Extra Log Research Articles

Adaptive Bayesian density estimation in sup-norm

We investigate the problem of deriving adaptive posterior rates of contraction on L∞ balls in density estimation. Although it is known that log-density priors can achieve optimal rates when the true density is sufficiently smooth, adaptive rates were still to be proven. Here we establish that the so-called spike-and-slab prior can achieve adaptive and optimal posterior contraction rates. Along the way, we prove a generic L∞ contraction result for log-density priors with independent wavelet coefficients. Interestingly, our approach is different from previous works on L∞ contraction and is reminiscent of the classical test-based approach used in Bayesian nonparametrics. Moreover, we require no lower bound on the smoothness of the true density, albeit the rates are deteriorated by an extra log(n) factor in the case of low smoothness.

A note on distance-preserving graph sparsification

We consider problems of the following type: given a graph G, how many edges are needed in the worst case for a sparse subgraph H that approximately preserves distances between a given set of node pairs P? Examples include pairwise spanners, distance preservers, reachability preservers, etc. There has been a trend in the area of simple constructions based on the hitting set technique, followed by somewhat more complicated constructions that improve over the bounds obtained from hitting sets by roughly a log factor. In this note, we point out that the simpler constructions based on hitting sets don't actually need an extra log factor in the first place. This simplifies and unifies a few proofs in the area, and it improves the size of the +4 pairwise spanner from O˜(np2/7) (Kavitha (2017) [13]) to O(np2/7).

CloudRaid: Detecting Distributed Concurrency Bugs via Log Mining and Enhancement

Cloud systems suffer from distributed concurrency bugs, which often lead to data loss and service outage. This paper presents <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CloudRaid</small> , a new automatical tool for finding distributed concurrency bugs efficiently and effectively. Distributed concurrency bugs are notoriously difficult to find as they are triggered by untimely interaction among nodes, i.e., unexpected message orderings. To detect concurrency bugs in cloud systems efficiently and effectively, <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CloudRaid</small> analyzes and tests automatically only the message orderings that are likely to expose errors. Specifically, <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CloudRaid</small> mines the logs from previous executions to uncover the message orderings that are feasible but inadequately tested. In addition, we also propose a log enhancing technique to introduce new logs automatically in the system being tested. These extra logs added improve further the effectiveness of <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CloudRaid</small> without introducing any noticeable performance overhead. Our log-based approach makes it well-suited for live systems. We have applied <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CloudRaid</small> to analyze six representative distributed systems: Hadoop2/Yarn, HBase, HDFS, Cassandra, Zookeeper, and Flink. <sc xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CloudRaid</small> has succeeded in testing 60 different versions of these six systems (10 versions per system) in 35 hours, uncovering 31 concurrency bugs, including nine new bugs that have never been reported before. For these nine new bugs detected, which have all been confirmed by their original developers, three are critical and have already been fixed.

Comparison of two functionalized fullerenes for antimicrobial photodynamic inactivation: Potentiation by potassium iodide and photochemical mechanisms

A new fullerene (BB4-PPBA) functionalized with a tertiary amine and carboxylic acid was prepared and compared with BB4 (cationic quaternary group) for antimicrobial photodynamic inactivation (aPDI). BB4 was highly active against Gram-positive methicillin resistant Staphylococcus aureus (MRSA) and BB4-PPBA was moderately active when activated by blue light. Neither compound showed much activity against Gram-negative Escherichia coli or fungus Candida albicans. Therefore, we examined potentiation by addition of potassium iodide. Both compounds were highly potentiated by KI (1–6 extra logs of killing). BB4-PPBA was potentiated more than BB4 against MRSA and E. coli, while for C. albicans the reverse was the case. Addition of azide potentiated aPDI mediated by BB4 against MRSA, but abolished the potentiation caused by KI with both compounds. The killing ability after light decayed after 24 h in the case of BB4, implying a contribution from hypoiodite as well as free iodine. Tyrosine was readily iodinated with BB4-PPBA plus KI, but less so with BB4. We conclude that the photochemical mechanisms of these two fullerenes are different. BB4-PPBA is more Type 2 (singlet oxygen) while BB4 is more Type 1 (electron transfer). There is also a possibility of direct bacterial killing by electron transfer, but this will require more study to prove.

