bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell sequencing of tumour infiltrating T cells efficiently identifies tumour-specific T cell receptors based on the T cell activation score
Authors: Zhang Chaoting , Li Shance , Shen Luyan , Teng Xia , Xiao Yefei , Yang Wenjun , Lu Zheming 
Published: May 2024

AbstractAdoptively transferred T cell receptor-engineered T cells are a promising cancer treatment strategy, and the identification of tumour-specific TCRs is essential. Previous studies reported that tumour-reactive T cells and TCRs could be isolated based on the expression of activation markers. However, since T cells with different cell states could not respond uniformly to activation but show a heterogeneous expression profile of activation and effector molecules, isolation of tumour-reactive T cells based on single activation or effector molecules could result in the absence of tumour-reactive T cells; thus, combinations of multiple activation and effector molecules could improve the efficiency of isolating tumour-specific TCRs. We enrolled two patients with lung adenocarcinoma and obtained their tumour infiltrating lymphocytes (TILs) and autologous tumour cells (ATCs). TILs were cocultured with the corresponding ATCs for 12 h and subjected to single-cell RNA sequencing. First, we identified three TCRs with the highest expression levels of IFNG and TNFRSF9 mRNA for each patient, yet only the top one or two recognized the corresponding ATCs in each patient. Next, we defined the activation score based on normalized expression levels of IFNG, IL2, TNF, IL2RA, CD69, TNFRSF9, GZMB, GZMA, GZMK, and PRF1 mRNA for each T cell and then identified three TCRs with the highest activation score for each patient. We found that all three TCRs in each patient could specifically identify corresponding ATCs. In conclusion, we established an efficient approach to isolate tumour-reactive TCRs based on combinations of multiple activation and effector molecules through single-cell RNA sequencing.
Longitudinal ultrasound-based AI model predicts axillary lymph node response to neoadjuvant chemotherapy in breast cancer: a multicenter study
Authors: Fu Ying , Lei Yu-Tao , Huang Yu-Hong , Mei Fang , Wang Song , Yan Kun , Wang Yi-Hua , Ma Yi-Han , Cui Li-Gang 
Published: May 2024

Abstract
Objectives
Developing a deep learning radiomics model from longitudinal breast ultrasound and sonographer’s axillary ultrasound diagnosis for predicting axillary lymph node (ALN) response to neoadjuvant chemotherapy (NAC) in breast cancer.

Methods
Breast cancer patients undergoing NAC followed by surgery were recruited from three centers between November 2016 and December 2022. We collected ultrasound images for extracting tumor-derived radiomics and deep learning features, selecting quantitative features through various methods. Two machine learning models based on random forest were developed using pre-NAC and post-NAC features. A support vector machine integrated these data into a fusion model, evaluated via the area under the curve (AUC), decision curve analysis, and calibration curves. We compared the fusion model’s performance against sonographer’s diagnosis from pre-NAC and post-NAC axillary ultrasonography, referencing histological outcomes from sentinel lymph node biopsy or axillary lymph node dissection.

Results
In the validation cohort, the fusion model outperformed both pre-NAC (AUC: 0.899 vs. 0.786, p < 0.001) and post-NAC models (AUC: 0.899 vs. 0.853, p = 0.014), as well as the sonographer’s diagnosis of ALN status on pre-NAC and post-NAC axillary ultrasonography (AUC: 0.899 vs. 0.719, p < 0.001). Decision curve analysis revealed patient benefits from the fusion model across threshold probabilities from 0.02 to 0.98. The model also enhanced sonographer’s diagnostic ability, increasing accuracy from 71.9% to 79.2%.

Conclusion
The deep learning radiomics model accurately predicted the ALN response to NAC in breast cancer. Furthermore, the model will assist sonographers to improve their diagnostic ability on ALN status before surgery.

Clinical relevance statement
Our AI model based on pre- and post-neoadjuvant chemotherapy ultrasound can accurately predict axillary lymph node metastasis and assist sonographer’s axillary diagnosis.

Key Points

Axillary lymph node metastasis status affects the choice of surgical treatment, and currently relies on subjective ultrasound.

