Spatially variant immune infiltration scoring in human cancer tissues

The Immunoscore is a method to quantify the immune cell infiltration within cancers to predict the disease prognosis. Previous immune profiling approaches relied on limited immune markers to establish patients’ tumor immunity. However, immune cells exhibit a higher-level complexity that is typically not obtained by the conventional immunohistochemistry methods. Herein, we present a spatially variant immune infiltration score, termed as SpatialVizScore, to quantify immune cells infiltration within lung tumor samples using multiplex protein imaging data. Imaging mass cytometry (IMC) was used to target 26 markers in tumors to identify stromal, immune, and cancer cell states within 26 human tissues from lung cancer patients. Unsupervised clustering methods dissected the spatial infiltration of cells in tissue using the high-dimensional analysis of 16 immune markers and other cancer and stroma enriched labels to profile alterations in the tumors’ immune infiltration patterns. Spatially resolved maps of distinct tumors determined the spatial proximity and neighborhoods of immune-cancer cell pairs. These SpatialVizScore maps provided a ranking of patients’ tumors consisting of immune inflamed, immune suppressed, and immune cold states, demonstrating the tumor’s immune continuum assigned to three distinct infiltration score ranges. Several inflammatory and suppressive immune markers were used to establish the cell-based scoring schemes at the single-cell and pixel-level, depicting the cellular spectra in diverse lung tissues. Thus, SpatialVizScore is an emerging quantitative method to deeply study tumor immunology in cancer tissues.

First Measurement of High-Energy Reactor Antineutrinos at Daya Bay

This Letter reports the first measurement of high-energy reactor antineutrinos at Daya Bay, with nearly 9000 inverse beta decay candidates in the prompt energy region of 8-12 MeV observed over 1958 days of data collection. A multivariate analysis is used to separate 2500 signal events from background statistically. The hypothesis of no reactor antineutrinos with neutrino energy above 10 MeV is rejected with a significance of 6.2 standard deviations. A 29% antineutrino flux deficit in the prompt energy region of 8-11 MeV is observed compared to a recent model prediction. We provide the unfolded antineutrino spectrum above 7 MeV as a data-based reference for other experiments. This result provides the first direct observation of the production of antineutrinos from several high-Q_{β} isotopes in commercial reactors.

Observation of a State X(2600) in the π^{+}π^{-}η' System in the Process J/ψ→γπ^{+}π^{-}η'

Based on (10087±44)×10^{6}  J/ψ events collected with the BESIII detector, the process J/ψ→γπ^{+}π^{-}η^{'} is studied using two largest decay channels of the η^{'} meson, η^{'}→γπ^{+}π^{-} and η^{'}→ηπ^{+}π^{-}, η→γγ. A new resonance, which we denote as the X(2600), is observed with a statistical significance larger than 20σ in the π^{+}π^{-}η^{'} invariant mass spectrum, and it has a connection to a structure around 1.5  GeV/c^{2} in the π^{+}π^{-} invariant mass spectrum. A simultaneous fit on the π^{+}π^{-}η^{'} and π^{+}π^{-} invariant mass spectra with the two η^{'} decay modes indicates that the mass and width of the X(2600) state are 2618.3±2.0_{-1.4}^{+16.3}  MeV/c^{2} and 195±5_{-17}^{+26}  MeV, where the first uncertainties are statistical, and the second systematic.

Observation of J/ψ Electromagnetic Dalitz Decays to X(1835), X(2120), and X(2370)

Using a sample of about 10^{10}  J/ψ events collected at a center-of-mass energy sqrt[s]=3.097  GeV with the BESIII detector, the electromagnetic Dalitz decays J/ψ→e^{+}e^{-}π^{+}π^{-}η^{'}, with η^{'}→γπ^{+}π^{-} and η^{'}→π^{+}π^{-}η, have been studied. The decay J/ψ→e^{+}e^{-}X(1835) is observed with a significance of 15σ, and also an e^{+}e^{-} invariant-mass dependent transition form factor of J/ψ→e^{+}e^{-}X(1835) is presented for the first time. The intermediate states X(2120) and X(2370) are also observed in the π^{+}π^{-}η^{'} invariant-mass spectrum with significances of 5.3σ and 7.3σ. The corresponding product branching fractions for J/ψ→e^{+}e^{-}X, X→π^{+}π^{-}η^{'} [X=X(1835), X(2120), and X(2370)] are reported.

