Accelerating genomic workflows using NVIDIA Parabricks.

Background: As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of traditional CPU computing infrastructures, Graphics Processing Units (GPUs) offer opportunities to accelerate genomic workflows by orders of magnitude. Here we benchmark one GPU-accelerated software suite called NVIDIA Parabricks on Amazon Web Services (AWS), Google Cloud Platform (GCP), and an NVIDIA DGX cluster.

The proliferation and clonal migration of B cells in the systemic and mucosal tissues of channel catfish suggests there is an interconnected mucosal immune system.

IgM transcripts from different mucosal and systemic tissues from a single adult channel catfish have been evaluated. Arrayed heavy chain cDNA libraries from each of these different mucosal and systemic tissues were separately constructed, hybridized with VH family specific probes and a variety of approaches were used to define their structural relationships. Baseline hybridization studies indicated that the tissue libraries had different VH expression patterns, and sequencing studies indicated this was not simply due to varying proportions of the same B cell population.

Contact resistance and phase slips in mesoscopic superfluid atom transport.

We have experimentally measured transport of superfluid, bosonic atoms in a mesoscopic system: a small channel connecting two large reservoirs. Starting far from equilibrium (superfluid in a single reservoir), we observe first resistive flow transitioning at a critical current into superflow, characterized by oscillations. We reproduce this full evolution with a simple electronic circuit model.

Electronic Transport and Possible Superconductivity at Van Hove Singularities in Carbon Nanotubes.

Van Hove singularities (VHSs) are a hallmark of reduced dimensionality, leading to a divergent density of states in one and two dimensions and predictions of new electronic properties when the Fermi energy is close to these divergences. In carbon nanotubes, VHSs mark the onset of new subbands. They are elusive in standard electronic transport characterization measurements because they do not typically appear as notable features and therefore their effect on the nanotube conductance is largely unexplored.

Bursting activity of substantia nigra pars reticulata neurons in mouse parkinsonism in awake and anesthetized states.

Electrophysiological changes in basal ganglia neurons are hypothesized to underlie motor dysfunction in Parkinson's disease (PD). Previous results in head-restrained MPTP-treated non-human primates have suggested that increased bursting within the basal ganglia and related thalamic and cortical areas may be a hallmark of pathophysiological activity. In this study, we investigated whether there is increased bursting in substantia nigra pars reticulata (SNpr) output neurons in anesthetized and awake, head-restrained unilaterally lesioned 6-OHDA mice when compared to control mice.

Resistive flow in a weakly interacting Bose-Einstein condensate.

We report the direct observation of resistive flow through a weak link in a weakly interacting atomic Bose-Einstein condensate. Two weak links separate our ring-shaped superfluid atomtronic circuit into two distinct regions, a source and a drain. Motion of these weak links allows for creation of controlled flow between the source and the drain.

A 30 mK, 13.5 T scanning tunneling microscope with two independent tips.

We describe the design, construction, and performance of an ultra-low temperature, high-field scanning tunneling microscope (STM) with two independent tips. The STM is mounted on a dilution refrigerator and operates at a base temperature of 30 mK with magnetic fields of up to 13.5 T.

Abnormal Bursting as a Pathophysiological Mechanism in Parkinson's Disease.

Despite remarkable advances in Parkinson's disease (PD) research, the pathophysiological mechanisms causing motor dysfunction remain unclear, possibly delaying the advent of new and improved therapies. Several such mechanisms have been proposed including changes in neuronal firing rates, the emergence of pathological oscillatory activity, increased neural synchronization, and abnormal bursting. This review focuses specifically on the role of abnormal bursting of basal ganglia neurons in PD, where a burst is a physiologically-relevant, transient increase in neuronal firing over some reference period or activity.

Hysteresis in a quantized superfluid 'atomtronic' circuit.

Atomtronics is an emerging interdisciplinary field that seeks to develop new functional methods by creating devices and circuits where ultracold atoms, often superfluids, have a role analogous to that of electrons in electronics. Hysteresis is widely used in electronic circuits-it is routinely observed in superconducting circuits and is essential in radio-frequency superconducting quantum interference devices. Furthermore, it is as fundamental to superfluidity (and superconductivity) as quantized persistent currents, critical velocity and Josephson effects.

In vivo electrophysiology of nigral and thalamic neurons in alpha-synuclein-overexpressing mice highlights differences from toxin-based models of parkinsonism.

Numerous studies have suggested that alpha-synuclein plays a prominent role in both familial and idiopathic Parkinson's disease (PD). Mice in which human alpha-synuclein is overexpressed (ASO) display progressive motor deficits and many nonmotor features of PD. However, it is unclear what in vivo pathophysiological mechanisms drive these motor deficits.

Bulk and surface tunneling hydrogen defects in alumina.

We perform ab initio calculations of hydrogen-based tunneling defects in alumina to identify deleterious two-level systems (TLS) in superconducting qubits. The defects analyzed include bulk hydrogenated Al vacancies, bulk hydrogen interstitial defects, and a surface OH rotor. The formation energies of the defects are first computed for an Al- and O-rich environment to give the likelihood of defect occurrence during growth.

Driving phase slips in a superfluid atom circuit with a rotating weak link.

We have observed well-defined phase slips between quantized persistent current states around a toroidal atomic (23Na) Bose-Einstein condensate. These phase slips are induced by a weak link (a localized region of reduced superfluid density) rotated slowly around the ring. This is analogous to the behavior of a superconducting loop with a weak link in the presence of an external magnetic field.

Analogs of basic electronic circuit elements in a free-space atom chip.

