The European Nucleotide Archive in 2023.

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide Sequence Database Collaboration (INSDC). It serves the bioinformatics community worldwide via the submission, processing, archiving and dissemination of sequence data. The ENA supports data types ranging from raw reads, through alignments and assemblies to functional annotation. The data is enriched with contextual information relating to samples and experimental configurations. In this article, we describe recent progress and improvements to ENA services. In particular, we focus upon three areas of work in 2023: FAIRness of ENA data, pandemic preparedness and foundational technology. For FAIRness, we have introduced minimal requirements for spatiotemporal annotation, created a metadata-based classification system, incorporated third party metadata curations with archived records, and developed a new rapid visualisation platform, the ENA Notebooks. For foundational enhancements, we have improved the INSDC data exchange and synchronisation pipelines, and invested in site reliability engineering for ENA infrastructure. In order to support genomic surveillance efforts, we have continued to provide ENA services in support of SARS-CoV-2 data mobilisation and have adapted these for broader pathogen surveillance efforts.

The European Nucleotide Archive in 2022.

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), offers those producing data an open and supported platform for the management, archiving, publication, and dissemination of data; and to the scientific community as a whole, it offers a globally comprehensive data set through a host of data discovery and retrieval tools. Here, we describe recent updates to the ENA's submission and retrieval services as well as focused efforts to improve connectivity, reusability, and interoperability of ENA data and metadata.

Exclusion of Axionlike-Particle Cogenesis Dark Matter in a Mass Window above 100 µeV.

We report the results of Phase 1b of the ORGAN experiment, a microwave cavity haloscope searching for dark matter axions in the 107.42-111.93 µeV mass range. The search excludes axions with two-photon coupling g_{aγγ}≥4×10^{-12} GeV^{-1} with 95% confidence interval, setting the best upper bound to date and with the required sensitivity to exclude the axionlike particle cogenesis model for dark matter in this range. This result was achieved using a tunable rectangular cavity, which mitigated several practical issues that become apparent when conducting high-mass axion searches, and was the first such axion search to be conducted with such a cavity. It also represents the most sensitive axion haloscope experiment to date in the ∼100 µeV mass region.

The European Nucleotide Archive in 2021.

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA's services and infrastructure that have been delivered over the past year.

The European Nucleotide Archive in 2020.

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scientific community and for the acceleration of the global research effort. Here we highlight the major developments to ENA services and content in 2020, focussing in particular on the recently released updated ENA browser, modernisation of our release process and our data coordination collaborations with specific research communities.

The European Nucleotide Archive in 2019.

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory's European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of nucleotide sequence data types. Making the world's public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource. Here, we outline ENA services and content in 2019 and provide an insight into selected key areas of development in this period.

Searching for Scalar Dark Matter via Coupling to Fundamental Constants with Photonic, Atomic, and Mechanical Oscillators.

We present a way to search for light scalar dark matter (DM), seeking to exploit putative coupling between dark matter scalar fields and fundamental constants, by searching for frequency modulations in direct comparisons between frequency stable oscillators. Specifically we compare a cryogenic sapphire oscillator (CSO), hydrogen maser (HM) atomic oscillator, and a bulk acoustic wave quartz oscillator (OCXO). This work includes the first calculation of the dependence of acoustic oscillators on variations of the fundamental constants, and demonstration that they can be a sensitive tool for scalar DM experiments. Results are presented based on 16 days of data in comparisons between the HM and OCXO, and 2 days of comparison between the OCXO and CSO. No evidence of oscillating fundamental constants consistent with a coupling to scalar dark matter is found, and instead limits on the strength of these couplings as a function of the dark matter mass are determined. We constrain the dimensionless coupling constant d_{e} and combination |d_{m_{e}}-d_{g}| across the mass band 4.4×10^{-19}≲m_{φ}≲6.8×10^{-14} eV c^{-2}, with most sensitive limits d_{e}≳1.59×10^{-1}, |d_{m_{e}}-dg|≳6.97×10^{-1}. Notably, these limits do not rely on maximum reach analysis (MRA), instead employing the more general coefficient separation technique. This experiment paves the way for future, highly sensitive experiments based on state-of-the-art acoustic oscillators, and we show that these limits can be competitive with the best current MRA-based exclusion limits.

Upconversion Loop Oscillator Axion Detection Experiment: A Precision Frequency Interferometric Axion Dark Matter Search with a Cylindrical Microwave Cavity.

First experimental results from a room-temperature tabletop phase-sensitive axion haloscope experiment are presented. The technique exploits the axion-photon coupling between two photonic resonator oscillators excited in a single cavity, allowing low-mass axions to be upconverted to microwave frequencies, acting as a source of frequency modulation on the microwave carriers. This new pathway to axion detection has certain advantages over the traditional haloscope method, particularly in targeting axions below 1 µeV (240 MHz) in energy. At the heart of the dual-mode oscillator, a tunable cylindrical microwave cavity supports a pair of orthogonally polarized modes (TM_{0,2,0} and TE_{0,1,1}), which, in general, enables simultaneous sensitivity to axions with masses corresponding to the sum and difference of the microwave frequencies. However, in the reported experiment, the configuration was such that the sum frequency sensitivity was suppressed, while the difference frequency sensitivity was enhanced. The results place axion exclusion limits between 7.44-19.38 neV, excluding a minimal coupling strength above 5×10^{-7} 1/GeV, after a measurement period of two and a half hours. We show that a state-of-the-art frequency-stabilized cryogenic implementation of this technique, ambitious but realizable, may achieve the best limits in a vast range of axion space.

