Cosmic Ray Background Removal With Deep Neural Networks in SBND

In liquid argon time projection chambers exposed to neutrino beams and running on or near surface levels, cosmic muons, and other cosmic particles are incident on the detectors while a single neutrino-induced event is being recorded. In practice, this means that data from surface liquid argon time projection chambers will be dominated by cosmic particles, both as a source of event triggers and as the majority of the particle count in true neutrino-triggered events. In this work, we demonstrate a novel application of deep learning techniques to remove these background particles by applying deep learning on full detector images from the SBND detector, the near detector in the Fermilab Short-Baseline Neutrino Program. We use this technique to identify, on a pixel-by-pixel level, whether recorded activity originated from cosmic particles or neutrino interactions.

PONDx: real-life utilization and decision impact of the 21-gene assay on clinical practice in Italy

Clinicopathological prognostic features have limited value to identify with precision newly diagnosed patients with hormone receptor (HR)-positive, HER2-negative breast cancer (BC), who would benefit from chemotherapy (CT) in addition to adjuvant hormonal therapy (HT). The 21-gene Oncotype DX Breast Recurrence Score® (RS) assay has been demonstrated to predict CT benefit, hence supporting personalized decisions on adjuvant CT. The multicenter, prospective, observational study PONDx investigated the real-life use of RS® results in Italy and its impact on treatment decisions. Physicians' treatment recommendations (HT ± CT) were documented before and after availability of RS results, and changes in recommendations were determined. In the HR+ HER2- early BC population studied (N = 1738), physicians recommended CT + HT in 49% of patients pre-RS. RS-guided treatment decisions resulted in 36% reduction of CT recommendations. PONDx confirms that RS results provide clinically relevant information for CT recommendation in early-stage BC, resulting in a reduction of more than a third of CT use.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

The novel Mechanical Ventilator Milano for the COVID-19 pandemic

This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world.

Unlocking mammalian regeneration through hypoxia inducible factor one alpha signaling

Historically, the field of regenerative medicine has aimed to heal damaged tissue through the use of biomaterials scaffolds or delivery of foreign progenitor cells. Despite 30 years of research, however, translation and commercialization of these techniques has been limited. To enable mammalian regeneration, a more practical approach may instead be to develop therapies that evoke endogenous processes reminiscent of those seen in innate regenerators. Recently, investigations into tadpole tail regrowth, zebrafish limb restoration, and the super-healing Murphy Roths Large (MRL) mouse strain, have identified ancient oxygen-sensing pathways as a possible target to achieve this goal. Specifically, upregulation of the transcription factor, hypoxia-inducible factor one alpha (HIF-1α) has been shown to modulate cell metabolism and plasticity, as well as inflammation and tissue remodeling, possibly priming injuries for regeneration. Since HIF-1α signaling is conserved across species, environmental or pharmacological manipulation of oxygen-dependent pathways may elicit a regenerative response in non-healing mammals. In this review, we will explore the emerging role of HIF-1α in mammalian healing and regeneration, as well as attempts to modulate protein stability through hyperbaric oxygen treatment, intermittent hypoxia therapy, and pharmacological targeting. We believe that these therapies could breathe new life into the field of regenerative medicine.

Can proteomics contribute to biomonitoring of aquatic pollution? A critical review

Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.

First Measurement of Differential Charged Current Quasielasticlike ν_{μ}-Argon Scattering Cross Sections with the MicroBooNE Detector

We report on the first measurement of flux-integrated single differential cross sections for charged-current (CC) muon neutrino (ν_{μ}) scattering on argon with a muon and a proton in the final state, ^{40}Ar (ν_{μ},μp)X. The measurement was carried out using the Booster Neutrino Beam at Fermi National Accelerator Laboratory and the MicroBooNE liquid argon time projection chamber detector with an exposure of 4.59×10^{19} protons on target. Events are selected to enhance the contribution of CC quasielastic (CCQE) interactions. The data are reported in terms of a total cross section as well as single differential cross sections in final state muon and proton kinematics. We measure the integrated per-nucleus CCQE-like cross section (i.e., for interactions leading to a muon, one proton, and no pions above detection threshold) of (4.93±0.76_{stat}±1.29_{sys})×10^{-38}  cm^{2}, in good agreement with theoretical calculations. The single differential cross sections are also in overall good agreement with theoretical predictions, except at very forward muon scattering angles that correspond to low-momentum-transfer events.

