bluuebunny/crossref_metadata_2025_split huggingface dataset:
AI analysis and modified type classification for endocytoscopic observation of esophageal lesions
Authors: Kumagai Youichi , Takubo Kaiyo , Sato Taku , Ishikawa Hiroyasu , Yamamoto Eisuke , Ishiguro Toru , Hatano Satoshi , Toyomasu Yoshitaka , Kawada Kenro , Matsuyama Takatoshi , Mochiki Erito , Ishida Hideyuki , Tada Tomohiro 
Published: March 2022

Abstract
Endocytoscopy (EC) facilitates real-time histological diagnosis of esophageal lesions in vivo. We developed a deep-learning artificial intelligence (AI) system for analysis of EC images and compared its diagnostic ability with that of an expert pathologist and nonexpert endoscopists. Our new AI was based on a vision transformer model (DeiT) and trained using 7983 EC images of the esophagus (2368 malignant and 5615 nonmalignant). The AI evaluated 114 randomly arranged EC pictures (33 ESCC and 81 nonmalignant lesions) from 38 consecutive cases. An expert pathologist and two nonexpert endoscopists also analyzed the same image set according to the modified type classification (adding four EC features of nonmalignant lesions to our previous classification). The area under the curve calculated from the receiver-operating characteristic curve for the AI analysis was 0.92. In per-image analysis, the overall accuracy of the AI, pathologist, and two endoscopists was 91.2%, 91.2%, 85.9%, and 83.3%, respectively. The kappa value between the pathologist and the AI, and between the two endoscopists and the AI showed moderate concordance; that between the pathologist and the two endoscopists showed poor concordance. In per-patient analysis, the overall accuracy of the AI, pathologist, and two endoscopists was 94.7%, 92.1%, 86.8%, and 89.5%, respectively. The modified type classification aided high overall diagnostic accuracy by the pathologist and nonexpert endoscopists. The diagnostic ability of the AI was equal or superior to that of the experienced pathologist. AI is expected to support endoscopists in diagnosing esophageal lesions based on EC images.
Fatty acid desaturase genetic variations and dietary omega-3 fatty acid intake associate with arterial stiffness
Authors: Bäck Magnus , Xhaard Constance , Rouget Raphael , Thuillier Quentin , Plunde Oscar , Larsson Susanna C. , Girerd Nicolas , Ferreira João Pedro , Boivin Jean-Marc , Bozec Erwan , Mercklé Ludovic , Zannad Faiez , Hoge Axelle , Guillaume Michèle , Dandine-Roulland Claire , Floch Edith Le , Bacq-Daian Delphine , Deleuze Jean-François , Van den Berghe Laurie , Nazare Julie-Anne , Laville Martine , Branlant Christiane , Behm-Ansmant Isabelle , Wagner Sandra , Rossignol Patrick 
Published: March 2022

Abstract

Aims
Long-chain polyunsaturated fatty acids (PUFAs) generate diverse bioactive lipid mediators, which tightly regulate vascular inflammation. The effects of omega-3 PUFA supplementation in cardiovascular prevention however remain controversial. In addition to direct dietary intake, fatty acid desaturases (FADS) determine PUFA levels. Increased arterial stiffness represents an independent predictor of mortality and cardiovascular events. The aim of the present study was to determine the association of PUFA intake, FADS1 genotype, and FADS expression with arterial stiffness.

Methods and results
A cross-sectional population-based cohort study of 1464 participants without overt cardiovascular disease was conducted. Dietary intake was assessed using a food frequency questionnaire. Arterial stiffness was assessed by carotid–femoral pulse wave velocity (cfPWV), and the FADS1 locus variant was determined. Blood cell transcriptomics was performed in a subset of 410 individuals. Pulse wave velocity was significantly associated with the FADS1 locus variant. Differential associations between PWV and omega-3 PUFA intake were observed depending on the FADS1 genotype. High omega-3 PUFA intake attenuated the FADS1 genotype-dependent associations. Carriers of the minor FADS1 locus variant exhibited increased expression of FADS2, which is associated with PWV.