Erratum: Upconversion Loop Oscillator Axion Detection Experiment: A Precision Frequency Interferometric Axion Dark Matter Search with a Cylindrical Microwave Cavity [Phys. Rev. Lett. 126, 081803 (2021)].

This corrects the article DOI: 10.1103/PhysRevLett.126.081803.

Rare Events Detected with a Bulk Acoustic Wave High Frequency Gravitational Wave Antenna.

This work describes the operation of a high frequency gravitational wave detector based on a cryogenic bulk acoustic wave cavity and reports observation of rare events during 153 days of operation over two separate experimental runs (run 1 and run 2). In both run 1 and run 2, two modes were simultaneously monitored. Across both runs, the third overtone of the fast shear mode (3B) operating at 5.506 MHz was monitored; whereas in run 1, the second mode was chosen to be the fifth overtone of the slow shear mode (5C) operating at 8.392 MHz. However, in run 2, the second mode was selected to be closer in frequency to the first mode; and it was chosen to be the third overtone of the slow shear mode (3C) operating at 4.993 MHz. Two strong events were observed as transients responding to energy deposition within acoustic modes of the cavity. The first event occurred during run 1 on 12 May 2019 (UTC), and it was observed in the 5.506 MHz mode; whereas the second mode at 8.392 MHz observed no event. During run 2, a second event occurred on 27 November 2019 (UTC) and was observed by both modes. Timings of the events were checked against available environmental observations as well as data from other detectors. Various possibilities explaining the origins of the events are discussed.

Direct search for dark matter axions excluding ALP cogenesis in the 63- to 67-µeV range with the ORGAN experiment.

The standard model axion seesaw Higgs portal inflation (SMASH) model is a well-motivated, self-contained description of particle physics that predicts axion dark matter particles to exist within the mass range of 50 to 200 micro-electron volts. Scanning these masses requires an axion haloscope to operate under a constant magnetic field between 12 and 48 gigahertz. The ORGAN (Oscillating Resonant Group AxioN) experiment (in Perth, Australia) is a microwave cavity axion haloscope that aims to search the majority of the mass range predicted by the SMASH model. Our initial phase 1a scan sets an upper limit on the coupling of axions to two photons of ∣gaγγ∣ ≤ 3 × 10-12 per giga-electron volts over the mass range of 63.2 to 67.1 micro-electron volts with 95% confidence interval. This highly sensitive result is sufficient to exclude the well-motivated axion-like particle cogenesis model for dark matter in the searched region.

Laser Powder Bed Fusion Additive Manufacturing of a Low-Modulus Ti-35Nb-7Zr-5Ta Alloy for Orthopedic Applications.

Laser powder bed fusion (L-PBF) was attempted here to additively manufacture a new generation orthopedic ß titanium alloy Ti-35Nb-7Zr-5Ta toward engineering patient-specific implants. Parts were fabricated using four different values of energy density (ED) input ranging from 46.6 to 54.8 J/mm3 through predefined laser beam parameters from prealloyed powders. All the conditions yielded parts of >98.5% of theoretical density. X-ray microcomputed tomography analyses of the fabricated parts revealed minimal imperfections with enhanced densification at a higher ED input. X-ray diffraction analysis indicated a marginally larger d-spacing and tensile residual stress at the highest ED input that is ascribed to the steeper temperature gradients. Cellular to columnar dendritic transformation was observed at the highest ED along with an increase in the size of the solidified features indicating the synergetic effects of the temperature gradient and solidification growth rate. Density measurements indicated ≈99.5% theoretical density achieved for an ED of 50.0 J/mm3. The maximum tensile strength of ≈660 MPa was obtained at an ED of 54.8 J/mm3 through the formation of the columnar dendritic substructure. High ductility ranging from 25 to 30% was observed in all the fabricated parts irrespective of ED. The assessment of cytocompatibility in vitro indicated good attachment and proliferation of osteoblasts on the fabricated samples that were similar to the cell response on commercially pure titanium, confirming the potential of the additively manufactured Ti-35Nb-7Zr-5Ta as a suitable material for biomedical applications. Taken together, these results demonstrate the feasibility of L-PBF of Ti-35Nb-7Zr-5Ta for potentially engineering patient-specific orthopedic implants.

Cross-Correlation Signal Processing for Axion and WISP Dark Matter Searches.

The search for dark matter is of fundamental importance to our understanding of the universe. Weakly interacting slim particles (WISPs) such as axions and hidden sector photons are well-motivated candidates for the dark matter. Some of the most sensitive and mature experiments to detect WISPs rely on microwave cavities, and the detection of weak photon signals. It is often suggested to power combine multiple cavities, which creates a host of technical concerns. We outline a scheme based on cross correlation for power combining cavities and increasing the signal-to-noise ratio of a candidate WISP signal.

