bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants
Authors: Sorkin Maria L. , Markham Kathleen K , Zorich Stevan , Menon Ananda , Edgeworth Kristen N. , Ricono Angela , Bryant Douglas , Bart Rebecca , Nusinow Dmitri A. , Greenham Kathleen 
Published: March 2023

Abstract
Background
Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive.

Results
We have developed self-assembled systems for both growing and monitoring plant fluorescence and bioluminescence for long-term experiments under controlled environmental conditions. This system combines environmental growth chambers with high-sensitivity CCD cameras, multi-wavelength LEDs, open-source software, and several options for coordinating lights with imaging. This easy-to-assemble system can be used for short and long-term imaging of bioluminescent reporters, acute light-response, circadian rhythms, delayed fluorescence, and fluorescent-protein-based assays in vivo.

Conclusions
We have developed two self-assembled imaging systems that will be useful to researchers interested in continuously monitoring in vivo reporter systems in various plant species.
A radiomics model for predicting the response to methylprednisolone in brain necrosis after radiotherapy for nasopharyngeal carcinoma
Authors: Zhuo Xiaohuang , Zhao Huiying , Chen Meiwei , Mu Youqing , Li Yi , Cai Jinhua , Li Honghong , Xu Yongteng , Tang Yamei 
Published: March 2023

Abstract
Background
Methylprednisolone is recommended as the front-line therapy for radiation-induced brain necrosis (RN) after radiotherapy for nasopharyngeal carcinoma. However, some patients fail to benefit from methylprednisolone or even progress. This study aimed to develop and validate a radiomic model to predict the response to methylprednisolone in RN.

Methods
Sixty-six patients receiving methylprednisolone were enrolled. In total, 961 radiomic features were extracted from the pre-treatment magnetic resonance imagings of the brain. Least absolute shrinkage and selection operator regression was then applied to construct the radiomics signature. Combined with independent clinical predictors, a radiomics model was built with multivariate logistic regression analysis. Discrimination, calibration and clinical usefulness of the model were assessed. The model was internally validated using 10-fold cross-validation.

Results
The radiomics signature consisted of 16 selected features and achieved favorable discrimination performance. The radiomics model incorporating the radiomics signature and the duration between radiotherapy and RN diagnosis, yielded an AUC of 0.966 and an optimism-corrected AUC of 0.967 via 10-fold cross-validation, which also revealed good discrimination. Calibration curves showed good agreement. Decision curve analysis confirmed the clinical utility of the model.

Conclusions
The presented radiomics model can be conveniently used to facilitate individualized prediction of the response to methylprednisolone in patients with RN.
Aryl hydrocarbon receptor nuclear translocator limits the recruitment and function of regulatory neutrophils against colorectal cancer by regulating the gut microbiota
Authors: Bi Yujing , Yang Qiuli , Li Zhengchao , Wang Yuexin , Wang Yufei , Jia Anna , Pan Zhiyuan , Yang Ruifu , Liu Guangwei 
Published: March 2023

Abstract
Background
Although the role and mechanism of neutrophils in tumors have been widely studied, the precise effects of aryl hydrocarbon receptor nuclear translocator (ARNT) on neutrophils remain unclear. In this study, we investigated the roles of ARNT in the function of CD11b+Gr1+ neutrophils in colitis-associated colorectal cancer.

Methods
Wild-type (WT), ARNT myeloid-specific deficient mice and a colitis-associated colorectal cancer mouse model were used in this study. The level and functions of CD11b+Gr1+ cells were evaluated by flow cytometry and confocal microscopy.

Results
We found that ARNT deficiency drives neutrophils recruitment, neutrophil extracellular trap (NET) development, inflammatory cytokine secretion and suppressive activities when cells enter the periphery from bone marrow upon colorectal tumorigenesis. ARNT deficiency displays similar effects to aryl hydrocarbon receptor (AHR) deficiency in neutrophils. CXCR2 is required for NET development, cytokine production and recruitment of neutrophils but not the suppressive activities induced by Arnt−/− in colorectal cancer. The gut microbiota is essential for functional alterations in Arnt−/− neutrophils to promote colorectal cancer growth. The colorectal cancer effects of Arnt−/− neutrophils were significantly restored by mouse cohousing or antibiotic treatment. Intragastric administration of the feces of Arnt−/− mice phenocopied their colorectal cancer effects.