P-524 Bi-allelic CFAP61 variants cause male infertility in humans and mice with severe oligoasthenoteratozoospermia

Study question

Are mutations in cilia and flagella-associated protein 61 (CFAP61) associated with human male infertility?

Summary answer

Bi-allelic variants ([NM_015585.4: c.1654C>T (p.R552C) and c.2911G>A (p.D971N), c.144-2A>G and c.1666G>A (p.G556R)] in CFAP61 were identified as contributory genetics factor in severe oligoasthenoteratozoospermia (OAT).

What is known already

Cfap61 knockout mice were infertile due to multiple morphological abnormalities of the sperm flagella (MMAF). However, so far there is no direct evidence that mutations of CFAP61 cause OAT and male infertility.

Study design, size, duration

Variant screening was performed by whole-exome sequencing (WES) from 325 infertile patients with OAT and 392 fertile individuals. A knockout mouse model was generate to confirm the candidate disease-causing gene, intracytoplasmic sperm injection (ICSI) was used to evaluate the efficiency of clinical treatment.

Participants/materials, setting, methods

A total 325 OAT-affected patients and 392 men with normal fertility were recruited from China. WES was performed, followed by Sanger sequencing validation. In silico bioinformatics predictions and in vitro functional analyses were performed to evaluate the impacts of candidate disease-causing variants. Hematoxylin and eosin (H&E) staining, electron microscopy, and immunofluorescence assays were performed to evaluate the sperm morphology. Two OAT-affected men with CFAP61 variants were treated by ICSI, and pregnancy outcomes were followed.

Main results and the role of chance

We identified bi-allelic CFAP61 variants [NM_015585.4: c.1654C>T (p.R552C) and c.2911G>A (p.D971N), c.144-2A>G and c.1666G>A (p.G556R)] in two (0.62%) of the 325 OAT-affected men. In silico bioinformatics analysis predicted that all four variants were deleterious, and in vitro functional analysis confirmed the deleterious effects of the mutants. Notably, H&E staining and electron microscopy analyses of the spermatozoa revealed multiple morphological abnormalities of sperm flagella, the absence of central pair microtubules, and mitochondrial sheath malformation in sperm flagella from man with CFAP61 variants. Further immunofluorescence assays revealed markedly reduced CFAP61 staining in the sperm flagella. In addition, Cfap61-deficient mice showed the OAT phenotype, suggesting that loss of function of CFAP61 was the cause of OAT. Two individuals accepted ICSI therapy using their own ejaculated sperm, and one of them succeeded in fathering a healthy baby.

Limitations, reasons for caution

Limitations include the lack of in vivo data from the one of patients, and the exact molecular mechanism should be further investigated.

Wider implications of the findings

Our findings indicate that CFAP61 is essential for spermatogenesis and that bi-allelic CFAP61 variants lead to OAT and male infertility in humans and mice. In addition, our results show that ICSI treatment can be recommended for CFAP61-related OAT.

Trial registration number

not applicable

Probing CP symmetry and weak phases with entangled double-strange baryons

Though immensely successful, the standard model of particle physics does not offer any explanation as to why our Universe contains so much more matter than antimatter. A key to a dynamically generated matter-antimatter asymmetry is the existence of processes that violate the combined charge conjugation and parity (CP) symmetry1. As such, precision tests of CP symmetry may be used to search for physics beyond the standard model. However, hadrons decay through an interplay of strong and weak processes, quantified in terms of relative phases between the amplitudes. Although previous experiments constructed CP observables that depend on both strong and weak phases, we present an approach where sequential two-body decays of entangled multi-strange baryon-antibaryon pairs provide a separation between these phases. Our method, exploiting spin entanglement between the double-strange Ξ- baryon and its antiparticle2 [Formula: see text], has enabled a direct determination of the weak-phase difference, (ξP - ξS) = (1.2 ± 3.4 ± 0.8) × 10-2 rad. Furthermore, three independent CP observables can be constructed from our measured parameters. The precision in the estimated parameters for a given data sample size is several orders of magnitude greater than achieved with previous methods3. Finally, we provide an independent measurement of the recently debated Λ decay parameter αΛ (refs. 4,5). The [Formula: see text] asymmetry is in agreement with and compatible in precision to the most precise previous measurement4.

