Final Report: Efficient Databases for MPC Microdata

The purpose of this grant was to develop the theory and practice of high-performance databases for massive streamed datasets. Over the last three years, we have developed fast indexing technology, that is, technology for rapidly ingesting data and storing that data so that it can be efficiently queried and analyzed. During this project we developed the technology so that high-bandwidth data streams can be indexed and queried efficiently. Our technology has been proven to work data sets composed of tens of billions of rows when the data streams arrives at over 40,000 rows per second. We achieved these numbers even on a single disk driven by two cores. Our work comprised (1) new write-optimized data structures with better asymptotic complexity than traditional structures, (2) implementation, and (3) benchmarking. We furthermore developed a prototype of TokuFS, a middleware layer that can handle microdata I/O packaged up in an MPI-IO abstraction

Don't Thrash: How to Cache Your Hash on Flash

This paper presents new alternatives to the well-known Bloom filter data structure. The Bloom filter, a compact data structure supporting set insertion and membership queries, has found wide application in databases, storage systems, and networks. Because the Bloom filter performs frequent random reads and writes, it is used almost exclusively in RAM, limiting the size of the sets it can represent. This paper first describes the quotient filter, which supports the basic operations of the Bloom filter, achieving roughly comparable performance in terms of space and time, but with better data locality. Operations on the quotient filter require only a small number of contiguous accesses. The quotient filter has other advantages over the Bloom filter: it supports deletions, it can be dynamically resized, and two quotient filters can be efficiently merged. The paper then gives two data structures, the buffered quotient filter and the cascade filter, which exploit the quotient filter advantages and thus serve as SSD-optimized alternatives to the Bloom filter. The cascade filter has better asymptotic I/O performance than the buffered quotient filter, but the buffered quotient filter outperforms the cascade filter on small to medium data sets. Both data structures significantly outperform recently-proposed SSD-optimized Bloom filter variants, such as the elevator Bloom filter, buffered Bloom filter, and forest-structured Bloom filter. In experiments, the cascade filter and buffered quotient filter performed insertions 8.6-11 times faster than the fastest Bloom filter variant and performed lookups 0.94-2.56 times faster.Comment: VLDB201

Adversarial Analyses of Window Backoff Strategies for Simple Multiple-Access Channels

Backoff strategies have typically been analyzed by making statistical assumptions on the distribution of problem inputs. Although these analyses have provided valuable insights into the efficacy of various backoff strategies, they leave open the question as to which backoff algorithms perform best in the worst case or on inputs, such as bursty inputs, that are not covered by the statistical models. This paper analyzes randomized backoff strategies using worst-case assumptions on the inputs. Specifically, we analyze algorithms for simple multiple-access channels, where the only feedback from each attempt to send a packet is a single bit indicating whether the transmission succeeded or the packet collided with another packet. We analyze a class of strategies, called window strategies, where each packet partitions time into a sequence (W₁, W₂,...) of windows. Within each window, the packet makes an access attempt during a single randomly selected slot. If its transmission is unsuccessful, it waits for its slot in the next window before retrying. We use delay-sequence arguments to show that for the batch problem, in which n packets all arrive at time 0, if every window has size W = Θ(n), then with high probability, all packets successfully transmit with makespan n lg lg n ± O(n). We use this result to analyze window backoff strategies with varying window sizes. Specifically, we show that the familiar binary exponential backoff algorithm, where Wk = Θ(2k), has makespan Θ(n lg n), and that more generally, for any constant r > 1, the r-exponential backoff algorithm in which Wk = Θ(rk) has makespan Θ(n lglg rn). We also show that for any constant r > 1, the r-polynomial backoff algorithm, in which Wk = Θ(kr), has makespan Θ((n/lg n)¹⁺¹/r). All of these batch strategies are monotonic, in the sense that the window size monotonically increases over time. We exhibit a monotonic backoff algorithm that achieves makespan Θ(n lg lg n/lg lg lg n). We prove that this algorithm, whose backoff is superpolynomial and subexponential, is optimal over all monotonic backoff schemes. In addition, we exhibit a simple backoff/backon algorithm, having window sizes that vary nonmonotonically according to a "sawtooth" pattern, that achieves the optimal makespan of Θ(n). We study the online setting using an adversarial queueing model. We define a (λ,T)-stream to be an input stream of packets in which at most n = λT packets arrive during any time interval of size T. In this model, to evaluate a given backoff algorithm (which does not know λ or T), we analyze the worst-case behavior of the algorithm over the class of (λ,T)-streams. Our results for the online setting focus on exponential backoff. We show that for any arrival rate λ, there exists a sufficiently large interval size T such that the throughput goes to 0 for some (λ,T)-stream. Moreover, there exists a sufficiently large constant c such that for any interval size T, if λ ⥠c lg lg n/lg n, the system is unstable in the sense that the arrival rate exceeds the throughput in the worst case. If, on the other hand, we have λ ⤠c/lg n for a sufficiently small constant c, then the system is stable. Surprisingly, the algorithms that guarantee smaller makespans in the batch setting require lower arrival rates to achieve stability than does exponential backoff, but when they are stable, they have better response times.Singapore-MIT Alliance (SMA

