Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards a Storage Stack for the Data Center

Towards a Storage Stack for the Data Center Ioan Alexandru Stefanovici Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2016 The storage stack in a data center consists of all the hardware and software layers involved in processing and persisting data to durable storage. The shift of the world’s computation to data centers is placing significant strain on the storage stack, leading to a stack that is unreliable and non-performant. This is caused in large part by a lack of understanding of the failure and performance characteristics of critical hardware components, and a lack of programmability and control over the numerous software layers in the stack. The broad goal of this thesis is to improve the storage stack by leveraging insights gained from empirical studies of real-world production systems, and by proposing a new paradigm for implementing and enhancing distributed storage functionality that enables the vertical specialization of the storage stack to a wide variety of customer and data center provider needs. The first part of this thesis studies the reliability of main memory in large-scale production systems. Our findings show that conventional wisdom about memory reliability is incorrect, and that physical hardware is in fact the main culprit for most errors in main memory in the field. As a result, existing memory error protection mechanisms are inadequate. We then use the insights gained from the empirical study to propose and evaluate a suitable error protection mechanism for future data centers. The second part of this thesis offers an empirical study of the effects of temperature on the performance and power consumption of the storage stack. Since cooling constitutes a large fraction of the total cost of ownership in a data center, increasing temperatures in a data center without sacrificing performance can have a huge impact on the power consumption and carbon footprint of data centers. The final part of this thesis proposes a new paradigm for implementing and enhancing distributed storage functionality by creating programmable APIs that allow dynamic configuration and control of the software stages along the storage stack, and designing and implementing an IO routing primitive for
Estimating probabilistic dark diversity based on the hypergeometric distribution

The biodiversity of a site includes the absent species from the region that are theoretically able to live in the site’s particular ecological conditions. These species constitute the dark diversity of the site. Unlike present species, dark diversity is unobservable and can only be estimated. Most existing methods to designate dark diversity act in a binary fashion. However, dark diversity is more suitably defined as a fuzzy set—in which the degree of certainty about species membership is expressed as a probability. We present a new method to estimate probabilistic dark diversity based on the hypergeometric distribution. The method relies on co-occurrences to infer the strength of the association between pairs of species and assign probabilistic adscription to dark diversity to absent species. We compare it with two established methods to estimate dark diversity (Beals index and favorability correction). To test the methods, we created simulations based on individual agents in which the suitability of each species in each site is known. We compared the ability of the methods to accurately predict suitability and the size of dark diversity, and compared their sensitivity to data availability. Further, we assessed the methods in two real datasets with nested sampling designs. Our simulations revealed that predictions of the Beals method were extremely sensitive to species frequency, and predicted suitability poorly. The Favorability transformation corrected this relationship, but did still predicted extremely low probabilities for species with very little information. The Hypergeometric method outperformed the Beals and Favorability methods in all considered aspects in the simulations and displayed better characteristics in the real datasets. Probabilistic consideratiosn of biodiversity will help to acknowledge the uncertainty associated with ecological information. Although the Beals method has been described as the best estimator of dark diversity, it should be preferred only when the goal is to predict future apperances of species. However, studies on dark diversity should focus on the ecological affinities of species. The Hypergeometric method is the most promising method to estimate probabilistic dark diversity and species pool composition based on co-occurrences.
Nanoscale dynamics of cholesterol in the cell membrane