Observation of the Singly Cabibbo Suppressed Decay Λ_{c}^{+}→nπ^{+}

The singly Cabibbo-suppressed decay Λ_{c}^{+}→nπ^{+} is observed for the first time with a statistical significance of 7.3σ by using 3.9  fb^{-1} of e^{+}e^{-} collision data collected at center-of-mass energies between 4.612 and 4.699 GeV with the BESIII detector at BEPCII. The branching fraction of Λ_{c}^{+}→nπ^{+} is measured to be (6.6±1.2_{stat}±0.4_{syst})×10^{-4}. By taking the upper limit of branching fractions of Λ_{c}^{+}→pπ^{0} from the Belle experiment, the ratio of branching fractions between Λ_{c}^{+}→nπ^{+} and Λ_{c}^{+}→pπ^{0} is calculated to be larger than 7.2 at the 90% confidence level, which disagrees with most predictions of the available phenomenological models. In addition, the branching fractions of the Cabibbo-favored decays Λ_{c}^{+}→Λπ^{+} and Λ_{c}^{+}→Σ^{0}π^{+} are measured to be (1.31±0.08_{stat}±0.05_{syst})×10^{-2} and (1.22±0.08_{stat}±0.07_{syst})×10^{-2}, respectively, which are consistent with previous results.

A proteomic approach to understand the impact of nodulation on salinity stress response in alfalfa (Medicago sativa L.)

Symbiotic nitrogen fixation in legumes is an important source of nitrogen supply in sustainable agriculture. Salinity is a key abiotic stress that negatively affects host plant growth, rhizobium-legume symbiosis and nitrogen fixation. This work investigates how the symbiotic relationship impacts plant response to salinity stress. We assayed the physiological changes and the proteome profile of alfalfa plants with active nodules (NA), inactive nodules (NI) or without nodules (NN) when plants were subjected to salinity stress. Our data suggest that NA plants respond to salinity stress through some unique signalling regulations. NA plants showed upregulation of proteins related to cell wall remodelling and reactive oxygen species scavenging, and downregulation of proteins involved in protein synthesis and degradation. The data also show that NA plants, together with NI plants, upregulated proteins involved in photosynthesis, carbon fixation and respiration, anion transport and plant defence against pathogens. The study suggests that the symbiotic relationship gave the host plant a better capacity to adjust key processes, probably to more efficiently use energy and resources, deal with oxidative stress, and maintain ion homeostasis and health during salinity stress.

Joint Determination of Reactor Antineutrino Spectra from ^{235}U and ^{239}Pu Fission by Daya Bay and PROSPECT

A joint determination of the reactor antineutrino spectra resulting from the fission of ^{235}U and ^{239}Pu has been carried out by the Daya Bay and PROSPECT Collaborations. This Letter reports the level of consistency of ^{235}U spectrum measurements from the two experiments and presents new results from a joint analysis of both data sets. The measurements are found to be consistent. The combined analysis reduces the degeneracy between the dominant ^{235}U and ^{239}Pu isotopes and improves the uncertainty of the ^{235}U spectral shape to about 3%. The ^{235}U and ^{239}Pu antineutrino energy spectra are unfolded from the jointly deconvolved reactor spectra using the Wiener-SVD unfolding method, providing a data-based reference for other reactor antineutrino experiments and other applications. This is the first measurement of the ^{235}U and ^{239}Pu spectra based on the combination of experiments at low- and highly enriched uranium reactors.

Measurement of the Cross Section for e^{+}e^{-}→Hadrons at Energies from 2.2324 to 3.6710 GeV

Based on electron-positron collision data collected with the BESIII detector operating at the Beijing Electron-Positron Collider II storage rings, the value of R≡σ(e^{+}e^{-}→hadrons)/σ(e^{+}e^{-}→μ^{+}μ^{-}) is measured at 14 center-of-mass energies from 2.2324 to 3.6710 GeV. The resulting uncertainties are less than 3.0% and are dominated by systematic uncertainties.

