Intrinsic polarity inversion in III-nitride waveguides for efficient nonlinear interactions.

III-nitrides provide a versatile platform for nonlinear photonics. In this work, we explore a new promising configuration - composite waveguides containing GaN and AlN layers with inverted polarity, i.e., having opposite signs of the χ(2) nonlinear coefficient. This configuration allows us to address the limiting problem of the mode overlap for nonlinear interactions. Our modelling predicts a significant improvement in the conversion efficiency. We confirm our theoretical prediction with the experimental demonstration of second harmonic generation with an efficiency of 4%W-1cm-2 using a simple ridge waveguide. This efficiency is an order of magnitude higher compared to the previously reported results for III-nitride waveguides. Further improvement, reaching a theoretical efficiency of 30%W-1cm-2, can be achieved by reducing propagation losses.

Measurement of the ν_{e}-Nucleus Charged-Current Double-Differential Cross Section at ⟨E_{ν}⟩=2.4 GeV Using NOvA.

The inclusive electron neutrino charged-current cross section is measured in the NOvA near detector using 8.02×10^{20} protons-on-target in the NuMI beam. The sample of GeV electron neutrino interactions is the largest analyzed to date and is limited by ≃17% systematic rather than the ≃7.4% statistical uncertainties. The double-differential cross section in final-state electron energy and angle is presented for the first time, together with the single-differential dependence on Q^{2} (squared four-momentum transfer) and energy, in the range 1 GeV≤E_{ν}<6 GeV. Detailed comparisons are made to the predictions of the GENIE, GiBUU, NEUT, and NuWro neutrino event generators. The data do not strongly favor a model over the others consistently across all three cross sections measured, though some models have especially good or poor agreement in the single differential cross section vs Q^{2}.

Search for Active-Sterile Antineutrino Mixing Using Neutral-Current Interactions with the NOvA Experiment.

This Letter reports results from the first long-baseline search for sterile antineutrinos mixing in an accelerator-based antineutrino-dominated beam. The rate of neutral-current interactions in the two NOvA detectors, at distances of 1 and 810 km from the beam source, is analyzed using an exposure of 12.51×10^{20} protons-on-target from the NuMI beam at Fermilab running in antineutrino mode. A total of 121 of neutral-current candidates are observed at the far detector, compared to a prediction of 122±11(stat.)±15(syst.) assuming mixing only between three active flavors. No evidence for ν[over ¯]_{µ}→ν[over ¯]_{s} oscillation is observed. Interpreting this result within a 3+1 model, constraints are placed on the mixing angles θ_{24}<25° and θ_{34}<32° at the 90% C.L. for 0.05 eV^{2}≤Δm_{41}^{2}≤0.5 eV^{2}, the range of mass splittings that produces no significant oscillations at the near detector. These are the first 3+1 confidence limits set using long-baseline accelerator antineutrinos.

First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NOvA.

The NOvA experiment has seen a 4.4σ signal of ν[over ¯]_{e} appearance in a 2 GeV ν[over ¯]_{µ} beam at a distance of 810 km. Using 12.33×10^{20} protons on target delivered to the Fermilab NuMI neutrino beamline, the experiment recorded 27 ν[over ¯]_{µ}→ν[over ¯]_{e} candidates with a background of 10.3 and 102 ν[over ¯]_{µ}→ν[over ¯]_{µ} candidates. This new antineutrino data are combined with neutrino data to measure the parameters |Δm_{32}^{2}|=2.48_{-0.06}^{+0.11}×10^{-3} eV^{2}/c^{4} and sin^{2}θ_{23} in the ranges from (0.53-0.60) and (0.45-0.48) in the normal neutrino mass hierarchy. The data exclude most values near δ_{CP}=π/2 for the inverted mass hierarchy by more than 3σ and favor the normal neutrino mass hierarchy by 1.9σ and θ_{23} values in the upper octant by 1.6σ.

Enhanced Higgs boson to τ(+)τ(-) search with deep learning.