Fabrication of Titanium-Niobium-Zirconium-Tantalium Alloy (TNZT) Bioimplant Components with Controllable Porosity by Spark Plasma Sintering.

Spark Plasma Sintering (SPS) is used to fabricate Titanium-Niobium-Zirconium-Tantalum alloy (TNZT) powder-based bioimplant components with controllable porosity. The developed densification maps show the effects of final SPS temperature, pressure, holding time, and initial particle size on final sample relative density. Correlations between the final sample density and mechanical properties of the fabricated TNZT components are also investigated and microstructural analysis of the processed material is conducted. A densification model is proposed and used to calculate the TNZT alloy creep activation energy. The obtained experimental data can be utilized for the optimized fabrication of TNZT components with specific microstructural and mechanical properties suitable for biomedical applications.

Next Generation of Phonon Tests of Lorentz Invariance Using Quartz BAW Resonators.

We demonstrate technological improvements in phonon sector tests of the Lorentz invariance that implement quartz bulk acoustic wave oscillators. In this experiment, room temperature oscillators with state-of-the-art phase noise are continuously compared on a platform that rotates at a rate of order of a cycle per second. The discussion is focused on improvements in noise measurement techniques, data acquisition, and data processing. Preliminary results of the second generation of such tests are given, and indicate that standard model extension coefficients in the matter sector can be measured at a precision of order 10-16 GeV after taking a year's worth of data. This is equivalent to an improvement of two orders of magnitude over the prior acoustic phonon sector experiment.

Tests of relativity by complementary rotating Michelson-Morley experiments.

We report relativity tests based on data from two simultaneous Michelson-Morley experiments, spanning a period of more than 1 yr. Both were actively rotated on turntables. One (in Berlin, Germany) uses optical Fabry-Perot resonators made of fused silica; the other (in Perth, Australia) uses microwave whispering-gallery sapphire resonators. Within the standard model extension, we obtain simultaneous limits on Lorentz violation for electrons (5 coefficients) and photons (8) at levels down to 10(-16), improved by factors between 3 and 50 compared to previous work.

Noise properties of microwave signals synthesized with femtosecond lasers.

We discuss various aspects of high resolution measurements of phase fluctuations at microwave frequencies. This includes methods to achieve thermal noise limited sensitivity, along with the improved immunity to oscillator amplitude noise. A few prototype measurement systems were developed to measure phase fluctuations of microwave signals extracted from the optical pulse trains generated by femtosecond lasers. This enabled first reliable measurements of the excess phase noise associated with optical-to-microwave frequency division. The spectral density of the excess phase noise was found to be -140 dBc/Hz at 100 Hz offset from the 10 GHz carrier which was almost 40 dB better than that of a high quality microwave synthesizer.

Room temperature measurement of the anisotropic loss tangent of sapphire using the whispering gallery mode technique.

The anisotropic loss tangent has been determined in monocrystalline sapphire for components parallel and perpendicular to the crystal axis, using the whispering gallery (WG) mode method. The Q-factors of quasi-TE and quasi-TM modes were measured precisely in four cylindrical sapphire resonators at room temperature, from which was determined a maximum attainable Q-factor of (2.1 +/- 0.2) x 10(5) at 9 GHz in a quasi-TM mode. Sapphire dielectric material from three different manufacturers was compared over the 270-345 K temperature range and the 5-16 GHz frequency range.

Second generation 50 K dual-mode sapphire oscillator.

Low-temperature, high-precision sapphire resonators exhibit a turning point in mode frequency-temperature dependence at around 10 K. This, along with sapphire's extremely low dielectric losses at microwave frequencies, results in oscillator fractional frequency stabilities on the order of 10(-15). At higher temperatures the lack of a turning point makes single-mode oscillators very sensitive to temperature fluctuations. By exciting two quasi-orthogonal whispering gallery (WG) modes in a single sapphire resonator, a turning point in the frequency-temperature dependence can be found in the beat frequency between the two modes. A temperature control technique based on mode frequency temperature dependence has been used to maintain the sapphire at this turning point and the fractional frequency instability of the beat frequency has been measured to be at a level of 4.3 X 10(-14) over 1 s, dropping to 3.5 X 10(-14) over 4 s integration time.

Long-term operation and performance of cryogenic sapphire oscillators.

Cryogenic sapphire oscillators (CSO) developed at the University of Western Australia (UWA) have now been in operation around the world continuously for many years. Such oscillators, due to their excellent spectral purity are essential for interrogating atomic frequency standards at the limit of quantum projection noise; otherwise aliasing effects will dominate the frequency stability due to the periodic sampling between successive interrogations of the atomic transition. Other applications, which have attracted attention in recent years, include tests on fundamental principles of physics, such as tests of Lorentz invariance. This paper reports on the long-term operation and performance of such oscillators. We compare the long-term drift of some different CSOs. The drift rates turn out to be linear over many years and in the same direction. However, the magnitude seems to vary by more than one order of magnitude between the oscillators, ranging from 10(14) per day to a few parts in 10(13) per day.