Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays

DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications

Collecting Duct Renal Cell Carcinoma Found to Involve the Collecting System During Partial Nephrectomy: A Case Report

Collecting duct carcinoma (CDC) is a rare and aggressive form of renal cell carcinoma (RCC) arising from the principal cells of the collecting duct.  One third of cases present with metastatic disease, but many present in a manner similar to conventional RCC or urothelial carcinoma (UC).  We discuss a case of CDC which presented as a small mass at the cortico-medullary junction, and was discovered at robotic partial nephrectomy (RPN) to be grossly involving the collecting system. A 62-year-old man presented with a small renal mass suspicious for RCC, which was found on computed tomography (CT) after an episode of gross hematuria.  After thorough workup, RPN was attempted; however, intraoperatively the mass was found to be involving the collecting system.  Radical nephroureterectomy was performed, and the pathology report revealed CDC.  CDC is a rare and aggressive form of RCC.  While many cases are metastatic at diagnosis, most patients present with the incidental finding of a small renal mass.  There are no reports of a CDC involving the collecting system at RPN after negative ureteroscopy preoperatively.  The adjuvant therapeutic options for CDC are limited, and long term survival is poor

New CC0\pi\ GENIE Model Tune for MicroBooNE

A novel tune has been made for the MicroBooNE experiment. The fit uses 4 new parameters within the GENIE v3.0.6 Monte Carlo program. Charged current pionless data from the T2K experiment was used. New uncertainties were obtained. These results will be used in future MicroBooNE analyses.Comment: 24 pages, 14 figure

Differential cross section measurement of charged current νe\nu_{e} interactions without final-state pions in MicroBooNE

In this letter we present the first measurements of an exclusive electron neutrino cross section with the MicroBooNE experiment using data from the Booster Neutrino Beamline at Fermilab. These measurements are made for a selection of charged-current electron neutrinos without final-state pions. Differential cross sections are extracted in energy and angle with respect to the beam for the electron and the leading proton. The differential cross section as a function of proton energy is measured using events with protons both above and below the visibility threshold. This is done by including a separate selection of electron neutrino events without reconstructed proton candidates in addition to those with proton candidates. Results are compared to the predictions from several modern generators, and we find the data agrees well with these models. The data shows best agreement, as quantified by $p$-value, with the generators that predict a lower overall cross section, such as GENIE v3 and NuWro

First measurement of quasi-elastic Λ\Lambda baryon production in muon anti-neutrino interactions in the MicroBooNE detector

We present the first measurement of the cross section of Cabibbo-suppressed $\Lambda$ baryon production, using data collected with the MicroBooNE detector when exposed to the neutrinos from the Main Injector beam at the Fermi National Accelerator Laboratory. The data analyzed correspond to $2.2 \times 10^{20}$ protons on target of neutrino mode running and $4.9 \times 10^{20}$ protons on target of anti-neutrino mode running. An automated selection is combined with hand scanning, with the former identifying five candidate $\Lambda$ production events when the signal was unblinded, consistent with the GENIE prediction of $5.3 \pm 1.1$ events. Several scanners were employed, selecting between three and five events, compared with a prediction from a blinded Monte Carlo simulation study of $3.7 \pm 1.0$ events. Restricting the phase space to only include $\Lambda$ baryons that decay above MicroBooNE's detection thresholds, we obtain a flux averaged cross section of $2.0^{+2.2}_{-1.7} \times 10^{-40}$ cm$^2/$Ar, where statistical and systematic uncertainties are combined

Measurement of neutral current single π0\pi^0 production on argon with the MicroBooNE detector

We report the first measurement of $\pi^0$ production in neutral current (NC) interactions on argon with average neutrino energy of $\lesssim1$~GeV. We use data from the MicroBooNE detector's 85-tonne active volume liquid argon time projection chamber situated in Fermilab's Booster Neutrino Beam and exposed to $5.89\times10^{20}$ protons on target for this measurement. Measurements of NC $\pi^0$ events are reported for two exclusive event topologies without charged pions. Those include a topology with two photons from the decay of the $\pi^0$ and one proton and a topology with two photons and zero protons. Flux-averaged cross-sections for each exclusive topology and for their semi-inclusive combination are extracted (efficiency-correcting for two-plus proton final states), and the results are compared to predictions from the \textsc{genie}, \textsc{neut}, and \textsc{NuWro} neutrino event generators. We measure cross sections of $1.243\pm0.185$ (syst) $\pm0.076$ (stat), $0.444\pm0.098\pm0.047$, and $0.624\pm0.131\pm0.075$ $[10^{-38}\textrm{cm}^2/\textrm{Ar}]$ for the semi-inclusive NC$\pi^0$, exclusive NC$\pi^0$+1p, and exclusive NC$\pi^0$+0p processes, respectively.Comment: 16 pages, 14 figures, 2 table

