A Bifunctional PARP-HDAC Inhibitor with Activity in Ewing Sarcoma

PURPOSE

Histone deacetylase (HDAC) inhibition has been shown to induce pharmacologic "BRCAness" in cancer cells with proficient DNA repair activity. This provides a rationale for exploring combination treatments with HDAC and PARP inhibition in cancer types that are insensitive to single-agent PARP inhibitors (PARPi). Here, we report the concept and characterization of a novel bifunctional PARPi (kt-3283) with dual activity toward PARP1/2 and HDAC enzymes in Ewing sarcoma cells.

EXPERIMENTAL DESIGN

Inhibition of PARP1/2 and HDAC was measured using PARP1/2, HDAC activity, and PAR formation assays. Cytotoxicity was assessed by IncuCyte live cell imaging, CellTiter-Glo, and spheroid assays. Cell-cycle profiles were determined using propidium iodide staining and flow cytometry. DNA damage was examined by γH2AX expression and comet assay. Inhibition of metastatic potential by kt-3283 was evaluated via ex vivo pulmonary metastasis assay (PuMA).

RESULTS

Compared with FDA-approved PARP (olaparib) and HDAC (vorinostat) inhibitors, kt-3283 displayed enhanced cytotoxicity in Ewing sarcoma models. The kt-3283-induced cytotoxicity was associated with strong S and G2-M cell-cycle arrest in nanomolar concentration range and elevated DNA damage as assessed by γH2AX tracking and comet assays. In three-dimensional spheroid models of Ewing sarcoma, kt-3283 showed efficacy in lower concentrations than olaparib and vorinostat, and kt-3283 inhibited colonization of Ewing sarcoma cells in the ex vivo PuMA model.

CONCLUSIONS

Our data demonstrate the preclinical justification for studying the benefit of dual PARP and HDAC inhibition in the treatment of Ewing sarcoma in a clinical trial and provides proof-of-concept for a bifunctional single-molecule therapeutic strategy.

Abstract 6194: A bifunctional inhibitor of PARP and HDAC enzymes with activity in Ewing sarcoma 3D spheroid and metastasis models

Introduction: Poly(ADP-ribose) polymerase (PARP) plays a major role in DNA repair and PARP inhibitors (PARPi) have shown promise in pre-clinical studies for the treatment of Ewing sarcoma (ES). While a clinical trial using olaparib as a single agent failed to show significant response against ES, combination therapies with PARPi have emerged as an area of interest. Deacetylation of histones, controlled by histone deacetylases (HDACs) is a key regulatory event in DNA repair and inhibition of HDACs has been shown to reduce ES tumor growth in vitro and in vivo. PARP inhibition combined with HDAC inhibition has demonstrated enhanced efficacy in pre-clinical studies in various tumor indications, and a clinical trial of olaparib and vorinostat combination therapy against metastatic breast cancer is currently ongoing. However, combination therapies can be limited in clinical utility due to overlapping toxicities and different pharmacokinetic profiles. Here, we report the efficacy of a novel bifunctional small-molecule compound, kt-3283, designed to have both PARP and HDAC inhibitory activities.

Materials and methods: PARP1 and PARP2 activity were measured using Trevigen Universal Colorimetric PARP Assay Kit, BPS Bioscience PARP2 Colorimetric PARP2 Assay Kit, and PARylation assay. HDAC activity was measured using HeLa cell nuclear extracts and a fluorogenic peptide-based biochemical assay. Cell survival EC50s were determined using live cell imaging with an Incucyte® S3 system and CellTiter Glo viability assay. Cell cycle analysis was performed by flow cytometry with propidium iodide staining. DNA damage was investigated by western blot, immunofluorescence, and comet assay. Spheroid assays were performed using the Incucyte® S3 spheroid analysis module and inhibition of metastases was assessed in a PUMA ES mouse model.

Results and discussion: Kt-3283 showed potent inhibition of PARP1/2 activity and PAR synthesis with IC50 values comparable to olaparib. Kt-3283 also showed inhibition of HDACs with an IC50 value in the low µM range. Cell survival EC50 values for the compound were also superior to those of olaparib and vorinostat in ES cell lines. Cell cycle and DNA damage analyses indicated S/G2/M cell cycle arrest and strong DNA damage upon treatment with kt-3283 at lower concentration range compared to olaparib and vorinostat. This compound also exhibited potent inhibition of 3D spheroid growth of ES cells with low µM EC50 values, and inhibited metastatic growth in a PUMA mouse model.

Conclusion: Kt-3283 shows potent inhibition of PARP1/2 and HDAC activities. It induces S and G2/M cell cycle arrest and DNA damage, and inhibits 3D spheroid growth and metastatic potential of ES cells. Further investigation of this bifunctional single-molecule inhibitor may offer a novel treatment opportunity for ES and other solid tumors with limited responses to PARPi.

Citation Format: Sarah Truong, Louise Ramos, Beibei Zhai, Jay Joshi, Fariba Ghaidi, Michael M. Lizardo, Taras Shyp, John Langlands, Dennis Brown, Jeffrey Bacha, Poul Sorensen, Wang Shen, Mads Daugaard. A bifunctional inhibitor of PARP and HDAC enzymes with activity in Ewing sarcoma 3D spheroid and metastasis models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6194.