The Higgs boson is thought to provide the interaction that imparts mass to the fundamental fermions, but while measurements at the Large Hadron Collider (LHC) are consistent with this hypothesis, current analysis techniques lack the statistical power to cross the traditional 5σ significance barrier without more data. Deep learning techniques have the potential to increase the statistical power of this analysis by automatically learning complex, high-level data representations. In this work, deep neural networks are used to detect the decay of the Higgs boson to a pair of tau leptons. A Bayesian optimization algorithm is used to tune the network architecture and training algorithm hyperparameters, resulting in a deep network of eight nonlinear processing layers that improves upon the performance of shallow classifiers even without the use of features specifically engineered by physicists for this application. The improvement in discovery significance is equivalent to an increase in the accumulated data set of 25%.

Pathogenesis and pathobiology of zoonotic brucellosis in humans.

Although human brucellosis has protean clinical manifestations, affected tissues usually exhibit signs of inflammation. The cellular and molecular bases of some immunopathological phenomena probably involved in the pathogenesis of infection with brucellae have been elucidated recently. Human osteoblasts and fibroblast-like synoviocytes produce cytokines, chemokines and matrix metalloproteinases in response to infection with brucellae and/or to stimulation by brucellae-infected monocytes. In turn, released cytokines promote the secretion of the metalloproteinases and induce osteoclastogenesis. These phenomena may underlie the bone loss and cartilage degradation found in brucellar arthritis and osteomyelitis. Brucella abortus and its lipoproteins elicit an inflammatory response in the central nervous system of mice, leading to astrogliosis, a characteristic feature of neurobrucellosis. Brucellae can also replicate in human endothelial cells, inducing an inflammatory response with increased expression of chemokines, interleukin-6 and adhesion molecules. Persistent brucellar infection of the endothelium would support development of endocarditis and other vascular manifestations. Thus, although the inflammatory phenomena triggered by brucellae are relatively mild, they are long-lasting as a result of the prolonged intracellular persistence of the bacteria in infected tissues and eventually lead to tissue damage.

Preliminary study of an immunochromatography test for serological diagnosis of canine brucellosis.

The most widely used screening test for the diagnosis of brucellosis in the dog is the rapid slide agglutination test in the presence of 2-mercaptoethanol (2ME-RSAT). The diagnosis is partially confirmed by the agar gel immunodiffusion test (AGID) and definitively confirmed by bacteriological isolation. Some chronic cases not detected by these tests may be detected by ELISA tests. The use of 2ME-RSAT in routine clinical practice requires a microscope and an experienced operator. An immunochromatographic diagnostic test for canine brucellosis (FASTest(®) Brucella c., Megacor, Hörbranz, Austria) has been recently released. In this study, we compared the diagnostic performance of the FASTest with those of 2ME-RSAT, AGID and ELISAs. Sera from 17 healthy dogs used as negative controls yielded negative results by FASTest, indicating a 100% specificity in this sample. Among 27 sera of dogs with acute or subacute brucellosis confirmed by B. canis isolation, all of which were positive by RSAT and ELISAs, the FASTest was positive in 24 cases and AGID in 23. In acute and subacute cases, the sensitivity of FASTest was 89%. Sera from six dogs with bacteriologically confirmed chronic brucellosis, which were positive by ELISAs but negative by 2ME-RSAT, were also tested; 1 was positive by FASTest and 4 were positive by AGID. These preliminary results indicate a good specificity of the FASTest (100% in this sample) but an unacceptable sensitivity as a screening test. In cases with chronic brucellosis, the sensitivity of the FASTest was lower than that of ELISAs but this assay could make a good intermediate test to be run after a positive RSAT and before running an AGID.

A photonic quantum information interface.

Quantum communication requires the transfer of quantum states, or quantum bits of information (qubits), from one place to another. From a fundamental perspective, this allows the distribution of entanglement and the demonstration of quantum non-locality over significant distances. Within the context of applications, quantum cryptography offers a provably secure way to establish a confidential key between distant partners. Photons represent the natural flying qubit carriers for quantum communication, and the presence of telecommunications optical fibres makes the wavelengths of 1,310 nm and 1,550 nm particularly suitable for distribution over long distances. However, qubits encoded into alkaline atoms that absorb and emit at wavelengths around 800 nm have been considered for the storage and processing of quantum information. Hence, future quantum information networks made of telecommunications channels and alkaline memories will require interfaces that enable qubit transfers between these useful wavelengths, while preserving quantum coherence and entanglement. Here we report a demonstration of qubit transfer between photons of wavelength 1,310 nm and 710 nm. The mechanism is a nonlinear up-conversion process, with a success probability of greater than 5 per cent. In the event of a successful qubit transfer, we observe strong two-photon interference between the 710 nm photon and a third photon at 1,550 nm, initially entangled with the 1,310 nm photon, although they never directly interacted. The corresponding fidelity is higher than 98 per cent.

