trunk: An Analysis of 1,702 Patients Treatedon Neoadjuvant Cooperative Osteosarcoma Study GroupProtocols
Authors: Bielack Stefan S. , Kempf-Bielack Beate , Delling Günter , Exner G. Ulrich , Flege Silke , Helmke Knut , Kotz Rainer , Salzer-Kuntschik Mechthild , Werner Matthias , Winkelmann Winfried , Zoubek Andreas , Jürgens Heribert , Winkler Kurt 
Published: September 2023

PURPOSE: To define prognostic factors for response and long-term outcome for a wide spectrum of osteosarcomas, extending well beyond those of the typical young patient with seemingly localized extremity disease. PATIENTS AND METHODS: A total of 1,702 consecutive newly diagnosed patients with high-grade osteosarcoma of the trunk or limbs registered into the neoadjuvant studies of the Cooperative Osteosarcoma Study Group before July 1998 were entered into an analysis of demographic, tumor-related, and treatment-related variables, response, and survival. The intended therapeutic strategy included preoperative and postoperative chemotherapy with multiple agents as well as surgery of all operable lesions. RESULTS: Axial tumor site, male sex, and a long history of symptoms were associated with poor response to chemotherapy in univariate and multivariate analysis. Actuarial 10-year overall and event-free survival rates were 59.8% and 48.9%. Among the variables assessable at diagnosis, patient age (actuarial 10-year survival ≥ 40, 41.6%; < 40, 60.2%; P = .012), tumor site (axial, 29.2%; limb, 61.7%; P < .0001), and primary metastases (yes, 26.7%; no, 64.4%; P < .0001), and for extremity osteosarcomas, also size (≥ one third, 52.5%; < one third, 66.7%; P < .0001) and location within the limb (proximal, 49.3%; other, 63.9%; P < .0001), had significant influence on outcome. Two additional important prognostic factors were treatment related: response to chemotherapy (poor, 47.2%; good, 73.4%; P < .0001) and the extent of surgery (incomplete, 14.6%; macroscopically complete, 64.8%; P < .0001). All factors except age maintained their significance in multivariate testing, with surgical remission and histologic response emerging as the key prognostic factors. CONCLUSION: Tumor site and size, primary metastases, response to chemotherapy, and surgical remission are of independent prognostic value in osteosarcoma.
Hyperbolic cones for casual diffeomorphisms
Authors: Rahimi Moghbeli S. , Molaei M. R. 
Published: September 2023

Abstract
This paper begins with introducing a new class of diffeomorphisms on pseudo-Riemannian manifolds which are called casual diffeomorphisms. We deduce a new pseudo-Riemannian metric via a casual diffeomorphism. We introduce a class of cones for a diffeomorphism, and we prove the existence of such cones for each p in a hyperbolic set of a casual diffeomorphism. As an example we find a hyperbolic casual diffeomorphism on a Schwarzschild pseudo-Riemannian manifold, and show that the whole manifold is a hyperbolic set for it.