Conclusion
Taken together, these findings point to FADS1 genotype-dependent associations of omega-3 PUFA intake on subclinical cardiovascular disease. These findings may have implications for identifying responders and non-responders to omega-3 PUFA supplementation and open up for personalized dietary counselling in cardiovascular prevention.
Genotype-independent plant transformation
Authors: Maren Nathan A , Duan Hui , Da Kedong , Yencho G Craig , Ranney Thomas G , Liu Wusheng 
Published: March 2022

Abstract
Plant transformation and regeneration remain highly species- and genotype-dependent. Conventional hormone-based plant regeneration via somatic embryogenesis or organogenesis is tedious, time-consuming, and requires specialized skills and experience. Over the last 40 years, significant advances have been made to elucidate the molecular mechanisms underlying embryogenesis and organogenesis. These pioneering studies have led to a better understanding of the key steps and factors involved in plant regeneration, resulting in the identification of crucial growth and developmental regulatory genes that can dramatically improve regeneration efficiency, shorten transformation time, and make transformation of recalcitrant genotypes possible. Co-opting these regulatory genes offers great potential to develop innovative genotype-independent genetic transformation methods for various plant species, including specialty crops. Further developing these approaches has the potential to result in plant transformation without the use of hormones, antibiotics, selectable marker genes, or tissue culture. As an enabling technology, the use of these regulatory genes has great potential to enable the application of advanced breeding technologies such as genetic engineering and gene editing for crop improvement in transformation-recalcitrant crops and cultivars. This review will discuss the recent advances in the use of regulatory genes in plant transformation and regeneration, and their potential to facilitate genotype-independent plant transformation and regeneration.
Mitogen-activated protein kinase 4 is obligatory for late pollen and early fruit development in tomato
Authors: Wang Jie , Li Mengzhuo , Zhuo Shibin , Liu Yue , Yu Xiaolin , Mukhtar Sidra , Ali Muhammad , Lu Gang 
Published: March 2022

AbstractMitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules regulating vegetative and reproductive development of plants. However, the molecular mechanisms of the SlMPK4 gene in tomato pollen and fruit development remain elusive. SlMPK4 is preferentially and highly expressed in tomato stamens and its mRNA levels increase during early flower development, peaking at the mature pollen stage. Either up- or downregulation of SlMPK4 expression had no significant effect on tomato vegetative growth. However, RNAi-mediated suppression of SlMPK4 caused defects in pollen development, resulting in pollen abortion. The aborted pollen grains were either malformed or collapsed and completely lacked viability, resulting in a predominantly reduced fruit set rate in RNAi lines compared with control and overexpressing transgenic plants. Interestingly, seed development was inhibited in RNAi lines. Moreover, &gt;12% of emasculated RNAi flowers developed seedless fruits without pollination. Anthers can produce typical microspore mother cells as well as uninucleate microspores, according to cytological investigations, while binucleate pollen ceased to produce typical mature pollen. Pollen abortion was further confirmed by transmission electron microscopy analysis at the binucleate stage in RNAi plants. The exine layer in aberrant pollen had a normal structure, while the intine layer appeared thicker. Suppression of SlMPK4 affects the transcript level of genes related to cell wall formation and modification, cell signal transduction, and metabolic and biosynthetic processes. A subset of genes that may be putative substrates of plant MAPKs were also differentially changed in RNAi transgenic flowers. Taken together, these results suggest that SlMPK4 plays a critical role in regulating pollen development and fruit development in tomato plants.
Ocean model-based covariates improve a marine fish stock assessment when observations are limited
Authors: du Pontavice Hubert , Miller Timothy J , Stock Brian C , Chen Zhuomin , Saba Vincent S 
Published: March 2022

Abstract
The productivity of many fish populations is influenced by the environment, but developing environment-linked stock assessments remain challenging and current management of most commercial species assumes that stock productivity is time-invariant. In the Northeast United States, previous studies suggest that the recruitment of Southern New England-Mid Atlantic yellowtail flounder is closely related to the strength of the Cold Pool, a seasonally formed cold water mass on the continental shelf. Here, we developed three new indices that enhance the characterization of Cold Pool interannual variations using bottom temperature from a regional hindcast ocean model and a global ocean data assimilated hindcast. We associated these new indices to yellowtail flounder recruitment in a state–space, age-structured stock assessment framework using the Woods Hole Assessment Model. We demonstrate that incorporating Cold Pool effects on yellowtail flounder recruitment reduces the retrospective patterns and may improve the predictive skill of recruitment and, to a lesser extent, spawning stock biomass. We also show that the performance of the assessment models that incorporated ocean model-based indices is improved compared to the model using only the observation-based index. Instead of relying on limited subsurface observations, using validated ocean model products as environmental covariates in stock assessments may both improve predictions and facilitate operationalization.
Boyden’s triad in the left lung: an interesting phenomenon
Authors: Zhang Min , Sun Wei-Jie , Wu Qing-Chen , Ge Ming-Jian 
Published: March 2022

Abstract

OBJECTIVES
Boyden’s triad of the right lung was first proposed in 2021. Here, we report 5 cases of this malformation found in the left lung.