Conclusion
Our results defined a new role for the transcription factor ARNT in regulating neutrophils recruitment and function and the gut microbiota with implications for the future combination of gut microbiota and immunotherapy approaches in colorectal cancer.
Is the diagnostic validity of conventional radiography for Lisfranc injury acceptable?
Authors: Chen Cheng , Jiang JianTao , Wang Cheng , Zou Jian , Shi ZhongMin , Yang YunFeng 
Published: March 2023

AbstractBackgroundLisfranc injuries mainly involve the tarsometatarsal joint complex and are commonly misdiagnosed or missed in clinical settings. Most medical institutions prefer to use conventional radiography. However, existing studies on conventional radiographs in Lisfranc injury lack a large population‐based sample, influencing the validity of the results. We aimed to determine the diagnostic validity and reliability of conventional radiography for Lisfranc injury and whether computed tomography can alter clinical decision‐making.MethodsThis retrospective study included 307 patients with, and 100 patients without, Lisfranc injury from January 2017 to December 2019. Diagnosis was confirmed using computed tomography. A senior and junior surgeon independently completed two assessments of the same set of anonymised conventional radiographs at least 3 months apart. The surgeons were then asked to suggest one of two treatment options (surgery or conservative treatment) for each case based on the radiographs and subsequently on the CT images.ResultsAll inter‐ and intra‐observer reliabilities were moderate to very good (all κ coefficients > 0.4). The mean (range) true positive rate was 81.8% (73.9%–87.0%), true negative rate was 90.0% (85.0%–94.0%), false positive rate was 10.0% (6.0%–15.0%), false negative rate was 18.2% (13.0%–26.1%), positive predictive value was 96.1% (93.8%–97.8%), negative predictive value was 62.4% (51.5%–69.7%), classification accuracy was 83.8% (76.7%–88.2%), and balanced error rate was 14.1% (10.2%–20.5%). Three‐column injuries were most likely to be recognized (mean rate, 92.1%), followed by intermediate‐lateral‐column injuries (mean rate, 81.5%). Medial‐column injuries were relatively difficult to identify (mean rate, 60.7%). The diagnostic rate for non‐displaced injuries (mean rate, 76.7%) was lower than that for displaced injuries (mean rate, 95.5%). The typical examples are given. A significant difference between the two surgeons was found in the recognition rate of non‐displaced injuries (p = 0.005). The mean alteration rate was 21.9%; the senior surgeon tended to a lower rate (15.6%) than the junior one (28.3%) (p < 0.001).ConclusionsThe sensitivity, specificity, and classification accuracy of conventional radiographs for Lisfranc injury were 81.8%, 90.0%, and 83.8%, respectively. Three‐column or displaced injuries were most likely to be recognized. The possibility of changing the initial treatment decision after subsequently evaluating computed tomography images was 21.9%. The diagnostic and clinical decision‐making of surgeons with different experience levels demonstrated some degree of variability. Protected weight‐bearing and a further CT scan should be considered if a Lisfranc injury is suspected and conventional radiography is negative.
Mitochondrial phylogenomics provides conclusive evidence that the family Ancyrocephalidae is deeply paraphyletic
Authors: Hao Cui-Lan , Wei Nian-Wen , Liu Yan-Jun , Shi Cai-Xia , Arken Kadirden , Yue Cheng 
Published: March 2023

Abstract
Background
Unresolved taxonomic classification and paraphyly pervade the flatworm class Monogenea: the class itself may be paraphyletic and split into Polyopisthocotylea and Monopisthocotylea; there are some indications that the monopisthocotylean order Dactylogyridea may also be paraphyletic; single-gene markers and some morphological traits indicate that the family Ancyrocephalidae is paraphyletic and intertwined with the family Dactylogyridae.

