A multiresolution approach to automated classification of protein subcellular location images

<p>Abstract</p> <p>Background</p> <p>Fluorescence microscopy is widely used to determine the subcellular location of proteins. Efforts to determine location on a proteome-wide basis create a need for automated methods to analyze the resulting images. Over the past ten years, the feasibility of using machine learning methods to recognize all major subcellular location patterns has been convincingly demonstrated, using diverse feature sets and classifiers. On a well-studied data set of 2D HeLa single-cell images, the best performance to date, 91.5%, was obtained by including a set of multiresolution features. This demonstrates the value of multiresolution approaches to this important problem.</p> <p>Results</p> <p>We report here a novel approach for the classification of subcellular location patterns by classifying in multiresolution subspaces. Our system is able to work with any feature set and any classifier. It consists of multiresolution (MR) decomposition, followed by feature computation and classification in each MR subspace, yielding local decisions that are then combined into a global decision. With 26 texture features alone and a neural network classifier, we obtained an increase in accuracy on the 2D HeLa data set to 95.3%.</p> <p>Conclusion</p> <p>We demonstrate that the space-frequency localized information in the multiresolution subspaces adds significantly to the discriminative power of the system. Moreover, we show that a vastly reduced set of features is sufficient, consisting of our novel modified Haralick texture features. Our proposed system is general, allowing for any combinations of sets of features and any combination of classifiers.</p

Altered expression of a putative progenitor cell marker DCAMKL1 in the rat gastric mucosa in regeneration, metaplasia and dysplasia

<p>Abstract</p> <p>Background</p> <p>Doublecortin and calcium/calmodulin-dependent protein kinase-like-1 (DCAMKL1) is a candidate marker for progenitor cells in the gastrointestinal mucosa. Lineage cells in the gastric mucosa are derived from progenitor cells, but this process can be altered after injury. Therefore, we explored DCAMKL1 expression under pathological conditions.</p> <p>Methods</p> <p>An immunohistochemical analysis was performed in rat stomach with acute superficial injury, chronic ulcer, intestinal metaplasia and dysplasia.</p> <p>Results</p> <p>DCAMKL1 was exclusively expressed in immature quiescent cells in the isthmus of normal fundic glands, where putative progenitor cells are thought to reside. DCAMKL1-positive cells and proliferating cells shed into the lumen after superficial injury and re-appeared during the regenerative process, mainly in the superficial mucosa. In the marginal mucosa around the active ulcer, parietal and chief cells diminished, foveolar hyperplasia was evident, and trefoil factor family 2 (TFF2)/spasmolytic polypeptide-expressing metaplasia (SPEM) emerged at the gland base. DCAMKL1 cells re-emerged in the deep mucosa juxtaposed with SPEM and proliferating cells. In the healing ulcer, the TFF2 cell population expanded and seemed to redifferentiate to chief cells, while proliferating cells and DCAMKL1 cells appeared above and below the TFF2 cells to promote healing. SPEM appeared and PCNA cells increased in the intestinalized mucosa, and DCAMKL1 was expressed in the proximity of the PCNA cells in the deep mucosa. DCAMKL1, PCNA and TFF2 were expressed in different dysplastic cells lining dilated glands near SPEM.</p> <p>Conclusion</p> <p>The ultrastructural appearance of DCAMKL1-positive cells and the expression patterns of DCAMKL1 in normal and pathological states indicate that the cells belong to a progenitor cell population. DCAMKL1 expression is closely associated with TFF2/SPEM cells after injury. DCAMKL1 cells repopulate close to proliferating, hyperplastic, metaplastic and dysplastic cells, and the progenitor zone shifts according to the pathological circumstances.</p

Observation of the decay Λ _b ⁰ → ψ(2S)pπ⁻

International audienceThe Cabibbo-suppressed decay Λ$_{b}^{0}$  → ψ(2S)pπ$^{−}$ is observed for the first time using a data sample collected by the LHCb experiment in proton-proton collisions corresponding to 1.0, 2.0 and 1.9 fb$^{−1}$ of integrated luminosity at centre-of-mass energies of 7, 8 and 13 TeV, respectively. The ψ(2S) mesons are reconstructed in the μ$^{+}$μ$^{−}$ final state. The branching fraction with respect to that of the Λ$_{b}^{0}$  → ψ(2S)pK$^{−}$ decay mode is measured to b

