BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites

BACKGROUND

Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mechanisms underpinning the activation of alternative promoters.

RESULTS

Here we describe how alternative cancer-testis-specific transcription is activated. We show that intergenic and intronic CTCF binding sites, which are transcriptionally inert in normal somatic cells, could be epigenetically reprogrammed into active de novo promoters in germ and cancer cells. BORIS/CTCFL, the testis-specific paralog of the ubiquitously expressed CTCF, triggers the epigenetic reprogramming of CTCF sites into units of active transcription. BORIS binding initiates the recruitment of the chromatin remodeling factor, SRCAP, followed by the replacement of H2A histone with H2A.Z, resulting in a more relaxed chromatin state in the nucleosomes flanking the CTCF binding sites. The relaxation of chromatin around CTCF binding sites facilitates the recruitment of multiple additional transcription factors, thereby activating transcription from a given binding site. We demonstrate that the epigenetically reprogrammed CTCF binding sites can drive the expression of cancer-testis genes, long noncoding RNAs, retro-pseudogenes, and dormant transposable elements.

CONCLUSIONS

Thus, BORIS functions as a transcription factor that epigenetically reprograms clustered CTCF binding sites into transcriptional start sites, promoting transcription from alternative promoters in both germ cells and cancer cells.

Upper Extremity Infection Related to Intravenous Drug Use: Considering the True Cost of the COVID-19 Pandemic and Lockdown

BACKGROUND

The COVID-19 pandemic caused significant morbidity and mortality in people who inject drugs (PWID). Upper extremity soft tissue infections are frequently associated with intravenous drug use (IVDU) due to poor compliance with aseptic technique. In Canada, multiple safe injection sites providing clean injection supplies closed, leaving many PWID with no alternatives to inject safely. It was hypothesized that these closures will correspond with increased morbidity and mortality among PWID. The main objective of this study was to determine the effect of the COVID-19 pandemic on the incidence of upper extremity infections in PWID.

METHODS

This was a retrospective chart review study. The primary outcome of interest was the frequency of upper extremity infections in PWID. Data were filtered to include only those patients presenting to the emergency department between March to June of 2019 and 2020. Chi-squared analysis was used to compare the number of IVDU patients among patients with upper extremity skin infections between these time periods.

RESULTS

The number of IVDU patients treated for upper extremity infections in Hamilton significantly increased during the pandemic, relative risk = 2.0 (95% confidence interval [CI]: 1.3-2.9, P = .0012,) while total upper extremity infections numbers have decreased overall. During the pandemic, PWID made up a larger proportion of upper extremity infections (χ2 = 10.444, P = .00123). Demographic data such as age and sex of IVDU patients presenting with upper extremity infection was not significantly affected by the pandemic.

CONCLUSIONS

The effect of the pandemic on accessing harm reduction services has led to evident increases in morbidity as described by this study. Further research on the impact of closures in PWID is needed to quantify these harms and work toward mitigation strategies.

An updated catalog of CTCF variants associated with neurodevelopmental disorder phenotypes

Introduction

CTCF-related disorder (CRD) is a neurodevelopmental disorder (NDD) caused by monoallelic pathogenic variants in CTCF. The first CTCF variants in CRD cases were documented in 2013. To date, 76 CTCF variants have been further described in the literature. In recent years, due to the increased application of next-generation sequencing (NGS), growing numbers of CTCF variants are being identified, and multiple genotype-phenotype databases cataloging such variants are emerging.

Methods

In this study, we aimed to expand the genotypic spectrum of CRD, by cataloging NDD phenotypes associated with reported CTCF variants. Here, we systematically reviewed all known CTCF variants reported in case studies and large-scale exome sequencing cohorts. We also conducted a meta-analysis using public variant data from genotype-phenotype databases to identify additional CTCF variants, which we then curated and annotated.

Results

From this combined approach, we report an additional 86 CTCF variants associated with NDD phenotypes that have not yet been described in the literature. Furthermore, we describe and explain inconsistencies in the quality of reported variants, which impairs the reuse of data for research of NDDs and other pathologies.

Discussion

From this integrated analysis, we provide a comprehensive and annotated catalog of all currently known CTCF mutations associated with NDD phenotypes, to aid diagnostic applications, as well as translational and basic research.

Study of n-Alkanethiol Self-Assembly Behavior on Iron Particles: Effect of Alkyl Chain Length and Adsorption Solvent on Resulting Iron-Based Magnetorheological Fluids

Self-assembled monolayers (SAMs) of organic molecules on metal surfaces are a type of inexpensive surface coating often used to improve metal substrate properties for sensors, electrochemistry, and nanofabrication applications. Iron, specifically, is one of the most commonly used metals, both as a pure metal and as an alloy due to its high conductivity, strong ferromagnetism, and low cost. However, magnetorheological fluids, which have shown impressive energy dampening in fields from civil infrastructure to biomedical devices utilizing iron dispersions, have suffered from low reliability and efficiency due to iron particle oxidation, corrosion, and settling. To understand the effect of self-assembled monolayers on iron and both the adsorbed particle's resistance against aggregation and performance impact, this work performs an in-depth study on alkanethiol-based self-assembled monolayers on iron particles. Adsorption of alkanethiols and the generation of SAMs on micron-sized iron particles were evaluated as a function of adsorption solvent polarity and alkanethiol chain length. Maximum alkanethiol loading, determined from appropriate isotherms, was found to strongly be a function of both parameters. Alkanethiol adsorption increased with increasing alkyl chain length and increasing solvent log P values in polar solvents. With respect to magnetorheologically relevant parameters, alkanethiol adsorption did not show any significant effect on both the magnetic properties of iron (as particles) and fluid on-state yield stress. The colloidal stability of n-alkanethiol adsorbed iron-based magnetorheological fluids (MRFs) was a function of both n-alkanethiol chain length and the iron particle adsorption solvent. MRFs composed of hexadecanethiol adsorbed iron prepared in polar solvents like methanol and ethanol showed excellent sedimentation stability compared to all other MRFs prepared in this study.