Potentiation by potassium iodide reveals that the anionic porphyrin TPPS4 is a surprisingly effective photosensitizer for antimicrobial photodynamic inactivation

We recently reported that addition of the non-toxic salt, potassium iodide can potentiate antimicrobial photodynamic inactivation of a broad-spectrum of microorganisms, producing many extra logs of killing. If the photosensitizer (PS) can bind to the microbial cells, then delivering light in the presence of KI produces short-lived reactive iodine species, while if the cells are added after light the killing is caused by molecular iodine produced as a result of singlet oxygen-mediated oxidation of iodide. In an attempt to show the importance of PS-bacterial binding, we compared two charged porphyrins, TPPS4 (thought to be anionic and not able to bind to Gram-negative bacteria) and TMPyP4 (considered cationic and well able to bind to bacteria). As expected TPPS4+light did not kill Gram-negative Escherichia coli, but surprisingly when 100mM KI was added, it was highly effective (eradication at 200nM+10J/cm2 of 415nm light). TPPS4 was more effective than TMPyP4 in eradicating the Gram-positive bacteria, methicillin-resistant Staphylococcus aureus and the fungal yeast Candida albicans (regardless of KI). TPPS4 was also highly active against E. coli after a centrifugation step when KI was added, suggesting that the supposedly anionic porphyrin bound to bacteria and Candida. This was confirmed by uptake experiments. We compared the phthalocyanine tetrasulfonate derivative (ClAlPCS4), which did not bind to bacteria or allow KI-mediated killing of E. coli after a spin, suggesting it was truly anionic. We conclude that TPPS4 behaves as if it has some cationic character in the presence of bacteria, which may be related to its delivery from suppliers in the form of a dihydrochloride salt.

Laboratory testing of enhanced biocide mitigation of an oilfield biofilm and its microbiologically influenced corrosion of carbon steel in the presence of oilfield chemicals

Microbiologically influenced corrosion (MIC) is prevalent in the oil and gas industry. Problematic biofilms cause MIC and reservoir souring. A high biocide concentration is usually required to mitigate biofilms compared with planktonic cells. This causes economic and environmental concerns. A biocide enhancer can make a biocide more effective using the same or lower biocide dosage. In this work, an equimolar mixture of 100 ppm (w/w) of four D-amino acids (D-methionine, D-tyrosine, D-tryptophan, and D-leucine) labeled as D-mix enhanced 100 ppm tetrakis (hydroxymethyl) phosphonium sulfate (THPS) against a field biofilm consortium on C1018 carbon steel coupons. In order to test chemical compatibilities, D-amino acids were added together with THPS and enhanced oil recovery chemicals (a polymer, a surfactant, a corrosion inhibitor, and a scale inhibitor) to treat the mature biofilm consortium. After a 7-day biofilm removal test in 125 ml anaerobic vials, the cocktail of 100 ppm THPS +100 ppm D-mix achieved extra logs of reduction in sessile cell counts compared with the 100 ppm THPS alone treatment. The combination also achieved lower weight loss and smaller maximum pit depths. Electrochemical tests corroborated the weight loss and pitting data.

Potassium Iodide Potentiates Antimicrobial Photodynamic Inactivation Mediated by Rose Bengal in In Vitro and In Vivo Studies.