METHODS
A total of 5280 patients with pulmonary lesions underwent three-dimensional computed tomography bronchography and angiography between January 2019 and January 2021, prior to surgery; 5 cases of this malformation were identified in the left lung. Bronchovascular patterns were analysed in each patient.

RESULTS
The incidence rate of Boyden’s triad in the left lung was 0.1%. This malformation was further divided into B3 on B4+5 type and B3 on B4 type. In B3 on B4+5 type, B3 was shifted downwards on the common trunk of B4+5, and A3 arose from the common trunk of A4+5 running alongside B3. In B3 on B4 type, B3 was shifted downwards on B4. A4 and A5 appeared separately. A3 arose from A4, running alongside B3; A5 arose from the common trunk of A8 − 10, and there was also an extraordinary ‘posterior vein’ (V. post): V1+2c. The incidence of V. post was 0.17%. An additional ‘fissure’ lies longitudinally between S1+2 and S3+4+5, nearly perpendicular to the oblique fissure, dividing the upper lobe into ‘two lobes’.

CONCLUSIONS
The B3 downwards-shifting malformation can be found on both lungs, and this is the first description of Boyden’s triad in the left lung; it appears to be much rarer than that in the right lung, with some accompanying unique variations.
The consequence of financial incentives for not prescribing antibiotics: a Japan’s nationwide quasi-experiment
Authors: Okubo Yusuke , Nishi Akihiro , Michels Karin B , Nariai Hiroki , Kim-Farley Robert J , Arah Onyebuchi A , Uda Kazuhiro , Kinoshita Noriko , Miyairi Isao 
Published: March 2022

Abstract

Background
For addressing antibiotic overuse, Japan designed a health care policy in which eligible medical facilities could claim a financial reward when antibiotics were not prescribed for early-stage respiratory and gastrointestinal infections. The policy was introduced in a pilot manner in paediatric clinics in April 2018.

Methods
We conducted a quasi-experimental, propensity score-matched, difference-in-differences (DID) design to determine whether the nationwide financial incentives for appropriate non-prescribing of antibiotics as antimicrobial stewardship [800 JPY (≈7.3 US D) per case] were associated with changes in prescription patterns, including antibiotics, and health care use in routine paediatric health care settings at a national level. Data consisted of 9 253 261 cases of infectious diseases in 553 138 patients treated at 10 180 eligible or ineligible facilities.

Results
A total of 2959 eligible facilities claimed 316 770 cases for financial incentives and earned 253 million JPY (≈2.29 million USD). Compared with ineligible facilities, the introduction of financial incentives in the eligible facilities was associated with an excess reduction in antibiotic prescriptions [DID estimate, -228.6 days of therapy (DOTs) per 1000 cases (95% CI, -272.4 to -184.9), which corresponded to a relative reduction of 17.8% (95% CI, 14.8 to 20.7)]. The introduction was also associated with excess reductions in drugs for respiratory symptoms [DID estimates, -256.9 DOTs per 1000 cases (95% CI, -379.3 to -134.5)] and antihistamines [DID estimate, -198.5 DOTs per 1000 cases (95% CI, -282.1 to -114.9)]. There was no excess in out-of-hour visits [DID estimate, -4.43 events per 1000 cases (95% CI, -12.8 to 3.97)] or hospitalizations [DID estimate, -0.08 events per 1000 cases (95% CI, -0.48 to 0.31)].

Conclusions
Our findings suggest that financial incentives to medical facilities for not prescribing antibiotics were associated with reductions in prescriptions for antibiotics without adverse health care consequences. Japan’s new health policy provided us with policy options for immediately reducing inappropriate antibiotic prescriptions by relatively small financial incentives.
A Blunted GPR183/Oxysterol Axis During Dysglycemia Results in Delayed Recruitment of Macrophages to the Lung During Mycobacterium tuberculosis Infection
Authors: Ngo Minh Dao , Bartlett Stacey , Bielefeldt-Ohmann Helle , Foo Cheng Xiang , Sinha Roma , Arachchige Buddhika Jayakody , Reed Sarah , Mandrup-Poulsen Thomas , Rosenkilde Mette Marie , Ronacher Katharina 
Published: March 2022

Abstract

Background
We previously reported that reduced GPR183 expression in blood from tuberculosis (TB) patients with diabetes is associated with more severe TB.