Abstract A024: In vitro efficacy of a novel dual PARP-HDAC inhibitor in ewing sarcoma

Introduction: Inhibition of poly-adenosine diphosphate-ribose polymerase (PARP) is an effective therapy against cancers with DNA damage repair (DDR) deficiencies, such as BRCA1 and BRCA2 defects. In preclinical studies, PARP inhibitors demonstrated potential therapeutic value in Ewing sarcoma (ES), though clinical trials with olaparib failed to show significant clinical benefit. While single agent therapy proved inefficacious in the clinical treatment of ES, combination therapies may show anti-tumour activity. A key regulatory event in DNA damage repair is acetylation and deacetylation of histones, controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Increased expression of HDACs have been correlated to more malignant phenotypes in sarcomas and inhibition of HDAC in ES has been shown to be effective in inhibiting tumor growth. HDAC inhibition combined with PARP inhibition has been shown to sensitize cells to treatment in vitro, however clinically, combination therapies often require sequential administration due to different pharmacokinetic profiles and overlapping toxicities, severely limiting clinical utility. Here, we evaluate the activity and efficacy of a novel bifunctional small-molecule compound designed to have both PARP and HDAC inhibiting activity. Methods: PARP1 activity was measured using the Trevigen Universal Colorimetric PARP Assay Kit and PARP2 activity was measured using the BPS Bioscience PARP2 Colorimetric PARP2 Assay Kit. HDAC activity was measured using HeLa nuclear extracts and a fluorogenic peptide-based biochemical assay. Cell survival EC50s were determined using live cell imaging with an Incucyte S3 system and the CellTiter Glo viability assay. Accumulation of phospho-histone H2AX (pH2AX) was detected by western blot using anti-phospho histone H2AX (Ser139) antibody from Cell Signaling Technologies. Results: A representative compound from the kt-3000 series showed potent inhibition of PARP1 and PARP2 with IC50 values in the low nM range, comparable to FDA-approved PARP inhibitors. The compound also showed inhibition of HDAC enzymes with IC50 values in the low µM range, slightly lower than the FDA-approved HDAC inhibitor, vorinostat. Cell survival EC50 values were superior to olaparib in ES cell lines in vitro. Treatment with the kt-3000 compound also resulted in the increased accumulation of pH2AX by western blot and increased S and G2/M cell cycle arrest compared to olaparib. Conclusion: Our kt-3000 compound shows potent inhibition of PARP1, PARP2, and HDAC, as well as induction of DNA damage and cell cycle arrest. Further development of these bifunctional single molecule inhibitors may result in a novel treatment opportunity for Ewing sarcoma.

Citation Format: Sarah Truong, Beibei Zhai, Fariba Ghaidi, Louise Ramos, Jay Joshi, Dennis Brown, Neil Sankar, John Langlands, Jeffrey Bacha, Wang Shen, Poul Sorensen, Mads Daugaard. In vitro efficacy of a novel dual PARP-HDAC inhibitor in ewing sarcoma [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A024.

Abstract 1058: Evaluation of a novel class of bifunctional DNA alkylating agent and PARP inhibitor

Introduction: Poly-adenosine diphosphate-ribose polymerase (PARP) inhibition is an effective, FDA-approved treatment against cancers with DNA damage repair (DDR) deficiencies, such as BRCA1 or BRCA2 mutations. PARP is a core component of single-strand break repair, so in tumors with DDR deficiencies, double-strand breaks (DSBs) and single-strand breaks (SSBs) accumulate and lead to cell death. Combining PARP inhibition with other DNA-damaging therapies, such as DNA alkylating agents, has proven to be more effective than PARP inhibition alone, as DNA alkylators can lead to the formation of DSBs. However, combination therapies often require sequential administration due to pharmacokinetic considerations and overlapping toxicities, severely limiting their clinical utility. Here, we evaluate a novel class of PARP inhibitors combined with DNA alkylating functionality, in formulation as a single molecule.

Methods: PARP1 activity was determined using the Trevigen Universal Colorimetric PARP Assay Kit and PARP2 activity was determined using the BPS Bioscience PARP2 Colorimetric Assay Kit. Methylator release was evaluated by measuring the appearance of a certain degradation product. Cell cycle analysis was performed using propidium iodide staining and quantified using flow cytometry. pH2AX expression as a measure of DNA double strand breaks (DSB) was quantified by flow cytometry using an Alexa Fluor 647-conjugated anti-H2AX phospho (Ser139) antibody from BioLegend. Detection of pH2AX by western blot and immunofluorescence assays was done using anti-phospho histone H2AX (Ser139) antibody from Cell Signaling Technologies.

Results: kt-4000 series compounds are potent inhibitors of both PARP1 and PARP2 with IC50 values in the low nM range, comparable to FDA-approved PARP inhibitors. The compounds release methylator in a similar manner as temozolomide, an FDA-approved DNA alkylating agent. They induce S-phase and G2/M cell cycle arrest in MCF7 cells and lead to accumulation of pH2AX by flow cytometry, western blot, and immunofluorescence assays.

Conclusion: Our novel class of PARP inhibitors combined with DNA alkylating function show potent inhibition of both PARP1 and PARP2. These compounds also lead to accumulation of H2AX phosphorylation, a sensitive marker for double-strand breaks, and S-phase and G2/M cell cycle arrest. Development of these bifunctional, single molecule therapies may extend the clinical utility of PARP inhibitors to DDR proficient disease and increase efficacy for DDR deficient disease.