Methods
To attempt to study the relationships of Ancyrocephalidae and Monopisthocotylea using a phylogenetic marker with high resolution, we sequenced mitochondrial genomes of two fish ectoparasites from the family Dactylogyridae: Dactylogyrus simplex and Dactylogyrus tuba. We conducted phylogenetic analyses using three datasets and three methods. Datasets were ITS1 (nuclear) and nucleotide and amino acid sequences of almost complete mitogenomes of almost all available Monopisthocotylea mitogenomes. Methods were maximum likelihood (IQ-TREE), Bayesian inference (MrBayes) and CAT-GTR (PhyloBayes).

Results
Both mitogenomes exhibited the ancestral gene order for Neodermata, and both were compact, with few and small intergenic regions and many and large overlaps. Gene sequences were remarkably divergent for nominally congeneric species, with only trnI exhibiting an identity value > 80%. Both mitogenomes had exceptionally low A + T base content and AT skews. We found evidence of pervasive compositional heterogeneity in the dataset and indications that base composition biases cause phylogenetic artefacts. All six mitogenomic analyses produced unique topologies, but all nine analyses produced topologies that rendered Ancyrocephalidae deeply paraphyletic. Mitogenomic data consistently resolved the order Capsalidea as nested within the Dactylogyridea.

Conclusions
The analyses indicate that taxonomic revisions are needed for multiple Polyopisthocotylea lineages, from genera to orders. In combination with previous findings, these results offer conclusive evidence that Ancyrocephalidae is a paraphyletic taxon. The most parsimonious solution to resolve this is to create a catch-all Dactylogyridae sensu lato clade comprising the current Ancyrocephalidae, Ancylodiscoididae, Pseudodactylogyridae and Dactylogyridae families, but the revision needs to be confirmed by another marker with a sufficient resolution.

Graphical Abstract
Clinical significance of obstructive sleep apnea in patients with acute coronary syndrome with or without prior stroke: a prospective cohort study
Authors: Wang Bin , Hao Wen , Fan Jingyao , Yan Yan , Gong Wei , Zheng Wen , Que Bin , Ai Hui , Wang Xiao , Nie Shaoping 
Published: March 2023

Abstract
Background and objective
Whether obstructive sleep apnea (OSA) is associated with worse prognosis in patients with acute coronary syndrome (ACS) with or without prior stroke remains unclear. We investigated the association of OSA with cardiovascular events in ACS patients with or without prior stroke.

Methods
Between June 2015 and January 2020, we prospectively recruited eligible ACS patients who underwent cardiorespiratory polygraphy during hospitalization. We defined OSA as an apnea hypopnea index (AHI) ≥ 15 events/hour. The primary composite end point was major adverse cardiovascular and cerebrovascular events (MACCEs), including cardiovascular death, myocardial infarction, stroke, ischemia-driven revascularization, or hospitalization for unstable angina or heart failure.

Results
Among 1927 patients enrolled, 207 patients had prior stroke (10.7%) and 1014 had OSA (52.6%). After a mean follow-up of 2.9 years, patients with stroke had significantly higher risk of MACCEs than those without stroke (hazard ratio [HR]:1.49; 95% confidence interval [CI]: 1.12–1.98, P = 0.007). The multivariate analysis showed that patients with OSA had 2.0 times the risk of MACCEs in prior stroke group (41 events [33.9%] vs 18 events [20.9%]; HR:2.04, 95% CI:1.13–3.69, P = 0.018), but not in non-prior stroke group (186 events [20.8%] vs 144 events [17.4]; HR:1.21, 95% CI 0.96–1.52, P = 0.10). No significant interaction was noted between prior stroke and OSA for MACCE (interaction P = 0.17).

