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

Phylogeography of Supralittoral Rocky Intertidal Ligia Isopods in the Pacific Region from Central California to Central Mexico

Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region.We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland.Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region

Ionization electron signal processing in single phase LArTPCs. Part I. Algorithm Description and quantitative evaluation with MicroBooNE simulation

© 2018 IOP Publishing Ltd and Sissa Medialab. We describe the concept and procedure of drifted-charge extraction developed in the MicroBooNE experiment, a single-phase liquid argon time projection chamber (LArTPC). This technique converts the raw digitized TPC waveform to the number of ionization electrons passing through a wire plane at a given time. A robust recovery of the number of ionization electrons from both induction and collection anode wire planes will augment the 3D reconstruction, and is particularly important for tomographic reconstruction algorithms. A number of building blocks of the overall procedure are described. The performance of the signal processing is quantitatively evaluated by comparing extracted charge with the true charge through a detailed TPC detector simulation taking into account position-dependent induced current inside a single wire region and across multiple wires. Some areas for further improvement of the performance of the charge extraction procedure are also discussed

Rejecting cosmic background for exclusive charged current quasi elastic neutrino interaction studies with Liquid Argon TPCs; a case study with the MicroBooNE detector

AbstractCosmic ray (CR) interactions can be a challenging source of background for neutrino oscillation and cross-section measurements in surface detectors. We present methods for CR rejection in measurements of charged-current quasielastic-like (CCQE-like) neutrino interactions, with a muon and a proton in the final state, measured using liquid argon time projection chambers (LArTPCs). Using a sample of cosmic data collected with the MicroBooNE detector, mixed with simulated neutrino scattering events, a set of event selection criteria is developed that produces an event sample with minimal contribution from CR background. Depending on the selection criteria used a purity between 50 and 80% can be achieved with a signal selection efficiency between 50 and 25%, with higher purity coming at the expense of lower efficiency. While using a specific dataset and selection criteria values optimized for the MicroBooNE detector, the concepts presented here are generic and can be adapted for various studies of exclusive $$\nu _{\mu }$$ ν μ CCQE interactions in LArTPCs.</jats:p

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

Biomechanical assessment of a distally fixed lateral extra-articular augmentation procedure in the treatment of anterolateral rotational laxity of the knee

Background: Most lateral extra-articular tenodesis (LET) procedures rely on passing a strip of the iliotibial band (ITB) under the fibular (lateral) collateral ligament and fixing it proximally to the femur. The Ellison procedure is a distally fixed lateral extra-articular augmentation procedure with no proximal fixation of the ITB. It has the potential advantages of maintaining a dynamic element of control of knee rotation and avoiding the possibility of overconstraint. Hypothesis: The modified Ellison procedure would restore native knee kinematics after sectioning of the anterolateral capsule, and closure of the ITB defect would decrease rotational laxity of the knee. Study Design: Controlled laboratory study. Methods: Twelve fresh-frozen cadaveric knees were tested in a 6 degrees of freedom robotic system through 0° to 90° of knee flexion to assess anteroposterior, internal rotation (IR), and external rotation laxities. A simulated pivot shift (SPS) was performed at 0°, 15°, 30°, and 45° of flexion. Kinematic testing was performed in the intact knee and anterolateral capsule–injured knee and after the modified Ellison procedure, with and without closure of the ITB defect. A novel pulley system was used to load the ITB at 30 N for all testing states. Statistical analysis used repeated measures analyses of variance and paired t tests with Bonferroni adjustments. Results: Sectioning of the anterolateral capsule increased anterior drawer and IR during isolated displacement and with the SPS (mean increase, 2° of IR; P < .05). The modified Ellison procedure reduced both isolated and coupled IR as compared with the sectioned state (P < .05). During isolated testing, IR was reduced close to that of the intact state with the modified Ellison procedure, except at 30° of knee flexion, when it was slightly overconstrained. During the SPS, IR with the closed modified Ellison was less than that in the intact state at 15° and 30° of flexion. No significant differences in knee kinematics were seen between the ITB defect open and closed. Conclusion: A distally fixed lateral augmentation procedure can closely restore knee laxities to native values in an anterolateral capsule–sectioned knee. Although the modified Ellison did result in overconstraint to isolated IR and coupled IR during SPS, this occurred only in the early range of knee flexion. Closure of the ITB defect had no effect on knee kinematics. Clinical Relevance: A distally fixed lateral extra-articular augmentation procedure provides an alternative to a proximally fixed LET and can reduce anterolateral laxity in the anterolateral capsule–injured knee and restore kinematics close to the intact state