Citation Format: Sarah Truong, Beibei Zhai, Fariba Ghaidi, Louise Ramos, Jay Joshi, Dennis Brown, Neil Sankar, John Langlands, Jeffrey Bacha, Wang Shen, Mads Daugaard. Evaluation of a novel class of bifunctional DNA alkylating agent and PARP inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1058.

An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly

Salmon lice have plagued the salmon farming industry and have negatively impacted salmon populations in the wild. In response, researchers have generated high density genetic maps, genome assemblies, transcriptomes, and whole-genome resequencing data to better understand this parasite. In this study, we used long-read sequencing technology to update the previous genome assemblies of Atlantic Ocean salmon lice with a more contiguous assembly and a more comprehensive gene catalog of Pacific Ocean salmon lice. We were also able to further characterize genomic features previously identified from other studies by using published resequenced genomes of 25 Atlantic and 15 Pacific salmon lice. One example was further characterizing the ZW sex chromosomes. For both the Atlantic and Pacific Ocean salmon lice subspecies, we found that the female W-chromosome is only a small fraction of the Z-chromosome and that the vast majority of the W and Z-chromosome do not contain conserved regions (i.e. pseudoautosomal regions). However, conserved orthologous protein sequences can still be identified between the W- and Z-chromosomes.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Abstract P081: In vitro activity and efficacy of novel dual PARP-HDAC inhibitors

Introduction: Inhibition of poly adenosine diphosphate-ribose polymerase (PARP) is an effective treatment strategy against tumors with homologous recombination (HR) DNA repair deficiencies. Combination treatments utilizing PARP inhibitors (PARPi) in concert with inhibitors of key DNA repair or PARPi-resistance pathways, may expand the utility of PARPi beyond cancers harboring germ-line HR deficiencies. Acetylation and deacetylation of histones is an important regulatory event in the DNA damage response. Combining histone deacetylation inhibitors (HDACi) and PARPi have sensitized PARPi-resistant cells to treatment; however, combination regimens often require sequential administration to manage overlapping toxicities and accommodate diverse pharmacokinetics, constituting a significant limitation of these strategies in a clinical setting. Here, we test the activity of kt-3000 series, a novel bi-functional class of small molecules with dual PARP and HDAC inhibitor activity in HR-proficient cancer cells where PARPi have historically lacked single-agent activity. Methods: PARP enzyme activity was measured using the Trevigen Universal Colorimetric PARP Assay Kit. HDAC activity was measured using nuclear extracts of treated cells and the HDAC Fluorometric Activity Assay Kit from Cayman Chemical, as per the manufacturer’s protocol. PARP activity was measured by fluorescence in C41 cells following compound treatment for 2 hours and PARP-activation with 1M H2O2 by staining cells with an anti-PARP Ab followed by a FITC-coupled secondary antibodies. Cell survival EC50 values were obtained by treating cells with a range of inhibitor concentrations, then quantifying cell confluency after 72-hours of treatment based on images taken with an Incucyte S3 system. Results: kt-3000 series compounds are potent inhibitors of PARP and HDAC with IC50 values for PARP enzyme activity in the low nM range, comparable to those of FDA-approved PARP inhibitors (olaparib, rucaparib, niraparib, and talazoparib) and IC50 values for the inhibition of HDAC activity comparable to FDA-approved HDAC inhibitors (panabinostat, belinostat, and vorinostat). Fluorescent assays of PARP activity in C41 cells also resulted in IC50 values in the nM range and cell survival EC50 values of the dual inhibitors are comparable to FDA-approved PARP inhibitors alone and in similar range with FDA-approved HDAC inhibitors alone. Conclusion: Our novel dual PARP-HDAC inhibitors show potent inhibition of PARP activity in vitro comparable to FDA-approved PARP inhibitors and also show potent inhibition of HDAC activity. The potency and activity of kt-3000 series compounds exhibit potential superiority to FDA-approved PARP inhibitors and HDAC inhibitors, in formulation as a single molecule. Development of these multi-target inhibitors will target unmet medical needs in the treatment of HR-proficient cancer types with dysregulation of histone deacetylation.

Citation Format: Sarah Truong, Fariba Ghaidi, Louise Ramos, Jay Joshi, Dennis Brown, Neil Sankar, John Langlands, Jeffrey Bacha, Wang Shen, Mads Daugaard. In vitro activity and efficacy of novel dual PARP-HDAC inhibitors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P081.

Odderon Exchange from Elastic Scattering Differences between pp and pp[over ¯] Data at 1.96 TeV and from pp Forward Scattering Measurements

We describe an analysis comparing the pp[over ¯] elastic cross section as measured by the D0 Collaboration at a center-of-mass energy of 1.96 TeV to that in pp collisions as measured by the TOTEM Collaboration at 2.76, 7, 8, and 13 TeV using a model-independent approach. The TOTEM cross sections, extrapolated to a center-of-mass energy of sqrt[s]=1.96  TeV, are compared with the D0 measurement in the region of the diffractive minimum and the second maximum of the pp cross section. The two data sets disagree at the 3.4σ level and thus provide evidence for the t-channel exchange of a colorless, C-odd gluonic compound, also known as the odderon. We combine these results with a TOTEM analysis of the same C-odd exchange based on the total cross section and the ratio of the real to imaginary parts of the forward elastic strong interaction scattering amplitude in pp scattering for which the significance is between 3.4σ and 4.6σ. The combined significance is larger than 5σ and is interpreted as the first observation of the exchange of a colorless, C-odd gluonic compound.