Cache-Oblivious Streaming B-Trees

A streaming B-tree is a dictionary that efficiently implements insertions and range queries. We present two cache-oblivious streaming B-trees, the shuttle tree, and the cache-oblivious lookahead array (COLA). For block-transfer size B and on N elements, the shuttle tree implements searches in optimal $O(log_{B+1}N)$ transfers, range queries of L successive elements in optimal $O(log_{B+1}N +L/B)$ transfers, and insertions in $O((log_{B+1}N)/B^{\Theta(1/(log log B)^2)}+(log^2N)/B)$ transfers, which is an asymptotic speedup over traditional B-trees if $B ≥ (log N)^{1+c log log log^2 N}$ for any constant c >1. A COLA implements searches in O(log N) transfers, range queries in O(log N + L/B) transfers, and insertions in amortized O((log N)/B) transfers, matching the bounds for a (cache-aware) buffered repository tree. A partially deamortized COLA matches these bounds but reduces the worst-case insertion cost to O(log N) if memory size $M = \Omega(log N)$. We also present a cache-aware version of the COLA, the lookahead array, which achieves the same bounds as Brodal and Fagerberg's (cache-aware) $B^{\epsilon}$-tree. We compare our COLA implementation to a traditional B-tree. Our COLA implementation runs 790 times faster for random insertions, 3.1 times slower for insertions of sorted data, and 3.5 times slower for searches.Engineering and Applied Science

