Miracle-dz/UniFAR-FTUs huggingface dataset:
CANDID: Classifying Assets in Networks by Determining Importance and Dependencies

CANDID: Classifying Assets in Networks by Determining Importance and Dependencies by Scott Michael Marshall Master of Science in Computer Science University of California, Berkeley Professor Sylvia Ratnasamy, Chair Professor Vern Paxson, Co-chair This thesis introduces CANDID, a passive NetFlow-based network traffic analysis platform targeted at inferring relationships and dependencies among services running on hosts in enterprise networks. These networks present challenges of great scale, complexity, and nonstop dynamism, which hinder the ability for network administrators to maintain insight into the complex relationships that exist in these networks. Consequently, administrators do not always know how best to proceed if a network failure occurs. CANDID strives to empower administrators by illuminating these relationships, such that they will be prepared to remedy complex service failures. The solutions presented here take the first steps towards understanding these complex in-network relationships, with a special focus on inferring one class of dependencies and detecting load balanced services. The focal point of this thesis is two radically different, yet complementary, strategies for inferring the presence of load balancing for pairs of systems. A case study using real NetFlow data from the network located at Lawrence Berkeley National Lab is leveraged to validate the strategies presented here. Promising results indicate this problem space is rich with unanswered research questions and is worthy of further exploration.
Crystal structure of tetraethylammonium chloride 3,4,5,6-tetrafluoro-1,2-diiodobenzene

Equimolar quantities of tetraethylammonium chloride (Et4NCl) and 3,4,5,6-tetrafluoro-1,2-diiodobenzene (o-DITFB or o-C6F4I2) have been co-crystallized in a solution of dichloromethane yielding a pure halogen-bonded compound, 3,4,5,6-tetrafluoro-1,2-diiodobenzene–tetraethyl ammonium chloride (2/1), Et4N+·Cl−·2C6F4I2, in the form of translucent needles. [(Et4NCl)(o-C6F4I2)2] packs in the C2/c space group. The asymmetric unit includes one molecule of DITFB, one Et4N+ cation located on a twofold rotation axis, and one chloride anion also located on a twofold rotation symmetry axis. This compound has an interesting halogen-bonding environment surrounding the halide. Here, the chloride anion acts as a tetradentate halogen bond acceptor and forms a distorted square-pyramidal geometry, with I⋯Cl−⋯I angles of 80.891 (6) and 78.811 (11)°, where two crystallographically distinct iodine atoms form halogen bonds with the chloride anion. Resulting from that square-pyramidal geometry are short contacts between some of the adjacent F atoms. Along the b axis, the halogen-bonding interaction results in a polymeric network, producing a sheet in which the two closest chloride ions are 7.8931 (6) Å apart. The Et4N+ cation alternates in columns with the halide ion. The expected short contacts (shorter than the sum of their van der Waals radii) are observed for the halogen bonds [3.2191 (2) and 3.2968 (2) Å], as well as almost linear angles [170.953 (6) and 173.529 (6)°].
Hepatocyte innervation in primates

The efferent innervation and some characteristics of nerve fibers of the liver lobule in the tree shrew, a primate, are described. Nerve endings on hepatocytes were encountered regularly and were determined to be efferent adrenergic nerves. Transmission electron microscopy revealed nerve endings and varicosities in close apposition to the hepatocytes adjacent to the connective tissue of the triads as well as within the liver lobule in the space of Disse. Fluorescence microscopy indicated the existence of adrenergic nerves with a similar distribution. Autoradiography of the avid uptake of exogenous [3H]norepinephrine indicated that all intralobular nerves are potentially norepinephrinergic (adrenergic). Chemical sympathectomy with 6-OH-dopamine resulted in the degeneration of all intralobular liver nerve fibers as revealed by fluorescence microscopy and electron microscopy. Substantial regeneration occurred after 60-90 days but was not completed by that time. Some nerves were also observed in close association with von Kupffer cells and endothelial cells. The functional significance of the efferent liver innervation is discussed.
Controls on the emission of plant volatiles through stomata: A sensitivity analysis