Clinical predictive models in equine medicine: A systematic review

Clinical predictive models use a patient's baseline demographic and clinical data to make predictions about patient outcomes and have the potential to aid clinical decision making. The extent of equine clinical predictive models is unknown in the literature. Using PubMed and Google Scholar, we systematically reviewed the predictive models currently described for use in equine patients. Models were eligible for inclusion if they were published in a peer-reviewed article as a multivariable model used to predict a clinical/laboratory/imaging outcome in an individual horse or herd. The agreement of at least two authors was required for model inclusion. We summarised the patient populations, model development methods, performance metric reporting, validation efforts, and, using PROBAST, assessed the risk of bias, and applicability concerns for these models. In addition, we summarised the index conditions for which models were developed and provided detailed information on included models. A total of ninety predictive models and 9 external validation studies were included in the final systematic review. A plurality of models (41%) was developed to predict outcomes associated with colic, e.g. need for surgery or survival to discharge. All included models were at high risk of bias, defined as failing one or more PROBAST signalling questions, primarily for analysis-related reasons. Importantly, a high risk of bias does not necessarily mean that models are unusable, but that they require more careful consideration prior to clinical use. Concerns for applicability were low for the majority of models. Systematic reviews such as this can serve to increase veterinarians' awareness of predictive models, including evaluation of their performance and their use in different patient populations.

Junior Medical Officers' knowledge of advance care directives and substitute decision making for people without decision making capacity: a cross sectional survey

Background

For the benefits of advance care planning to be realised during a hospital admission, the treating team must have accurate knowledge of the law pertaining to implementation of advance care directives (ACDs) and substitute decision making.

Aims

To determine in a sample of Junior Medical Officers (JMOs): (1) knowledge of the correct order to approach people as substitute decision makers if a patient does not have capacity to consent to treatment; (2) knowledge of the legal validity of ACDs when making healthcare decisions for persons without capacity to consent to treatment, including the characteristics associated with higher knowledge; and (3) barriers to enacting ACDs.

Methods

A cross-sectional survey was conducted at five public hospitals in New South Wales, Australia. Interns, residents, registrars, and trainees on clinical rotation during the recruitment period were eligible to participate. Consenting participants completed an anonymous pen-and-paper survey.

Results

A total of 118 JMOs completed a survey (36% return rate). Fifty-five percent of participants were female and 56.8% were aged 20–29 years. Seventy-five percent of JMOs correctly identified a Guardian as the first person to approach if a patient did not have decision-making capacity, and 74% correctly identified a person’s spouse or partner as the next person to approach. Only 16.5% identified all four persons in the correct order, and 13.5% did not identify any in the correct order. The mean number of correct responses to the questions assessing knowledge of the legal validity of ACDs was 2.6 (SD = 1.1) out of a possible score of 6. Only 28 participants (23.7%) correctly answered four or more knowledge statements correctly. None of the explored variables were significantly associated with higher knowledge of the legal validity of ACDs. Uncertainty about the currency of ACDs and uncertainty about the legal implications of relying on an ACD when a patient’s family or substitute decision maker disagree with it were the main barriers to enacting ACDs.

Conclusion

JMOs knowledge of the legal validity of ACDs for persons without decision making capacity and the substitute decision making hierarchy is limited. There is a clear need for targeted education and training to improve knowledge in this area for this cohort.

Junior medical doctors' decision making when using advance care directives to guide treatment for people with dementia: a cross-sectional vignette study

Background

Junior medical doctors have a key role in discussions and decisions about treatment and end-of-life care for people with dementia in hospital. Little is known about junior doctors’ decision-making processes when treating people with dementia who have advance care directives (ACDs), or the factors that influence their decisions. To describe among junior doctors in relation to two hypothetical vignettes involving patients with dementia: (1) their legal compliance and decision-making process related to treatment decisions; (2) the factors influencing their clinical decision-making; and (3) the factors associated with accurate responses to one hypothetical vignette.

Method

A cross-sectional survey of junior doctors, including trainees, interns, registrars and residents, on clinical rotation in five public hospitals located in one Australian state. The anonymous, investigator-developed survey was conducted between August 2018 and June 2019. Two hypothetical vignettes describing patients with dementia presenting to hospital with an ACD and either: (1) bacterial pneumonia; or (2) suspected stroke were presented in the survey. Participants were asked to indicate whether they would commence treatment, given the ACD instructions described in each vignette.

Results

Overall, 116 junior doctors responded (35% consent rate). In Vignette 1, 58% of respondents (n = 67/116) selected the legally compliant option (i.e. not commence treatment). Participants who chose the legally compliant option perceived ‘following patient wishes’ (n = 32/67; 48%) and ‘legal requirements to follow ACDs’ (n = 32/67; 48%) as equally important reasons for complying with the ACD. The most common reason for not selecting the legally compliant option in Vignette 1 was the ‘ACD is relevant in my decision-making process, but other factors are more relevant’ (n = 14/37; 38%). In Vignette 2, 72% of respondents (n = 83/116) indicated they would commence treatment (i.e. not follow the ACD) and 18% (n = 21/116) selected they would not commence treatment. (i.e. follow the ACD). Similar reasons influenced participant decision-making in Vignette 2, a less legally certain scenario.

Conclusions

There are critical gaps in junior doctors’ compliance with the law as it relates to the implementation of ACDs. Despite there being differences in relation to the legal answer and its certainty, clinical and ethical factors guided decision-making over and above the law in both vignettes. More education and training to guide junior doctors’ clinical decision-making and ensure compliance with the law is required.