Our AI model outperformed sonographer’s visual diagnosis on axillary ultrasound.

Our deep learning radiomics model can improve sonographers’ diagnosis and might assist in surgical decision-making.
An assessment of effective slope as a parameter for turbulent drag prediction over multi-scaled roughness
Authors: Ramani A. , Schilt L. , Nugroho B. , Busse A. , Jelly T. O. , Monty J. P. , Hutchins N. 
Published: May 2024

AbstractThe streamwise effective slope ($${\rm ES}_x$$

ES
x

), which is the mean absolute streamwise gradient of the roughness, is considered to be a key parameter in predicting the drag penalty of rough-wall turbulent boundary-layers. However, many real-world rough surfaces are multi-scaled. For such surfaces, $${\rm ES}_x$$

ES
x

can be unbounded and its value can be dominated by scales of the topography that are invisible to the flow. To illustrate this, a campaign of drag balance measurements was conducted with a set of machined surfaces. A baseline surface is prepared with fine machining parameters. By coarsening the machining precision, artefacts called ‘scallops’ are introduced which increases the ‘measured’ $${\rm ES}_x$$

ES
x

without changing other geometrical statistics. The drag of the ‘scalloped’ surfaces is higher than the baseline surface, with the relative drag increase scaling with the viscous scaled scallop height, but only when their height exceeds $$2\sim 3$$

2
∼
3

times the viscous length scale. Further, the drag of one of the ‘scalloped’ cases, even when the scallop height is $$\mathcal {O}(10)$$

O
(
10
)

viscous units, is seen to be much lower ($$\sim 28$$

∼
28

%) than a case with matched $${\rm ES}_x$$

ES
x

, but where the $${\rm ES}_x$$

ES
x

results from larger scale features. These findings confirm that for multi-scaled surfaces, $${\rm ES}_x$$

ES
x

may be a misleading topographical metric for drag (or $$k_s$$

k
s

) prediction and one must consider which scales contribute to the average slope of a surface.
Critical Subgraphs of Schrijver Graphs for the Fractional Chromatic Number
Authors: Gujgiczer Anna , Simonyi Gábor 
Published: May 2024

AbstractSchrijver graphs are vertex-color-critical subgraphs of Kneser graphs having the same chromatic number. They also share the value of their fractional chromatic number but Schrijver graphs are not critical for that. Here we present an induced subgraph of every Schrijver graph that is vertex-critical with respect to the fractional chromatic number. These subgraphs turn out to be isomorphic with certain circular complete graphs. We also characterize the critical edges within this subgraph.
Escalation of tropical cyclone impacts on the northwestern Bay of Bengal over the past decade
Authors: Wu Dijia , Ju Xia , Sun Jia , Hu Xiaomin , Xiong Xuejun 
Published: May 2024

AbstractTropical cyclones have resulted in casualties and economic losses in the areas surrounding the Bay of Bengal (BoB). Thus, a comprehensive investigation of these tropical cyclones holds vital implications for disaster preparedness and mitigation. This paper compares the occurrence of storms in the last two decades, i.e., 2002–2011 and 2012–2021, and results reveal that such storms exhibited predominantly a northwesterly track towards the northwestern BoB, with a severer intensity but equal total storm frequencies. Over the past decade, a southeast-northwest pathway (SNP) was identified, demonstrating a higher incidence of severe tropical cyclones (STC, with lifetime maximum intensity ≥ 64 knots) over the BoB. Further analysis of the changes in the environmental conditions between these two decades indicates that a southeasterly anomaly in the steering flow contributed to the formation of the SNP. During the same period, the more favorable oceanic conditions during the last decade, including higher sea surface temperatures, a greater upper ocean heat content, a thicker warm water layer, and a thicker barrier layer beneath the SNP, favored the development of these storms by providing more heat energy to the storms. The atmospheric conditions, including increased air-sea heat fluxes, moisture, and instability within the lower troposphere, as well as reduced vertical wind shear, facilitated the development of convection within these storm systems. These favorable conditions improved the potential for storm development into STCs and elevated the risk of the northwestern BoB being impacted by more destructive storms.
Experiments and numerical modelling of secondary flows of blood and shear-thinning blood analogue fluids in rotating domains
Authors: Kelly Nathaniel S. , Gill Harinderjit S. , Cookson Andrew N. , Fraser Katharine H. 
Published: May 2024