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.

First-line carboplatin/nab-paclitaxel in advanced ovarian cancer patients, after hypersensitivity reaction to solvent-based taxanes: a single-institution experience.

One of the major challenges related to solvent-based taxanes administration in clinical practice is the high rate of hypersensitivity reactions (HSRs). Nab-paclitaxel is a solvent-free, albumin-bound, paclitaxel, which minimize the risk of HSR occurrence. In this single-institution, retrospective analysis, we evaluated stage IIIc-IV epithelial ovarian cancer (EOC) patients, treated with first-line carboplatin/nab-paclitaxel (± bevacizumab), after the occurrence of an HSR with solvent-based paclitaxel (and/or docetaxel). Between April 2012 and December 2018, ten patients (20.8%) received carboplatin/nab-paclitaxel (± bevacizumab) after the occurrence of an HSR to solvent-based taxanes. Among the evaluable patients, ORR was 100%. At median follow-up of 28.5 months, median PFS was 16.7 months, and median OS was 65.4 months, respectively. Median received dose intensity (DI) was 86% and 80% of the projected DI for nab-paclitaxel and carboplatin, respectively. There were no treatment-related grade 4 adverse events. Most relevant treatment-related grade 3 adverse events were: asthenia (10%), hypertransaminasemia (10%), neutropenia (20%), thrombocytopenia (20%), and anemia (10%). No HSR recurrence was observed. The high rate of HSR occurrence could limit first-line treatment options in clinical practice. Carboplatin/nab-paclitaxel association could represent a valid treatment option in this setting.

The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental temporal lobe epilepsy.

Gene and protein expressions display circadian oscillations, which can be disrupted in diseases in most body organs. Whether these oscillations occur in the healthy hippocampus and whether they are altered in epilepsy are not known. We identified more than 1200 daily oscillating transcripts in the hippocampus of control mice and 1600 in experimental epilepsy, with only one-fourth oscillating in both conditions. Comparison of gene oscillations in control and epilepsy predicted time-dependent alterations in energy metabolism, which were verified experimentally. Although aerobic glycolysis remained constant from morning to afternoon in controls, it increased in epilepsy. In contrast, oxidative phosphorylation increased in control and decreased in epilepsy. Thus, the control hippocampus shows circadian molecular remapping, which is altered in epilepsy. We suggest that the hippocampus operates in a different functioning mode in epilepsy. These alterations need to be considered when studying epilepsy mechanisms, designing drug treatments, and timing their delivery.

Learning in the machine: Recirculation is random backpropagation.

Learning in physical neural systems must rely on learning rules that are local in both space and time. Optimal learning in deep neural architectures requires that non-local information be available to the deep synapses. Thus, in general, optimal learning in physical neural systems requires the presence of a deep learning channel to communicate non-local information to deep synapses, in a direction opposite to the forward propagation of the activities. Theoretical arguments suggest that for circular autoencoders, an important class of neural architectures where the output layer is identical to the input layer, alternative algorithms may exist that enable local learning without the need for additional learning channels, by using the forward activation channel as the deep learning channel. Here we systematically identify, classify, and study several such local learning algorithms, based on the general idea of recirculating information from the output layer to the hidden layers. We show through simulations and mathematical derivations that these algorithms are robust and converge to critical points of the global error function. In most cases, we show that these recirculation algorithms are very similar to an adaptive form of random backpropagation, where each hidden layer receives a linearly transformed, slowly-varying, version of the output error.

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas.

BACKGROUND AND PURPOSE: The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation. MATERIALS AND METHODS: MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 (IDH1) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification. RESULTS: Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features. CONCLUSIONS: Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training.

Mitochondrial mutations in cancer.