VOC distribution between gas- and liquid-phases (Henry’s law constant, H ,P a m 3 mol � 1 ) and varying internal diffusion conductances in the liquid- and gas-phases. The model was parameterized for three contrasting leaf architectures (conifer, sclerophyll, and mesophytic leaves). The sensitivity analysis indicated that the volatile H value is the key variable affecting the stomatal sensitivity of VOC emissions. Differences in leaf architecture, in particular in leaf liquid volume to area ratio, also modified the emission responses to changes in stomatal aperture, but these structural effects were superimposed by compound gas/liquid phase partitioning. The results of this analysis indicate that major effort in parameterization of dynamic VOC emission models should be directed toward obtaining reliable gas/liquid-phase equilibria for various plant volatiles, and that these models may readily be applied for leaves with contrasting architecture. INDEX TERMS: 0315 Atmospheric Composition and Structure: Biosphere/atmosphere interactions; 0365 Atmospheric Composition and Structure: Troposphere—composition and chemistry; KEYWORDS: emission model, leaf architecture, Henry’s law constant, liquid-phase conductance
Translation of Overlay Models of Student Knowledge for Relative Domains Based on Domain Ontology Mapping

The effectiveness of an adaptive educational system in many respects depends on the precision of modeling assumptions it makes about a student. One of the well-known challenges in student modeling is to adequately assess the initial level of student's knowledge when s/he starts working with a system. Sometimes potentially handful data are available as a part of user model from a system used by the student before. The usage of external user modeling information is troublesome because of differences in system architecture, knowledge representation, modeling constraints, etc. In this paper, we argue that the implementation of underlying knowledge models in a sharable format, as domain ontologies-along with application of automatic ontology mapping techniques for model alignment-can help to overcome the “new-user” problem and will greatly widen opportunities for student model translation. Moreover, it then becomes possible for systems from relevant domains to rely on knowledge transfer and reuse those portions of the student models that are related to overlapping concepts.
Automatic analysis of in-the-wild mobile eye-tracking experiments using object, face and person detection

In this paper we present a novel method for the automatic analysis of mobile eye-tracking data in natural environments. Mobile eye-trackers generate large amounts of data, making manual analysis very time-consuming. Available solutions, such as marker-based analysis minimize the manual labour but require experimental control, making real-life experiments practically unfeasible. We present a novel method for processing this mobile eye-tracking data by applying object, face and person detection algorithms. Furthermore we present a temporal smoothing technique to improve the detection rate and we trained a new detection model for occluded person and face detections. This enables the analysis to be performed on the object level rather than the traditionally used coordinate level. We present speed and accuracy results of our novel detection scheme on challenging, large-scale real-life experiments.
The Fragility Index in a Cohort of Pediatric Randomized Controlled Trials

Data suggest inadequacy of common statistical techniques for reporting outcomes in clinical trials. The Fragility Index can measure how many events the statistical significance hinges on, and may facilitate better interpretation of trial results. This study aimed to assess the Fragility Index in pediatric randomized controlled trials (RCTs) with statistically significant findings published in high-quality medical journals. A Fragility Index was calculated on included trials with dichotomous positive outcomes. Analysis of the relationship between trial characteristics and the Fragility Index was performed. Of the 429 abstracts screened, 17 met the inclusion criteria and underwent analysis. The median Fragility Index was 7 with an interquartile range of 2–11. In 41% of the studies, the number of patients lost to follow-up or withdrawn prior to analysis was equal to or greater than the Fragility Index. There was no correlation between the RCT sample size and the Fragility Index (r = 0.249, p = 0.335) nor the event group size and the Fragility Index (r = 0.250, p = 0.334). There was a strong negative correlation between the original p-value and the Fragility Index (r = −0.700, p = 0.002). The Fragility Index is a calculated metric that may assist in applying clinical relevance to statistically significant outcomes in pediatric randomized controlled trials with dichotomous outcomes.
Anisotropic enhancement of group velocity in a homogenized dielectric composite medium