Cholesterol constitutes ∼30–40% of the mammalian plasma membrane, a larger fraction than of any other single component. It is a major player in numerous signaling processes as well as in shaping molecular membrane architecture. However, our knowledge of the dynamics of cholesterol in the plasma membrane is limited, restricting our understanding of the mechanisms regulating its involvement in cell signaling. Here, we applied advanced fluorescence imaging and spectroscopy approaches on in vitro (model membranes) and in vivo (live cells and embryos) membranes as well as in silico analysis to systematically study the nanoscale dynamics of cholesterol in biological membranes. Our results indicate that cholesterol diffuses faster than phospholipids in live membranes, but not in model membranes. Interestingly, a detailed statistical diffusion analysis suggested two-component diffusion for cholesterol in the plasma membrane of live cells. One of these components was similar to a freely diffusing phospholipid analogue, whereas the other one was significantly faster. When a cholesterol analogue was localized to the outer leaflet only, the fast diffusion of cholesterol disappeared, and it diffused similarly to phospholipids. Overall, our results suggest that cholesterol diffusion in the cell membrane is heterogeneous and that this diffusional heterogeneity is due to cholesterol's nanoscale interactions and localization in the membrane.
Parents as Learning Partners in the development of t echnological Fluency

This paper presents research on parent support of the development of new media skills and technological fluency. Parents’ roles in their children’s learning were identified based on in terviews with eight middle school students and their parents. All eight students were highly experienced with technology activities. Seven distinct parental roles that supported learning were identified and defined: Teacher, Collaborator, Learning Broker, Resource Provider, Nontechnical Consultant, Employer, and Learner. The parents in this sample varied in their level of technological knowledge, though in every family at least one parent worked in the computer industry as an engineer or designer. The paper presents the approach used to identify these roles, the coding system used, and examples of each role across the cases. The diversity and density of roles played by parents for individual students are also quantified. Findings indicate that for these eight learners parents play signifi cant roles in supporting creative technologically mediated activities. The findings highlight the importance of understanding family-based learning relationships when considering pathways to early expertise with new media.
Eltrombopag enables initiation and completion of pegylated interferon/ribavirin therapy in Japanese HCV-infected patients with chronic liver disease and thrombocytopenia

To investigate the efficacy of eltrombopag for the treatment of thrombocytopenia in patients with chronic hepatitis C, a phase II, single-arm, open-label study with a 9-week pre-antiviral phase was conducted, followed by a 48-week antiviral phase and a 24-week follow-up phase. The proportion of patients who achieved a platelet count threshold, the proportion of patients who maintained a platelet count >50,000/µl, sustained virological response (SVR) rates and safety parameters were evaluated. Of the 45 enrolled patients (median age, 59 years; median platelet count, 63,000/µl; 98% with Child-Pugh class A), 43 (96%) achieved the platelet count threshold during the pre-antiviral phase. A total of 13 patients (29%) experienced ≥1 adverse event (AE), of which headache and vomiting were the most common, and 41 patients (mostly receiving eltrombopag 12.5 mg or 25 mg) entered the antiviral phase, of which 36 (88%) maintained the platelet count threshold; no patient platelet count decreased below 25,000/µl. Nine patients (22%) achieved an SVR at the 24-week follow-up. Grade ≥3 AEs occurred in 25 patients (61%). A total of 8 serious AEs occurred in five patients (12%). No mortality, thromboembolic events (TEEs), or cataract progression were reported. Eltrombopag increased the platelet count in chronic hepatitis C virus-infected patients with cirrhosis and thrombocytopenia and enabled them to initiate and complete interferon-based antiviral therapy (NCT01636778; first submitted: July 05, 2012).
Insights about the formation of a complex impact structure formed in basalt from numerical modeling: The Vista Alegre structure, southern Brazil

We present the outcomes of simulations of the formation of the Vista Alegre impact structure, Paraná Basin, Brazil. The target comprised a thick sequence of volcanic rocks of predominantly basaltic composition of the Serra Geral Formation that had been deposited on top of sedimentary rocks (sandstones) of the Pirambóia/Botucatu formations. The cratering process was modeled using the iSALE shock physics code. Our best‐fit model suggests that (1) the crater was originally ~10 km in size; (2) it was formed in ~115 s by a stony projectile of 1000 m in diameter, for an assumed impact velocity of 12 km s−1; (3) target rocks underwent a peak pressure of ~20 GPa, in agreement with previous petrographic investigations of shock deformation. Furthermore, the model points out that the sedimentary strata below the layer of volcanic rocks were raised by ~650 meters at the central part of the crater, which resulted in the current partial exposure of the sandstones at the surface. The outcomes of our modeling suggest that parameters like cohesion and strength of the target rocks, after shock compression, determined the final morphology of the crater, especially the absence of a topographically prominent central peak. Finally, the results of the numerical modeling are roughly in agreement with gravity data over the structure, in particular with respect to the presence of the uplifted sedimentary strata, which are responsible for a low gravity signature at the center of the structure.
Single-Event Upsets in SRAMs With Scaling Technology Nodes Induced by Terrestrial, Nuclear Reactor, and Monoenergetic Neutrons