Timber identification of Autranella, Baillonella and Tieghemella in the taxonomically challenging Sapotaceae family

BACKGROUND

To enforce timber import laws and perform timber species identification, the identity of the botanical species must be well-defined. Since the Sapotaceae family is known as a taxonomically challenging family, we focus in this study on the four most valuable Sapotaceae timber species from tropical Africa: Autranella congolensis (De Wild.) A.Chev., Baillonella toxisperma Pierre, Tieghemella africana Pierre and Tieghemella heckelii (A.Chev.) Pierre ex Dubard. The wood anatomical characteristic fiber lumen fraction and Direct Analysis in Real Time-Time of Flight Mass Spectrometry (DART-TOFMS) were used to differentiate the four species and to make inferences on species delineation and taxonomic identity.

RESULTS

We observed differences in the fiber lumen fraction measurements and discerned two groups: (1) A. congolensis and B. toxisperma, and (2) T. africana and T. heckelii. In addition, all Mann-Whitney U comparisons and differences in distributions (Kolmogorov-Smirnov) for the fiber lumen fraction measurements were significant between all species. When permutating the data between species within those two groups, significant differences were still found between the species within those groups. This could indicate that the fiber lumen fraction is not diagnostic to discern the species. DART-TOFMS analysis showed that A. congolensis and B. toxisperma have distinct chemotypes, while T. heckelii and T. africana have remarkably similar chemotypes.

CONCLUSIONS

Based on our observations of similar chemotype and weakly differentiated fiber lumen ratio, we support an alternative taxonomic hypothesis that considers Tieghemella monotypic, because of the strong resemblance between T. heckelii and T. africana. Larger sample sizes and further research is required to develop methodology for the identification of these species. A taxonomic study utilizing molecular genetics would be beneficial to assess the status of the genus and the species limits. This could have implications towards their potential inclusion on CITES appendices if there is ever need for them to be listed. If Tieghemella africana and T. heckelii remain two distinct species, they should both be listed. Screening agents should be aware that the morphological and chemical differences between T. africana and T. heckelii are minimal.

Acute onset of blisters in an infant with acrodermatitis enteropathica: A case report

We represent a pediatric case of the congenital disorder caused by zinc malabsorption, acrodermatitis enteropathica, presenting with acute onsetof blisters. Although blisters can be seen in this condition, it is not always a key feature and can therefore be overlooked when considering a differential diagnosis of acute blistering in infancy. We therefore review the common and less common features of this cutaneous eruption as well as provide an extensive differential diagnosis for acute blistering in infancy. We also emphasize the importance of lifelong treatment with zinc supplementation in these children.

Sleep Apnea in Maintenance Hemodialysis: A Mixed-Methods Study

Rationale & Objective

More than 50% of hemodialysis patients experience sleep disturbance and most have coexisting sleep apnea. However, how sleep apnea affects sleep and the overall experience of patients with chronic kidney disease treated by hemodialysis has not been evaluated.

Study Design

A mixed-methods design, incorporating cross-sectional observational and descriptive qualitative methodologies.

Setting & Participants

Patients receiving maintenance hemodialysis in Newcastle, New South Wales, Australia, with newly diagnosed sleep apnea (apnea-hypopnea index ≥ 5 per hour).

Assessments

In-laboratory polysomnography to assess sleep apnea and objective sleep parameters. Epworth Sleepiness Scale to assess daytime symptoms. A semi-structured qualitative interview to explore patient experience.

Analytical Approach

Descriptive and iterative thematic analysis.

Results

We analyzed 36 patients with newly diagnosed sleep apnea and interviewed 26 (mean age, 62 years, median apnea-hypopnea index, 32 per hour). Severity of sleep apnea did not affect patients’ sleep duration, sleep efficiency, or self-reported Epworth Sleepiness Scale score. From the qualitative interviews, 4 themes emerged: “broken sleep” related to short sleep duration, with waking and dozing off a common sleep cycle, caused by uncontrolled pain and dialysis. Many participants reported regularly “feeling unrefreshed” on waking. “Impact of sleep disturbance” included reduced physical, mental, and self-management capacity. Finally, interviewees described the need to use strategies to “soldier on” with symptoms.

Limitations

Participants’ views are only transferrable to hemodialysis patients with sleep apnea.

Conclusions

Our findings suggest that severity of sleep apnea does not affect sleep time or patient-reported daytime sleepiness; however, hemodialysis patients with sleep apnea report disturbed and unrefreshed sleep and the debilitating effects of sleep disturbance is profound. Broken and unrefreshed sleep were the dominant symptoms of sleep apnea and should be assessed routinely to identify patients with sleep apnea and improve quality of life in patients with chronic kidney disease treated with hemodialysis.

Knowledge and confidence of junior medical doctors in discussing and documenting resuscitation plans: A cross-sectional survey

BACKGROUND

A Resuscitation Plan is a medically authorised order to use or withhold resuscitation interventions. Absence of appropriate resuscitation orders exposes patients to the risk of invasive medical interventions that may be of questionable benefit depending on individual circumstances.

AIMS

To describe among junior doctors: (1) self-reported confidence discussing and completing resuscitation plans; (2) knowledge of resuscitation policy including whether resuscitation plans are legally enforceable and key triggers for completion; and (3) the factors associated with higher knowledge of triggers for completing resuscitation plans.

METHODS

A cross-sectional survey was conducted at five hospitals. Junior doctors on clinical rotation were approached at scheduled training sessions, before or after ward rounds, or at change of rotation orientation days and provided with a pen-and-paper survey.

RESULTS

A total of 118 junior doctors participated. Most felt confident discussing (79%, n = 92) and documenting (87%, n = 102) resuscitation plans with patients. However, only 45% of doctors (n = 52) correctly identified that resuscitation plans are legally enforceable medical orders. On average, doctors correctly identified 6.8 (SD = 1.8) out of 10 triggers for completing a resuscitation plan. Doctors aged >30 years were four times more likely to have high knowledge of triggers for completing resuscitation plans (OR 4.28 (95% CI 1.54 to 11.89), p = 0.0053).

