Ref HAL: hal-04699141_v1
Ref Arxiv: 2312.14278
DOI: 10.1039/D3SM01740K
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Soft amorphous materials are viscoelastic solids ubiquitously found around us, from clays and cementitious pastes to emulsions and physical gels encountered in food or biomedical engineering. Under an external deformation, these materials undergo a noteworthy transition from a solid to a liquid state that reshapes the material microstructure. This yielding transition was the main theme of a workshop held from January 9 to 13, 2023 at the Lorentz Center in Leiden. The manuscript presented here offers a critical perspective on the subject, synthesizing insights from the various brainstorming sessions and informal discussions that unfolded during this week of vibrant exchange of ideas. The result of these exchanges takes the form of a series of open questions that represent outstanding experimental, numerical, and theoretical challenges to be tackled in the near future.

Ref HAL: lirmm-04694873_v1
DOI: 10.1002/pd.6489
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Objective This study involved very early post‐mortem (PM) examination of human fetal anatomy at 8 weeks of gestation (WG) using whole‐body multimodal micro‐imaging: micro‐CT and high‐field MRI (HF‐MRI). We discuss the potential place of this imaging in early first‐trimester virtual autopsy. Methods We performed micro‐CT after different contrast‐bath protocols including diffusible iodine‐based contrast‐enhanced (dice) and HF‐MRI with a 9.4 T machine with qualitative and quantitative evaluation and obtained histological sections. Results Nine fetuses were included: the crown–rump length was 10–24 mm and corresponded to 7 and 9 WG according to the Robinson formula. The Carnegie stages were 17–21. Dice micro‐CT and HF‐MRI presented high signal to noise ratio, >5, according to the Rose criterion, and for allowed anatomical phenotyping in these specimens. Imaging did not alter the histology, allowing immunostaining and pathological examination. Conclusion PM non‐destructive whole‐body multimodal micro‐imaging: dice micro‐CT and HF‐MRI allows for PM human fetal anatomy study as early as 8 WG. It paves the way to virtual autopsy in the very early first trimester. Obtaining a precision phenotype, even regarding miscarriage products, allows a reverse phenotyping to select variants of interest in genome‐wide analysis, offering potential genetic counseling for bereaved parents.

Ref HAL: hal-04694631_v1
Ref Arxiv: 2408.16819
Ref INSPIRE: 2823269
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Generating functions of BPS indices, counting states of D4-D2-D0 black holes in Calabi-Yau compactifications of type IIA string theory and identified with rank 0 Donaldson- Thomas invariants, are examples of mock modular forms. They have a quite complicated modular anomaly expressed as a sum over three different types of trees weighted by generalized error functions and their derivatives. We show that this anomaly can be significantly simplified, which in turn simplfies finding the corresponding mock modular generating functions.

Ref HAL: hal-04693176_v1
Ref Arxiv: 2408.16674
Ref INSPIRE: 2822771
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We extend previous next-to-next-to leading order (NNLO) calculations of the QCD pressure at zero temperature and non-zero baryonic densities using the renormalization group optimized perturbation theory (RGOPT), which entails an all-order RG-invariant resummation. First, we consider the approximation of three massless quark flavors, and then adding the running strange quark mass dependence. The resulting pressure displays a sizeably reduced sensitivity to variations of the arbitrary renormalization scale as compared to the state-of-the-art NNLO results. This confirms previous NLO investigations that the RGOPT resummation scheme provides improved convergence properties and reduced renormalization scale uncertainties, thus being a promising prescription to improve perturbative QCD at high and mid range baryonic densities.