Terrestrial, nuclear reactor, and monoenergetic neutron-induced single-event upset (SEU) in SRAMs with different technology nodes more than <inline-formula> <tex-math notation="LaTeX">$1.50~\mu \text{m}$ </tex-math></inline-formula>–40 nm were explored experimentally. Monte Carlo simulation was accomplished in Geant4 software to calculate neutron-induced SEU cross section and energy deposition of neutron-induced secondary particles in SRAMs. The results indicate that the neutron-induced SEU cross section in SRAMs changes in a nonmonotonic way with the scaling down of technology nodes. For 0.5–0.13-<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> SRAMs from HITACHI series, SEU cross section increases with the decrease of technology node, both in terrestrial and nuclear reactor neutrons. For <inline-formula> <tex-math notation="LaTeX">$0.13~\mu \text{m}$ </tex-math></inline-formula>–40 nm SRAMs from ISIS series, SEU cross section decreases with the decrease of technology node, and this trend keeps the same in 2.5 MeV, 14 MeV, and reactor neutron irradiation, respectively. The threshold energy of neutron-induced SEU decreases sharply with the decreasing technology nodes, and 16 O, 28 Si, <inline-formula> <tex-math notation="LaTeX">$\alpha $ </tex-math></inline-formula> particles, and 24 Mg are the main secondary particles inducing SEU.
Demographics and the Natural Real Interest Rate: Historical and Projected Paths for the Euro Area

This paper employs an aggregate representation of an overlapping generation (OLG) model quantifying a decrease of the natural real interest rate in the range of -1.7 and -0.4 percentage points in the euro area between 1990 and 2030 due to demographics alone. Two channels contribute to this downward impact: the increasing scarcity of effective labor input and the increasing willingness to save by individuals due to longer life expectancy. The decrease of the aggregate saving rate as individuals retire has an upward impact which is never strong enough. Mitigating factors are: higher substitutability between labor and capital, higher intertemporal elasticity of substitution in consumption, reforms aiming at increasing the relative productivity of older cohorts, the participation rate and the retirement age. The simulated path of the natural real interest rate is consistent with recent econometric estimates: an upward trend in the 70s and 80s and a prolonged decline afterward. JEL Classification: E17, E21, E43, E52, J11
Novelty and the bounds of unknowledge in economics

Economic development and growth are driven by the emergence of new technologies, new products and services, new institutions, new policies, and so on. Important though it is, the emergence of novelty is not well understood. Epistemological and methodological problems make it a difficult research topic. They imply a ‘bound of unknowledge’ (Shackle) for economic theorizing wherever novelty occurs in economic life. To make progress, this paper takes stock of the problems. The methodological consequences for causal explanations and the modelling of economics dynamics are discussed, and some possibilities for positively theorizing about novelty are outlined.
Former food products have no detrimental effects on diet digestibility, growth performance and selected plasma variables in post-weaning piglets