CONCLUSION

Most junior doctors feel confident discussing and documenting resuscitation plans. There is a need to improve knowledge about legal obligations to follow completed resuscitation plans, and about when resuscitation plans should be completed to ensure they are completed with patients who are most at risk. This article is protected by copyright. All rights reserved.

Measurement of f_{s}/f_{u} Variation with Proton-Proton Collision Energy and B-Meson Kinematics

The ratio of the B_{s}^{0} and B^{+} fragmentation fractions f_{s} and f_{u} is studied with B_{s}^{0}→J/ψϕ and B^{+}→J/ψK^{+} decays using data collected by the LHCb experiment in proton-proton collisions at 7, 8, and 13 TeV center-of-mass energies. The analysis is performed in bins of B-meson momentum, longitudinal momentum, transverse momentum, pseudorapidity, and rapidity. The fragmentation-fraction ratio f_{s}/f_{u} is observed to depend on the B-meson transverse momentum with a significance of 6.0σ. This dependency is driven by the 13 TeV sample (8.7σ), while the results for the other collision energies are not significant when considered separately. Furthermore, the results show a 4.8σ evidence for an increase of f_{s}/f_{u} as a function of collision energy.

Observation of Several Sources of CP Violation in B^{+}→π^{+}π^{+}π^{-} Decays

Observations are reported of different sources of CP violation from an amplitude analysis of B^{+}→π^{+}π^{+}π^{-} decays, based on a data sample corresponding to an integrated luminosity of 3  fb^{-1} of pp collisions recorded with the LHCb detector. A large CP asymmetry is observed in the decay amplitude involving the tensor f_{2}(1270) resonance, and in addition significant CP violation is found in the π^{+}π^{-}S wave at low invariant mass. The presence of CP violation related to interference between the π^{+}π^{-}S wave and the P wave B^{+}→ρ(770)^{0}π^{+} amplitude is also established; this causes large local asymmetries but cancels when integrated over the phase space of the decay. The results provide both qualitative and quantitative new insights into CP -violation effects in hadronic B decays.

Measurement of Charged Hadron Production in Z-Tagged Jets in Proton-Proton Collisions at sqrt[s]=8 TeV

The production of charged hadrons within jets recoiling against a Z boson is measured in proton-proton collision data at sqrt[s]=8  TeV recorded by the LHCb experiment. The charged-hadron structure of the jet is studied longitudinally and transverse to the jet axis for jets with transverse momentum p_{T}>20  GeV and in the pseudorapidity range 2.5<η<4. These are the first measurements of jet hadronization at these forward rapidities and also the first where the jet is produced in association with a Z boson. In contrast to previous hadronization measurements at the Large Hadron Collider, which are dominated by gluon jets, these measurements probe predominantly light-quark jets which are found to be more longitudinally and transversely collimated with respect to the jet axis when compared to the previous gluon dominated measurements. Therefore, these results provide valuable information on differences between quarks and gluons regarding nonperturbative hadronization dynamics.

Amplitude Analysis of B^{±}→π^{±}K^{+}K^{-} Decays

The first amplitude analysis of the B^{±}→π^{±}K^{+}K^{-} decay is reported based on a data sample corresponding to an integrated luminosity of 3.0  fb^{-1} of pp collisions recorded in 2011 and 2012 with the LHCb detector. The data are found to be best described by a coherent sum of five resonant structures plus a nonresonant component and a contribution from ππ↔KK S-wave rescattering. The dominant contributions in the π^{±} K^{∓} and K^{+} K^{-} systems are the nonresonant and the B^{±}→ρ(1450)^{0}π^{±} amplitudes, respectively, with fit fractions around 30%. For the rescattering contribution, a sizable fit fraction is observed. This component has the largest CP asymmetry reported to date for a single amplitude of (-66±4±2)%, where the first uncertainty is statistical and the second systematic. No significant CP violation is observed in the other contributions.

Search for the Lepton-Flavor-Violating Decays B_{s}^{0}→τ^{±}μ^{∓} and B^{0}→τ^{±}μ^{∓}

Results are reported from a search for the rare decays B_{s}^{0}→τ^{±}μ^{∓} and B^{0}→τ^{±}μ^{∓}, where the τ lepton is reconstructed in the channel τ^{-}→π^{-}π^{+}π^{-}ν_{τ}. These processes are effectively forbidden in the standard model, but they can potentially occur at detectable rates in models of new physics that can induce lepton-flavor-violating decays. The search is based on a data sample corresponding to 3  fb^{-1} of proton-proton collisions recorded by the LHCb experiment in 2011 and 2012. The event yields observed in the signal regions for both processes are consistent with the expected standard model backgrounds. Because of the limited mass resolution arising from the undetected τ neutrino, the B_{s}^{0} and B^{0} signal regions are highly overlapping. Assuming no contribution from B^{0}→τ^{±}μ^{∓}, the upper limit B(B_{s}^{0}→τ^{±}μ^{∓})<4.2×10^{-5} is obtained at 95% confidence level. If no contribution from B_{s}^{0}→τ^{±}μ^{∓} is assumed, a limit of B(B^{0}→τ^{±}μ^{∓})<1.4×10^{-5} is obtained at 95% confidence level. These results represent the first limit on B(B_{s}^{0}→τ^{±}μ^{∓}) and the most stringent limit on B(B^{0}→τ^{±}μ^{∓}).