Ref HAL: hal-04669355_v1
PMID 39071735
DOI: 10.1093/noajnl/vdae044
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Background: Radiological follow-up of diffuse low-grade gliomas (LGGs) growth is challenging. Approximative visual assessment still predominates over objective quantification due to the complexity of the pathology. The infiltrating character, diffuse borders and presence of surgical cavities demand LGG-based linear measurement rules to efficiently and precisely assess LGG evolution over time.Methods: We compared optimized 1D, 2D, and 3D linear measurements with manual volume segmentation as a reference to assess LGG tumor growth in 36 patients with LGG (340 magnetic resonance imaging scans), using the clinically important mean tumor diameter (MTD) and the velocity diameter expansion (VDE). LGG-specific progression thresholds were established using the high-grade gliomas-based RECIST, Macdonald, and RANO criteria, comparing the sensitivity to identify progression/non-progression for each linear method compared to the ground truth established by the manual segmentation.Results: 3D linear volume approximation correlated strongly with manually segmented volume. It also showed the highest sensitivity for progression detection. The MTD showed a comparable result, whereas the VDE highlighted that caution is warranted in the case of small tumors with multiple residues. Novel LGG-specific progression thresholds, or the critical change in estimated tumor volume, were increased for the 3D (from 40% to 52%) and 2D methods (from 25% to 33%) and decreased for the 1D method (from 20% to 16%). Using the 3D method allowed a ~5-minute time gain.Conclusions: While manual volumetric assessment remains the gold standard for calculating growth rate, the 3D linear method is the best time-efficient standardized alternative for radiological evaluation of LGGs in routine use.

Ref HAL: hal-04693484_v1
DOI: 10.1016/j.carbon.2024.119487
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Poly(N-isopropylacrylamide) (PNIPAM) is one of the most well studied thermoresponsive polymers and its microgels undergo a reversible volume phase transition (VPT) at temperatures close to that of the human body. Coupling this property with the unique optical properties of single-walled carbon nanotubes (SWCNT) in the near infrared (NIR) leads to interesting nanohybrids that could be used as multi-responsive sensors/actuators for biological applications.We show the synthesis of thermoresponsive SWCNT/PNIPAM hybrids using two different non-covalent strategies, preserving the nanotube optical properties such as fluorescence. The first strategy involves the dispersion of the SWCNT in water with sodium dodecyl sulfate (SDS), and subsequent in situ synthesis of PNIPAM microgels inside the SDS coatings around the nanotubes. The second strategy starts with modifying the nanotubes with a pyrene derivative, which in turn is used as the starting point for the in situ polymerization of the PNIPAM microgels, thus ensuring that the polymer grows around the nanotubes. In both cases, we obtain hybrids showing a phase transition at temperatures close to that of the human body, with the absorption and fluorescence spectra of the hybrids in the NIR changing in response to the changing dielectric environment. These systems could be used as actuators/sensors in biological systems.

Ref HAL: hal-04693471_v1
DOI: 10.1007/s00894-024-06068-y
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ContextSingle-wall carbon nanotubes (SWCNT) dispersed in water with the help of sodium dodecyl sulfate (SDS) surfactants exhibit a temperature dependent near infrared (NIR) exciton spectrum. Due to their biocompatibility and NIR spectrum falling within the transparent window for biological tissue, SWCNTs hold potential for sensing temperature inside cells. Here, we seek to elucidate the mechanism responsible for this temperature dependence, focusing on changes in the water coverage of the SWCNT as the surfactant structure changes with temperature. We compare optical absorption spectra in the UV–Vis-IR range and fully atomistic molecular dynamics (MD) simulations. The observed temperature dependence of the spectra for various SWCNTs may be attributed to changes in the dielectric environment and its impact on excitons. MD simulations reveal that the adsorbed SDS molecules effectively shield the SWCNT, with ~ 70% of water molecules removed from the first two adlayers; this coverage shows a modest temperature dependence. Although we are not able to directly demonstrate how this influences the NIR spectrum, this represents a potential pathway given the strong influence of the water environment on the excitons in SWCNTs.MethodsOptical absorption measurements were carried out in the UV–Vis-NIR range using a Varian Cary 5000 spectrophotometer in a temperature-controlled environment. PeakFit™ v. 4.06 was used as peak-fitting program in the spectral range 900–1400 nm (890–1380 meV) as a function of the temperature. Fully atomistic molecular dynamics simulations were conducted using the NAMD2 package. The CHARMM force field comprising two-body bond stretching, three-body angle deformation, four-body dihedral angle deformation, and nonbonded interactions (electrostatic and Lennard–Jones 6–16 potentials) was employed.