The metabolism of solid tumors is associated with high lactate production while growing in oxygen (aerobic glycolysis) suggesting that tumors may have defects in mitochondrial function. The mitochondria produce cellular energy by oxidative phosphorylation (OXPHOS), generate reactive oxygen species (ROS) as a by-product, and regulate apoptosis via the mitochondrial permeability transition pore (mtPTP). The mitochondria are assembled from both nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) genes. The mtDNA codes for 37 genes essential of OXPHOS, is present in thousands of copies per cell, and has a very high mutations rate. In humans, severe mtDNA mutations result in multisystem disease, while some functional population-specific polymorphisms appear to have permitted humans to adapt to new environments. Mutations in the nDNA-encoded mitochondrial genes for fumarate hydratase and succinate dehydrogenase have been linked to uterine leiomyomas and paragangliomas, and cancer cells have been shown to induce hexokinase II which harnesses OXPHOS adenosine triphosphate (ATP) production to drive glycolysis. Germline mtDNA mutations at nucleotides 10398 and 16189 have been associated with breast cancer and endometrial cancer. Tumor mtDNA somatic mutations range from severe insertion-deletion and chain termination mutations to mild missense mutations. Surprisingly, of the 190 tumor-specific somatic mtDNA mutations reported, 72% are also mtDNA sequence variants found in the general population. These include 52% of the tumor somatic mRNA missense mutations, 83% of the tRNA mutations, 38% of the rRNA mutations, and 85% of the control region mutations. Some associations might reflect mtDNA sequencing errors, but analysis of several of the tumor-specific somatic missense mutations with population counterparts appear legitimate. Therefore, mtDNA mutations in tumors may fall into two main classes: (1) severe mutations that inhibit OXPHOS, increase ROS production and promote tumor cell proliferation and (2) milder mutations that may permit tumors to adapt to new environments. The former may be lost during subsequent tumor oxygenation while the latter may become fixed. Hence, mitochondrial dysfunction does appear to be a factor in cancer etiology, an insight that may suggest new approaches for diagnosis and treatment.

SCRATCH: a protein structure and structural feature prediction server.

SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at http://www.igb.uci.edu/servers/psss.html.

High Incidence of Respiratory Involvement in a Cluster of Brucella suis-Infected Workers from a Pork Processing Plant in Argentina.

Epidemiological and clinical aspects of Brucella suis infection in 17 workers from a pork processing plant in Argentina occurring between January 2014 and July 2015 are presented. All patients reported working 9 h daily without adequate personal protection garment. Blood cultures were positive for Brucella spp. in 14 of the 17 patients (82.3%). All isolates were identified as B. suis biovar 1. Although fever, sweats, asthenia, myalgia and hepatic involvement were the most frequent clinical manifestations, an unusually high incidence of respiratory involvement was found. From 13 patients in which chest radiography was performed, four (30%) had radiological abnormalities, including lobar pneumonia in two cases (one with pleural effusion) and interstitial involvement in other two. The high frequency of respiratory involvement in our series makes necessary to consider brucellosis in the differential diagnosis of respiratory diseases in pork processing plant employees.

Use of enrofloxacin in the treatment of canine brucellosis in a dog kennel (clinical trial).

To date, no totally effective antibiotic for the eradication of canine brucellosis has been found. The purpose of this study was to evaluate the efficacy of enrofloxacin in a kennel infected with Brucella canis. Twelve dogs, 2 males and 10 females (including 1 in estrus, 3 pregnant, and 6 in anestrus) infected with B. canis were given 5 mg/kg of enrofloxacin orally every 12 h for 30 days. Females received additional courses of enrofloxacin during the estral and luteal phases of the subsequent cycles (0-2 cycles). They were repeatedly mated by infected males. A serological follow-up was carried out for 38 months. The clinical, serological and bacteriological findings were recorded. In a trial carried out 14 months after the beginning of this study, all dogs were negative on the Rapid Slide Agglutination Test (RSAT). No abortions were observed. All mated female dogs conceived and gave birth to healthy puppies. Cultures of postpartum vaginal discharges (lochia) were negative for B. canis. Similar to other treatments, although enrofloxacin was not completely efficacious in treating canine brucellosis, it maintained fertility and avoided the recurrence of abortions, transmission of the disease to the puppies and dissemination of microorganisms during parturition. We inferred that enrofloxacin could be used as an alternative drug for the treatment of canine brucellosis.