Measurement of CP-Violating and Mixing-Induced Observables in B_{s}^{0}→ϕγ Decays

A time-dependent analysis of the B_{s}^{0}→ϕγ decay rate is performed to determine the CP -violating observables S_{ϕγ} and C_{ϕγ} and the mixing-induced observable A_{ϕγ}^{Δ}. The measurement is based on a sample of pp 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_{ϕγ}=0.43±0.30±0.11, C_{ϕγ}=0.11±0.29±0.11, and A_{ϕγ}^{Δ}=-0.67_{-0.41}^{+0.37}±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_{s}^{0} decays. The results are consistent with the standard model predictions.

First Observation of the Radiative Decay Λ_{b}^{0}→Λγ

The radiative decay Λ_{b}^{0}→Λγ is observed for the first time using a data sample of proton-proton collisions corresponding to an integrated luminosity of 1.7  fb^{-1} collected by the LHCb experiment at a center-of-mass energy of 13 TeV. Its branching fraction is measured exploiting the B^{0}→K^{*0}γ decay as a normalization mode and is found to be B(Λ_{b}^{0}→Λγ)=(7.1±1.5±0.6±0.7)×10^{-6}, where the quoted uncertainties are statistical, systematic, and systematic from external inputs, respectively. This is the first observation of a radiative decay of a beauty baryon.

Observation of an Excited B_{c}^{+} State

Using pp collision data corresponding to an integrated luminosity of 8.5  fb^{-1} recorded by the LHCb experiment at center-of-mass energies of sqrt[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/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 2.2σ (3.2σ) 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 Mass Difference Between Neutral Charm-Meson Eigenstates

We report a measurement of the mass difference between neutral charm-meson eigenstates using a novel approach that enhances sensitivity to this parameter. We use 2.3×10^{6} D^{0}→K_{S}^{0}π^{+}π^{-} decays reconstructed in proton-proton collisions collected by the LHCb experiment in 2011 and 2012. Allowing for CP violation in mixing and in the interference between mixing and decay, we measure the CP-averaged normalized mass difference x_{CP}=[2.7±1.6(stat)±0.4(syst)]×10^{-3} and the CP-violating parameter Δx=[-0.53±0.70(stat)±0.22(syst)]×10^{-3}. The results are consistent with CP symmetry. These determinations are the most precise from a single experiment and, combined with current world-average results, yield the first evidence that the masses of the neutral charm-meson eigenstates differ.

Observation of a Narrow Pentaquark State, P_{c}(4312)^{+}, and of the Two-Peak Structure of the P_{c}(4450)^{+}

A narrow pentaquark state, P_{c}(4312)^{+}, decaying to J/ψp, is discovered with a statistical significance of 7.3σ in a data sample of Λ_{b}^{0}→J/ψpK^{-} decays, which is an order of magnitude larger than that previously analyzed by the LHCb Collaboration. The P_{c}(4450)^{+} pentaquark structure formerly reported by LHCb is confirmed and observed to consist of two narrow overlapping peaks, P_{c}(4440)^{+} and P_{c}(4457)^{+}, where the statistical significance of this two-peak interpretation is 5.4σ. The proximity of the Σ_{c}^{+}D[over ¯]^{0} and Σ_{c}^{+}D[over ¯]^{*0} thresholds to the observed narrow peaks suggests that they play an important role in the dynamics of these states.

Observation of CP Violation in Charm Decays

A search for charge-parity (CP) violation in D^{0}→K^{-}K^{+} and D^{0}→π^{-}π^{+} decays is reported, using pp collision data corresponding to an integrated luminosity of 5.9  fb^{-1} collected at a center-of-mass energy of 13 TeV with the LHCb detector. The flavor of the charm meson is inferred from the charge of the pion in D^{*}(2010)^{+}→D^{0}π^{+} decays or from the charge of the muon in B[over ¯]→D^{0}μ^{-}ν[over ¯]_{μ}X decays. The difference between the CP asymmetries in D^{0}→K^{-}K^{+} and D^{0}→π^{-}π^{+} decays is measured to be ΔA_{CP}=[-18.2±3.2(stat)±0.9(syst)]×10^{-4} for π-tagged and ΔA_{CP}=[-9±8(stat)±5(syst)]×10^{-4} for μ-tagged D^{0} mesons. Combining these with previous LHCb results leads to ΔA_{CP}=(-15.4±2.9)×10^{-4}, where the uncertainty includes both statistical and systematic contributions. The measured value differs from zero by more than 5 standard deviations. This is the first observation of CP violation in the decay of charm hadrons.

Search for CP Violation in D_{s}^{+}→K_{S}^{0}π^{+}, D^{+}→K_{S}^{0}K^{+}, and D^{+}→ϕπ^{+} Decays

A search for charge-parity (CP) violation in Cabibbo-suppressed D_{s}^{+}→K_{S}^{0}π^{+}, D^{+}→K_{S}^{0}K^{+}, and D^{+}→ϕπ^{+} decays is reported using proton-proton collision data, corresponding to an integrated luminosity of 3.8  fb^{-1}, collected at a center-of-mass energy of 13 TeV with the LHCb detector. High-yield samples of kinematically and topologically similar Cabibbo-favored D_{(s)}^{+} decays are analyzed to subtract nuisance asymmetries due to production and detection effects, including those induced by CP violation in the neutral kaon system. The results areA_{CP}(D_{s}^{+}→K_{S}^{0}π^{+})=(1.3±1.9±0.5)×10^{-3},A_{CP}(D^{+}→K_{S}^{0}K^{+})=(-0.09±0.65±0.48)×10^{-3},A_{CP}(D^{+}→ϕπ^{+})=(0.05±0.42±0.29)×10^{-3},where the first uncertainties are statistical and the second systematic. They are the most precise measurements of these quantities to date, and are consistent with CP symmetry. A combination with previous LHCb measurements, based on data collected at 7 and 8 TeV, is also reported.