Operationalising the "One Health" approach in India: facilitators of and barriers to effective cross-sector convergence for zoonoses prevention and control

BACKGROUND

There is a strong policy impetus for the One Health cross-sectoral approach to address the complex challenge of zoonotic diseases, particularly in low/lower middle income countries (LMICs). Yet the implementation of this approach in LMIC contexts such as India has proven challenging, due partly to the relatively limited practical guidance and understanding on how to foster and sustain cross-sector collaborations. This study addresses this gap by exploring the facilitators of and barriers to successful convergence between the human, animal and environmental health sectors in India.

METHODS

A mixed methods study was conducted using a detailed content review of national policy documents and in-depth semi-structured interview data on zoonotic disease management in India. In total, 29 policy documents were reviewed and 15 key informant interviews were undertaken with national and state level policymakers, disease managers and experts operating within the human-animal-environment interface of zoonotic disease control.

RESULTS

Our findings suggest that there is limited policy visibility of zoonotic diseases, although global zoonoses, especially those identified to be of pandemic potential by international organisations (e.g. CDC, WHO and OIE) rather than local, high burden endemic diseases, have high recognition in the existing policy agenda setting. Despite the widespread acknowledgement of the importance of cross-sectoral collaboration, a myriad of factors operated to either constrain or facilitate the success of cross-sectoral convergence at different stages (i.e. information-sharing, undertaking common activities and merging resources and infrastructure) of cross-sectoral action. Importantly, participants identified the lack of supportive policies, conflicting departmental priorities and limited institutional capacities as major barriers that hamper effective cross-sectoral collaboration on zoonotic disease control. Building on existing informal inter-personal relationships and collaboration platforms were suggested by participants as the way forward.

CONCLUSION

Our findings point to the importance of strengthening existing national policy frameworks as a first step for leveraging cross-sectoral capacity for improved disease surveillance and interventions. This requires the contextual adaptation of the One Health approach in a manner that is sensitive to the underlying socio-political, institutional and cultural context that determines and shapes outcomes of cross-sector collaborative arrangements.

Primary cutaneous anaplastic large-cell lymphoma: a review of the SEER database from 2005 to 2016

INTRODUCTION

Primary cutaneous anaplastic large-cell lymphoma (PC-ALCL) is a rare T-cell lymphoma. A prior analysis of the Surveillance, Epidemiology, and End Results (SEER) database reported only 157 cases of localized primary cutaneous CD30+ T-cell lymphoproliferative disorders (PC-ALCL and lymphomatoid papulosis) from 1973 to 2004. Our analysis of the SEER database since 2004 is the largest to date and our results improve our understanding of this disease and their potential prognostic factors.

METHODS

We used the SEER database to retrospectively identify patients. Survival was analysed using the Kaplan-Meier method, and log-rank tests were used to compare survival distributions.

RESULTS

There were 501 cases of PC-ALCL recorded from 2005 to 2016. Overall survival rates at 5 and 10 years were found to be 80.6% (95% CI 76.3%-84.3%) and 61.5% (95% CI 54.1%-68.1%) respectively. Age ≥ 60 years [hazard ratio (HR) = 1.09, P = 0.001 and use of chemotherapy (HR = 1.86, P = 0.01)] were associated with lower overall survival. In contrast to the 1973-2004 cohort, the head and neck site was not significantly associated with prognosis on multivariate analysis.

CONCLUSION

PC-ALCL has been increasingly recognized over the past decade. Age > 60 years and use of chemotherapy are associated with a worse outcome. Contrary to prior studies, location was not associated with poor survival.

Spin reorientation in antiferromagnetic Dy2FeCoO6 double perovskite

We explored the electronic and magnetic properties of the lanthanide double perovskite Dy₂FeCoO₆ by combining magnetization, Raman and Mössbauer spectroscopy and neutron diffraction along with density functional theory (DFT) calculations. Our magnetization measurements revealed two magnetic phase transitions in Dy₂FeCoO₆. First, a paramagnetic to antiferromagnetic transition at T _N = 248 K and subsequently, a spin reorientation transition at T _SR = 86 K. In addition, a field-induced magnetic phase transition with a critical field of H _c ≈ 20 kOe is seen at 2 K. Neutron diffraction data suggested cation-disordered orthorhombic structure for Dy₂FeCoO₆ in Pnma space group which is supported by Raman scattering results. The magnetic structures ascertained through representational analysis indicate that at T _N, a paramagnetic state is transformed to Γ₅(Cx, Fy, Az) antiferromagnetic structure while, at T _SR, Fe/Co moments undergo a spin reorientation to Γ₃(Gx, Ay, Fz). The refined magnetic moment of (Fe/Co) is 1.47(4) μ _B at 7 K. The antiferromagnetic structure found experimentally is supported through the DFT calculations which predict an insulating electronic state in Dy₂FeCoO₆.