Rose bengal (RB) is a halogenated xanthene dye that has been used to mediate antimicrobial photodynamic inactivation for several years. While RB is highly active against Gram-positive bacteria, it is largely inactive in killing Gram-negative bacteria. We have discovered that addition of the nontoxic salt potassium iodide (100 mM) potentiates green light (540-nm)-mediated killing by up to 6 extra logs with the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, the Gram-positive bacterium methicillin-resistant Staphylococcus aureus, and the fungal yeast Candida albicans The mechanism is proposed to be singlet oxygen addition to iodide anion to form peroxyiodide, which decomposes into radicals and, finally, forms hydrogen peroxide and molecular iodine. The effects of these different bactericidal species can be teased apart by comparing the levels of killing achieved in three different scenarios: (i) cells, RB, and KI are mixed together and then illuminated with green light; (ii) cells and RB are centrifuged, and then KI is added and the mixture is illuminated with green light; and (iii) RB and KI are illuminated with green light, and then cells are added after illumination with the light. We also showed that KI could potentiate RB photodynamic therapy in a mouse model of skin abrasions infected with bioluminescent P. aeruginosa.

Mitigation of the Desulfovibrio vulgaris biofilm using alkyldimethylbenzylammonium chloride enhanced by d-amino acids

d-tyrosine and d-methionine that are naturally occurring chemicals were investigated as enhancers for alkyldimethylbenzylammonium chloride (ADBAC) against the Desulfovibrio vulgaris biofilm on C1018 coupons surfaces in ATCC 1249 culture medium. The 7-day biofilm prevention results showed that the d-amino acids alone had only limited effects on SRB sessile cell counts. Ten ppm (w/w) ADBAC alone achieved a 1-log reduction in SRB sessile cell count compared with the untreated control. The combination of 1 ppm d-tyrosine + 10 ppm ADBAC achieved 3 extra log reduction and 50 ppm d-methionine + 10 ppm ADBAC achieved 2 extra log reduction compared with the 10 ppm ADBAC alone treatment. In the biofilm removal test, both combinations exhibited 2 extra log reduction compared with the 10 ppm ADBAC alone treatment. These results were supported by scanning electron microscope images and confocal laser scanning microscope images of the biofilms.

Factors involved in treatment durability and immunological recovery in a cohort of HIV-positive patients receiving atazanavir-based regimens.

IntroductionSince antiretroviral therapy must be taken lifelong, persistence and safety have become the goals to achieve. Protease inhibitors, in particular atazanavir (ATV) with or without ritonavir (r), represent a highly prescribed class in real life long-term treatment.MethodsWe conducted a retrospective cohort study in HIV-1-positive patients who were followed at the Infectious Diseases Unit, DIBIC Luigi Sacco, University of Milan. Data regarding viral load, CD4 lymphocytes and the mean blood chemistry parameters were collected at baseline, first, third, sixth months from the beginning of therapy and then every six months. Factors related to persistence of therapy with ATV and time-dependent probability to reach a CD4 cells count >500 cells/µL were evaluated with Kaplan-Meier curve and Cox model.ResultsA total of 1030 patients were evaluated: 183 received therapy with ATV/r as naïve, 653 switched to ATV/r as a second or following line and 194 switched to unboosted ATV from previous ATV-free regimens. A total of 138 patients shifted to unboosted ATV from a previous ATV/r regimen (17 from naïve ATV/r and 121 from experienced ATV/r). The median duration of therapy was 38 months (95% CI 29–73) in ATV/r naïve patients, 36 months (95% CI 23–53) in unboosted ATV group and 35 months (95% CI 31–43) in patients switched to ATV/r. We observed no significant difference in the persistence of the three regimens (p=0.149). Female (HR=1.317; 95% CI 1.073–1.616 p=0.008) and patients with CD4<200 cells/µL at baseline (HR=1.433 95% CI 1.086–1.892 p=0.011) were at increased risk of regimen interruption, whereas starting therapy with a backbone containing abacavir (HR=0.725; 95% CI 0.533–0.987 p=0.041) resulted protective. In multivariate analysis no significant difference between the three regimens was observed regarding reaching a count of CD4 cells >500 cells/µL. Factors associated to a poor CD4 gain were each extra Log of viral load at baseline (HR=0.915; 95% CI 0.852–0.982 p=0.014) and CD4<200 cells/µL at ATV start (HR=0.197; 95%CI 0.138–0.281 p<0.0001); conversely, females (HR=1.262; 95%CI 1.032–1.543 p=0.023) had a higher probability of CD4 recovery.ConclusionsAntiretroviral regimens containing atazanavir with or without ritonavir were durable and well tolerated, an elevated viral load and CD4 <200 cells/µL at baseline resulted related to regimen discontinuation and reduced CD4 recovery.