[Research progress in pathogenesis and control of Enterococcus faecalis with persistent infection in root canals]

Root canal therapy is the common treatment for endodontic infections. Successful root canal therapy depends on favorable root canal preparation, root canal medication and three-dimensional obturation of the root canal system. The key to successful root canal therapy is to prevent re-infection of the highly complex root canal systems by removing infecious biofilms and bacterial toxins in the root canal system. The present paper reviews the pathogenic mechanism of the Enterococcus faecalis in the harsh environment of root canal system, the inflammation and immunity of refractory periapical periodontitis and the progress of infection control methods.

First Measurement of Polarizations in the Decay D^{0}→ωφ

Using a data sample corresponding to an integrated luminosity of 2.93  fb^{-1} collected at a center-of-mass energy sqrt[s]=3.773  GeV by the BESIII detector, the decay D^{0}→ωϕ is observed for the first time. The branching fraction is measured to be (6.48±0.96±0.40)×10^{-4} with a significance of 6.3σ, where the first and second uncertainties are statistical and systematic, respectively. An angular analysis reveals that the ϕ and ω mesons from the D^{0}→ωϕ decay are transversely polarized. The 95% confidence level upper limit on longitudinal polarization fraction is set to be less than 0.24, which is inconsistent with current theoretical expectations and challenges our understanding of the underlying dynamics in charm meson decays.

Association of High Muscle Mass with Carotid Atherosclerosis: A Community-Based Population Cohort Study

OBJECTIVES

Although low muscle mass may make an under-appreciated contribution to increasing the risk of cardiovascular diseases, no prospective studies have explored the association between low muscle mass and carotid atherosclerosis. We investigated whether muscle mass was related to a higher carotid intima-media thickness (C-IMT) and carotid artery plaque in a community-based population.

METHODS

The study included 1,253 asymptomatic participants without known cardiovascular disease, who underwent carotid ultrasonography at baseline in 2013-2014 and received a re-examination in 2015-2016. The skeletal muscle mass index was estimated using a bioelectrical impedance analyzer. We assessed the relationship between the skeletal muscle mass index and the development of C-IMT and carotid plaque, both, using multivariate-adjusted logistic regression models.

RESULTS

During the follow up, 400 (51.0%) subjects with normal C-IMT at baseline developed elevated C-IMT and 215 (17.2%) subjects developed carotid plaque. The risk of elevated C-IMT occurrence linearly decreased with an increase in skeletal muscle mass index quintiles or its continuous data, after multivariate-adjustment in men and women, respectively (both P for trend < 0.05; both P < 0.05). Subgroup analyses showed that this association was BMI-dependent. Besides, there was an inverse association between a high skeletal muscle mass index and carotid artery plaque in women, but the association disappeared after multivariate adjustment. In men, the skeletal muscle mass index was not associated with the incidence of carotid plaque.

CONCLUSIONS

Skeletal muscle mass was inversely associated with the incidence of carotid atherosclerosis, suggesting muscle mass maintenance may play a role in modifying atherosclerosis.

Measurement of the Absolute Branching Fraction of D_{s}^{+}→τ^{+}ν_{τ} via τ^{+}→e^{+}ν_{e}ν[over ¯]_{τ}

Using a dataset of 6.32  fb^{-1} of e^{+}e^{-} annihilation data collected with the BESIII detector at center-of-mass energies between 4178 and 4226 MeV, we have measured the absolute branching fraction of the leptonic decay D_{s}^{+}→τ^{+}ν_{τ} via τ^{+}→e^{+}ν_{e}ν[over ¯]_{τ}, and find B_{D_{s}^{+}→τ^{+}ν_{τ}}=(5.27±0.10±0.12)×10^{-2}, where the first uncertainty is statistical and the second is systematic. The precision is improved by a factor of 2 compared to the previous best measurement. Combining with f_{D_{s}^{+}} from lattice quantum chromodynamics calculations or the |V_{cs}| from the CKMfitter group, we extract |V_{cs}|=0.978±0.009±0.012 and f_{D_{s}^{+}}=(251.1±2.4±3.0)  MeV, respectively. Combining our result with the world averages of B_{D_{s}^{+}→τ^{+}ν_{τ}} and B_{D_{s}^{+}→μ^{+}ν_{μ}}, we obtain the ratio of the branching fractions B_{D_{s}^{+}→τ^{+}ν_{τ}}/B_{D_{s}^{+}→μ^{+}ν_{μ}}=9.72±0.37, which is consistent with the standard model prediction of lepton flavor universality.

