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Strongly consistent distributed systems are easy to reason about but face fundamental limitations in availability and performance. Weakly consistent systems can be implemented with very high performance but place a burden on the application developer to reason about complex interleavings of execution. Invariant confluence provides a formal framework for understanding when we can get the best of both worlds. An invariant confluent object can be efficiently replicated with no coordination needed to preserve its invariants. However, actually determining whether or not an object is invariant confluent is challenging. In this paper, we establish conditions under which a commonly used sufficient condition for invariant confluence is both necessary and sufficient, and we use this condition to design (a) a general-purpose interactive invariant confluence decision procedure and (b) a novel sufficient condition that can be checked automatically. We then take a step beyond invariant confluence and introduce a generalization of invariant confluence, called segmented invariant confluence, that allows us to replicate non-invariant confluent objects with a small amount of coordination. We implemented these formalisms in a prototype called Lucy and found that our decision procedures efficiently handle common real-world workloads including foreign keys, rollups, escrow transactions, and more. We also found that segmented invariant confluent replication can deliver up to an order of magnitude more throughput than linearizable replication for low contention workloads and comparable throughput for medium to high contention workloads.

In emails, information abounds. Whether it be a bill reminder, a hotel confirmation, or a shipping notification, our emails contain useful bits of information that enable a number of applications. Most of this email traffic is machine-generated, sent from a business to a human. These business-to-consumer emails are typically instantiated from a set of email templates, and discovering these templates is a key step in enabling a variety of intelligent experiences. Existing email information extraction systems typically separate information extraction into two steps: an offline template discovery process (called template induction) that is periodically run on a sample of emails, and an online email annotation process that applies discovered templates to emails as they arrive. Since information extraction requires an email's template to be known, any delay in discovering a newly created template causes missed extractions, lowering the overall extraction coverage. In this paper, we present a novel system called Crusher that discovers templates completely online, reducing template discovery delay from a week (for the existing MapReduce-based batch system) to minutes. Furthermore, Crusher has a resource consumption footprint that is significantly smaller than the existing batch system. We also report on the surprising lesson we learned that conventional stream processing systems do not present a good framework on which to build Crusher. Crusher delivers an order of magnitude more throughput than a prototype built using a stream processing engine. We hope that these lessons help designers of stream processing systems accommodate a broader range of applications like online template induction in the future.

Quorum systems are a powerful mechanism for ensuring the consistency of replicated data. Production systems usually opt for majority quorums due to their simplicity and fault tolerance, but majority quorum systems provide poor throughput and scalability. Alternatively, researchers have invented a number of theoretically "optimal" quorum systems, but the underlying theory ignores many practical complexities such as machine heterogeneity and workload skew. In this paper, we conduct a pragmatic re-examination of quorum systems. We enrich the current theory on quorum systems with a number of practical refinements to find quorum systems that provide higher throughput, lower latency, and lower network load. We also develop a library Quoracle that precisely quantifies the available trade-offs between quorum systems to empower engineers to find optimal quorum systems, given a set of objectives for specific deployments and workloads. Our tool is available online at: https://github.com/mwhittaker/quoracle., To be published in PaPoC 2021 (https://papoc-workshop.github.io/2021/)

Traditionally, the high cost of network communication between servers has hidden the impact of cross-core coordination in replicated systems. However, new technologies, like kernel-bypass networking and faster network links, have exposed hidden bottlenecks in distributed systems. This paper explores how to build multicore-scalable, replicated storage systems. We introduce a new guideline for their design, called the Zero-Coordination Principle. We use this principle to design a new multicore-scalable, in-memory, replicated, key-value store, called Meerkat. Unlike existing systems, Meerkat eliminates all cross-core and cross-replica coordination, both of which pose a scalability bottleneck. Our experiments found that Meerkat is able to scale up to 80 hyper-threads and execute 8.3 million transactions per second. Meerkat represents an improvement of 12X on state-of-the-art, fault-tolerant, in-memory, transactional storage systems built using leader-based replication and a shared transaction log.

Protein aggregation into amyloid fibrils is a ubiquitous phenomenon across the spectrum of neurodegenerative disorders and type 2 diabetes. A common strategy against amyloidogenesis is to minimize the populations of toxic oligomers and protofibrils by inhibiting protein aggregation with small molecules or nanoparticles. However, melanin synthesis in nature is realized by accelerated protein fibrillation to circumvent accumulation of toxic intermediates. Accordingly, we designed and demonstrated the use of star-shaped poly(2-hydroxyethyl acrylate) (PHEA) nanostructures for promoting aggregation while ameliorating the toxicity of human islet amyloid polypeptide (IAPP), the peptide involved in glycemic control and the pathology of type 2 diabetes. The binding of PHEA elevated the β-sheet content in IAPP aggregates while rendering a new morphology of "stelliform" amyloids originating from the polymers. Atomistic molecular dynamics simulations revealed that the PHEA arms served as rodlike scaffolds for IAPP binding and subsequently accelerated IAPP aggregation by increased local peptide concentration. The tertiary structure of the star nanoparticles was found to be essential for driving the specific interactions required to impel the accelerated IAPP aggregation. This study sheds new light on the structure-toxicity relationship of IAPP and points to the potential of exploiting star polymers as a new class of therapeutic agents against amyloidogenesis.

