On Predictive Modeling for Optimizing Transaction Execution in Parallel OLTP Systems

A new emerging class of parallel database management systems (DBMS) is designed to take advantage of the partitionable workloads of on-line transaction processing (OLTP) applications. Transactions in these systems are optimized to execute to completion on a single node in a shared-nothing cluster without needing to coordinate with other nodes or use expensive concurrency control measures. But some OLTP applications cannot be partitioned such that all of their transactions execute within a single-partition in this manner. These distributed transactions access data not stored within their local partitions and subsequently require more heavy-weight concurrency control protocols. Further difficulties arise when the transaction's execution properties, such as the number of partitions it may need to access or whether it will abort, are not known beforehand. The DBMS could mitigate these performance issues if it is provided with additional information about transactions. Thus, in this paper we present a Markov model-based approach for automatically selecting which optimizations a DBMS could use, namely (1) more efficient concurrency control schemes, (2) intelligent scheduling, (3) reduced undo logging, and (4) speculative execution. To evaluate our techniques, we implemented our models and integrated them into a parallel, main-memory OLTP DBMS to show that we can improve the performance of applications with diverse workloads.Comment: VLDB201

Fault-tolerant distributed transactions for partitioned OLTP databases

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 103-112).This thesis presents Dtxn, a fault-tolerant distributed transaction system designed specifically for building online transaction processing (OLTP) databases. Databases have traditionally been designed as general purpose data processing tools. By being designed only for OLTP workloads, Dtxn can be more efficient. It is designed to support very large databases by partitioning data across a cluster of commodity servers in a data center. Combining multiple servers together allows systems built with Dtxn to be cost effective, highly available, scalable, and fault-tolerant. Dtxn provides three novel features. First, it provides reusable infrastructure for building a distributed OLTP database out of single machine databases. This allows developers to take a specialized backend storage engine and use it across multiple machines, without needing to re-implement the distributed transaction infrastructure. We used Dtxn to build four different applications: a simple key/value store, a specialized TPC-C implementation, a main-memory OLTP database, and a traditional disk-based OLTP database. Second, Dtxn provides a novel concurrency control mechanism called speculative concurrency control, designed for main memory OLTP workloads that are primarily composed of transactions with a single round of communication between the application and database. Speculative concurrency control executes one transaction at a time, with no concurrency control overhead. In cases where there may be stalls due to network communication, it speculates future transactions. Our results show that this provides significantly better throughput than traditional two-phase locking, outperforming it by a factor of two on the TPC-C benchmark. Finally, Dtxn supports live migration, allowing part of the data on one server to be moved to another server while processing transactions. Our experiments show that our approach has nearly no visible impact on throughput or latency when moving data under moderate to high loads. It has significantly less impact than the best commercially available systems when the database is overloaded. The period of time where the throughput is reduced is less than half as long as failing over to another replica or using virtual machine migration.by Evan Philip Charles Jones.Ph.D

CMB polarimetry with BICEP: instrument characterization, calibration, and performance

BICEP is a ground-based millimeter-wave bolometric array designed to target the primordial gravity wave signature on the polarization of the cosmic microwave background (CMB) at degree angular scales. Currently in its third year of operation at the South Pole, BICEP is measuring the CMB polarization with unprecedented sensitivity at 100 and 150 GHz in the cleanest available 2% of the sky, as well as deriving independent constraints on the diffuse polarized foregrounds with select observations on and off the Galactic plane. Instrument calibrations are discussed in the context of rigorous control of systematic errors, and the performance during the first two years of the experiment is reviewed.Comment: 12 pages, 15 figures, updated version of a paper accepted for Millimeter and Submillimeter Detectors and Instrumentation for Astronomy IV, Proceedings of SPIE, 7020, 200

Persistent net release of carbon dioxide and methane from an Alaskan lowland boreal peatland complex

Permafrost degradation in peatlands is altering vegetation and soil properties and impacting net carbon storage. We studied four adjacent sites in Alaska with varied permafrost regimes, including a black spruce forest on a peat plateau with permafrost, two collapse scar bogs of different ages formed following thermokarst, and a rich fen without permafrost. Measurements included year-round eddy covariance estimates of net carbon dioxide (CO2), mid-April to October methane (CH4) emissions, and environmental variables. From 2011 to 2022, annual rainfall was above the historical average, snow water equivalent increased, and snow-season duration shortened due to later snow return. Seasonally thawed active layer depths also increased. During this period, all ecosystems acted as slight annual sources of CO2 (13–59 g C m−2 year−1) and stronger sources of CH4 (11–14 g CH4 m−2 from ~April to October). The interannual variability of net ecosystem exchange was high, approximately ±100 g C m−2 year−1, or twice what has been previously reported across other boreal sites. Net CO2 release was positively related to increased summer rainfall and winter snow water equivalent and later snow return. Controls over CH4 emissions were related to increased soil moisture and inundation status. The dominant emitter of carbon was the rich fen, which, in addition to being a source of CO2, was also the largest CH4 emitter. These results suggest that the future carbon-source strength of boreal lowlands in Interior Alaska may be determined by the area occupied by minerotrophic fens, which are expected to become more abundant as permafrost thaw increases hydrologic connectivity. Since our measurements occur within close proximity of each other (≤1 km2), this study also has implications for the spatial scale and data used in benchmarking carbon cycle models and emphasizes the necessity of long-term measurements to identify carbon cycle process changes in a warming climate