Measuring quantitative proteomic distance between Spanish beef breeds

Estimates of quantitative proteomic distance between populations have not been reported to date. Here, quantitative proteomic distances between three Spanish bovine breeds (Asturiana de los Valles, AV; Retinta, RE; and Rubia Gallega, RG) were estimated from two-dimensional electrophoresis profiles of meat samples of longissimus thoracis muscle at 2 h post-mortem. Statistically significant distances were detected between AV/RG and the most genetically different RE breed, using the novel QD measure of quantitative proteomic distance. In total, 18 differentially abundant myofibrillar and sarcoplasmic proteins/isoforms contributing to proteomic distances between breeds were confidently identified by tandem mass spectrometry. The fast skeletal myosin regulatory light chain 2 followed by other five interacting proteins exhibited the most pronounced relative change between breeds. In addition, most differentially represented proteins could be associated with variations in meat tenderness. Therefore, they could be candidate biomarkers for molecular breeding programs and authentication of the three Spanish beef breeds.

Early-life ketamine exposure attenuates the preference for ethanol in adolescent Sprague-Dawley rats

Ketamine, a noncompetitive N-methyl-d-aspartate (NMDA) receptor antagonist, produces quick and effective antidepressant results in depressed juvenile and adult individuals. The long-term consequences of using ketamine in juvenile populations are not well known, particularly as it affects vulnerability to drugs of abuse later in life, given that ketamine is also a drug of abuse. Thus, the current study examined whether early-life ketamine administration produces long-term changes in the sensitivity to the rewarding effects of ethanol, as measured using the conditioned place preference (CPP) paradigm. On postnatal day (PD) 21, juvenile male and female rats were pretreated with ketamine (0.0 or 20 mg/kg) for 10 consecutive days (i.e., PD 21-30) and then evaluated for ethanol-induced CPP (0.0, 0.125, 0.5, or 2.0 g/kg) from PD 32-39. Results revealed that early-life ketamine administration attenuated the rewarding properties of ethanol in male rats, as ketamine pretreated rats failed to exhibit ethanol-induced CPP at any dose compared to saline pretreated rats, which showed an increased preference towards the ethanol-paired compartment in a dose-dependent manner. In females, ethanol-induced CPP was generally less robust compared to males, but ketamine pretreatment resulted in a rightward shift in the dose-response curve, given that ketamine pretreated rats needed a higher dose of ethanol compared to saline pretreated rats to exhibit ethanol-induced CPP. When considered together, the findings suggest that early use of ketamine does not appear to enhance the vulnerability to ethanol later in life, but in contrast, it may attenuate the rewarding effects of ethanol.

Bio-hybrid gold nanoparticles as SERS probe for rapid bacteria cell identification

This study reports the utilization of engineered molecular networks between bacteriophage (or phage) and gold nanoparticles (AuNPs) prepared ablating a high purity gold target in water by nanosecond laser source. Gold colloids are assembled with P9b phage clone, displaying the specific peptide (QRKLAAKLT), able to bind P. aeruginosa. The single components and assembled systems were characterized by spectroscopic and electronic techniques, such as the conventional optical absorption and micro-Raman spectroscopies as well as the Dynamic Light Scattering (DLS) and Scanning Transmission Electron Microscopy (STEM) techniques. The performance of the AuNPs-phage assembly as substrate for Surface-Enhanced Raman Spectroscopy (SERS) was tested against the detection of the characteristics Raman vibrational features of the Pseudomonas aeruginosa bacteria.

1156Coronary artery bypass grafting vs. FFR-guided PCI in diabetic patients with multivessel disease

Background

In diabetic patients with multivessel coronary disease (MVD), coronary artery bypass grafting (CABG) has shown long-term benefits in mortality over percutaneous coronary revascularization (PCI). Nevertheless, the impact of fractional flow reserve (FFR)-guided PCI on clinical outcomes has never been investigated in these patients.

Purpose

To evaluate the long-term (5-year) clinical outcome of diabetic patients with MVD treated with FFR-guided PCI compared to CABG.

Methods

From February 2010 to February 2018, all diabetic patients undergoing coronary angiography in one centre (n=4622) were screened for inclusion. The inclusion criterion was presence of at least two-vessels CAD defined as with diameters stenosis ≥50%. In case of intermediate coronary stenosis (%DS 30–70%), FFR was performed at the discretion of the operator. Revascularization was performed when FFR ≤0.80. Exclusion criteria were ST-elevation myocardial infarction, prior CABG, and moderate or severe valvular heart dysfunction.