Postoperative Nausea and Vomiting Implications in Neostigmine versus Sugammadex

Purpose/Background: Postoperative nausea and vomiting (PONV) is a frequent complaint in the postoperative period, which can delay discharge, result in readmission, and increase cost for patients and facilities. Inducing paralysis is common in anesthesia, as is utilizing the drugs neostigmine and sugammadex as reversal agents for non-depolarizing neuromuscular blockers. Many studies are available that compare these two drugs to determine if neostigmine increases the risk of PONV over sugammadex. Sugammadex has a more favorable pharmacologic profile and may improve patient outcomes by reducing PONV. Methods: This review included screening a total of 39 studies and peer-reviewed articles that looked at patients undergoing general anesthesia who received non-depolarizing neuromuscular blockers requiring either neostigmine or sugammadex for reversal, along with their respective PONV rates. 8 articles were included, while 31 articles were removed based on our exclusion criteria. These were published between 2014 and 2020 exclusively. The key words used were “neostigmine”, “sugammadex”, “PONV”, along with combinations “paralytic reversal agents and PONV”. This search was performed on the scholarly database MEDLINE. The data items were PONV rates in neostigmine group, PONV rates in sugammadex group, incidence of postoperative analgesic consumption in neostigmine group, and incidence of postoperative analgesic consumption in sugammadex group. Results: Despite numerical differences being noted in the incidence of PONV with sugammadex over reversal with neostigmine, there did not appear to be any statistically significant data in the multiple peer-reviewed trials included in our review, for not one of the 8 studies concluded that there was a higher incidence of PONV in one drug or the other of an y clinical relevance. Although the side-effect profile tended to be better in the sugammadex group than neostigmine in areas other than PONV, there was not sufficient evidence to conclude that one drug was superior to the other in causing a direct reduction of PONV. Implications for Nursing Practice: There were variable but slight differences noted between both drug groups in PONV rates, but it remained that none of the studies determined it was statically significant or clinically conclusive. This review did, however, note other advantages to sugammadex over neostigmine, including its pharmacologic profile of more efficiently reversing non-depolarizing neuromuscular blocking drugs and its more favorable pharmacokinetics. This lack of statistically significant evidence found within these studies consequentially does not support pharmacologic decision-making of one drug in favor of the other for reducing PONV; therefore, PONV alone is not a sufficient rationale for a provider to justify using one reversal over another at the current time until further research proves otherwise

Final Report: Efficient Databases for MPC Microdata

The purpose of this grant was to develop the theory and practice of high-performance databases for massive streamed datasets. Over the last three years, we have developed fast indexing technology, that is, technology for rapidly ingesting data and storing that data so that it can be efficiently queried and analyzed. During this project we developed the technology so that high-bandwidth data streams can be indexed and queried efficiently. Our technology has been proven to work data sets composed of tens of billions of rows when the data streams arrives at over 40,000 rows per second. We achieved these numbers even on a single disk driven by two cores. Our work comprised (1) new write-optimized data structures with better asymptotic complexity than traditional structures, (2) implementation, and (3) benchmarking. We furthermore developed a prototype of TokuFS, a middleware layer that can handle microdata I/O packaged up in an MPI-IO abstraction

Specialized intensive inpatient rehabilitation is crucial and time-sensitive for functional recovery from disorders of consciousness

BackgroundDisorders of consciousness (DoCs) after severe brain injury are considered to be conditions with dire prognosis. Despite the accumulating evidence, inpatient rehabilitation is often denied by payers referring to the Medicare/Medicaid criteria, under the assumption that such patients will not “actively” participate in therapy or make “measurable improvements.”ObjectiveThis study aimed to report on the effectiveness and efficiency of a specialized inpatient DoC rehabilitation program based on measurable clinical parameters.MethodsA retrospective cohort study was conducted. The cohort comprised 137 patients with DoC admitted to a specialized acute inpatient rehabilitation program between January 2014 and October 2018. Patients were categorized as having been admitted at the acute stage (<=28 days post-injury), subacute stage (29–365 days following a traumatic brain injury (TBI) or 29–90 days following a non-TBI), or chronic stage (>365 days following a TBI or >90 days following a non-TBI). Outcomes included changes in level of consciousness (based on the Coma Recovery Scale–Revised (CRS-R), while also acknowledging scenarios beyond those captured by the CRS-R via Individualized Qualitative Behavioral Assessment and team consensus); Functional Independence Measure (FIM) levels; achievements in decannulation and initiation of oral diet; and time to those achievements.ResultsThe rates of emergence from a minimally conscious state were 90, 62, and 18% among patients admitted at the acute, subacute, and chronic stages, respectively. Among patients who emerged, 100, 85, and 67%, respectively, had measurable FIM scores. Approximately 60 and 20% of patients at the acute and subacute stages, respectively, required moderate assistance or less in transfer/communication/eating/grooming/upper body dressing by the time of discharge from Phase I admission. The decannulation rates were 94, 67, and 17%. The oral diet initiation rates were 70, 23, and 6%. The time to reach these achievements lengthened as chronicity increased. There was a weak positive correlation (rs = 0.308) in the case of decannulation and a strong positive correlation (rs = 0.606, both p < 0.01) in the case of oral diet between days since injury on admission and days to the achievement after admission. Patients with TBI and hypoxic brain injury had comparable recovery rates when admitted at the acute and subacute stages.ConclusionSpecialized intensive inpatient rehabilitation is crucial and time-sensitive for functional recovery from DoC caused by TBI and hypoxic–ischemic brain injury. Specific goals and different outcome measures need to be developed to appraise the benefits of acute inpatient rehabilitation for DoC