Abstract The effect of a diet based on former food products (FFP) as alternative feed ingredients on in vitro and in vivo digestibility of dry matter (DM), pig growth performance, and selected plasma biochemical variables were evaluated. After an adaptation period (7 d), 12 post-weaning piglets (28 days-old) were housed for 16 d in individual pens and assigned to two experimental groups: Control (n = 6), received a standard diet and FFP (n = 6), received a diet in which conventional cereals (wheat, barley, and corn), plasma powder and whey powder, were partially replaced by 30% FFP. During the experiment, stool and blood samples were also collected for DM in vivo digestibility and for plasma biochemical measurements, respectively. The results revealed that both in vitro and in vivo digestibility values were higher (p<.05) for FFP diets compared to the control diets. At the end of the experiment, no differences in BW were observed between groups (p=.61). ADG and ADFI were not affected by dietary treatment. Conversely, piglets on the FFP diet showed a lower FCR (p<.01). Finally, dietary treatment also affected plasma glucose and urea, which in pigs fed FFPs increased and decreased, respectively. Taken together, these results suggest that the use of FFPs up to a level of 30% in post-weaning diets has no detrimental effects on pig growth performance, although more studies are needed to confirm these results. Highlights CFormer foodstuffs products (FFPs) are valuable alternative feed ingredients. FFPs can partially replace cereal grains in post-weaning piglet’s diets without affecting growth performance.
Rapid WUI growth in a natural amenity-rich region in central-western Patagonia, Argentina

The wildland–urban interface (WUI) is a focal area for human environmental conflicts including wildfires. The WUI grows because new houses are built, and in developed countries, housing growth can be very rapid in areas with natural amenities. However, it is not clear if natural amenity-driven WUI growth is limited to developed countries, or also prevalent in developing countries. Amenity-driven WUI growth may be particularly rapid there, owing to a rapidly growing middle class. Our objectives were to (i) map the current WUI; (ii) quantify recent WUI growth; and (iii) analyse relationships between the WUI and both fire ignition points and wildfire perimeters in the region of El Bolson, in Central Andean Patagonia, Argentina. We mapped the current WUI based on housing information derived from census data, topographic maps, high-resolution imagery and land-cover data. We found that the WUI contained 96.6% of all buildings in 2016 even though the WUI covered only 6.4% of the study area. Between 1981 and 2016, the WUI increased in area by 76%, and the number of houses by 74%. Furthermore, 77% of the recent fires in the region occurred in the WUI, highlighting the need to balance development with wildfire risk and other human–environmental problems.
Highly Siderophile Elements in Earth, Mars, the Moon, and Asteroids.

The highly siderophile elements (HSE: Os, Ir, Ru, Rh, Pt, Pd, Re, Au) are key tracers of planetary accretion and differentiation processes due to their affinity for metal relative to silicate. Under low-pressure conditions the HSE are defined by having metal–silicate partition coefficients in excess of 104 (e.g., Kimura et al. 1974; Jones and Drake 1986; O’Neill et al. 1995; Borisov and Palme 1997; Mann et al. 2012). The HSE are geochemically distinct in that, with the exception of Au, they have elevated melting points relative to iron (1665 K), low vapour pressures, and are resistant to corrosion or oxidation. Under solar nebular conditions, Re, Os, Ir, Ru, Rh, and Pt, along with the moderately siderophile elements (MSE) Mo and W, condense as refractory-metal alloys. Palladium and Au are not as refractory and condense in solid solution with FeNi metal (Palme 2008). Assuming abundances of the HSE in materials that made up the bulk Earth were broadly similar to modern chondrite meteorites, mass balance calculations suggest that >98% of these elements reside in the metallic core (O’Neill and Palme 1998). In practical terms, the resultant low HSE abundance inventories in differentiated silicate crusts and mantles enables the use of these elements in order to effectively track metallic core formation and the subsequent additions of HSE-rich impactors to planets and asteroids (Fig. 1). In detail, the absolute and relative abundances of the HSE in planetary materials are also affected by mantle and crustal processes including melting, metasomatism, fractional crystallization, and crust-mantle remixing, as well as later impact processing, volatility of Re under oxidizing conditions, and low-temperature secondary alteration (cf., Day 2013; Gannoun et al. 2016, this volume). In the absence of metal, the HSE are chalcophile, so these elements are also affected by processes …
Deep Water Cycling and Sea Level Change Since the Breakup of Pangea