First Measurement of Inclusive Muon Neutrino Charged Current Differential Cross Sections on Argon at E_{ν}∼0.8 GeV with the MicroBooNE Detector

We report the first measurement of the double-differential and total muon neutrino charged current inclusive cross sections on argon at a mean neutrino energy of 0.8 GeV. Data were collected using the MicroBooNE liquid argon time projection chamber located in the Fermilab Booster neutrino beam and correspond to 1.6×10^{20} protons on target of exposure. The measured differential cross sections are presented as a function of muon momentum, using multiple Coulomb scattering as a momentum measurement technique, and the muon angle with respect to the beam direction. We compare the measured cross sections to multiple neutrino event generators and find better agreement with those containing more complete treatment of quasielastic scattering processes at low Q^{2}. The total flux integrated cross section is measured to be 0.693±0.010(stat)±0.165(syst)×10^{-38}  cm^{2}.

Measurement of the Effective Weak Mixing Angle in pp[over ¯]→Z/γ^{*}→ℓ^{+}ℓ^{-} Events

We present a measurement of the effective weak mixing angle parameter sin^{2}θ_{eff}^{ℓ} in pp[over ¯]→Z/γ^{*}→μ^{+}μ^{-} events at a center-of-mass energy of 1.96 TeV, collected by the D0 detector at the Fermilab Tevatron Collider and corresponding to 8.6  fb^{-1} of integrated luminosity. The measured value of sin^{2}θ_{eff}^{ℓ}[μμ]=0.23016±0.00064 is further combined with the result from the D0 measurement in pp[over ¯]→Z/γ^{*}→e^{+}e^{-} events, resulting in sin^{2}θ_{eff}^{ℓ}[comb]=0.23095±0.00040. This combined result is the most precise measurement from a single experiment at a hadron collider and is the most precise determination using the coupling of the Z/γ^{*} to light quarks.

The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

The development and operation of liquid-argon time-projection chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.

Combined Forward-Backward Asymmetry Measurements in Top-Antitop Quark Production at the Tevatron

The CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of sqrt[s]=1.96  TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is A_{FB}^{tt[over ¯]}=0.128±0.025. The combined inclusive and differential asymmetries are consistent with recent standard model predictions.

Limits on Active to Sterile Neutrino Oscillations from Disappearance Searches in the MINOS, Daya Bay, and Bugey-3 Experiments

Searches for a light sterile neutrino have been performed independently by the MINOS and the Daya Bay experiments using the muon (anti)neutrino and electron antineutrino disappearance channels, respectively. In this Letter, results from both experiments are combined with those from the Bugey-3 reactor neutrino experiment to constrain oscillations into light sterile neutrinos. The three experiments are sensitive to complementary regions of parameter space, enabling the combined analysis to probe regions allowed by the Liquid Scintillator Neutrino Detector (LSND) and MiniBooNE experiments in a minimally extended four-neutrino flavor framework. Stringent limits on sin^{2}2θ_{μe} are set over 6 orders of magnitude in the sterile mass-squared splitting Δm_{41}^{2}. The sterile-neutrino mixing phase space allowed by the LSND and MiniBooNE experiments is excluded for Δm_{41}^{2}<0.8  eV^{2} at 95%  CL_{s}.

Improved Search for a Light Sterile Neutrino with the Full Configuration of the Daya Bay Experiment

This Letter reports an improved search for light sterile neutrino mixing in the electron antineutrino disappearance channel with the full configuration of the Daya Bay Reactor Neutrino Experiment. With an additional 404 days of data collected in eight antineutrino detectors, this search benefits from 3.6 times the statistics available to the previous publication, as well as from improvements in energy calibration and background reduction. A relative comparison of the rate and energy spectrum of reactor antineutrinos in the three experimental halls yields no evidence of sterile neutrino mixing in the 2×10^{-4}≲|Δm_{41}^{2}|≲0.3  eV^{2} mass range. The resulting limits on sin^{2}2θ_{14} are improved by approx imately a factor of 2 over previous results and constitute the most stringent constraints to date in the |Δm_{41}^{2}|≲0.2  eV^{2} region.

Evidence for a B_{s}^{0}π^{±} State

We report evidence for a narrow structure, X(5568), in the decay sequence X(5568)→B_{s}^{0}π^{±}, B_{s}^{0}→J/ψϕ, J/ψ→μ^{+}μ^{-}, ϕ→K^{+}K^{-}. This is evidence for the first instance of a hadronic state with valence quarks of four different flavors. The mass and natural width of this state are measured to be m=5567.8±2.9(stat)_{-1.9}^{+0.9}(syst)  MeV/c^{2} and Γ=21.9±6.4(stat)_{-2.5}^{+5.0}(syst)  MeV/c^{2}. If the decay is X(5568)→B_{s}^{*}π^{±}→B_{s}^{0}γπ^{±} with an unseen γ, m(X(5568)) will be shifted up by m(B_{s}^{*})-m(B_{s}^{0})∼49  MeV/c^{2}. This measurement is based on 10.4  fb^{-1} of pp[over ¯] collision data at sqrt[s]=1.96  TeV collected by the D0 experiment at the Fermilab Tevatron collider.