Under certain circumstances, the group velocity in a homogenized composite medium (HCM) can exceed the group velocity in its component material phases. This phenomenon is explored for a uniaxial dielectric HCM comprising isotropic component material phases distributed as oriented spheroidal particles. The theoretical approach is based upon the Bruggeman homogenization formalism. Enhancement in group velocity in the HCM with respect to the component material phases turns out to be sensitively dependent upon the shape of the component spheroids and their alignment relative to the direction of propagation.
Derivation of point of departure (PoD) estimates in genetic toxicology studies and their potential applications in risk assessment

Genetic toxicology data have traditionally been employed for qualitative, rather than quantitative evaluations of hazard. As a continuation of our earlier report that analyzed ethyl methanesulfonate (EMS) and methyl methanesulfonate (MMS) dose–response data (Gollapudi et al., 2013), here we present analyses of 1‐ethyl‐1‐nitrosourea (ENU) and 1‐methyl‐1‐nitrosourea (MNU) dose–response data and additional approaches for the determination of genetic toxicity point‐of‐departure (PoD) metrics. We previously described methods to determine the no‐observed‐genotoxic‐effect‐level (NOGEL), the breakpoint‐dose (BPD; previously named Td), and the benchmark dose (BMD10) for genetic toxicity endpoints. In this study we employed those methods, along with a new approach, to determine the non‐linear slope‐transition‐dose (STD), and alternative methods to determine the BPD and BMD, for the analyses of nine ENU and 22 MNU datasets across a range of in vitro and in vivo endpoints. The NOGEL, BMDL10 and BMDL1SD PoD metrics could be readily calculated for most gene mutation and chromosomal damage studies; however, BPDs and STDs could not always be derived due to data limitations and constraints of the underlying statistical methods. The BMDL10 values were often lower than the other PoDs, and the distribution of BMDL10 values produced the lowest median PoD. Our observations indicate that, among the methods investigated in this study, the BMD approach is the preferred PoD for quantitatively describing genetic toxicology data. Once genetic toxicology PoDs are calculated via this approach, they can be used to derive reference doses and margin of exposure values that may be useful for evaluating human risk and regulatory decision making. Environ. Mol. Mutagen. 55:609–623, 2014. © 2014 The Authors. Environmental and Molecular Mutagenesis Published by Wiley Periodicals, Inc.
Predicting Infiltration and Ground-Water Mounds for Artificial Recharge

Planning systems for the artificial recharge of ground water via surface infiltration requires site investigations to predict infiltration rates and land requirements. Also, the ability of the vadose zone to transmit water to the underlying aquifer must be assessed, and aquifer conditions must be evaluated to predict the rise of ground-water mounds and to determine where ground water must eventually be pumped up again to prevent ground-water mounds below recharge areas from rising too high. A simple technique is presented to convert data from short-duration single-cylinder infiltrometer tests to final infiltration rates for large areas. Also, simple equations are developed to estimate heights of perched ground-water mounds above restricting layers in the vadose zone, to estimate how far from the recharge area ground water must be pumped, and to what depth to create a steady-state system with constant height of the ground-water mound in the recharge area. The procedures are useful for feasibility studies and the preliminary design of recharge projects, including long-term underground storage or water banking.
Glycine Betaine Uptake by the ProXVWZ ABC Transporter Contributes to the Ability of Mycobacterium tuberculosis To Initiate Growth in Human Macrophages

ABSTRACT Mycobacterium tuberculosis maintains a large genetic capacity necessary for growth in different environments during infection and survival upon aerosol transmission to new hosts. Screening for bacterial RNAs produced in response to host interactions produced candidate lists where we noted proXVWZ, annotated as encoding a putative glycine betaine or proline transporter. As high surface-to-volume ratios make bacterial cells particularly vulnerable to changes in water availability, we investigated the contributions of this transporter to the ability of M. tuberculosis to colonize macrophages. An H37Rv proXVWZ mutant was impaired for initial survival and intracellular growth and exhibited reduced growth at elevated medium osmolarity. This defect could be complemented by restoring proXVWZ and was attributable to a failure to accumulate the compatible solute glycine betaine. We then demonstrated that ProXVWZ allows M. tuberculosis to obtain betaine from host macrophages and thereby contributes to early steps in colonizing this niche.
Evaluation of riparian forests established by the Conservation Reserve Enhancement Program (CREP) in Virginia