Measurement of the mass and production rate of Ξb− baryons

The first measurement of the production rate of Ξ − b baryons in p p collisions relative to that of Λ 0 b baryons is reported, using data samples collected by the LHCb experiment, and corresponding to integrated luminosities of 1, 2 and 1.6     fb − 1 at √ s = 7 , 8 and 13 TeV, respectively. In the kinematic region 2 &lt; η &lt; 6 and p T &lt; 20     GeV / c , we measure f Ξ − b f Λ 0 b B ( Ξ − b → J / ψ Ξ − ) B ( Λ 0 b → J / ψ Λ ) = ( 10.8 ± 0.9 ± 0.8 ) × 10 − 2 [ √ s = 7 , 8     TeV ], f Ξ − b f Λ 0 b B ( Ξ − b → J / ψ Ξ − ) B ( Λ 0 b → J / ψ Λ ) = ( 13.1 ± 1.1 ± 1.0 ) × 10 − 2 [ √ s = 13     TeV ], where f Ξ − b and f Λ 0 b are the fragmentation fractions of b quarks into Ξ − b and Λ 0 b baryons, respectively; B represents branching fractions; and the uncertainties are due to statistical and experimental systematic sources. The values of f Ξ − b / f Λ 0 b are obtained by invoking SU(3) symmetry in the Ξ − b → J / ψ Ξ − and Λ 0 b → J / ψ Λ decays. Production asymmetries between Ξ − b and ¯ Ξ + b baryons are also reported. The mass of the Ξ − b baryon is also measured relative to that of the Λ 0 b baryon, from which it is found that m ( Ξ − b ) = 5796.70 ± 0.39 ± 0.15 ± 0.17     MeV / c 2 , where the last uncertainty is due to the precision on the known Λ 0 b mass. This result represents the most precise determination of the Ξ − b mass

Measurement of CP -violating and mixing-induced observables in Bs0→ϕγ decays

A time-dependent analysis of the B 0 s → ϕ γ decay rate is performed to determine the C P -violating observables S ϕ γ and C ϕ γ and the mixing-induced observable A Δ ϕ γ . The measurement is based on a sample of p p collision data recorded with the LHCb detector, corresponding to an integrated luminosity of 3     fb − 1 at center-of-mass energies of 7 and 8 TeV. The measured values are S ϕ γ = 0.43 ± 0.30 ± 0.11 , C ϕ γ = 0.11 ± 0.29 ± 0.11 , and A Δ ϕ γ = − 0.67 + 0.37 − 0.41 ± 0.17 , where the first uncertainty is statistical and the second systematic. This is the first measurement of the observables S and C in radiative B 0 s decays. The results are consistent with the standard model predictions

Observation of an Excited Bc⁺ state

Using p p collision data corresponding to an integrated luminosity of 8.5     fb − 1 recorded by the LHCb experiment at center-of-mass energies of √ s = 7 , 8, and 13 TeV, the observation of an excited B + c state in the B + c π + π − invariant-mass spectrum is reported. The observed peak has a mass of 6841.2 ± 0.6 ( stat ) ± 0.1 ( syst ) ± 0.8 ( B + c )     MeV /\ud c 2 , where the last uncertainty is due to the limited knowledge of the B + c mass. It is consistent with expectations of the B ∗ c ( 2 3 S 1 ) + state reconstructed without the low-energy photon from the B ∗ c ( 1 3 S 1 ) + → B + c γ decay following B ∗ c ( 2 3 S 1 ) + → B ∗ c ( 1 3 S 1 ) + π + π − . A second state is seen with a global (local) statistical significance of 2.2 σ ( 3.2 σ ) and a mass of 6872.1 ± 1.3 ( stat ) ± 0.1 ( syst ) ± 0.8 ( B + c )     MeV / c 2 , and is consistent with the B c ( 2 1 S 0 ) + state. These mass measurements are the most precise to date