To account for confounders, we compared outcomes by calculating an adjusted Kaplan-Meier estimator using inverse probability of treatment weighting (IPTW). Propensity score variables included age, sex, smoking habit, hypertension, hyperlipidemia, insulin therapy, family history of CAD, chronic obstructive pulmonary disease (COPD), glomerular filtration rate (GFR), prior myocardial infarction, peripheral vascular disease (PVD), admission for NSTEMI, ejection fraction, number of angiographic stenotic vessels. Odds ratios were calculated using generalized linear models (GLM). The primary endpoint was major adverse cardiovascular and cerebrovascular events (MACCE), defined as all-cause death, myocardial infarction and stroke. Secondary endpoints were the individual component of MACCE and any repeated revascularization.

Results

A total of 538 diabetic patients with MVD were included in the analysis. Among them, 317 (59%) patients underwent CABG and 221 (41%) FFR-guided PCI.

Patients treated with FFR-guided PCI had more often COPD as compared to patients in the CABG-group, but patients treated with CABG had lower GFR, more PVD, higher number of angiographic stenotic vessels (2.8±0.4 vs. 2.5±0.5; p<0.01) and higher Syntax score (20±7 vs. 14±6; p<0.01) as compared to the FFR-guided PCI group.

Clinical follow-up was obtained in 95% of the patients at a median follow-up of 5 years.

The incidence of MACCE was similar in the CABG and in the FFR-guided PCI group [27% vs. 29%; OR (95% CI) 1.05 (0.68–1.63); p=0.74]. No differences were found in the individual components of MACCE. Repeat revascularization was more frequent in the FFR-guided PCI group than in the CABG group [27% vs. 7%; OR (95% CI) 4.3 (2.35–7.9); p<0.01].

Conclusions

In diabetic patients with MVD undergoing FFR-guided PCI, no differences in major adverse events were observed at a median follow-up of 5 years compared with CABG.

P1233Differential effects of five risk variants for atrial fibrillation at the 4q25 region on L-type calcium current and transient inward currents in human atrial myocytes

Background

An increasing number of single nucleotide polymorphisms (SNPs) at the chromosomal region 4q25 have been associated with risk of atrial fibrillation (AF) and we have recently reported that carriers of the rs13143308 risk variant have an increased incidence of spontaneous calcium release-induce transient inward currents (ITI). However, it is not known if different 4q25 variants have similar effects.

Purpose

This study aimed to compare the effects of five SNPs at 4q25 on L-type calcium current (ICa) and ITI frequency, features that are altered in patients with AF.

Methods

To avoid confounding effects of AF on calcium homeostasis, atrial samples from 63 patients without AF were genotyped and divided into groups according to the genotype of the SNPs rs1448818, rs6817105, rs13143308, rs6843082, rs3853443 ordered according to their location and identified by the three last digits + an R for risk or N for normal variants. ICa density and ITI frequency were measured with perforated patch clamp technique in atrial myocytes from these patients.

Results

Three SNPs 818, 308 and 443 segregated independently of the genotype at the other loci. The 105 and 082 loci always co-segregated with 308 but never together. The ICa density was smaller in carriers of 818R and 443N variants (−1.6±0.3pA/pF, p=0.01) or 818N and 443R variants (−1.6±0.4pA/pF, p=0.02) than in patients with 818N and 443N variants (−3.2±0.4pA/pF), independently of the genotype at 105, 308 and 082 (these loci did not affect ICa). In contrast, to this, the ITI frequency was increased only in myocytes from patients carrying 105R, 308R and 082N (1.4±0.2events/min, p<0.001) or 105N, 308R and 082R (1.6±0.5events/min, p=0.002) when compared to patients with 105N, 308N and 082N (0.36±0.09events/min) independently of the genotypes at 818 and 443, or when compared to patients without risk at any of the five loci (0.55±0.30events/min). The table shows schematically the qualitative effects of the different risk variants.