Observation of D^{0}→K_{1}(1270)^{-}e^{+}ν_{e}

Using 2.93  fb^{-1} of e^{+}e^{-} collision data taken with the BESIII detector at a center-of-mass energy of 3.773 GeV, the observation of the D^{0}→K_{1}(1270)^{-}e^{+}ν_{e} semileptonic decay is presented. The statistical significance of the decay D^{0}→K_{1}(1270)^{-}e^{+}ν_{e} is greater than 10σ. The branching fraction of D^{0}→K_{1}(1270)^{-}e^{+}ν_{e} is measured to be (1.09±0.13_{-0.16}^{+0.09}±0.12)×10^{-3}. Here, the first uncertainty is statistical, the second is systematic, and the third originates from the assumed branching fraction of K_{1}(1270)^{-}→K^{-}π^{+}π^{-}. The fraction of longitudinal polarization in D^{0}→K_{1}(1270)^{-}e^{+}ν_{e} is determined for the first time to be 0.50±0.19_{stat}±0.08_{syst}.

First Measurement of the Absolute Branching Fraction of Λ→pμ^{-}ν[over ¯]_{μ}

The absolute branching fraction of Λ→pμ^{-}ν[over ¯]_{μ} is reported for the first time based on an e^{+}e^{-} annihilation sample of 10×10^{9}  J/ψ events collected with the BESIII detector at sqrt[s]=3.097  GeV. The branching fraction is determined to be B(Λ→pμ^{-}ν[over ¯]_{μ})=[1.48±0.21(stat)±0.08(syst)]×10^{-4}, which is improved by about 30% in precision over the previous indirect measurements. Combining this result with the world average of B(Λ→pe^{-}ν[over ¯]_{e}), we obtain the ratio {[Γ(Λ→pμ^{-}ν[over ¯]_{μ})]/[Γ(Λ→pe^{-}ν[over ¯]_{e})]} to be 0.178±0.028, which agrees with the standard model prediction assuming lepton flavor universality. The asymmetry of the branching fractions of Λ→pμ^{-}ν[over ¯]_{μ} and Λ[over ¯]→p[over ¯]μ^{+}ν_{μ} is also determined, and no evidence for CP violation is found.

Propensity score matched analysis of cleft closure in complete atrioventricular septal defect repair

BACKGROUND

Repair of complete atrioventricular septal defect (cAVSD) is achieved with low mortality. However, there is a high rate of reoperation on the left atrioventricular valve (LAVV), which is often attributed to non-closure of the cleft. Although non-closure of the cleft has been reported to be a risk factor for reoperation, no randomized-controlled or propensity-matched trials have ever been performed. We investigated the effect of cleft closure on outcomes following cAVSD repair.

METHODS

We reviewed 455 patients who underwent cAVSD repair between 1990 and 2019. To determine the effect of cleft closure, propensity score matching was performed on risk factors for reoperation following cAVSD repair.

RESULTS

Median age was 3.6 months (mean 9.6±20.4), median weight was 4.3 kg (mean 4.7±4.3kg) and 41.9% (191/455) were male. Early mortality was 2.9% (13/455), and survival was 89.8±1.9% at 20 years. Early reoperation was a risk factor for mortality (p=0.004). Freedom from reoperation was 72.5±4.0% at 20 years. Freedom from LAVV reoperation was 74.1±4.0% at 20 years. Preoperative severe LAVV regurgitation (p<0.001) and early postoperative moderate or greater LAVV regurgitation (p=0.007) were risk factors for reoperation, while trisomy 21 (p=0.03) and recent era of surgery (p=0.02) were protective. Propensity score matching yielded 106 pairs. There were no differences in long-term survival (p=0.71) or reoperation (p=0.26) between the two groups.

CONCLUSIONS

Repair of cAVSD can be achieved with low mortality and good long-term survival, however, the reoperation rate remains high. Similar freedom from reoperation can be achieved with or without closure of the LAVV cleft.