Manipulating of matter with light: From atoms to bubbles

This thesis concerns the interaction between matter and light, in particular the coherent manipulation and directed motion of cold atoms in a Hamiltonian system in the fully chaotic regime. The system under scrutiny is the cold atom realisation of the delta kicked rotor, a paradigm system for the study of quantum chaos in which ultra-cold caesium atoms are periodically 'kicked' by a symmetric (and in this case far-detuned) optical lattice. Experiments demonstrate quantum features such as dynamical localisation, and asymmetric diffusion is achieved as a result of mixed (chaotic and regular) classical dynamics. Further experiments make an exploration of phase space past the momentum boundary, a manifestation of finite-width kicks, and by reducing system symmetries it is shown that directed atomic motion in this Hamiltonian system can result from purely chaotic dynamics alone. The second part of this thesis describes the design and construction of a computer-controlled scanning-beam laser tweezers for the manipulation of dielectric microspheres and micron-sized protein-coated bubbles. Evidence for the three-dimensional trapping and the automated two-dimensional manipulation of these neutral particles in time-shared optical traps is presented. The preparation and plans for biological research applications is also detailed, the work of which marks the beginning of future biophysical collaborations

Low Mass Printable Devices for Energy Capture, Storage, and Use

The energy-efficient, environmentally friendly technology that will be presented is the result of a Space Act Agreement between NthDegree Technologies Worldwide, Inc., and the National Aeronautics and Space Administration's (NASA's) Marshall Space Flight Center (MSFC). The work combines semiconductor and printing technologies to advance lightweight electronic and photonic devices having excellent potential for commercial and exploration applications. Device development involves three projects that relate to energy generation and consumption: (1) a low-mass efficient (low power, low heat emission) micro light-emitting diode (LED) area lighting device; (2) a low-mass omni-directional efficient photovoltaic (PV) device with significantly improved energy capture; and (3) a new approach to building super-capacitors. These three technologies, energy capture, storage, and usage (e.g., lighting), represent a systematic approach for building efficient local micro-grids that are commercially feasible; furthermore, these same technologies, appropriately replacing lighting with lightweight power generation, will be useful for enabling inner planetary missions using smaller launch vehicles and to facilitate surface operations during lunar and planetary surface missions. The PV device model is a two sphere, light trapped sheet approximately 2-mm thick. The model suggests a significant improvement over current thin film systems. For lighting applications, all three technology components are printable in-line by printing sequential layers on a standard screen or flexographic direct impact press using the three-dimensional printing technique (3DFM) patented by NthDegree. One primary contribution to this work in the near term by the MSFC is to test the robustness of prototype devices in the harsh environments that prevail in space and on the lunar surface. It is anticipated that this composite device, of which the lighting component has passed off-gassing testing, will function appropriately in such environments consistent with NASA s exploration missions. Advanced technologies such as this show promise for both space flight and terrestrial applications

Toward Early-Warning Detection of Gravitational Waves from Compact Binary Coalescence

Rapid detection of compact binary coalescence (CBC) with a network of advanced gravitational-wave detectors will offer a unique opportunity for multi-messenger astronomy. Prompt detection alerts for the astronomical community might make it possible to observe the onset of electromagnetic emission from (CBC). We demonstrate a computationally practical filtering strategy that could produce early-warning triggers before gravitational radiation from the final merger has arrived at the detectors.Comment: 16 pages, 7 figures, published in ApJ. Reformatted preprint with emulateap

Automated Additive Construction (AAC) for Earth and Space Using In-situ Resources

Using Automated Additive Construction (AAC), low-fidelity large-scale compressive structures can be produced out of a wide variety of materials found in the environment. Compressionintensive structures need not utilize materials that have tight specifications for internal force management, meaning that the production of the building materials do not require costly methods for their preparation. Where a certain degree of surface roughness can be tolerated, lower-fidelity numerical control of deposited materials can provide a low-cost means for automating building processes, which can be utilized in remote or extreme environments on Earth or in Space. For space missions where every kilogram of mass must be lifted out of Earth’s gravity well, the promise of using in-situ materials for the construction of outposts, facilities, and installations could prove to be enabling if significant reduction of payload mass can be achieved. In a 2015 workshop sponsored by the Keck nstitute for Space Studies, on the topic of Three Dimensional (3D) Additive Construction For Space Using In-situ Resources, was conducted with additive construction experts from around the globe in attendance. The workshop explored disparate efforts, methods, and technologies and established a proposed framework for the field of Additive Construction Using In-situ Resources. This paper defines the field of Automated Additive Construction Using In-situ Resources, describes the state-of-the-art for various methods, establishes a vision for future efforts, identifies gaps in current technologies, explores investment opportunities, and proposes potential technology demonstration missions for terrestrial, International Space Station (ISS), lunar, deep space zero-gravity, and Mars environments