First demonstration of O(1 ns)\mathcal{O}(1\,\text{ns}) timing resolution in the MicroBooNE liquid argon time projection chamber

MicroBooNE is a neutrino experiment located in the Booster Neutrino Beamline (BNB) at Fermilab, which collected data from 2015 to 2021. MicroBooNE's liquid argon time projection chamber (LArTPC) is accompanied by a photon detection system consisting of 32 photomultiplier tubes used to measure the argon scintillation light and determine the timing of neutrino interactions. Analysis techniques combining light signals and reconstructed tracks are applied to achieve a neutrino interaction time resolution of $\mathcal{O}(1\,\text{ns})$. The result obtained allows MicroBooNE to access the ns neutrino pulse structure of the BNB for the first time. The timing resolution achieved will enable significant enhancement of cosmic background rejection for all neutrino analyses. Furthermore, the ns timing resolution opens new avenues to search for long-lived-particles such as heavy neutral leptons in MicroBooNE, as well as in future large LArTPC experiments, namely the SBN program and DUNE

Search for heavy neutral leptons in electron-positron and neutral-pion final states with the MicroBooNE detector

We present the first search for heavy neutral leptons (HNL) decaying into $\nu e^+e^-$ or $\nu\pi^0$ final states in a liquid-argon time projection chamber using data collected with the MicroBooNE detector. The data were recorded synchronously with the NuMI neutrino beam from Fermilab's Main Injector corresponding to a total exposure of $7.01 \times 10^{20}$ protons on target. We set upper limits at the $90\%$ confidence level on the mixing parameter $\lvert U_{\mu 4}\rvert^2$ in the mass ranges $10\le m_{\rm HNL}\le 150$ MeV for the $\nu e^+e^-$ channel and $150\le m_{\rm HNL}\le 245$ MeV for the $\nu\pi^0$ channel, assuming $\lvert U_{e 4}\rvert^2 = \lvert U_{\tau 4}\rvert^2 = 0$. These limits represent the most stringent constraints in the mass range $35<m_{\rm HNL}<175$ MeV and the first constraints from a direct search for $\nu\pi^0$ decays.Comment: Version as accepted by Physical Review Letters, some presentational changes and updated references, no changes to result

First measurement of η\eta production in neutrino interactions on argon with MicroBooNE

We present a measurement of $\eta$ production from neutrino interactions on argon with the MicroBooNE detector. The modeling of resonant neutrino interactions on argon is a critical aspect of the neutrino oscillation physics program being carried out by the DUNE and Short Baseline Neutrino programs. $\eta$ production in neutrino interactions provides a powerful new probe of resonant interactions, complementary to pion channels, and is particularly suited to the study of higher-order resonances beyond the $\Delta(1232)$. We measure a flux-integrated cross section for neutrino-induced $\eta$ production on argon of $3.22 \pm 0.84 \; \textrm{(stat.)} \pm 0.86 \; \textrm{(syst.)}$ $10^{-41}{\textrm{cm}}^{2}$/nucleon. By demonstrating the successful reconstruction of the two photons resulting from $\eta$ production, this analysis enables a novel calibration technique for electromagnetic showers in GeV accelerator neutrino experiments

First Measurement of Differential Cross Sections for Muon Neutrino Charged Current Interactions on Argon with a Two-proton Final State in the MicroBooNE Detector

We present the first measurement of differential cross sections for charged-current muon neutrino interactions on argon with one muon, two protons, and no pions in the final state. Such interactions leave the target nucleus in a two-particle two-hole state; these states are of great interest, but currently there is limited information about their production in neutrino-nucleus interactions. Detailed investigations of the production of two-particle two-hole states are vital to support upcoming experiments exploring the nature of the neutrino, and the development of the liquid-argon time-projection-chamber has made possible the isolation of such final states. The opening angle between the two protons, the angle between the total proton momentum and the muon, and the total transverse momentum of the final state system are sensitive to the underlying physics processes as embodied in a variety of models. Realistic initial-state momentum distributions are shown to be important in reproducing the data.Comment: To be submitted to PR