Risk variant rs1448818C rs6817105C rs13143308T rs6843082T rs3853445C ICa Decreased Unchanged Unchanged Unchanged Decreased ITI Unchanged Increased Increased Increased Unchanged

Conclusion

Different SNPs at the chromosomal region 4q25 are associated with differential pathological changes in intracellular calcium homeostasis. Risk variants at rs1448818 or rs3853445 cause loss of ICa without affecting ITI frequency while a risk variant at rs13143308 elevates the ITI frequency without affecting ICa. These findings afford a framework for stratification of pharmacological therapy based on the functional effects of the 4q25 risk variants

Acknowledgement/Funding

SAF2017-88019; Marato2015-20-30; SGR2017-1769; CIBERCV

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}.

Recoil Directionality Experiment

Directional sensitivity to nuclear recoils could provide a smoking gun for a possible discovery of dark matter in the form of WIMPs. A hint of directional dependence of the response of a dual-phase liquid argon Time Projection Chamber was found in the SCENE experiment. Given the potential importance of such a capability in the frame work of dark matter searches, a new dedicated experiment, ReD (Recoil Directionality), was designed in the framework of the DarkSide Collaboration, in order to scrutinize this hint. This contribution will describe the performance of the detectors achieved during the first test-beam, the current status of ReD and the perspectives for physics measurements during the forthcoming beam-time.

Proteomic footprint of ultrasound intensification on sliced dry-cured ham subjected to mild thermal conditions

Ultrasound can intensify the heating process used to correct texture defects in dry-cured hams. The effect of ultrasound-assisted heating on the proteome of sliced dry-cured ham was evaluated. Dry-cured hams with high proteolysis index (PI > 36) were sliced, vacuum packed and subjected to conventional (CV) and ultrasound-assisted (US) thermal treatments. Comparative proteome profiling between sample groups was assessed by two-dimensional electrophoresis (2-DE) coupled to tandem mass spectrometry. It was found that protein fragmentation increased markedly after US thermal treatment. Specifically, fragments of the major myofibrillar protein, actin, were abundantly over-represented following US heating. In addition, five unfragmented sarcoplasmic proteins (i.e. fatty acid-binding protein, peroxiredoxin-6, superoxide dismutase, carbonyl reductase and aminoacylase) showed increased abundance in the US sample group. These results suggest candidate biomarkers to monitor proteolysis intensity and proteolysis-independent effects linked to cured ham quality by ultrasound application. SIGNIFICANCE: The present proteome profiling study of treated dry-cured ham demonstrates the impact of ultrasound action on proteins. Moreover, negative organoleptic effects can be appearing with ultrasound treatment due to proteolysis increase. Therefore, the proteolysis monitoring could help to control these effects. In this regards, our results suggest that actin can be a candidate biomarker to monitor proteolysis intensity.

Clinical outcomes of hepatitis C treatment before and after kidney transplantation and its impact on time to transplant: A multicenter study

Waitlist time for kidney transplantation is long but may be shortened with the utilization of hepatitis C positive allografts. We retrospectively reviewed the course of 36 hepatitis C positive patients awaiting kidney transplantation at 2 large centers within the same health system, with near-identical care delivery models with the exception of timing of hepatitis C treatment, to determine the impact of timing of hepatitis C treatment on access to transplant, waitlist time, and treatment efficacy and tolerability. The majority of patients had hepatitis C genotype 1a or 1b, and all received direct acting antiviral therapy with 100% treatment response. One patient underwent transplantation in the pretransplant treatment group. The 1-year transplantation rate was 12.5% vs 67.9% (P = .0013) in those treated posttransplantation. The median waitlist time in the posttransplant group was 122 (interquartile range [IQR] 21.5, 531.0) days, which was significantly shorter than the center's regional and national wait time. Pathologic review revealed no difference in allograft quality. Overall treatment related adverse events were not different between the 2 groups. A strategy of posttransplant hepatitis C treatment increased access to transplant and reduced waitlist time. Delaying treatment until after transplant did not appear to adversely affect recipients' kidney allograft or overall survival.

Constraints on Sub-GeV Dark-Matter-Electron Scattering from the DarkSide-50 Experiment

We present new constraints on sub-GeV dark-matter particles scattering off electrons based on 6780.0 kg d of data collected with the DarkSide-50 dual-phase argon time projection chamber. This analysis uses electroluminescence signals due to ionized electrons extracted from the liquid argon target. The detector has a very high trigger probability for these signals, allowing for an analysis threshold of three extracted electrons, or approximately 0.05 keVee. We calculate the expected recoil spectra for dark matter-electron scattering in argon and, under the assumption of momentum-independent scattering, improve upon existing limits from XENON10 for dark-matter particles with masses between 30 and 100  MeV/c^{2}.