Absolute polarization angle calibration using polarized diffuse Galactic emission observed by BICEP

We present a method of cross-calibrating the polarization angle of a polarimeter using BICEP Galactic observations. \bicep\ was a ground based experiment using an array of 49 pairs of polarization sensitive bolometers observing from the geographic South Pole at 100 and 150 GHz. The BICEP polarimeter is calibrated to +/-0.01 in cross-polarization and less than +/-0.7 degrees in absolute polarization orientation. BICEP observed the temperature and polarization of the Galactic plane (R.A= 100 degrees ~ 270 degrees and Dec. = -67 degrees ~ -48 degrees). We show that the statistical error in the 100 GHz BICEP Galaxy map can constrain the polarization angle offset of WMAP Wband to 0.6 degrees +\- 1.4 degrees. The expected 1 sigma errors on the polarization angle cross-calibration for Planck or EPIC are 1.3 degrees and 0.3 degrees at 100 and 150 GHz, respectively. We also discuss the expected improvement of the BICEP Galactic field observations with forthcoming BICEP2 and Keck observations.Comment: 13 pages, 10 figures and 2 tables. To appear in Proceedings of SPIE Astronomical Telescopes and Instrumentation 201

The DEEP2 Galaxy Redshift Survey: Design, Observations, Data Reduction, and Redshifts

We describe the design and data sample from the DEEP2 Galaxy Redshift Survey, the densest and largest precision-redshift survey of galaxies at z ~ 1 completed to date. The survey has conducted a comprehensive census of massive galaxies, their properties, environments, and large-scale structure down to absolute magnitude M_B = -20 at z ~ 1 via ~90 nights of observation on the DEIMOS spectrograph at Keck Observatory. DEEP2 covers an area of 2.8 deg^2 divided into four separate fields, observed to a limiting apparent magnitude of R_AB=24.1. Objects with z < 0.7 are rejected based on BRI photometry in three of the four DEEP2 fields, allowing galaxies with z > 0.7 to be targeted ~2.5 times more efficiently than in a purely magnitude-limited sample. Approximately sixty percent of eligible targets are chosen for spectroscopy, yielding nearly 53,000 spectra and more than 38,000 reliable redshift measurements. Most of the targets which fail to yield secure redshifts are blue objects that lie beyond z ~ 1.45. The DEIMOS 1200-line/mm grating used for the survey delivers high spectral resolution (R~6000), accurate and secure redshifts, and unique internal kinematic information. Extensive ancillary data are available in the DEEP2 fields, particularly in the Extended Groth Strip, which has evolved into one of the richest multiwavelength regions on the sky. DEEP2 surpasses other deep precision-redshift surveys at z ~ 1 in terms of galaxy numbers, redshift accuracy, sample number density, and amount of spectral information. We also provide an overview of the scientific highlights of the DEEP2 survey thus far. This paper is intended as a handbook for users of the DEEP2 Data Release 4, which includes all DEEP2 spectra and redshifts, as well as for the publicly-available DEEP2 DEIMOS data reduction pipelines. [Abridged]Comment: submitted to ApJS; data products available for download at http://deep.berkeley.edu/DR4

Limits to Rest-Frame Ultraviolet Emission From Far-Infrared-Luminous z~6 Quasar Hosts