AbstractThe transition from concentric primary flow to non-tangential secondary flow of blood was investigated using experimental steady shear rheometry and numerical modelling. The aims were to: assess the difference in secondary flow in a Newtonian versus shear-thinning blood analogue; and measure the secondary flow in the blood. Both experiments and numerical modelling showed that the transition from primary to secondary flow was the same in a Newtonian fluid and a shear-thinning blood analogue. Experiments showed whole blood transitioned to secondary flow at lower modified Reynolds numbers than the Newtonian fluid; and transition was haematocrit dependent with higher RBC concentrations transitioning at lower modified Reynolds numbers. These results indicate that modelling blood as a purely shear-thinning fluid does not predict the correct secondary flow fields in whole blood; non-Newtonian effects beyond shear-thinning behaviour are influential, and incorporating effects such as multiphase contributions and viscoelasticity, yield stress and thixotropy is necessary.
Prevalence of vestibular disease in France: analysis of prescription data from a national health insurance database
Authors: Grill Eva , Darrouzet Vincent , Mansmann Ulrich , Chabbert Christian 
Published: May 2024

AbstractVestibular problems are frequent reasons for primary care consultations. However, there is considerable uncertainty about the prevalence and cost of vestibular disorders. Despite ambiguous effectiveness data, the histamine analogue betahistine is widely and almost exclusively used for treatment of vertigo. Prescription of betahistine can, therefore, be used as a proxy estimate for prevalence. We used openly available claims data from the French health insurance data warehouse, defining annual prevalence of vestibular disease as the number of people who received at least one betahistine prescription that year. Dosage and pack size of each prescribed formulation were extracted to calculate the sum of betahistine in mg and the Defined Daily Dose (DDD) for age and sex strata and in total. To estimate the relative impact of one landmark trial, the BEMED study, we compared prescriptions from the years 2014/2015 to prescriptions in 2019/2022. A total of 735,121 (2014), 694,705 (2015), 614,431 (2019), and 562,476 (2022) persons filled in a prescription of betahistine. Patients were predominantly older and female. Average amount dispensed per year and per person increased from 4422.54 mg during the pre-BEMED period to 4736.90 mg during the post-BEMED period. DDD decreased from 130 Mio per year in 2014/2015 to 116 Mio per year in 2019/2022. Total costs for betahistine decreased by 42% from 21,615,037 Euro in 2014 to 12,894,249 Euro in 2022. Vestibular disease is frequent in France and has a relevant impact on population health. Despite conflicting clinical evidence, betahistine continues to be prescribed widely in medical practice.
Quantitative analysis of intestinal perfusion with indocyanine green (ICG) and methylene blue (MB) using a single clinically approved fluorescence imaging system: a demonstration in a porcine model
Authors: Heuvelings Danique J. I. , Scheepers Max H. M. C. , Al-Difaie Zaid , Okamoto Nariaki , Diana Michele , Stassen Laurents P. S. , Bouvy Nicole D. , Al-Taher Mahdi 
Published: May 2024

Abstract
Background
Near-infrared fluorescence (NIRF) angiography with intraoperative administration of indocyanine green (ICG) has rapidly disseminated in clinical practice. Another clinically approved, and widely available dye, methylene blue (MB), has up to now not been used for this purpose. Recently, we demonstrated promising results for the real-time evaluation of intestinal perfusion using this dye. The primary aim of this study was to perform a quantitative analysis of bowel perfusion assessment for both ICG and MB.

Methods
Four mature female Landrace pigs underwent laparotomy under general anesthesia. An ischemic bowel loop with five regions of interest (ROIs) with varying levels of perfusion was created in each animal. An intravenous (IV) injection of 0.25 mg/kg–0.50 mg/kg MB was administered after 10 min, followed by NIRF imaging in MB mode and measurement of local lactate levels in all corresponding ROIs. This procedure was repeated in ICG mode (IV dose of 0.2 mg/kg) after 60 min. The quest spectrum fluorescence camera (Quest Medical Imaging, Middenmeer, The Netherlands) was used for NIRF imaging of both MB and ICG.