Methods
To further elucidate the role of GPR183 and its oxysterol ligands in the lung, we studied dysglycemic mice infected with Mycobacterium tuberculosis (Mtb).

Results
We found upregulation of the oxysterol-producing enzymes CH25H and CYP7B1 and increased concentrations of 25-hydroxycholesterol upon Mtb infection in the lungs of mice. This was associated with increased expression of GPR183 indicative of oxysterol-mediated recruitment of GPR183-expressing immune cells to the lung. CYP7B1 was predominantly expressed by macrophages in TB granulomas. CYP7B1 expression was significantly blunted in lungs from dysglycemic animals, which coincided with delayed macrophage infiltration. GPR183-deficient mice similarly had reduced macrophage recruitment during early infection.

Conclusions
Taken together, we demonstrate a requirement of the GPR183/oxysterol axis for positioning of macrophages to the site of infection and add an explanation to more severe TB in diabetes patients.
Antibiotic resistance: calling time on the ‘silent pandemic’
Authors: Mendelson Marc , Sharland Michael , Mpundu Mirfin 
Published: March 2022

Abstract
It is time to stop referring to the antibiotic resistance pandemic as ‘silent’. Continuing to use such a term denies the reality that antibiotic-resistant bacterial infections, driven by misuse and abuse of antibiotics by humans against microbial ecosystems that we should be living in symbiosis with, is wrong. Both our terminology and who the real ‘enemy’ is in relation to antibiotic resistance demands serious reconsideration.
Determination of Orellanine in Human Biological Matrices Using Liquid Chromatography with High-Resolution Mass Spectrometry Detection: A Validated Method Applied to Suspected Poisoning Cases
Authors: Flament Estelle , Guitton Jérôme , Gicquel Thomas , Paret Nathalie , Jarrier Nathalie , Creusat Gaelle , Tournoud Christine , Labadie Magali , Gaulier Jean-Michel , Gaillard Yvan 
Published: March 2022

AbstractConsumption of mushrooms can become unsafe for the consumer in case of confusion. Some fungi of Cortinarius genus contain the nephrotoxic mycotoxin orellanine responsible for their toxicity. Related case poisoning diagnosis is a challenge for both clinicians and analysts because of a long latency period between intake and toxic syndrome, the lack of available information in literature and the numerous pitfalls of orellanine identification/quantification in biological samples. In this situation, we propose an analytical method designed for the orellanine detection and/or quantification in biological matrices such as plasma, urine and whole blood, in a context of related intoxication suspected case. Using 1 mL biological sample volume, this liquid chromatographic with high-resolution mass spectrometry detection method (i) exhibits a limit of quantification for orellanine of 0.5 µg/L in plasma and urine and (ii) enables orellanine detection in whole blood with a limit of detection of 0.5 µg/L. This validated analytical method was successfully applied to 10 suspected intoxication cases.
Heavy drought reduces the decomposition rate of the mixed litters of two composite invasive alien plants
Authors: Yu Youli , Cheng Huiyuan , Wang Congyan , Du Daolin 
Published: March 2022

AbstractCompositae family comprises the largest number of species of invasive alien plants (IAPs) in China. Two IAPs can co-invade the same habitat. Drought can alter the litter decomposition of IAPs and soil enzyme activities. This study aims to estimate the independent and combined effects of two composite IAPs (Bidens pilosa and Solidago canadensis) on litter decomposition and soil enzyme activities under drought. A polyethylene litterbags experiment (5 g litters of B. pilosa, 5 g litters of S. canadensis or 5 g litters of B. pilosa and S. canadensis in an equal proportion per polyethylene litterbag) was performed. The polyethylene litterbags were treated with a gradient of drought, i.e. control, light level of drought and heavy level of drought. The decomposition coefficient of the two composite IAPs and soil enzyme activities was determined. The co-invasion of the two composite IAPs posed a synergistic effect on urease activity. The mixed litters of two composite IAPs and the litters of B. pilosa had higher decomposition rates than S. canadensis. Urease activity was increased in light droughts, but it was decreased in heavy drought. Heavy drought reduced the decomposition rate of the mixed litters of two composite IAPs and the litters of B. pilosa. Drought did not affect the decomposition rate of S. canadensis litters. Thus, heavy drought can decrease the nutrient cycling rate under the co-invasion of the two composite IAPs and the independent invasion of B. pilosa rather than the independent invasion of S. canadensis.
Estimating cluster masses from SDSS multiband images with transfer learning
Authors: Lin Sheng-Chieh , Su Yuanyuan , Liang Gongbo , Zhang Yuanyuan , Jacobs Nathan , Zhang Yu 
Published: March 2022