Neuropathology of COVID-19 (neuro-COVID): clinicopathological update

Coronavirus disease 2019 (COVID-19) is emerging as the greatest public health crisis in the early 21st century. Its causative agent, Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), is an enveloped single-stranded positive-sense ribonucleic acid virus that enters cells via the angiotensin converting enzyme 2 receptor or several other receptors. While COVID-19 primarily affects the respiratory system, other organs including the brain can be involved. In Western clinical studies, relatively mild neurological dysfunction such as anosmia and dysgeusia is frequent (~70-84%) while severe neurologic disorders such as stroke (~1-6%) and meningoencephalitis are less common. It is unclear how much SARS-CoV-2 infection contributes to the incidence of stroke given co-morbidities in the affected patient population. Rarely, clinically-defined cases of acute disseminated encephalomyelitis, Guillain-Barré syndrome and acute necrotizing encephalopathy have been reported in COVID-19 patients. Common neuropathological findings in the 184 patients reviewed include microglial activation (42.9%) with microglial nodules in a subset (33.3%), lymphoid inflammation (37.5%), acute hypoxic-ischemic changes (29.9%), astrogliosis (27.7%), acute/subacute brain infarcts (21.2%), spontaneous hemorrhage (15.8%), and microthrombi (15.2%). In our institutional cases, we also note occasional anterior pituitary infarcts. COVID-19 coagulopathy, sepsis, and acute respiratory distress likely contribute to a number of these findings. When present, central nervous system lymphoid inflammation is often minimal to mild, is detected best by immunohistochemistry and, in one study, indistinguishable from control sepsis cases. Some cases evince microglial nodules or neuronophagy, strongly supporting viral meningoencephalitis, with a proclivity for involvement of the medulla oblongata. The virus is detectable by reverse transcriptase polymerase chain reaction, immunohistochemistry, or electron microscopy in human cerebrum, cerebellum, cranial nerves, olfactory bulb, as well as in the olfactory epithelium; neurons and endothelium can also be infected. Review of the extant cases has limitations including selection bias and limited clinical information in some cases. Much remains to be learned about the effects of direct viral infection of brain cells and whether SARS-CoV-2 persists long-term contributing to chronic symptomatology

Technology dictates algorithms: Recent developments in read alignment

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of genomic data in the form of nucleotide sequences or reads. Aligning reads onto reference genomes enables the identification of individual-specific genetic variants and is an essential step of the majority of genomic analysis pipelines. Aligned reads are essential for answering important biological questions, such as detecting mutations driving various human diseases and complex traits as well as identifying species present in metagenomic samples. The read alignment problem is extremely challenging due to the large size of analyzed datasets and numerous technological limitations of sequencing platforms, and researchers have developed novel bioinformatics algorithms to tackle these difficulties. Importantly, computational algorithms have evolved and diversified in accordance with technological advances, leading to todays diverse array of bioinformatics tools. Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads. We provide rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read aligners. We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques. We also discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology, including whole transcriptome, adaptive immune repertoire, and human microbiome studies

Intermittent Screening and Treatment versus Intermittent Preventive Treatment of Malaria in Pregnancy: A Randomised Controlled Non-Inferiority Trial