Observation of B_{(s)}^{0}→J/ψpp[over ¯] Decays and Precision Measurements of the B_{(s)}^{0} Masses

The first observation of the decays B_{(s)}^{0}→J/ψpp[over ¯] is reported, using proton-proton collision data corresponding to an integrated luminosity of 5.2  fb^{-1}, collected with the LHCb detector. These decays are suppressed due to limited available phase space, as well as due to Okubo-Zweig-Iizuka or Cabibbo suppression. The measured branching fractions are B(B^{0}→J/ψpp[over ¯])=[4.51±0.40(stat)±0.44(syst)]×10^{-7}, B(B_{s}^{0}→J/ψpp[over ¯])=[3.58±0.19(stat)±0.39(syst)]×10^{-6}. For the B_{s}^{0} meson, the result is much higher than the expected value of O(10^{-9}). The small available phase space in these decays also allows for the most precise single measurement of both the B^{0} mass as 5279.74±0.30(stat)±0.10(syst)  MeV and the B_{s}^{0} mass as 5366.85±0.19(stat)±0.13(syst)  MeV.

Search for Lepton-Universality Violation in B^{+}→K^{+}ℓ^{+}ℓ^{-} Decays

A measurement of the ratio of branching fractions of the decays B^{+}→K^{+}μ^{+}μ^{-} and B^{+}→K^{+}e^{+}e^{-} is presented. The proton-proton collision data used correspond to an integrated luminosity of 5.0  fb^{-1} recorded with the LHCb experiment at center-of-mass energies of 7, 8, and 13 TeV. For the dilepton mass-squared range 1.1<q^{2}<6.0  GeV^{2}/c^{4} the ratio of branching fractions is measured to be R_{K}=0.846_{-0.054}^{+0.060}_{-0.014}^{+0.016}, where the first uncertainty is statistical and the second systematic. This is the most precise measurement of R_{K} to date and is compatible with the standard model at the level of 2.5 standard deviations.

Model-Independent Observation of Exotic Contributions to B^{0}→J/ψK^{+}π^{-} Decays

An angular analysis of B^{0}→J/ψK^{+}π^{-} decays is performed, using proton-proton collision data corresponding to an integrated luminosity of 3  fb^{-1} collected with the LHCb detector. The m(K^{+}π^{-}) spectrum is divided into fine bins. In each m(K^{+}π^{-}) bin, the hypothesis that the three-dimensional angular distribution can be described by structures induced only by K^{*} resonances is examined, making minimal assumptions about the K^{+}π^{-} system. The data reject the K^{*}-only hypothesis with a large significance, implying the observation of exotic contributions in a model-independent fashion. Inspection of the m(J/ψπ^{-}) vs m(K^{+}π^{-}) plane suggests structures near m(J/ψπ^{-})=4200 and 4600 MeV.

First Measurement of Charm Production in its Fixed-Target Configuration at the LHC

The first measurement of heavy-flavor production by the LHCb experiment in its fixed-target mode is presented. The production of J/ψ and D^{0} mesons is studied with beams of protons of different energies colliding with gaseous targets of helium and argon with nucleon-nucleon center-of-mass energies of sqrt[s_{NN}]=86.6 and 110.4 GeV, respectively. The J/ψ and D^{0} production cross sections in pHe collisions in the rapidity range [2, 4.6] are found to be σ_{J/ψ}=652±33(stat)±42(syst)   nb/nucleon and σ_{D^{0}}=80.8±2.4(stat)±6.3(syst)  μb/nucleon, where the first uncertainty is statistical and the second is systematic. No evidence for a substantial intrinsic charm content of the nucleon is observed in the large Bjorken-x region.

Abstract PD4-04: Role of breast MRI in predicting pathologically negative nodes after neoadjuvant chemotherapy in cN0 patients in the I-SPY2 trial

Background

In clinically node-negative (cN0) breast cancer patients with triple negative (TN) and HER2+ disease and breast pathological complete response (breast pCR), low rates of nodal positivity after neoadjuvant chemotherapy (NAC) have been demonstrated. In these patients, the omission of surgical axillary staging has been proposed. However, this information is not routinely known preoperatively. We aimed to validate the correlation between pathologic breast response and pathologic nodal status, and evaluate the relationship between response of the breast tumor on MRI and pathologic nodal status after NAC in cN0 patients in the I-SPY2 trial.

Methods

We identified all patients with cT1-4 cN0 breast cancer prior to NAC from graduated arms of the I-SPY2 trial, a prospective neoadjuvant chemotherapy trial. Absence of residual disease post-NAC was defined as longest diameter (LD) of 0 mm on MRI. Breast pCR was defined as the absence of invasive tumor in the breast at surgery. Associations between ypN0 and patient, MRI, and tumor characteristics were assessed using chi-square tests and univariate regression.

Results

Of 365 cT1-4 cN0 patients included, 128 had HR+/HER2- tumors (35%), 60 HR+/HER2+ tumors (16%), 34 HR-/HER2+ tumors (9%) and 143 TN tumors (39%). Overall, 283 patients (78%) were ypN0 after NAC and 152 patients (42%) had a breast pCR. ypN0 rate was higher in patients with a breast pCR than those with residual disease (93% vs 66%, p&lt;0.001). Patients with HR-/HER2+ and TN tumors were more likely to be ypN0 (97% and 87% respectively) than patients with HR+/HER2- and HR+/HER2+ disease (66% and 71% respectively, p&lt;0.001). Other characteristics associated with ypN0 were tumor grade (grade I 57%, grade II 66%, grade III 84%; p=0.002), MammaPrint Classification (High Risk 1 68% and High Risk 2 87%; p&lt;0.001) and absence of residual tumor in the breast on MRI (87% vs 72% in patients with evidence of tumor on MRI post-NAC/pre-surgery; p=0.003).