Using a thermal sample of laser-cooled rubidium atoms, we have constructed a neutral-atom circuit analogous to an electronic capacitor discharged through a resistor. The atoms are confined using what we call a free-space atom chip, an optical dipole trap created using a generalized phase-contrast imaging technique. We have also calculated theoretical values for the capacitance and resistance, which agree with our experiments, as well as theoretical value for an atomic analog of electrical inductance.

Detection of bursts and pauses in spike trains.

Midbrain dopaminergic neurons in vivo exhibit a wide range of firing patterns. They normally fire constantly at a low rate, and speed up, firing a phasic burst when reward exceeds prediction, or pause when an expected reward does not occur. Therefore, the detection of bursts and pauses from spike train data is a critical problem when studying the role of phasic dopamine (DA) in reward related learning, and other DA dependent behaviors.

Disinhibition bursting of dopaminergic neurons.

Substantia nigra pars compacta (SNpc) dopaminergic neurons receive strong tonic inputs from GABAergic neurons in the substantia nigra pars reticulata (SNpr) and globus pallidus (GP), and glutamatergic neurons in the subthalamic nucleus. The presence of these tonic inputs raises the possibility that phasic disinhibition may trigger phasic bursts in dopaminergic neurons. We first applied constant NMDA and GABA(A) conductances onto a two-compartment single cell model of the dopaminergic neuron (Kuznetsov et al.

Superflow in a toroidal Bose-Einstein condensate: an atom circuit with a tunable weak link.

We have created a long-lived (≈40 s) persistent current in a toroidal Bose-Einstein condensate held in an all-optical trap. A repulsive optical barrier across one side of the torus creates a tunable weak link in the condensate circuit, which can affect the current around the loop. Superflow stops abruptly at a barrier strength such that the local flow velocity at the barrier exceeds a critical velocity.

High-frequency, short-latency disinhibition bursting of midbrain dopaminergic neurons.

During reinforcement and sequence learning, dopaminergic neurons fire bursts of action potentials. Dopaminergic neurons in vivo receive strong background excitatory and inhibitory inputs, suggesting that one mechanism by which bursts may be produced is disinhibition. Unfortunately, these inputs are lost during slice preparation and are not precisely controlled during in vivo experiments.

Application of a NMDA receptor conductance in rat midbrain dopaminergic neurons using the dynamic clamp technique.

Neuroscientists study the function of the brain by investigating how neurons in the brain communicate. Many investigators look at changes in the electrical activity of one or more neurons in response to an experimentally-controlled input. The electrical activity of neurons can be recorded in isolated brain slices using patch clamp techniques with glass micropipettes.

A dynamic role for GABA receptors on the firing pattern of midbrain dopaminergic neurons.

Dopaminergic neurons are subject to a significant background GABAergic input in vivo. The presence of this GABAergic background might be expected to inhibit dopaminergic neuron firing. However, dopaminergic neurons are not all silent but instead fire in single-spiking and burst firing modes.

Patterns of receptor revision in the immunoglobulin heavy chains of a teleost fish.

H chain cDNA libraries were constructed from the RNA derived from seven different organs and tissues from the same individual catfish. Sequence analysis of >300 randomly selected clones identified clonal set members within the same or different tissues, and some of these represented mosaic or hybrid sequences. These hybrids expressed V(H) members of the same or different V(H) families within different regions of the same clone.

Disruption of NMDAR-dependent burst firing by dopamine neurons provides selective assessment of phasic dopamine-dependent behavior.

Midbrain dopamine (DA) neurons fire in 2 characteristic modes, tonic and phasic, which are thought to modulate distinct aspects of behavior. However, the inability to selectively disrupt these patterns of activity has hampered the precise definition of the function of these modes of signaling. Here, we addressed the role of phasic DA in learning and other DA-dependent behaviors by attenuating DA neuron burst firing and subsequent DA release, without altering tonic neural activity.

The nucleotide targets of somatic mutation and the role of selection in immunoglobulin heavy chains of a teleost fish.

Sequence analysis of H chain cDNA derived from the spleen of an individual catfish has shown that somatic mutation occurs within both the VH- and JH-encoded regions. Somatic mutation preferentially targets G and C nucleotides with approximately balanced frequencies, resulting in the predominant accumulation of G-to-A and C-to-T substitutions that parallel the activation-induced cytidine deaminase nucleotide exchanges known in mammals. The overall mutation rate of A nucleotides is not significantly different from that expected by sequence-insensitive mutations, and a significant bias exists against mutations occurring in T.

Macroscopic tunnel splittings in superconducting phase qubits.

Prototype Josephson-junction based qubit coherence times are too short for quantum computing. Recent experiments probing superconducting phase qubits have revealed previously unseen fine splittings in the transition energy spectra. These splittings have been attributed to new microscopic degrees of freedom (microresonators), a previously unknown source of decoherence.

Spectroscopy of three-particle entanglement in a macroscopic superconducting circuit.

We study the quantum mechanical behavior of a macroscopic, three-body, superconducting circuit. Microwave spectroscopy on our system, a resonator coupling two large Josephson junctions, produced complex energy spectra well explained by quantum theory over a large frequency range. By tuning each junction separately into resonance with the resonator, we first observe strong coupling between each junction and the resonator.

Patterns of gene divergence and VL promoter activity in immunoglobulin light chain clusters of the channel catfish.

The structure and genomic organization of V, J, and C segments in multiple gene clusters of the G class of catfish light (L) chain were determined to study evolutionary patterns of cluster divergence and regulatory function. The results showed that the organizational pattern is conserved; two VL segments reside in opposite transcriptional orientation to a pseudogene JL segment (psiJ), a functional JL segment, and a CL segment. Structures within the central V-psiJ-J-C regions indicate that cluster duplication occurred after the V-V-psiJ-J-C organization became fixed.