Radiologic presentation of chronic granulomatous prostatitis mimicking locally advanced prostate adenocarcinoma

We present a case of nonspecific granulomatous prostatitis (GP), a clinical mimic of prostate adenocarcinoma. A 54-year-old man presented with lower urinary tract symptoms and raised prostate-specific antigen. Magnetic resonance imaging showed features consistent with prostate cancer, including low T2-signal intensity in the peripheral and transition zones with signs of extracapsular extension. Diffusion-weighted imaging showed high-signal intensity, with low apparent diffusion coefficient values, whereas dynamic contrast enhancement demonstrated a type 3 washout curve, similar to that found in prostate cancer. Transperineal sector-guided prostate biopsy confirmed nonspecific GP, and the patient was treated conservatively. We discuss and compare nonspecific, chronic GP as a radiologic mimic of prostate adenocarcinoma patient.

Evidence for Simultaneous Production of J/ψ and ϒ Mesons

We report evidence for the simultaneous production of J/ψ and ϒ mesons in 8.1  fb^{-1} of data collected at sqrt[s]=1.96  TeV by the D0 experiment at the Fermilab pp[over ¯] Tevatron Collider. Events with these characteristics are expected to be produced predominantly by gluon-gluon interactions. In this analysis, we extract the effective cross section characterizing the initial parton spatial distribution, σ_{eff}=2.2±0.7(stat)±0.9(syst)  mb.

Overview of ion source characterization diagnostics in INTF

INdian Test Facility (INTF) is envisaged to characterize ITER diagnostic neutral beam system and to establish the functionality of its eight inductively coupled RF plasma driver based negative hydrogen ion source and its beamline components. The beam quality mainly depends on the ion source performance and therefore, its diagnostics plays an important role for its safe and optimized operation. A number of diagnostics are planned in INTF to characterize the ion source performance. Negative ions and its cesium contents in the source will be monitored by optical emission spectroscopy (OES) and cavity ring down spectroscopy. Plasma near the extraction region will be studied using standard electrostatic probes. The beam divergence and negative ion stripping losses are planned to be measured using Doppler shift spectroscopy. During initial phase of ion beam characterization, carbon fiber composite based infrared imaging diagnostics will be used. Safe operation of the beam will be ensured by using standard thermocouples and electrical voltage-current measurement sensors. A novel concept, based on plasma density dependent plasma impedance measurement using RF electrical impedance matching parameters to characterize the RF driver plasma, will be tested in INTF and will be validated with OES data. The paper will discuss about the overview of the complete INTF diagnostics including its present status of procurement, experimentation, interface with mechanical systems in INTF, and integration with INTF data acquisition and control systems.

Inclusive Production of the X(4140) State in pp[over ¯] Collisions at D0

We present a study of the inclusive production of the X(4140) state with the decay to the J/ψϕ final state in hadronic collisions. Based on 10.4  fb^{-1} of pp[over ¯] collision data collected by the D0 experiment at the Fermilab Tevatron collider, we report the first evidence for the prompt production of an X(4140) state and find the fraction of X(4140) events originating from b hadrons to be f_{b}=0.39±0.07(stat)±0.10(syst). The ratio of the nonprompt X(4140) production rate to the B_{s}^{0} yield in the same channel is R=0.19±0.05(stat)±0.07(syst). The values of the mass M=4152.5±1.7(stat)_{-5.4}^{+6.2}(syst)  MeV and width Γ=16.3±5.6(stat)±11.4(syst)  MeV are consistent with previous measurements.

Clinical outcomes in patients with nonfunctioning pituitary adenomas managed conservatively

CONTEXT

The natural history and the optimum management of patients with nonfunctioning pituitary adenomas (NFPAs) are unclear.

OBJECTIVE

Our objective was to characterize the natural history of patients with NFPAs managed conservatively.

DESIGN AND PATIENTS

We conducted a retrospective analysis of patients presenting to a tertiary referral centre between 1986 and 2009. Patients with pituitary adenomas and no clinical or biochemical evidence of hormonal hypersecretion were included. Those presenting with apoplexy or a radiological follow-up period of less than 1 year were excluded. The pituitary imaging for all patients was re-examined by two neuroradiologists in consensus.

OUTCOME MEASURES

The outcome measures were change in tumour size and pituitary hormone function.

RESULTS

Sixty-six patients were managed conservatively for a mean follow-up period of 4·3 years (range: 1-14·7). Forty-seven (71%) had a macroadenoma, and nineteen (29%) had a microadenoma. Tumour size decreased or remained stable in 40% of macroadenomas and 47% of microadenomas. The median annual growth rate of enlarging macroadenomas and microadenomas was 1·0 mm/year and 0·4 mm/year, respectively. The median annual growth rate of macroadenomas was significantly higher than that of microadenomas (P < 0·01). Sixty-eight percentage of patients with a macroadenoma had pituitary hormone deficiency in one or more axes, compared to 42% of those with a microadenoma.

CONCLUSION

Patients with NFPAs without optic chiasm compression can be managed conservatively. All patients need pituitary function assessment, irrespective of tumour size. These findings provide clinically relevant data for the management of patients with NFPAs.