In patients with HR-/HER2+, HR+/HER2+, HR-/HER2+ or TN disease and a breast pCR, ypN0 rate was respectively 82%, 96%, 96% and 97% (table 1). In patients with HR+/HER2-, HR+/HER2+, HR-/HER2+ or TN disease and with no evidence of residual disease in the breast on MRI, rate of ypN0 was 71%, 80%, 94% and 96% respectively.

Conclusion

In cT1-4 cN0 breast cancer patients with HR+/HER2+, HR-/HER2+ and TN tumors and a breast pCR, ypN0 rates after NAC are extremely high. In patients with HR-/HER2+ and TN tumors with no residual breast disease on MRI after NAC and pre-surgery, ypN0 rates are high enough to consider omission of axillary surgery. In patients with HR+ tumors, MRI is unsufficiently predictive for pathological response and can therefore not be used to select ypN0 patients. Research on the prediction of ypN0 in cN+ I-SPY2 patients is ongoing.

Nodal status in patients with pCR and absence of residual disease on MRI Number of positive nodesBreast Cancer Subtype0123AllBreast pCR     HR+/HER2-27(82)2(6)4(12)033(100)HR+/HER2+24(96)01(4)025(100)HR-/HER2+24(96)1(4)0025(100)TN67(97)2(3)0069(100)Absence of residual disease on MRI     HR+/HER2-24(71)7(21)3(9)034(100)HR+/HER2+16(80)3(15)01(5)20(100)HR-/HER2+15(94)1(6)0016(100)TN54(96)2(4)0056(100)

Citation Format: van der Noordaa ME, Esserman L, Yau C, Mukhtar R, Price E, Hylton N, Abe H, Wolverton D, Crane EP, Ward KA, Nelson M, Niell BL, Oh K, Brandt KR, Bang DH, Ojeda-Fournier H, Eghtedari M, Sheth PA, Bernreuter WK, Umphrey H, Rosen MA, Dogan B, Yang W, Joe B, van 't Veer L, Hirst G, Lancaster R, Wallace A, Alvaredo M, Symmans F, Asare S, Boughey JC, I-SPY2 Consortium. Role of breast MRI in predicting pathologically negative nodes after neoadjuvant chemotherapy in cN0 patients in the I-SPY2 trial [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD4-04.

Neuropeptide signaling regulates the susceptibility of developing C. elegans to anoxia

Inadequate delivery of oxygen to organisms during development can lead to cell dysfunction/death and life-long disabilities. Although the susceptibility of developing cells to low oxygen conditions changes with maturation, the cellular and molecular pathways that govern responses to low oxygen are incompletely understood. Here we show that developing Caenorhabditis elegans are substantially more sensitive to anoxia than adult animals and that this sensitivity is controlled by nervous system generated hormones (e.g., neuropeptides). A screen of neuropeptide genes identified and validated nlp-40 and its receptor aex-2 as a key regulator of anoxic survival in developing worms. The survival-promoting action of impaired neuropeptide signaling does not rely on five known stress resistance pathways and is specific to anoxic insult. Together, these data highlight a novel cell non-autonomous pathway that regulates the susceptibility of developing organisms to anoxia.

Measurement of the Charm-Mixing Parameter y_{CP}

A measurement of the charm-mixing parameter y_{CP} using D^{0}→K^{+}K^{-}, D^{0}→π^{+}π^{-}, and D^{0}→K^{-}π^{+} decays is reported. The D^{0} mesons are required to originate from semimuonic decays of B^{-} and B[over ¯]^{0} mesons. These decays are partially reconstructed in a data set of proton-proton collisions at center-of-mass energies of 7 and 8 TeV collected with the LHCb experiment and corresponding to an integrated luminosity of 3  fb^{-1}. The y_{CP} parameter is measured to be (0.57±0.13(stat)±0.09(syst))%, in agreement with, and as precise as, the current world-average value.

Observation of Two Resonances in the Λ_{b}^{0}π^{±} Systems and Precise Measurement of Σ_{b}^{±} and Σ_{b}^{*±} Properties

The first observation of two structures consistent with resonances in the final states Λ_{b}^{0}π^{-} and Λ_{b}^{0}π^{+} is reported using samples of pp collision data collected by the LHCb experiment at sqrt[s]=7 and 8 TeV, corresponding to an integrated luminosity of 3  fb^{-1}. The ground states Σ_{b}^{±} and Σ_{b}^{*±} are also confirmed and their masses and widths are precisely measured.

Fluctuation, invisibility, fatigue - the barriers to maintaining employment with systemic lupus erythematosus: results of an online survey

Objectives

Systemic lupus erythematosus (SLE) is associated with high levels of workplace disability and unemployment. The objective of this study was to understand the reasons for this and to describe the barriers and facilitators of employment identified by people with SLE to develop appropriate solutions. Unemployment, as well as unsuitable work, has adverse health outcomes.

Methods

Adults with SLE completed a UK-specific online survey, through the LUPUS UK website, designed to find out more about the difficulties and successes that people with SLE have in maintaining employment. The survey was predominantly qualitative, to understand participants’ employment experiences to generate possible solutions.

Results

Three hundred and ninety-three people gave detailed responses to the survey within eight weeks. Every respondent reported a detrimental effect of SLE on their ability to work: 40.45% had left employment because of it. The themes of concern to respondents were unambiguous: (i) the difficulties of working (and career damage) with SLE, (ii) fear and anxiety overshadowing work/family life, (iii) the greater potential to remain in some employment or stay in full employment when modifications of work pattern and support from management and colleagues were available. SLE-related fatigue, its invisibility and fluctuating nature were felt to be the main barriers to maintaining employment. Numerous respondents could work only part-time and anxiety was high regarding their future ability to continue working. Many had taken substantial pay reductions and refused offered promotions to preserve their health. Distress due to loss of work and the benefits it brings were reported by every respondent who had left work.