Transverse oscillating bubble enhanced laser‑driven betatron X‑ray radiation generation

Ultrafast high-brightness X-ray pulses have proven invaluable for a broad range of research. Such pulses are typically generated via synchrotron emission from relativistic electron bunches using large-scale facilities. Recently, significantly more compact X-ray sources based on laser-wakefield accelerated (LWFA) electron beams have been demonstrated. In particular, laser-driven sources, where the radiation is generated by transverse oscillations of electrons within the plasma accelerator structure (so-called betatron oscillations) can generate highly-brilliant ultrashort X-ray pulses using a comparably simple setup. Here, we experimentally demonstrate a method to markedly enhance the parameters of LWFA-driven betatron X-ray emission in a proof-of-principle experiment. We show a significant increase in the number of generated photons by specifically manipulating the amplitude of the betatron oscillations by using our novel Transverse Oscillating Bubble Enhanced Betatron Radiation scheme. We realize this through an orchestrated evolution of the temporal laser pulse shape and the accelerating plasma structure. This leads to controlled off-axis injection of electrons that perform large-amplitude collective transverse betatron oscillations, resulting in increased radiation emission. Our concept holds the promise for a method to optimize the X-ray parameters for specific applications, such as time-resolved investigations with spatial and temporal atomic resolution or advanced high-resolution imaging modalities, and the generation of X-ray beams with even higher peak and average brightness

Thermomechanical data of polyurethane shape memory polymer: Considering varying compositions

This article presents data from the investigation of the thermal characteristics and mechanical behaviors of twelve different compositions of a polyurethane shape memory polymer (SMP). Each of the SMP compositions has a unique molar ratio of three monomers: (i) hexamethylene diisocyanate (HDI), (ii) N,N,N′,N′-Tetrakis(2-Hydroxypropyl)ethylenediamine (HPED), and (iii) Triethanolamine (TEA). The thermal characteristic datasets for each composition include the glass transition temperatures, as obtained from differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA), and the thermal degradation thresholds, as found from thermogravimetric analysis (TGA). The mechanical behaviors of the SMPs are represented by the failure stresses and strains, as obtained by cyclic tensile testing and failure testing, respectively. The interpretation of these measurements as well as a discussion of the potential usage of candidate SMP compositions for medical devices can be found in the companion article by Kunkel et al. (2018) [1], “Synthesis and characterization of bio-compatible shape memory polymers with potential applications to endovascular embolization of intracranial aneurysms.”Funding from the Oklahoma Center for the Advancement of Science and Technology (OCAST, HR18-002) and the Oklahoma Shared Clinical and Translational Resources (OSCTR, NIGMS U54GM104938) are gratefully acknowledged. CHL was also supported by the institutional start-up funds from the School of Aerospace and Mechanical Engineering, the IBEST SEED Funding for Interdisciplinary Research, and the Faculty Investment Program from the Research Council at the University of Oklahoma (OU). Open Access fees paid for in whole or in part by the University of Oklahoma Libraries.Ye

West Nile Virus Viremia in Eastern Chipmunks (Tamias striatus) Sufficient for Infecting Different Mosquitoes

Chipmunks might play a role in enzootic WNV cycles and be an amplifying host for mosquitoes that infect humans