BACKGROUND: The effectiveness of intermittent preventive treatment of malaria in pregnancy (IPTp) may be compromised by the spread of resistance to sulphadoxine/pyrimethamine (SP) across Africa. But little information exists on alternative drugs for IPTp or alternative strategies for the prevention of malaria in pregnancy. Therefore, we have investigated whether screening with a rapid diagnostic test and treatment of those who are positive (IST) at routine antenatal clinic attendances is as effective and as safe as SP-IPTp in pregnant women. METHODS AND FINDINGS: During antenatal clinic sessions in six health facilities in Ghana held between March 2007 and September 2007, 3333 pregnant women who satisfied inclusion criteria were randomised into three intervention arms (1) standard SP-IPTp, (2) IST and treatment with SP or (3) IST and treatment with amodiaquine+artesunate (AQ+AS). All women received a long-lasting insecticide treated net. Study women had a maximum of three scheduled follow-up visits following enrollment. Haemoglobin concentration and peripheral parasitaemia were assessed between 36 and 40 weeks of gestation. Birth weight was measured at delivery or within 72 hours for babies delivered at home. Parasite prevalence at enrollment in primigravidae and in multigravidae was 29.6% and 10.2% respectively. At 36-40 weeks of gestation the prevalence of asymptomatic parasitaemia was 12.1% in study women overall and was very similar in all treatment groups. The risk of third trimester severe anaemia or low birth weight did not differ significantly between the three treatment groups regardless of gravidity. IST with AQ+AS or SP was not inferior to SP-IPTp in reducing the risk of low birth weight (RD  =  -1.17[95%CI; -4.39-1.02] for IST-SP vs. SP-IPTp and RD = 0.78[95%CI; -2.11-3.68] for IST-AQAS vs. SP-IPTp); third trimester severe anaemia (RD = 0.29[95%CI; -0.69-1.30] for IST-SP vs. SP-IPTp and RD  =  -0.36[95%CI;-1.12-0.44] for IST-AQAS vs. SP-IPTp). CONCLUSION: The results of this study suggest that in an area of moderately high malaria transmission, IST with SP or AS+AQ may be a safe and effective strategy for the control of malaria in pregnancy. However, it is important that these encouraging findings are confirmed in other geographical areas and that the impact of IST on placental malaria is investigated. TRIAL REGISTRATION: ClinicalTrials.gov NCT00432367 [NCT00432367]

Implications For The Origin Of GRB 051103 From LIGO Observations

We present the results of a LIGO search for gravitational waves (GWs) associated with GRB 051103, a short-duration hard-spectrum gamma-ray burst (GRB) whose electromagnetically determined sky position is coincident with the spiral galaxy M81, which is 3.6 Mpc from Earth. Possible progenitors for short-hard GRBs include compact object mergers and soft gamma repeater (SGR) giant flares. A merger progenitor would produce a characteristic GW signal that should be detectable at the distance of M81, while GW emission from an SGR is not expected to be detectable at that distance. We found no evidence of a GW signal associated with GRB 051103. Assuming weakly beamed gamma-ray emission with a jet semi-angle of 30 deg we exclude a binary neutron star merger in M81 as the progenitor with a confidence of 98%. Neutron star-black hole mergers are excluded with > 99% confidence. If the event occurred in M81 our findings support the the hypothesis that GRB 051103 was due to an SGR giant flare, making it the most distant extragalactic magnetar observed to date.Comment: 8 pages, 3 figures. For a repository of data used in the publication, go to: https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=15166 . Also see the announcement for this paper on ligo.org at: http://www.ligo.org/science/Publication-GRB051103/index.ph

ADAM8 signaling drives neutrophil migration and ARDS severity

Acute respiratory distress syndrome (ARDS) results in catastrophic lung failure and has an urgent, unmet need for improved early recognition and therapeutic development. Neutrophil influx is a hallmark of ARDS and is associated with the release of tissue-destructive immune effectors, such as matrix metalloproteinases (MMPs) and membrane-anchored metalloproteinase disintegrins (ADAMs). Here, we observed using intravital microscopy that Adam8–/– mice had impaired neutrophil transmigration. In mouse pneumonia models, both genetic deletion and pharmacologic inhibition of ADAM8 attenuated neutrophil infiltration and lung injury while improving bacterial containment. Unexpectedly, the alterations of neutrophil function were not attributable to impaired proteolysis but resulted from reduced intracellular interactions of ADAM8 with the actin-based motor molecule Myosin1f that suppressed neutrophil motility. In 2 ARDS cohorts, we analyzed lung fluid proteolytic signatures and identified that ADAM8 activity was positively correlated with disease severity. We propose that in acute inflammatory lung diseases such as pneumonia and ARDS, ADAM8 inhibition might allow fine-tuning of neutrophil responses for therapeutic gain