Conclusion

SLE presents specific difficulties for maintaining employment – fatigue, fluctuation and invisibility – not addressed by current anti-discrimination legislation or currently available ‘reasonable adjustments’. This study demonstrates that (i) employment is an important area of concern for people with SLE, (ii) SLE has significant detrimental effects on individuals’ ability to participate and progress in employment, (iii) legislators and employers need information about SLE as invisibility and fluctuation cause hidden problems, and (iv) more data is needed to inform workplace adjustments if individual distress and societal loss of skills are to be addressed.

Evidence for an η c ( 1 S ) π - resonance in B 0 → η c ( 1 S ) K + π - decays

A Dalitz plot analysis of B 0 → η c ( 1 S ) 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 Te V , 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 η c ( 1 S ) 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 Me V and 152 ± 58 - 35 + 60 Me V , respectively. The spin-parity assignments J P = 0 + and J P = 1 - are both consistent with the data. In addition, the first measurement of the B 0 → η c ( 1 S ) K + π - branching fraction is performed and gives B ( B 0 → η c ( 1 S ) 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.

Search for lepton-flavour-violating decays of Higgs-like bosons

A search is presented for a Higgs-like boson with mass in the range 45 to 195 GeV / c 2 decaying into a muon and a tau lepton. The dataset consists of proton-proton interactions at a centre-of-mass energy of 8 TeV , collected by the LHCb experiment, corresponding to an integrated luminosity of 2 fb - 1 . The tau leptons are reconstructed in both leptonic and hadronic decay channels. An upper limit on the production cross-section multiplied by the branching fraction at 95% confidence level is set and ranges from 22 pb for a boson mass of 45 GeV / c 2 to 4 pb for a mass of 195 GeV / c 2 .

Measurement of Antiproton Production in p-He Collisions at sqrt[s_{NN}]=110 GeV

The cross section for prompt antiproton production in collisions of protons with an energy of 6.5 TeV incident on helium nuclei at rest is measured with the LHCb experiment from a data set corresponding to an integrated luminosity of 0.5  nb^{-1}. The target is provided by injecting helium gas into the LHC beam line at the LHCb interaction point. The reported results, covering antiproton momenta between 12 and 110  GeV/c, represent the first direct determination of the antiproton production cross section in p-He collisions, and impact the interpretation of recent results on antiproton cosmic rays from space-borne experiments.

First Observation of the Doubly Charmed Baryon Decay Ξ_{cc}^{++}→Ξ_{c}^{+}π^{+}

The doubly charmed baryon decay Ξ_{cc}^{++}→Ξ_{c}^{+}π^{+} is observed for the first time, with a statistical significance of 5.9σ, confirming a recent observation of the baryon in the Λ_{c}^{+}K^{-}π^{+}π^{+} final state. The data sample used corresponds to an integrated luminosity of 1.7  fb^{-1}, collected by the LHCb experiment in pp collisions at a center-of-mass energy of 13 TeV. The Ξ_{cc}^{++} mass is measured to be 3620.6±1.5(stat)±0.4(syst)±0.3(Ξ_{c}^{+})  MeV/c^{2} and is consistent with the previous result. The ratio of branching fractions between the decay modes is measured to be [B(Ξ_{cc}^{++}→Ξ_{c}^{+}π^{+})×B(Ξ_{c}^{+}→pK^{-}π^{+})]/[B(Ξ_{cc}^{++}→Λ_{c}^{+}K^{-}π^{+}π^{+})×B(Λ_{c}^{+}→pK^{-}π^{+})]=0.035±0.009(stat)±0.003(syst).

Measurement of Angular and CP Asymmetries in D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} Decays

The first measurements of the forward-backward asymmetry of the dimuon pair (A_{FB}), the triple-product asymmetry (A_{2ϕ}), and the charge-parity-conjugation asymmetry (A_{CP}), in D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} decays are reported. They are performed using data from proton-proton collisions collected with the LHCb experiment from 2011 to 2016, corresponding to a total integrated luminosity of 5  fb^{-1}. The asymmetries are measured to be A_{FB}(D^{0}→π^{+}π^{-}μ^{+}μ^{-})=(3.3±3.7±0.6)%, A_{2ϕ}(D^{0}→π^{+}π^{-}μ^{+}μ^{-})=(-0.6±3.7±0.6)%, A_{CP}(D^{0}→π^{+}π^{-}μ^{+}μ^{-})=(4.9±3.8±0.7)%, A_{FB}(D^{0}→K^{+}K^{-}μ^{+}μ^{-})=(0±11±2)%, A_{2ϕ}(D^{0}→K^{+}K^{-}μ^{+}μ^{-})=(9±11±1)%, A_{CP}(D^{0}→K^{+}K^{-}μ^{+}μ^{-})=(0±11±2)%, where the first uncertainty is statistical and the second systematic. The asymmetries are also measured as a function of the dimuon invariant mass. The results are consistent with the standard model predictions.

Measurement of the Ω_{c}^{0} Baryon Lifetime

We report a measurement of the lifetime of the Ω_{c}^{0} baryon using proton-proton collision data at center-of-mass energies of 7 and 8 TeV, corresponding to an integrated luminosity of 3.0  fb^{-1} collected by the LHCb experiment. The sample consists of about 1000  Ω_{b}^{-}→Ω_{c}^{0}μ^{-}ν[over ¯]_{μ}X signal decays, where the Ω_{c}^{0} baryon is detected in the pK^{-}K^{-}π^{+} final state and X represents possible additional undetected particles in the decay. The Ω_{c}^{0} lifetime is measured to be τ_{Ω_{c}^{0}}=268±24±10±2  fs, where the uncertainties are statistical, systematic, and from the uncertainty in the D^{+} lifetime, respectively. This value is nearly four times larger than, and inconsistent with, the current world-average value.