Pulsed electric fields cause sublethal injuries in the outer membrane of Enterobacter sakazakii facilitating the antimicrobial activity of citral

The objective was to evaluate the relation of sublethal injury in the outer membrane of Enterobacter sakazakii to the inactivating effect of the combination of pulsed electric fields (PEF) treatments and citral. The occurrence of sublethal injury in the outer membrane was measured using selective recovery media containing bile salts. Loss of membrane integrity was measured by the increased uptake of the fluorescent dye propidium iodide (PI). PEF caused nonpermanent and permanent envelope permeabilization of Ent. sakazakii at pH 4·0. After PEF, most surviving cells showed transient cell permeabilization and sublethal injury in their outer membranes. The simultaneous application of a mild PEF treatment (100 pulses, 25 kV cm(-1) ) and 200 μl l(-1) of citral to cells suspended in pH 4·0 buffer at a final concentration of 10(7) cells per ml showed an outstanding synergistic lethal effect, causing the inactivation of more than two extra log(10) cycles. Our results confirm that the detection of sublethal injury in the outer membrane after PEF may contribute to the identification of the treatment conditions under which PEF may act synergistically with hydrophobic compounds such as citral. Knowledge about the mechanism of microbial inactivation by PEF will aid the establishment of successful combined preservation treatments.

Bacterial resistance after pulsed electric fields depending on the treatment medium pH

The objective was to evaluate and compare the pulsed electric field (PEF) resistance of four Gram-positive ( Bacillus subtilis, Listeria monocytogenes, Lactobacillus plantarum, Staphylococcus aureus) and four Gram-negative ( Escherichia coli, E. coli O157:H7, Salmonella serotype Senftenberg 775W, Yersinia enterocolitica) bacterial strains under the same treatment conditions. Microbial characteristics such as cell size, shape or type of the cell envelopes did not exert the expected influence on microbial PEF resistance. The most PEF resistant bacteria depended on the treatment medium pH. For instance, L. monocytogenes, which showed the highest PEF resistance at pH 7.0, was one of the most sensitive at pH 4.0. The most PEF resistant strains at pH 4.0 were the Gram-negatives E. coli O157:H7 and S. Senftenberg. A subsequent holding of PEF-treated cells in pH 4.0 for 2 h increased the degree of inactivation up to 4 extra Log 10 cycles depending on the bacterial strain investigated. Under these treatment conditions, the most PEF resistant bacterial strains were still the pathogens S. Senftenberg and E. coli O157:H7. Industrial relevance The design of appropriate food preservation processes by PEF requires the selection of an adequate target bacterial strain, which should correspond to the most PEF resistant microorganism contaminating food. This study indicates that the pH of the treatment medium plays an important role in determining this target bacterial strain. On the other hand, the combination of PEF and subsequent holding under acidic conditions has been proven to be an effective method in order to achieve a higher level of microbial inactivation.

Approximation algorithms for optimization problems in graphs with superlogarithmic treewidth

We present a generic scheme for approximating NP-hard problems on graphs of treewidth k = ω ( log n ) . When a tree-decomposition of width ℓ is given, the scheme typically yields an ℓ / log n -approximation factor; otherwise, an extra log k factor is incurred. Our method applies to several basic subgraph and partitioning problems, including the maximum independent set problem.

A numerical method for the generalized airfoil equation based on the de la Vallée Poussin interpolation

The authors consider the generalized airfoil equation in some weighted Hölder–Zygmund spaces with uniform norms. Using a projection method based on the de la Vallée Poussin interpolation, they reproduce the estimates of the L 2 case by cutting off the typical extra log m factor which seemed inevitable to have dealing with the uniform norm, because of the unboundedness of the Lebesgue constants. The better convergence estimates do not produce a greater computational effort: the proposed numerical procedure leads to solve a simple tridiagonal linear system, the condition number of which tends to a finite limit as the dimension of the system tends to infinity, whatever natural matrix norm is considered. Several numerical tests are given.