Conclusions
Among ACS patients, the presence of OSA was associated with an increased risk of cardiovascular events in patients with prior stroke. Further trials exploring the efficacy of OSA treatment in high-risk patients with ACS and prior stroke are warranted.
Trial registration Clinicaltrials.gov identifier NCT03362385.
Change of serum lipoproteins and its potential use in stratifying patients with sepsis among neonates
Authors: Guo Junfei , Lai Weiming , Wu Yongbing , Li Huan , Fu Zhenhua , Mu Xiaoping 
Published: March 2023

Abstract
Background
Changes of serum lipoprotein concentration during bacteremia or sepsis are observed and lipoproteins concentration facilitate the evaluation severity of sepsis in adults, but its clinical usage is still unclear. Here, we analyzed the lipoprotein concentration in neonates with sepsis and discussed its use in stratifying patients.

Methods
This is a retrospective study involved 88 culture-proven septic patients. Clinical and microbiology data of involved patients were collected via inquiring databases of our institute. Patients were grouped according to blood culture results or procalcitonin level; the difference between groups were analyzed.

Results
Compared with uninfected group, there is no change of triglyceride (TG) concentrations and significant decrease of Total cholesterol (TC) concentration in septic patients. There is no significant difference between Gram-positive and Gram-negative-related septic patients in terms of serum TG and TC concentration. Other than group with procalcitonin level of 0.5–2 ng/ml, both serum TG and TC concentration were decreased while serum procalcitonin level increasing.

Conclusions
Our results indicated that serum lipoprotein concentration may be recommended to help diagnosis of bacteria and to evaluate the severity of sepsis.
Effect of replacement of soybean oil by Hermetia illucens fat on performance, digestibility, cecal microbiome, liver transcriptome and liver and plasma lipidomes of broilers
Authors: Schäfer Lea , Grundmann Sarah M. , Maheshwari Garima , Höring Marcus , Liebisch Gerhard , Most Erika , Eder Klaus , Ringseis Robert 
Published: March 2023

Abstract
Background
In contrast to protein-rich insect meal, the feed potential of insect fat is generally less explored and knowledge about the suitability of insect fat as a fat source specifically in broiler diets is still limited. In view of this, the present study aimed to comprehensively investigate the effect of partial (50%) and complete replacement of soybean oil with insect fat from Hermetia illucens (HI) larvae in broiler diets on performance, fat digestibility, cecal microbiome, liver transcriptome and liver and plasma lipidomes. Thus, 100 male, 1-day-old Cobb 500 broilers were randomly assigned to three groups and fed three different diets with either 0 (group HI-0, n = 30), 2.5% (group HI-2.5, n = 35) or 5.0% (HI-5.0, n = 35) Hermetia illucens (HI) larvae fat for 35 d.

Results
Body weight gain, final body weight, feed intake, and feed:gain ratio during the whole period and apparent ileal digestibility coefficient for ether extract were not different between groups. Cecal microbial diversity did not differ between groups and taxonomic analysis revealed differences in the abundance of only four low-abundance bacterial taxa among groups; the abundances of phylum Actinobacteriota, class Coriobacteriia, order Coriobacteriales and family Eggerthellaceae were lower in group HI-5.0 compared to group HI-2.5 (P < 0.05). Concentrations of total and individual short-chain fatty acids in the cecal digesta were not different between the three groups. Liver transcriptomics revealed a total of 55 and 25 transcripts to be differentially expressed between groups HI-5.0 vs. HI-0 and groups HI-2.5 vs. HI-0, respectively (P < 0.05). The concentrations of most lipid classes, with the exception of phosphatidylethanolamine, phosphatidylglycerol and lysophosphatidylcholine in the liver and cholesterylester and ceramide in plasma (P < 0.05), and of the sum of all lipid classes were not different between groups.