ABSTRACTThe total masses of galaxy clusters characterize many aspects of astrophysics and the underlying cosmology. It is crucial to obtain reliable and accurate mass estimates for numerous galaxy clusters over a wide range of redshifts and mass scales. We present a transfer-learning approach to estimate cluster masses using the ugriz-band images in the SDSS Data Release 12. The target masses are derived from X-ray or SZ measurements that are only available for a small subset of the clusters. We designed a semisupervised deep learning model consisting of two convolutional neural networks. In the first network, a feature extractor is trained to classify the SDSS photometric bands. The second network takes the previously trained features as inputs to estimate their total masses. The training and testing processes in this work depend purely on real observational data. Our algorithm reaches a mean absolute error (MAE) of 0.232 dex on average and 0.214 dex for the best fold. The performance is comparable to that given by redMaPPer, 0.192 dex. We have further applied a joint integrated gradient and class activation mapping method to interpret such a two-step neural network. The performance of our algorithm is likely to improve as the size of training data set increases. This proof-of-concept experiment demonstrates the potential of deep learning in maximizing the scientific return of the current and future large cluster surveys.
Particle-in-cell simulations of high-frequency waves driven by pickup ion ring-beam distributions in the outer heliosheath
Authors: Mousavi Ameneh , Liu Kaijun , Sadeghzadeh Sina 
Published: March 2022

ABSTRACT
Scattering of pickup ion ring-beam distributions in the outer heliosheath is a fundamental element in the spatial retention scenario of the energetic neutral atom (ENA) ribbon observed by the Interstellar Boundary EXplorer (IBEX). According to our earlier linear instability analysis, pickup ion ring-beam distributions trigger magnetic field-aligned, right-hand polarized unstable waves in two separate frequency ranges which are near and far above the proton cyclotron frequency, respectively. We have performed hybrid simulations to study the unstable waves near the proton cyclotron frequency. However, the high-frequency waves well above the proton cyclotron frequency are beyond the reach of hybrid simulations. In this paper, particle-in-cell simulations are carried out to study the parallel- and antiparallel-propagating high-frequency waves excited by the outer heliosheath pickup ions at different pickup angles as well as the scattering of the pickup ions by the waves excited. In the early stages of the simulations, the results confirm the excitation of the parallel-propagating, right-hand polarized high-frequency waves as predicted by the earlier linear analysis. Later in the simulations, enhanced antiparallel-propagating modes also emerge. Furthermore, the evolution of the pickup ion ring-beam distributions of the selected pickup angles reveals that the high-frequency waves do not significantly contribute to the pickup ion scattering. These results are favourable regarding the plausibility of the spatial retention scenario of the IBEX ENA ribbon.
Instability from high-order resonant chains in wide-separation massive planet systems
Authors: Murphy Matthew M , Armitage Philip J 
Published: March 2022

ABSTRACTDiversity in the properties of exoplanetary systems arises, in part, from dynamical evolution that occurs after planet formation. We use numerical integrations to explore the relative role of secular and resonant dynamics in the long-term evolution of model planetary systems, made up of three equal mass giant planets on initially eccentric orbits. The range of separations studied is dominated by secular processes, but intersects chains of high-order mean-motion resonances. Over time-scales of 108 orbits, the secular evolution of the simulated systems is predominantly regular. High-order resonant chains, however, can be a significant source of angular momentum deficit (AMD), leading to instability. Using a time series analysis based on a Hilbert transform, we associate instability with broad islands of chaotic evolution. Previous work has suggested that first-order resonances could modify the AMD of nominally secular systems and facilitate secular chaos. We find that higher order resonances, when present in chains, can have similar impacts.