Forested riparian buffer strips are recommended as an agricultural best management practice for protection of water quality and for wildlife habitat. Since the 1990s, federal and state conservation agencies in Virginia have been involved in establishment of riparian buffers under the auspices of programs, such as the Conservation Reserve Enhancement Program (CREP). Riparian buffers established by the CREP program are considered to be beneficial towards the protection of water quality. However, the benefit is based upon assumption that planted trees and shrubs survive and grow. Little evaluation has been done within the state to document the success of the establishment efforts. We evaluated 63 riparian planting sites located in the Coastal Plain, Piedmont, and Ridge and Valley physiographic provinces of Virginia. Overall, the riparian forests in the Coastal Plain and Piedmont were fully stocked due to a combination of planted and natural regeneration. Riparian forests in the Ridge and Valley region were inadequately stocked, and the region has problems with invasive, exotic species. Major recommendations for improving the success of future riparian restoration and establishment efforts are to (1) include the potential for natural regeneration when planning CREP plantings, (2) stop mechanized operations in the riparian buffers that reduce planted and natural regeneration (e.g., mowing and disking), (3) reduce herbivory (particularly cattle) within the riparian buffer, and (4) control invasive exotic species as necessary.
Conductance fluctuations in gold point contacts: an atomistic picture

This paper concerns an experimental and theoretical study of the transition between two consecutive conductance plateaus as obtained in breaking gold contact experiments. The experimental measurements performed at 100 K with a scanning tunneling microscope and variable elongation speeds show that the transitions between consecutive plateaus can appear in the conductance traces as an abrupt conductance step, a smooth quasicontinuous change or as large amplitude conductance fluctuations. The theoretical calculations based on a non-orthogonal tight-binding Hamiltonian have shown that for a given deformation there are several structures having close and competing energies. We discuss the relation between the temperature, sampling frequency, stretching speed and energy barriers which can explain the conditions for the observation of the three kinds of conductance traces.
A Finite-Volume Method for Nonlinear Nonlocal Equations with a Gradient Flow Structure

We propose a positivity preserving entropy decreasingfinitevolumescheme for nonlinear nonlocal equations with a gradient flow structure. These properties al- low for accurate computations of stationary states and long-time asymptotics demon- strated by suitably chosen test cases in which these featuresoftheschemearee ssential. The proposed scheme is able to cope with non-smooth stationary states, different time scales including metastability, as well as concentrations and self-similar behavior in- duced by singular nonlocal kernels. We use the scheme to explore properties of these equations beyond their present theoretical knowledge. AMS subject classifications :6 5M08, 35R09, 34B10
Implicit and Explicit Representations of Hand Position in Tool Use

Understanding the interactions of visual and proprioceptive information in tool use is important as it is the basis for learning of the tool's kinematic transformation and thus skilled performance. This study investigated how the CNS combines seen cursor positions and felt hand positions under a visuo-motor rotation paradigm. Young and older adult participants performed aiming movements on a digitizer while looking at rotated visual feedback on a monitor. After each movement, they judged either the proprioceptively sensed hand direction or the visually sensed cursor direction. We identified asymmetric mutual biases with a strong visual dominance. Furthermore, we found a number of differences between explicit and implicit judgments of hand directions. The explicit judgments had considerably larger variability than the implicit judgments. The bias toward the cursor direction for the explicit judgments was about twice as strong as for the implicit judgments. The individual biases of explicit and implicit judgments were uncorrelated. Biases of these judgments exhibited opposite sequential effects. Moreover, age-related changes were also different between these judgments. The judgment variability was decreased and the bias toward the cursor direction was increased with increasing age only for the explicit judgments. These results indicate distinct explicit and implicit neural representations of hand direction, similar to the notion of distinct visual systems.
Compressive photography based on lens array with coded mask