Conclusions
Partial and complete replacement of soybean oil with HI larvae fat in broiler diets had no effect on growth performance and only modest, but no adverse effects on the cecal microbiome and the metabolic health of broilers. This suggests that HI larvae fat can be used as an alternative fat source in broiler diets, thereby, making broiler production more sustainable.
Effect of growth stage on Italian ryegrass (Lolium multiflorum Lam.) silage fermentation from microbiological perspective
Authors: Yin Xuejing , Long Jiangyu , Zhao Jie , Wang Siran , Dong Zhihao , Li Junfeng , Shao Tao 
Published: March 2023

Abstract
Background
Italian ryegrass is a temperate climate crop, which is widely cultivated in the winter fallow paddy fields of subtropical China. The utilization efficiency of Italian ryegrass depends greatly on its growth stage at harvest. Previous studies have reported the optimum stage for harvesting various forage to balance their quality and quantity. However, when considering the practice condition, such as rainy or unavailability of harvest equipment, the harvest stage of forage cannot always be implemented according to the production schedules. Thus, to characterize the effect of growth stage on the silage fermentation profile, bacterial community construction and metabolisms of carbohydrates and amino acids, Italian ryegrass were naturally ensiled at the filling stage (FSN) and the dough stage (DSN), respectively. After ensiling for 1, 3, 7, 15, 30, and 60 days, triplicate silos were opened for sampling.

Results
The growth of Italian ryegrass increased the pH, dry matter, neutral, and acid detergent fiber contents, but decreased buffering capacity, crude protein and water-soluble carbohydrates contents, and the epiphytic microbiota of Italian ryegrass harvested at the filling stage was simpler than that harvested at the dough stage. During ensiling, FSN had lower pH and higher organic acid content than DSN. The bacterial succession rate in FSN was also faster than DSN, which showed that Lactobacillus becomes the dominant genus in the early stage of ensiling. The predicted metabolisms revealed that carbohydrate and amino acid metabolisms were the two main metabolisms in silage fermentation. When compared with epiphytic microbiota, ensiling enhanced carbohydrate metabolism and diminished amino acid metabolism. The difference of these two metabolisms between FSN and DSN was obvious at the early stage of ensiling.

Conclusions
Growth stage affected the chemical and microbial composition of Italian ryegrass, so as to the fermentation profile, bacterial community and its metabolisms intensity. Italian ryegrass harvested at the filling stage was prone to ferment. The complexity of epiphytic microbiota made Italian ryegrass harvested at the dough stage more difficult to ferment.

Graphical Abstract
The burden of firearm injuries on the hospital system, 2000–2020
Authors: Davoudi Anis , Woodworth Lindsey 
Published: March 2023

Abstract
Background
Firearm injuries are a long-running yet preventable public health concern in the USA. We analyzed national inpatient data to determine the burden of firearm injuries on the USA hospital system. For each year from 2000–2014 and 2016–2020, we calculated the annual frequency of firearm hospitalization in the USA overall and by the intent of the shooter. We also calculated the rate of firearm hospitalizations per 100,000 inpatient encounters. For each outcome, we used regression analysis to estimate the average year-over-year change. Finally, we explored the types of firearms responsible for firearm hospitalizations.

Findings
Each year during 2000–2020 (excluding 2015), there were an average of 30,428 firearm hospitalizations in the USA. On average, firearm hospitalizations represented 84 out of every 100,000 inpatient encounters each year. There was not a statistically significant year-over-year increase in firearm hospitalizations for either the periods 2000–2014 or 2016–2020. However, firearm hospitalizations were noticeably higher in 2020 than in other years. Until 2019, the most frequent intent among firearm hospitalizations was assault. Beginning in 2019, assaults were outnumbered by unintentional firearm hospitalizations. According to diagnosis codes, handguns were used more often than rifles/shotguns/larger firearms in firearm injuries that resulted in hospitalization for the intents assault (27.93% handguns; 5.87% rifles/shotguns/larger firearms), unintentional (23.94% handguns; 10.48% rifles/shotguns/larger firearms), self-harm (46.63% handguns; 14.35% rifles/shotguns/larger firearms) and undetermined (17.82% handguns; 6.21% rifles/shotguns/larger firearms). Frequently, the type of firearm responsible for the hospitalization was not recorded in the patient’s diagnosis code.

Conclusion
Firearm injuries inflict a significant burden on the hospital system in the USA. While firearm hospitalizations were unusually high in 2020, there is not strong evidence that the burden of firearm injuries on the hospital system is changing over time. The frequent non-identification of the type of firearm responsible for the injury in hospital patients’ diagnosis code complicates injury surveillance efforts.