Search for Violation of CPT and Lorentz Invariance in Bs(0) Meson Oscillations

We present the first search for CPT-violating effects in the mixing of Bs(0) mesons using the full Run II data set with an integrated luminosity of 10.4  fb(-1) of proton-antiproton collisions collected using the D0 detector at the Fermilab Tevatron Collider. We measure the CPT-violating asymmetry in the decay Bs(0)→μ(±)Ds(±) as a function of celestial direction and sidereal phase. We find no evidence for CPT-violating effects and place limits on the direction and magnitude of flavor-dependent CPT- and Lorentz-invariance violating coupling coefficients. We find 95% confidence intervals of Δa⊥<1.2×10(-12)  GeV and (-0.8<ΔaT-0.396ΔaZ<3.9)×10(-13)  GeV.

Tevatron Combination of Single-Top-Quark Cross Sections and Determination of the Magnitude of the Cabibbo-Kobayashi-Maskawa Matrix Element V_{tb}

We present the final combination of CDF and D0 measurements of cross sections for single-top-quark production in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV. The data correspond to total integrated luminosities of up to 9.7 fb^{-1} per experiment. The t-channel cross section is measured to be σ_{t}=2.25_{-0.31}^{+0.29} pb. We also present the combinations of the two-dimensional measurements of the s- vs t-channel cross section. In addition, we give the combination of the s+t channel cross section measurement resulting in σ_{s+t}=3.30_{-0.40}^{+0.52} pb, without assuming the standard model value for the ratio σ_{s}/σ_{t}. The resulting value of the magnitude of the top-to-bottom quark coupling is |V_{tb}|=1.02_{-0.05}^{+0.06}, corresponding to |V_{tb}|>0.92 at the 95% C.L.

Pharmacological Characterization of ZYAN1, a Novel Prolyl Hydroxylase Inhibitor for the Treatment of Anemia

Prolyl hydroxylase (PHD) inhibitors stabilize hypoxia inducible factor (HIF), and exert antianemic effect by potentiating erythropoietin (EPO) expression and down-regulation of hepcidin. ZYAN1 is a novel PHD inhibitor under clinical development for the treatment of anemia. The pharmacodynamic effects of acute and chronic dosing of ZYAN1 were assessed in normal and 5/6 nephrectomized Wistar rats. The effect of ZYAN1 was also investigated in cisplatin-induced anemia using C57 mice. Acute treatment with ZYAN1 increased circulating EPO levels (10.3 ± 3.7 and 40.0 ± 8.5 fold rise at 15 and 30 mg/kg, respectively), reticulocyte count (4.2 ± 0.5 and 6.0 ± 0.2 fold rise at 15 and 30 mg/kg, respectively) and stabilized HIF (28% increase at 45 mg/kg) in normal rats. Nephrectomized rats showed similar dose-related pharmacodynamic effects. In a 28-day study in nephrectomized rats, ZYAN1 administered every alternate day, caused increase in hemoglobin (1.9 ± 0.3 and 2.5 ± 0.4 g/dL) and RBC count (10.7 ± 4.0 and 14.0 ± 4.1%) at 15 and 30 mg/kg respectively. In cisplatin-treated mice also an increase in hemoglobin (3.4 ± 0.2 and 5.9 ± 0.2 g/dL) and RBC count (22.5 ± 2.2 and 37.3 ± 1.7%) at 15 and 30 mg/kg respectively was observed. ZYAN1's effects on hemoglobin and RBC count were distinct from darbepoietin. ZYAN1 demonstrated hematinic potential by combined effects on EPO release and efficient iron utilization. The efficacy of ZYAN1 in disease models of different etiologies suggests that it will be useful in treating wide spectrum of anemia patients.

Measurement of the Effective Weak Mixing Angle in pp[over ¯]→Z/γ^{*}→e^{+}e^{-} Events

We present a measurement of the fundamental parameter of the standard model, the weak mixing angle sin^{2}θ_{eff}^{ℓ} which determines the relative strength of weak and electromagnetic interactions, in pp[over ¯]→Z/γ^{*}→e^{+}e^{-} events at a center of mass energy of 1.96 TeV, using data corresponding to 9.7 fb^{-1} of integrated luminosity collected by the D0 detector at the Fermilab Tevatron. The effective weak mixing angle is extracted from the forward-backward charge asymmetry as a function of the invariant mass around the Z boson pole. The measured value of sin^{2}θ_{eff}^{ℓ}=0.23147±0.00047 is the most precise measurement from light quark interactions to date, with a precision close to the best LEP and SLD results.

Soil biota effects on local abundances of three grass species along a land-use gradient

Biotic plant-soil interactions and land-use intensity are known to affect plant individual fitness as well as competitiveness and therefore plant-species abundances in communities. Therefore, a link between soil biota and land-use intensity on local abundance of plant species in grasslands can be expected. In two greenhouse experiments, we investigated the effects of soil biota from grassland sites differing in land-use intensity on three grass species that vary in local abundances along this land-use gradient. We were interested in those soil-biota effects that are associated with land-use intensity, and whether these effects act directly or indirectly. Therefore, we grew the three plant species in two separate experiments as single individuals and in mixtures and compared their performance. As single plants, all three grasses showed a similar performance with and without soil biota. In contrast, in mixtures growth of the species in response to the presence or absence of soil biota differed. This resulted in different soil-biota effects that tend to correspond with patterns of species-specific abundances in the field for two of the three species tested. Our results highlight the importance of indirect interactions between plants and soil microorganisms and suggest that combined effects of soil biota and plant-plant interactions are involved in structuring plant communities. In conclusion, our experiments suggest that soil biota may have the potential to alter effects of plant-plant interactions and therefore influence plant-species abundances and diversity in grasslands.