Results
Intraoperative NIRF imaging of bowel perfusion assessment with MB and ICG was successful in all studied animals. Ingress (i/s) levels were calculated and correlated with local lactate levels. Both MB and ICG ingress values showed a significant negative correlation (r = − 0.7709; p =  < 0.001; r = − 0.5367, p = 0.015, respectively) with local lactate levels. This correlation was stronger for MB compared to ICG, although ICG analysis showed higher absolute ingress values.

Conclusion
Our fluorescence quantification analysis validates the potential to use MB for bowel perfusion assessment besides the well-known and widely used ICG. Further human studies are necessary to translate our findings to clinical applications.
Detection and classification of human respiration under building debris model using VHF/UHF waves
Authors: Niyaz Özden , Tüylü Tolgahan , Mahouti Peyman , Erkmen Burcu , Türker Tokan Nurhan 
Published: May 2024

AbstractDetecting live humans in buildings that have collapsed due to disasters and identifying their condition of health is of great importance for search and rescue operations. Although various methods have been used for this purpose, there are still critical challenges to ensure accurate and rapid life-saving operations. Immediate detection of the presence of living humans under debris combined with the assessment of their vital signs is a crucial factor. This research endeavors to introduce a previously unexplored method: the use of artificial neural network-based techniques to detect human respiration under building debris by generating novel simulation-derived electromagnetic data. To achieve this, a realistic three-dimensional debris model was integrated into an electromagnetic simulation program and complemented by a phantom simulating anterior–posterior body movements indicative of respiration. Measurements of magnitude and phase between 150 and 650 MHz were performed under different conditions. Using surrogate models based on artificial neural networks, noise with different signal-to-noise ratios within the selected frequencies was introduced. These models were used to perform two different steps. Firstly, the presence of respiration of living humans trapped under debris was successfully detected with a success rate of 99.97%. Secondly, the difficult task of classifying the respiration patterns of the human was accomplished with an impressive accuracy of 99.69%, providing a solid basis for proof of concept.
On a theorem by Schlenk
Authors: Bähni Yannis 
Published: May 2024

AbstractIn this paper we prove a generalisation of Schlenk’s theorem about the existence of contractible periodic Reeb orbits on stable, displaceable hypersurfaces in symplectically aspherical, geometrically bounded, symplectic manifolds, to a forcing result for contractible twisted periodic Reeb orbits. We make use of holomorphic curve techniques for a suitable generalisation of the Rabinowitz action functional in the stable case in order to prove the forcing result. As in Schlenk’s theorem, we derive a lower bound for the displacement energy of the displaceable hypersurface in terms of the action value of such periodic orbits. The main application is a forcing result for noncontractible periodic Reeb orbits on quotients of certain symmetric star-shaped hypersurfaces. In this case, the lower bound for the displacement energy is explicitly given by the difference of the two periods. This theorem can be applied to many physical systems including the Hénon–Heiles Hamiltonian and Stark–Zeeman systems. Further applications include a new proof of the well-known fact that the displacement energy is a relative symplectic capacity on $${\mathbb {R}}^{2n}$$

R

2
n

and that the Hofer metric is indeed a metric.
Revisiting the bicontinental allopolyploid origin of Australasian Lepidium species with amplicon sequencing of 15 nuclear genes
Authors: Smissen Rob D. , Walker Susan , Heenan Peter B. 
Published: May 2024

