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1. PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data

   https://doi.org/10.1186/s13059-021-02341-y  

   Song, Dongyuan; Li, Jingyi Jessica (April 2021, Genome Biology)

   Abstract To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. However, existing methods do not account for pseudotime inference uncertainty, and they have either ill-posedp-values or restrictive models. Here we propose PseudotimeDE, a DE gene identification method that adapts to various pseudotime inference methods, accounts for pseudotime inference uncertainty, and outputs well-calibratedp-values. Comprehensive simulations and real-data applications verify that PseudotimeDE outperforms existing methods in false discovery rate control and power. 

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2. Live‐Cell Imaging of Guanosine Tetra‐ and Pentaphosphate (p)ppGpp with RNA‐based Fluorescent Sensors**

   https://doi.org/10.1002/anie.202111170  

   Sun, Zhining; Wu, Rigumula; Zhao, Bin; Zeinert, Rilee; Chien, Peter; You, Mingxu (October 2021, Angewandte Chemie International Edition)

   Abstract Guanosine tetra‐ and pentaphosphate, (p)ppGpp, are important alarmone nucleotides that regulate bacterial survival in stressful environment. A direct detection of (p)ppGpp in living cells is critical for our understanding of the mechanism of bacterial stringent response. However, it is still challenging to image cellular (p)ppGpp. Here, we report RNA‐based fluorescent sensors for the live‐cell imaging of (p)ppGpp. Our sensors are engineered by conjugating a recently identified (p)ppGpp‐specific riboswitch with a fluorogenic RNA aptamer, Broccoli. These sensors can be genetically encoded and enable direct monitoring of cellular (p)ppGpp accumulation. Unprecedented information on cell‐to‐cell variation and cellular dynamics of (p)ppGpp levels is now obtained under different nutritional conditions. These RNA‐based sensors can be broadly adapted to study bacterial stringent response. 

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3. Towards the understanding of the genuine three-body interaction for p–p–p and p–p–$$\Lambda $$

   https://doi.org/10.1140/epja/s10050-023-00998-6  

   Acharya, S.; Adamová, D.; Adler, A.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmad, S.; Ahn, S. U.; Ahuja, I.; et al (July 2023, The European Physical Journal A)

   Abstract Three-body nuclear forces play an important role in the structure of nuclei and hypernuclei and are also incorporated in models to describe the dynamics of dense baryonic matter, such as in neutron stars. So far, only indirect measurements anchored to the binding energies of nuclei can be used to constrain the three-nucleon force, and if hyperons are considered, the scarce data on hypernuclei impose only weak constraints on the three-body forces. In this work, we present the first direct measurement of the p–p–p and p–p– $$\Lambda $$ Λ systems in terms of three-particle correlation functions carried out for pp collisions at $$\sqrt{s} = 13$$ s = 13 TeV. Three-particle cumulants are extracted from the correlation functions by applying the Kubo formalism, where the three-particle interaction contribution to these correlations can be isolated after subtracting the known two-body interaction terms. A negative cumulant is found for the p–p–p system, hinting to the presence of a residual three-body effect while for p–p– $$\Lambda $$ Λ the cumulant is consistent with zero. This measurement demonstrates the accessibility of three-baryon correlations at the LHC. 

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4. Study of the p–p–K$$^{+}$$ and p–p–K$$^{-}$$ dynamics using the femtoscopy technique

   https://doi.org/10.1140/epja/s10050-023-01139-9  

   Acharya, S; Adamová, D; Adler, A; Aglieri_Rinella, G; Agnello, M; Agrawal, N; Ahammed, Z; Ahmad, S; Ahn, S U; Ahuja, I; et al (December 2023, The European Physical Journal A)

   Abstract The interactions of kaons (K) and antikaons ($$\mathrm {\overline{K}}$$ $\overline{K}$) with few nucleons (N) were studied so far using kaonic atom data and measurements of kaon production and interaction yields in nuclei. Some details of the three-body KNN and$$\mathrm {\overline{K}}$$ $\overline{K}$NN dynamics are still not well understood, mainly due to the overlap with multi-nucleon interactions in nuclei. An alternative method to probe the dynamics of three-body systems with kaons is to study the final state interaction within triplet of particles emitted in pp collisions at the Large Hadron Collider, which are free from effects due to the presence of bound nucleons. This Letter reports the first femtoscopic study of p–p–K$$^+$$ ${}^{+}$and p–p–K$$^-$$ ${}^{-}$correlations measured in high-multiplicity pp collisions at$$\sqrt{s}$$ $\sqrt{s}$= 13 TeV by the ALICE Collaboration. The analysis shows that the measured p–p–K$$^+$$ ${}^{+}$and p–p–K$$^-$$ ${}^{-}$correlation functions can be interpreted in terms of pairwise interactions in the triplets, indicating that the dynamics of such systems is dominated by the two-body interactions without significant contributions from three-body effects or bound states. 

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5. Coulomb-free 1S0 p − p scattering length from the quasi-free p + d → p + p + n reaction and its relation to universality

   https://doi.org/10.1038/s42005-023-01221-0  

   Tumino, Aurora; Rapisarda, Giuseppe G.; La Cognata, Marco; Oliva, Alessandro; Kievsky, Alejandro; Bertulani, Carlos A.; D’Agata, Giuseppe; Gattobigio, Mario; Guardo, Giovanni L.; Lamia, Livio; et al (May 2023, Communications Physics)

   Abstract The Coulomb-free¹S₀proton-proton (p-p) scattering length relies heavily on numerous and distinct theoretical techniques to remove the Coulomb contribution. Here, it has been determined from the half-off-the-energy-shellp-pscattering cross section measured at center-of-mass energies below 1 MeV using the quasi-freep + d → p + p + nreaction. A Bayesian data-fitting approach using the expression of the s-wave nucleon-nucleon scattering cross section returned ap-pscattering length$${a}_{pp}=-18.1{7}_{-0.58}^{+0.52}{| }_{stat}\pm 0.0{1}_{syst}$$ $a_{pp}=-18.17_{-0.58}^{+0.52}{\mid }_{stat}\pm 0.01_{syst}$fm and effective ranger₀ = 2.80 ± 0.05_stat ± 0.001_systfm. A model based on universality concepts has been developed to interpret this result. It accounts for the short-range interaction as a whole, nuclear and residual electromagnetic, according to what the s-wave phase-shiftδdoes in the description of low-energy nucleon-nucleon scattering data. We conclude that our parameters are representative of the short-range physics and propose to assess the charge symmetry breaking of the short-range interaction instead of just the nuclear interaction. This is consistent with the current understanding that the charge dependence of nuclear forces is due to different masses of up-down quarks and their electromagnetic interactions. This achievement suggests that these properties have a lesser than expected impact in the context of the charge symmetry breaking. 

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