Plenoptic camera records the 4D light field data by storing the spatial information and angular information. Meanwhile, it introduces the trade-off between spatial resolution and angular resolution. We proposed a new camera design which has been modulated in Fourier domain. High resolution 4D light field could be reconstructed from the coded image by sparse reconstruction. A simulation is carried out to evaluate the performance of the camera design. The reconstructed light field has a better performance than the conventional plenoptic camera.
Three-Dimensional Dynamics of the Subsurface Countercurrents and Equatorial Thermostad. Part II: Influence of the Large-Scale Ventilation and of Equatorial Winds

Sensitivity tests are performed to assess the respective influences of the large-scale ventilation and of the near-equatorial winds on the dynamics of the the subsurface countercurrents (SCCs) and thermostad. They show that the intensity of the inertial jets is a function of the potential vorticity (PV) values at subduction and that stronger jets are favored by low PV injection, forced in the authors’ framework either by a deep mixed layer at subduction and/or by an injection of PV at lower latitudes. Such circumstances lead to a strong meridional shoaling of the thermocline near the equator. The resulting inertial jets occur at about 3 8N in the western part of the basin and are the poleward limit of a near-0 PV region and of an equatorial thermostad. A necessary condition for the existence of inertial jets is that the equatorial wind fetch is large enough, otherwise only weak time-mean eastward currents are produced by a nonlinear rectification of instability waves farther away from the equator. The presence of a North Equatorial Countercurrent does not constitute a barrier for equatorward motions within the lower thermocline, and inertial jets are still controlled by the meridional slope of the SSCs’ layer setup through the establishment of tropical PV pools predicted by ventilation theory.
The Sima de los Huesos Hominids Date to Beyond U/Th Equilibrium (>350 kyr) and Perhaps to 400–500 kyr: New Radiometric Dates

The Sima de los Huesos site of the Atapuerca complex near Burgos, Spain contains the skeletal remains of at least 28 individuals in a mud breccia underlying an accumulation of the Middle Pleistocene cave bear (U. deningeri). Earlier dating estimates of 200 to 320 kyr were based on U-series and ESR methods applied to bones, made inaccurate by unquantifiable uranium cycling. We report here on a new discovery within the Sima de los Huesos of human bones stratigraphically underlying an in situ speleothem. U-series analyses of the speleothem shows the lower part to be at isotopic U/Th equilibrium, translating to a firm lower limit of 350 kyr for the SH hominids. Finite dates on the upper part suggest a speleothem growth rate of c. 1 cm/32 kyr. This rate, along with paleontological constraints, place the likely age of the hominids in the interval of 400 to 600 kyr.
The crystal structure of the aldose reductase.NADPH binary complex.

Aldose reductase is an NADPH-dependent oxidoreductase that catalyzes the reduction of a broad range of aldehydes, including glucose. Since aldose reductase has been strongly implicated in the development of the chronic complications of diabetes mellitus, much effort has been devoted to understanding the structure and mechanism of this enzyme, and many aldose reductase inhibitors have been developed as potential drugs for the treatment of these complications. We describe here the 2.75 A crystal structure of recombinant human aldose reductase (Cys-298 to Ser mutant) complexed with NADPH. This mutant displays unusual kinetic behavior characterized by high Km/high Vmax substrate kinetics and reduced sensitivity to certain aldose reductase inhibitors. The crystal structure revealed that the enzyme is a beta/alpha-barrel with the coenzyme-binding domain located at the carboxyl-terminal end of the parallel strands of the barrel. The enzyme undergoes a large conformational change upon binding NADPH which involves the reorientation of loop 7 to a position which appears to lock the coenzyme into place. NADPH is bound to aldose reductase in an unusual manner, more similar to FAD- rather than NAD(P)-dependent oxidoreductases. No disulfide bridges were observed in the crystal structure.