We report on a Hubble Space Telescope search for rest-frame ultraviolet emission from the host galaxies of five far-infrared-luminous $z\simeq{}6$ quasars and the $z=5.85$ hot-dust free quasar SDSS J0005-0006. We perform 2D surface brightness modeling for each quasar using a Markov-Chain Monte-Carlo estimator, to simultaneously fit and subtract the quasar point source in order to constrain the underlying host galaxy emission. We measure upper limits for the quasar host galaxies of $m_J>22.7$ mag and $m_H>22.4$ mag, corresponding to stellar masses of $M_\ast<2\times10^{11}M_\odot$. These stellar mass limits are consistent with the local $M_{\textrm{BH}}$-$M_\ast$ relation. Our flux limits are consistent with those predicted for the UV stellar populations of $z\simeq6$ host galaxies, but likely in the presence of significant dust ($\langle A_{\mathrm{UV}}\rangle\simeq 2.6$ mag). We also detect a total of up to 9 potential $z\simeq6$ quasar companion galaxies surrounding five of the six quasars, separated from the quasars by 1.4''-3.2'', or 8.4-19.4 kpc, which may be interacting with the quasar hosts. These nearby companion galaxies have UV absolute magnitudes of -22.1 to -19.9 mag, and UV spectral slopes $\beta$ of -2.0 to -0.2, consistent with luminous star-forming galaxies at $z\simeq6$. These results suggest that the quasars are in dense environments typical of luminous $z\simeq6$ galaxies. However, we cannot rule out the possibility that some of these companions are foreground interlopers. Infrared observations with the James Webb Space Telescope will be needed to detect the $z\simeq6$ quasar host galaxies and better constrain their stellar mass and dust content.Comment: 22 pages, 13 figures. Accepted for publication in Ap

Self-Renewal of Acute Lymphocytic Leukemia Cells Is Limited by the Hedgehog Pathway Inhibitors Cyclopamine and IPI-926

Conserved embryonic signaling pathways such as Hedgehog (Hh), Wingless and Notch have been implicated in the pathogenesis of several malignancies. Recent data suggests that Hh signaling plays a role in normal B-cell development, and we hypothesized that Hh signaling may be important in precursor B-cell acute lymphocytic leukemia (B-ALL). We found that the expression of Hh pathway components was common in human B-ALL cell lines and clinical samples. Moreover, pathway activity could be modulated by Hh ligand or several pathway inhibitors including cyclopamine and the novel SMOOTHENED (SMO) inhibitor IPI-926. The inhibition of pathway activity primarily impacted highly clonogenic B-ALL cells expressing aldehyde dehydrogenase (ALDH) by limiting their self-renewal potential both in vitro and in vivo. These data demonstrate that Hh pathway activation is common in B-ALL and represents a novel therapeutic target regulating self-renewal and persistence of the malignant clone

Different paths to the modern state in Europe: the interaction between domestic political economy and interstate competition

Theoretical work on state formation and capacity has focused mostly on early modern Europe and on the experience of western European states during this period. While a number of European states monopolized domestic tax collection and achieved gains in state capacity during the early modern era, for others revenues stagnated or even declined, and these variations motivated alternative hypotheses for determinants of fiscal and state capacity. In this study we test the basic hypotheses in the existing literature making use of the large date set we have compiled for all of the leading states across the continent. We find strong empirical support for two prevailing threads in the literature, arguing respectively that interstate wars and changes in economic structure towards an urbanized economy had positive fiscal impact. Regarding the main point of contention in the theoretical literature, whether it was representative or authoritarian political regimes that facilitated the gains in fiscal capacity, we do not find conclusive evidence that one performed better than the other. Instead, the empirical evidence we have gathered lends supports to the hypothesis that when under pressure of war, the fiscal performance of representative regimes was better in the more urbanized-commercial economies and the fiscal performance of authoritarian regimes was better in rural-agrarian economie

Timing of Favorable Conditions, Competition and Fertility Interact to Govern Recruitment of Invasive Chinese Tallow Tree in Stressful Environments

The rate of new exotic recruitment following removal of adult invaders (reinvasion pressure) influences restoration outcomes and costs but is highly variable and poorly understood. We hypothesize that broad variation in average reinvasion pressure of Triadica sebifera (Chinese tallow tree, a major invader) arises from differences among habitats in spatiotemporal availability of realized recruitment windows. These windows are periods of variable duration long enough to permit establishment given local environmental conditions. We tested this hypothesis via a greenhouse mesocosm experiment that quantified how the duration of favorable moisture conditions prior to flood or drought stress (window duration), competition and nutrient availability influenced Triadica success in high stress environments. Window duration influenced pre-stress seedling abundance and size, growth during stress and final abundance; it interacted with other factors to affect final biomass and germination during stress. Stress type and competition impacted final size and biomass, plus germination, mortality and changes in size during stress. Final abundance also depended on competition and the interaction of window duration, stress type and competition. Fertilization interacted with competition and stress to influence biomass and changes in height, respectively, but did not affect Triadica abundance. Overall, longer window durations promoted Triadica establishment, competition and drought (relative to flood) suppressed establishment, and fertilization had weak effects. Interactions among factors frequently produced different effects in specific contexts. Results support our ‘outgrow the stress’ hypothesis and show that temporal availability of abiotic windows and factors that influence growth rates govern Triadica recruitment in stressful environments. These findings suggest that native seed addition can effectively suppress superior competitors in stressful environments. We also describe environmental scenarios where specific management methods may be more or less effective. Our results enable better niche-based estimates of local reinvasion pressure, which can improve restoration efficacy and efficiency by informing site selection and optimal Management