AbstractNew Zealand is home to 16 endemic species of Lepidium (Brassicaceae), including two species considered to have become extinct since European colonisation and an additional species shared with Australia. Previous meiotic chromosome counts suggest at least some are high polyploids. A hybrid origin has been proposed for several of them, with African and American species implicated as parents. We generated amplicon sequence data for 15 genes derived from targeted enrichment data from a selection of species endemic to New Zealand, and of African, American, and Australian origin naturalised in New Zealand. These were analysed, along with publicly available genomic data from other Lepidium species. Our results are consistent with earlier work in supporting two main groups of endemic New Zealand Lepidium, corresponding to different dominant nrDNA sequences. Our data suggest that these two groups differ in ploidy (one octoploid, the ploidy of the other uncertain). The octoploid species combine four distinguishable subgenomes and the other species may be the products of allopolyploidisation between octoploid species and a diploid species closely related to, if not, L. africanum. Previously proposed links to American Lepidium are also supported, with at least two Australasian Lepidium subgenomes related to subgenomes present in American polyploid species. The affinities of two further subgenomes present in Australasian Lepidium remain to be determined, but they may also be of American origin. One New Zealand endemic species, L. naufragorum, displays sequences broadly consistent with it being the octodecaploid product of hybridisation between octoploid and decaploid New Zealand groups.
The impact of changing climate on the spread of the widely expanding species Ambrosia artemisiifolia in Slovakia
Authors: Hrabovský Michal , Kubalová Silvia , Kanka Róbert 
Published: May 2024

AbstractThe invasion of common ragweed in Slovakia was analysed based on 1635 collected records. More than 70 years have passed since the first record was sampled in 1949. Since then, it has spread in two waves, first in the lowlands, next to farmland and human settlements, and later in the mountains, on the roadsides. In the present, it is probably expanded in half of the territory of Slovakia. It is changing habitat preferences and adapting to new environments. Using eleven environmental and geographical variables, the species distribution modelling was performed to obtain probability of occurrence in high resolution (30 s) in Slovakia. Four predictions were calculated based on two models. The first prediction was based on the first model trained on ragweed records before the start of the second expansion wave in 2000. The second prediction is based on the first model and predicts the present distribution according to current climatic conditions, which have changed in twenty years. The third prediction was based on the second model, trained on all 1635 collected records from 1949 to 2022. The fourth prediction based on the second model shows the potential distribution in 2040–2061. Comparing the predictions, the climatic changes explain current expansion of common ragweed in mountains since the air temperature is the main factor shaping distribution of common ragweed in Slovakia.
Comparison of stochastic stability boundaries for parametrically forced systems with application to ship rolling motion
Authors: Maki Atsuo , Maruyama Yuuki , Liu Yaliu , Dostal Leo 
Published: May 2024

AbstractNumerous accidents caused by parametric rolling have been reported on container ships and pure car carriers (PCCs). Considering this dangerous phenomenon, the parametric rolling in irregular seas is examined in this paper based on the stability of the systems origin, which corresponds to the upright condition of the vessel. It provides a novel theoretical explanation of the instability mechanism for two cases: white-noise parametric excitation and colored-noise parametric excitation. Moreover, the authors confirm the usefulness of the previously provided formulae by Roberts and Dostal by means of numerical examples.
Sex ratio and sex-specific chick mortality in a species with moderate sexual size dimorphism and female brood desertion
Authors: Banach Agata , Flis Adam , Kusal Bartłomiej , Łożyńska Halszka , Ledwoń Mateusz 
Published: May 2024

AbstractAn equal sex ratio at the population level is the usual, evolutionarily stable condition. However, at the individual level, it may be adaptive for parents to manipulate the sex of their offspring, especially in species with sexual size dimorphism (SSD) when the costs and benefits of producing sons and daughters can vary. In this study, we investigated the hatching sex ratio (HSR) and fledging sex ratio (FSR) in the Whiskered Tern (Chlidonias hybrida). Despite the fact that SSD exists in Whiskered Terns already at the chick stage, HSR and FSR did not deviate from parity at the population level. We tested the dependence of HSR, FSR and the survival probability of males and females on the individual hatching date, average egg volume (in a clutch) and the number of nestlings. None of these factors influenced HSR. Survival probability was negatively correlated with the number of hatchlings. The proportion of females among the fledglings was positively correlated with the average egg volume per clutch. To better explore the effect of egg volume on the sex ratio, we tested the relationship between exact egg volume and hatchling sex or hatching success at the individual level; but despite the quite large sample size, our analyses failed to reveal any relationship. The sex ratio was equal among chicks that were found dead in a nest, mostly due to starvation, but more female than male chicks disappeared from nests (mostly due to predation), primarily in the first week of life. This indicates that females may be easier to predate, very likely by frogs hunting small chicks.