First‐order variations in sea level exhibit amplitudes of ∼200 m over periods that coincide with those of supercontinental cycles (∼300–500 Myr). Proposed mechanisms for this sea level change include processes that change the container volume of the ocean basins and the relative elevation of continents. Here we investigate how unbalanced rates of water exchange between Earth's surface and mantle interior, resulting from fluctuations in tectonic rates, can cause sea level changes. Previous modeling studies of subduction water fluxes suggest that the amount of water that reaches sub‐arc depths is well correlated with the velocity and age of the subducting plate. We use these models to calibrate a parameterization of the deep subduction water flux, which we together with a parameterization of mid‐ocean ridge outgassing, then apply to reconstructions of Earth's tectonic history. This allows us to estimate the global water fluxes between the oceans and mantle for the past 230 Myr and compute the associated sea level change. Our model suggests that a sea level drop of up to 130 m is possible over this period and that it was partly caused by the ∼150Ma rift pulse that opened the Atlantic and forced rapid subduction of old oceanic lithosphere. This indicates that deep water cycling may be one of the more important sea level changing mechanisms on supercontinental time scales and provides a more complete picture of the dynamic interplay between tectonics and sea level change.
Targeting the Nucleosome Core Particle with Polyamide Dimers

The Nucleosome Core Particle (NCP) is the minimal unit in eukaryotic chromatin and a unique target for DNA-binding polyamides. The ability to modulate the stability of nucleosomes would be a useful tool for molecular biology and gene regulation. A series of polyamide clamps designed to differentiate between the NCP and B-form DNA were synthesized and analyzed using DNase I footprinting. In addition, a new polyamide dimer designed to bind to and stabilize the NCP was synthesized. Finally, the NCP was used to perform the DNA-templated ligation of alkyneand azide-functionalized polyamides.
Implant Insertion Methods and Periimplant Tissues – Experimental Study

The replacement of missing teeth with dental implants has become predictable treatment modality over the past several decades. The function of dental implants depends on the process of osseointegration, defined by Branemark (Branemark, 1985, as cited in Abrahamsson & Cardaropoli, 2006) as „direct structural and functional connection between living ordered bone and the surface of load carrying implant“. The process through which osseointegration is achieved depends on several factors, such as biocompatibility of the metal used as well as the design and surface characteristics of the implant, the condition of the implant socket, the surgical technique used and the loading conditions applied (Abrahamsson & Cardaropoli, 2006). Endosteal implants are available in various designs, forms and materials. The earliest implant designs were one-component devices, i.e. implant body and implant abutment were connected in a single unit. Those implants could only be inserted in one-stage surgical method and are collectively referred to as “one-stage” or non-submerged implant systems. When inserted, implants penetrate through the oral mucosa into the oral cavity thus risking the possible contamination and/or early loading that could result in implant failure. Within the past five decades numerous types of implant designs have evolved. Almost all of them have a common characteristic: they consist of two parts – the implant body and the implant abutment or transmucosal part. The first part (implant body) is placed into the bone socket and covered with mucoperiosteal flap. The second part (implant abutment) is connected to the implant after a period of healing in the secondary surgical procedure. These designs are recommended for so called “two-stage” or submerge surgical approach, and the components of the soft tissue cover, epithelial and subepithelial tissue, act as a barrier between the internal (bone tissue) and external (oral cavity) environment. The studies on both surgical methods have been well documented (Adell et al., 1990, as cited in Heydenrijk et al., 2002; Lindquist et al., 1996; Ericsson et al., 1996; Buser et al., 1996; Levy et al., 1996; Bragger et al., 1998; Abrahamsson et al., 1999; Hermann et al., 2001; Lindquist et al., Heydenrijk et al., 2002). On the basis of early research in dogs, Branemark and his coworkers introduced submerged implant placement believing it was one of the key prerequisites for osseointegration (Weber & Cochran, 1998). Namely, implants were placed under cover of the oral mucosa for a healing period of 3-6 months and after that period a second surgical procedure was