Measurement of the CKM angle γ using<i> B</i>^± → <i>DK</i>^± with D → K _S ⁰ π⁺π⁻, K _S ⁰ K⁺K⁻ decays

A binned Dalitz plot analysis of $B^\pm \to D K^\pm$ decays, with $D\to K_\text{S}^0\pi^+\pi^-$ and $D\to K_\text{S}^0K^+K^-$, is used to perform a measurement of the CP-violating observables $x_{\pm}$ and $y_{\pm}$, which are sensitive to the Cabibbo-Kobayashi-Maskawa angle $\gamma$. The analysis is performed without assuming any $D$ decay model, through the use of information on the strong-phase variation over the Dalitz plot from the CLEO collaboration. Using a sample of proton-proton collision data collected with the LHCb experiment in 2015 and 2016, and corresponding to an integrated luminosity of 2.0$\,\text{fb}^{-1}$, the values of the CP violation parameters are found to be $x_- = ( 9.0 \pm 1.7 \pm 0.7 \pm 0.4) \times 10^{-2}$, $y_- = ( 2.1 \pm 2.2 \pm 0.5 \pm 1.1) \times 10^{-2}$, $x_+ = (- 7.7 \pm 1.9 \pm 0.7 \pm 0.4) \times 10^{-2}$, and $y_+ = (- 1.0 \pm 1.9 \pm 0.4 \pm 0.9) \times 10^{-2}$. The first uncertainty is statistical, the second is systematic, and the third is due to the uncertainty on the strong-phase measurements. These values are used to obtain $\gamma = \left(87\,^{+11}_{-12}\right)^\circ$, $r_B = 0.086^{+ 0.013}_{-0.014}$, and $\delta_B = (101 \pm 11)^\circ$, where $r_B$ is the ratio between the suppressed and favoured $B$-decay amplitudes and $\delta_B$ is the corresponding strong-interaction phase difference. This measurement is combined with the result obtained using 2011 and 2012 data collected with the \lhcb experiment, to give $\gamma = \left(80\,^{+10}_{\,-9}\right)^\circ$, $r_B = 0.080 \pm 0.011$, and $\delta_B = (110 \pm 10)^\circ$.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2018-017.html. Version 2 includes minor changes made during journal revie

Evidence for an ηc(1S)π- resonance in B0→ηc(1S)K+π- decays

A Dalitz plot analysis of B0→ηc(1S)K+π- decays is performed using data samples of pp collisions collected with the LHCb detector at centre-of-mass energies of s=7,8 and 13TeV , corresponding to a total integrated luminosity of 4.7fb-1 . A satisfactory description of the data is obtained when including a contribution representing an exotic ηc(1S)π- resonant state. The significance of this exotic resonance is more than three standard deviations, while its mass and width are 4096±20-22+18MeV and 152±58-35+60MeV , respectively. The spin-parity assignments JP=0+ and JP=1- are both consistent with the data. In addition, the first measurement of the B0→ηc(1S)K+π- branching fraction is performed and gives B(B0→ηc(1S)K+π-)=(5.73±0.24±0.13±0.66)×10-4, where the first uncertainty is statistical, the second systematic, and the third is due to limited knowledge of external branching fractions

Evidence for an ηc(1S) π− Resonance in B0 → ηc(1S) K+ π− Decays

A Dalitz plot analysis of B0 → ηc(1S) K+ π− decays is performed using data samples of pp collisions collected with the LHCb detector at centre-of-mass energies of √s =7, 8 and 13 TeV, corresponding to a total integrated luminosity of 4.7 fb^−1. A satisfactory description of the data is obtained when including a contribution representing an exotic ηc(1S) π− resonant state. The significance of this exotic resonance is more than three standard deviations, while its mass and width are 4096 ± 20{−22}{+18} MeV and 152 ± 58{−35}{+60} MeV, respectively. The spin-parity assignments JP = 0+ and JP = 1− are both consistent with the data. In addition, the first measurement of the B0 → ηc(1S) K+ π− branching fraction is performed and gives B(B0 → ηc(1S) K+ π−) = (5.73 ± 0.24 ± 0.13 ± 0.66) × 10^−4, where the first uncertainty is statistical, the second systematic, and the third is due to limited knowledge of external branching fractions