Two-Dimensional Gauge Theories of the Symmetric Group S n in the Large-n Limit

We study the two-dimensional gauge theory of the symmetric group S n describing the statistics of branched n-coverings of Riemann surfaces. We consider the theory defined on the disc and on the sphere in the large-n limit. A non trivial phase structure emerges, with various phases corresponding to different connectivity properties of the covering surface. We show that any gauge theory on a two-dimensional surface of genus zero is equivalent to a random walk on the gauge group manifold: in the case of S n , one of the phase transitions we find can be interpreted as a cutoff phenomenon in the corresponding random walk. A connection with the theory of phase transitions in random graphs is also pointed out. Finally we discuss how our results may be related to the known phase transitions in Yang-Mills theory. We discover that a cutoff transition occurs also in two dimensional Yang-Mills theory on a sphere, in a large N limit where the coupling constant is scaled with N with an extra log N compared to the standard ‘t Hooft scaling.

Bacterial survival rate on tooth‐ and interdental brushes in relation to the use of toothpaste

AbstractBackground, aims: Previous studies indicated that oral hygiene aids can play a rôle in the intra‐oral translocation of pathogens. The survival rate of cariogenic and periodontopathogenic species on toothbrushes, with and without toothpaste, and interdental brushes was presently investigated.Material and methods: 12 periodontitis patients had their interdental spaces professionally cleaned with interdental brushes and their teeth with new toothbrushes with or without different dentifrices. Each time brushes were rinsed with tap water and stored dry at room temperature. At different time intervals an interdental brush or 4 tufts from a toothbrush were processed for vitality staining and selective and non‐selective culturing procedures.Results: Immediately after rinsing, a toothbrush without toothpaste harboured 107, 108 and 107 colony forming units (CFU) of respectively aerobic, anaerobic and black pigmented species. An insignificant decrease occurred the first 24 hours and after 48 hours still 104 CFU of aerobic and anaerobic species could be cultured. No periodontopathogen remained detectable at 8 hours, except for Fusobacterium nucleatum. The proportion of vital bacteria decreased in 48 hours from 50% to 30%. Comparable results were obtained for interdental brushes. The bacterial survival rate on toothbrushes was significantly reduced by the use of a detergent containing toothpaste by 2 log at baseline, another 2 log at 4 hours and an extra log more at 8 hours for aerobic and anaerobic species. A toothpaste without detergent only had an insignificant bactericidal effect.Conclusion: Toothpaste detergents decrease the survival rate of pathogenic species on a toothbrush and can thus limit the risk for bacterial translocation.

Bacterial survival rate on tooth- and interdental brushes in relation to the use of toothpaste.

Previous studies indicated that oral hygiene aids can play a rôle in the intra-oral translocation of pathogens. The survival rate of cariogenic and periodontopathogenic species on toothbrushes, with and without toothpaste, and interdental brushes was presently investigated. 12 periodontitis patients had their interdental spaces professionally cleaned with interdental brushes and their teeth with new toothbrushes with or without different dentifrices. Each time brushes were rinsed with tap water and stored dry at room temperature. At different time intervals an interdental brush or 4 tufts from a toothbrush were processed for vitality staining and selective and non-selective culturing procedures. Immediately after rinsing, a toothbrush without toothpaste harboured 10(7), 10(8) and 10(7) colony forming units (CFU) of respectively aerobic, anaerobic and black pigmented species. An insignificant decrease occurred the first 24 hours and after 48 hours still 10(4) CFU of aerobic and anaerobic species could be cultured. No periodontopathogen remained detectable at 8 hours, except for Fusobacterium nucleatum. The proportion of vital bacteria decreased in 48 hours from 50% to 30%. Comparable results were obtained for interdental brushes. The bacterial survival rate on toothbrushes was significantly reduced by the use of a detergent containing toothpaste by 2 log at baseline, another 2 log at 4 hours and an extra log more at 8 hours for aerobic and anaerobic species. A toothpaste without detergent only had an insignificant bactericidal effect. Toothpaste detergents decrease the survival rate of pathogenic species on a toothbrush and can thus limit the risk for bacterial translocation.