Tevatron constraints on models of the Higgs boson with exotic spin and parity using decays to bottom-antibottom quark pairs

Combined constraints from the CDF and D0 Collaborations on models of the Higgs boson with exotic spin J and parity P are presented and compared with results obtained assuming the standard model value JP=0+. Both collaborations analyzed approximately 10  fb(-) of proton-antiproton collisions with a center-of-mass energy of 1.96 TeV collected at the Fermilab Tevatron. Two models predicting exotic Higgs bosons with JP=0- and JP=2+ are tested. The kinematic properties of exotic Higgs boson production in association with a vector boson differ from those predicted for the standard model Higgs boson. Upper limits at the 95% credibility level on the production rates of the exotic Higgs bosons, expressed as fractions of the standard model Higgs boson production rate, are set at 0.36 for both the JP=0- hypothesis and the JP=2+ hypothesis. If the production rate times the branching ratio to a bottom-antibottom pair is the same as that predicted for the standard model Higgs boson, then the exotic bosons are excluded with significances of 5.0 standard deviations and 4.9 standard deviations for the JP=0- and JP=2+ hypotheses, respectively.

Measurement of the B(s)(0) lifetime in the flavor-specific decay channel B(s)(0)→D(s)(-)μ(+)νX

We present an updated measurement of the B(s)(0) lifetime using the semileptonic decays B(s)(0)→D(s)(-)μ(+)νX, with D(s)(-)→ϕπ(-) and ϕ→K(+)K(-) (and the charge conjugate process). This measurement uses the full Tevatron Run II sample of proton-antiproton collisions at √[s]=1.96  TeV, comprising an integrated luminosity of 10.4  fb(-1). We find a flavor-specific lifetime τ(fs)(B(s)(0))=1.479±0.010(stat)±0.021(syst)  ps. This technique is also used to determine the B(0) lifetime using the analogous B(0)→D(-)μ(+)νX decay with D(-)→ϕπ(-) and ϕ→K(+)K(-), yielding τ(B(0))=1.534±0.019(stat)±0.021(syst)  ps. Both measurements are consistent with the current world averages, and the B(s)(0) lifetime measurement is one of the most precise to date. Taking advantage of the cancellation of systematic uncertainties, we determine the lifetime ratio τ(fs)(B(s)(0))/τ(B(0))=0.964±0.013(stat)±0.007(syst).

Measurement of the forward-backward asymmetry in the production of B(±) mesons in pp̄ collisions at √s=1.96 TeV

We present a measurement of the forward-backward asymmetry in the production of B(±) mesons, A(FB)(B(±)), using B(±)→J/ψK(±) decays in 10.4  fb(-1) of pp̄ collisions at sqrt[s]=1.96  TeV collected by the D0 experiment during Run II of the Tevatron collider. A nonzero asymmetry would indicate a preference for a particular flavor, i.e., b quark or ̄b antiquark, to be produced in the direction of the proton beam. We extract A(FB)(B(±)) from a maximum likelihood fit to the difference between the numbers of forward- and backward-produced B(±) mesons. We measure an asymmetry consistent with zero: A(FB)(B(±))=[-0.24±0.41  (stat)±0.19  (syst)]%.

Constraints on models for the Higgs boson with exotic spin and parity in VH → Vbb final states

We present constraints on models containing non-standard-model values for the spin J and parity P of the Higgs boson H in up to 9.7 fb(-1) of pp collisions at sqrt[s] = 1.96 TeV collected with the D0 detector at the Fermilab Tevatron Collider. These are the first studies of Higgs boson J(P) with fermions in the final state. In the ZH → ℓℓbb, WH → ℓνbb, and ZH → ννbb final states, we compare the standard model (SM) Higgs boson prediction, J(P) = 0(+), with two alternative hypotheses, J(P) = 0(-) and J(P) = 2(+). We use a likelihood ratio to quantify the degree to which our data are incompatible with non-SM J(P) predictions for a range of possible production rates. Assuming that the production rate in the signal models considered is equal to the SM prediction, we reject the J(P) = 0(-) and J(P) = 2(+) hypotheses at the 97.6% CL and at the 99.0% CL, respectively. The expected exclusion sensitivity for a J(P) = 0(-) (J(P) = 2(+)) state is at the 99.86% (99.94%) CL. Under the hypothesis that our data are the result of a combination of the SM-like Higgs boson and either a J(P) = 0(-) or a J(P) = 2(+) signal, we exclude a J(P) = 0(-) fraction above 0.80 and a J(P) = 2(+) fraction above 0.67 at the 95% CL. The expected exclusion covers J(P) = 0(-) (J(P) = 2(+)) fractions above 0.54 (0.47).

Precision measurement of the top quark mass in lepton + jets final States

We measure the mass of the top quark in lepton+jets final states using the full sample of pp collision data collected by the D0 experiment in Run II of the Fermilab Tevatron Collider at sqrt[s] = 1.96 TeV, corresponding to 9.7 fb(-1) of integrated luminosity. We use a matrix element technique that calculates the probabilities for each event to result from tt production or background. The overall jet energy scale is constrained in situ by the mass of the W boson. We measure m(t) = 174.98 ± 0.76 GeV. This constitutes the most precise single measurement of the top-quark mass.