[Detection of anti-Brucella spp. antibodies in swine by agglutination techniques and indirect ELISA in the Buenos Aires and La Pampa provinces, Argentina]. / Detección de anticuerpos anti-Brucella spp. en cerdos mediante técnicas de aglutinación y ELISA indirecto en las provincias de Buenos Aires y La Pampa, Argentina.

Porcine brucellosis is one of the most important zoonoses in this country. Currently, there is no control program for porcine brucellosis in Argentina and the epidemiological situation is still unknown. The purpose of our study was to detect anti-Brucella spp. antibodies in swine in the southwest of the Buenos Aires province and the east of the La Pampa province. Blood samples were obtained when animals were slaughtered. The presence of anti-brucella antibodies was studied by the buffered plate agglutination test (BPA), the tube agglutination test (SAT), the 2-mercaptoethanol (2-ME) agglutination test and indirect ELISA tests, using the cytosolic fraction from Brucella abortus S19 (CYT), and lipopolysaccharide (LPS)-free cytosolic proteins (CP). Out of a total of 325 samples analyzed, 17.8% reacted positively to BPA, 13.8% to SAT, 8.0% to 2-ME, 21.0% to ELISA-CYT and 10.0% to ELISA-CP. These results agree with the few data available in our country and suggest that brucellosis screening should be extended to other regions.

Naturally occurring nucleosome positioning signals in human exons and introns.

We describe the structural implications of a periodic pattern found in human exons and introns by hidden Markov models. We show that exons (besides the reading frame) have a specific sequential structure in the form of a pattern with triplet consensus non-T(A/T)G, and a minimal periodicity of roughly ten nucleotides. The periodic pattern is also present in intron sequences, although the strength per nucleotide is weaker. Using two independent profile methods based on triplet bendability parameters from DNase I experiments and nucleosome positioning data, we show that the pattern in multiple alignments of internal exon and intron sequences corresponds to a periodic "in phase" bending potential towards the major groove of the DNA. The nucleosome positioning data show that the consensus triplets (and their complements) have a preference for locations on a bent double helix where the major groove faces inward and is compressed. The in-phase triplets are located adjacent to GCC/GGC triplets known to have the strongest bias in their positioning on the nuclesome. Analysis of mRNA sequences encoding proteins with known tertiary structure exclude the possibility that the pattern is a consequence of the previously well-known periodicity caused by the encoding of alpha-helices in proteins. Finally, we discuss the relation between the bending potential of coding and non-coding regions and its impact on the translational positioning of nucleosomes and the recognition of genes by the transcriptional machinery.

DNA structure in human RNA polymerase II promoters.

The fact that DNA three-dimensional structure is important for transcriptional regulation begs the question of whether eukaryotic promoters contain general structural features independently of what genes they control. We present an analysis of a large set of human RNA polymerase II promoters with a very low level of sequence similarity. The sequences, which include both TATA-containing and TATA-less promoters, are aligned by hidden Markov models. Using three different models of sequence-derived DNA bendability, the aligned promoters display a common structural profile with bendability being low in a region upstream of the transcriptional start point and significantly higher downstream. Investigation of the sequence composition in the two regions shows that the bendability profile originates from the sequential structure of the DNA, rather than the general nucleotide composition. Several trinucleotides known to have high propensity for major groove compression are found much more frequently in the regions downstream of the transcriptional start point, while the upstream regions contain more low-bendability triplets. Within the region downstream of the start point, we observe a periodic pattern in sequence and bendability, which is in phase with the DNA helical pitch. The periodic bendability profile shows bending peaks roughly at every 10 bp with stronger bending at 20 bp intervals. These observations suggest that DNA in the region downstream of the transcriptional start point is able to wrap around protein in a manner reminiscent of DNA in a nucleosome. This notion is further supported by the finding that the periodic bendability is caused mainly by the complementary triplet pairs CAG/CTG and GGC/GCC, which previously have been found to correlate with nucleosome positioning. We present models where the high-bendability regions position nucleosomes at the downstream end of the transcriptional start point, and consider the possibility of interaction between histone-like TAFs and this area. We also propose the use of this structural signature in computational promoter-finding algorithms.