Underbalanced Drilling With Coiled Tubing: A Safe, Economical Method For Drilling And Completing Gas Wells

Abstract With the recent resurgence of the gas market and the continued commitment of the oil and gas industry to pursue safe, efficient and economical technology to stay competitive and viable, Underbalanced drilling with coiled Tubing is a natural progression for the 1990s and beyond. The successful marriage of conventional drilling technology with the obvious advantages of coiled tubing have brought about a new wave of economical gas wells which can be drilled and completed for a fraction of the cost of cased, cemented, perforated and stimulated wells. This study looks at coiled tubing drilling technology and its advantages. The methodology is discussed and case studies are examined. A peek into the development of this technology is offered and future developments are postulated. Why Drill Underbalanced? There have been many papers written over the years discussing formation damage and resultant loss of production and reserves. The debate over the subsequent ability to remove this formation damage via various stimulation and hydraulic fracturing techniques is a broad topic. However, all debate aside, if formation damage is avoided, or at least minimized from the outset, the technique used to eradicate the formation damage becomes a moot point. Hydraulic fracturing goes well beyond the scope of merely removing formation damage, but serves to increase effective drainage area and potentially tap into other permeability channels such as natural fracture conduits. However, in many areas where there is underlying water, the potential also exists to create a conduit into these zones and effectively negate the ability to produce the well. Barefoot Completions The increasing proliferation of barefoot completions is testament to the industry's push for more economical means of producing marginal gas reservoirs. One of the downsides to barefoot completions is the potential costs incurred by running and cementing casing and then finding that the reservoir is not economical to tie-in. This represents an increase in expenditure over "drill and abandon" costs. However, it has been this author's observation that when such a well is drilled, often considerable expense is incurred in running extra electric logs and testing. Casing is frequently run to attempt stimulation that will reduce potential formation damage. Setting casing above the zone of interest and then drilling into the zone underbalanced serves two main goals: First, formation damage is minimized and second, the well is production tested while being drilled. This serves to minimize the need for extensive formation evaluation and provides the means to cost effectively determine the merits of tieing in the well. Often high permeability reservoirs are subject to losses of circulation. Incremental costs in lost circulation material and additional rig time can be incurred and cementing difficulties are also probable. Setting casing above these zones can improve the probability of achieving a good cement job and can eliminate the costs and problems associated with a loss of circulation. Why Coiled Tubing? The next consideration involves the technique employed to drill the reservoir underbalanced. There are essentially three options to consider to complete a well underbalanced: drilling rig, service rig and coiled tubing rig.

Adaptive hypothesis testing using wavelets

Let a function f be observed with a noise. We wish to test the null hypothesis that the function is identically zero, against a composite nonparametric alternative: functions from the alternative set are separated away from zero in an integral (e.g., $L_2$) norm and also possess some smoothness properties. The minimax rate of testing for this problem was evaluated in earlier papers by Ingster and by Lepski and Spokoiny under different kinds of smoothness assumptions. It was shown that both the optimal rate of testing and the structure of optimal (in rate) tests depend on smoothness parameters which are usually unknown in practical applications. In this paper the problem of adaptive (assumption free) testing is considered. It is shown that adaptive testing without loss of efficiency is impossible. An extra log log-factor is inessential but unavoidable payment for the adaptation. A simple adaptive test based on wavelet technique is constructed which is nearly minimax for a wide range of Besov classes.

What Is Reservoir Management?

This paper describes practical aspects of reservoir management and new approaches being used today, with emphasis on the multidisciplinary team approach. Case studies are presented that illustrate the effectiveness of this approach. In addition, specific attributes of a successful reservoir-management organization and program are highlighted.