Systematically reasoning about the fine-grained causes of events in a real-world distributed system is challenging. Causality, from the distributed systems literature, can be used to compute the causal history of an arbitrary event in a distributed system, but the event's causal history is an over-approximation of the true causes. Data provenance, from the database literature, precisely describes why a particular tuple appears in the output of a relational query, but data provenance is limited to the domain of static relational databases. In this paper, we present wat-provenance: a novel form of provenance that provides the benefits of causality and data provenance. Given an arbitrary state machine, wat-provenance describes why the state machine produces a particular output when given a particular input. This enables system developers to reason about the causes of events in real-world distributed systems. We observe that automatically extracting the wat-provenance of a state machine is often infeasible. Fortunately, many distributed systems components have simple interfaces from which a developer can directly specify wat-provenance using a technique we call wat-provenance specifications. Leveraging the theoretical foundations of wat-provenance, we implement a prototype distributed debugging framework called Watermelon.

The utility of biodegradable nanosized drug carriers for the local and controlled delivery of therapeutics to the lungs has prompted significant interest in the development of inhalable nanomedicines. Still, little is known about how these systems are cleared from the lungs, including the kinetics of the structural lipids. Most preclinical and clinical studies to date have evaluated the lung clearance of loaded drugs, which in many cases poorly reflects the kinetics of the nanocarrier, or the bulk-labelled particles. This study therefore aimed to describe and compare the pulmonary pharmacokinetic behaviour and patterns of lung clearance of two commonly explored inhalable nanocarriers (anionic ∼150 nm liposomes and solid lipid nanoparticles [SLNs]) in rats by following the

Network measurement is an essential component of many SDN applications, but most existing controller platforms force programmers to implement measurement tasks by installing fine-grained forwarding rules on switches---an approach that significantly increases configuration and management complexity. This paper proposes a radically different approach: rather than implementing measurement tasks directly on network switches, we argue for pushing measurement to the edge and utilizing the abundant resources available on end hosts. At a technical level, our approach is based on two key ideas: (i) we express measurement tasks using programs in a high-level, declarative query language, and (ii) we use program analysis to calculate predicates that can be used to answer queries at the edge of the network. We present an implementation of our approach on top of the NetKAT framework, we develop case studies illustrating the benefits of our approach, and we conduct experiments that quantify performance on realistic benchmarks.

We have developed a portable and extensible set of tools and applications for control of a remote transmission electron microscope (TEM). These tools will be used to develop a system for automatically acquiring large numbers of high quality images from a TEM in a routine, robust, and efficient manner. In particular we plan to develop applications that allow for data collection from specimens preserved in vitreous ice. Copyright 1997 Academic Press. Copyright 1997 Academic Press

Kinesin motors convert chemical energy from ATP hydrolysis into unidirectional movement. To understand how kinesin motors bind to and move along microtubules, we fit the atomic structure of the motor domain of Ncd (a kinesin motor involved in meiosis and mitosis) into three-dimensional density maps of Ncd–microtubule complexes calculated by cryo-electron microscopy and image analysis. The model reveals that Ncd shares an extensive interaction surface with the microtubule, and that a portion of the binding site involves loops that contain conserved residues. In the Ncd dimer, the microtubule-bound motor domain makes intimate contact with its partner head, which is dissociated from the microtubule. This head–head interaction may be important in positioning the dissociated head to take a step to the next binding site on the microtubule protofilament.

Brush border myosin I (BBMI) is a single-headed molecular motor. Its catalytic domain exhibits extensive sequence homology to the catalytic domain of myosin II, while its tail lacks the coiled-coil nature of myosin II. The BBMI tail domain contains at least three IQ motifs and binds calmodulin. Addition of calcium removes one of these calmodulin light chains, with effects on ATPase activity and motility in in vitro assays. Using the techniques of cryoelectron microscopy and helical image analysis we have calculated three-dimensional (3D) maps of BBMI-decorated actin filaments prepared in the presence and absence of calcium. The 3D maps describe a BBMI catalytic domain that is strikingly similar to the catalytic domain of myosin II subfragment 1 (S1), with the exception of a short amino-terminal region of the heavy chain, which is absent from BBMI. The tail domains of BBMI and S1 are highly divergent in structure, continuing on from their respective motor domains with very different geometries. Addition of calcium to BBMI, and the concomitant loss of a calmodulin light chain, results in an extensive reorganization of mass in the tail domain.

We describe a set of procedures and algorithms which have been developed to provide an efficient and reliable method for reconstructing a three-dimensional density map from specimens with helical symmetry. These procedures build on the original MRC helical processing suite, with extensions principally developed using the SUPRIM image processing package. Actomyosin is used as a model specimen to demonstrate the utility of this repackaged and expanded set of routines. The time required to complete a three-dimensional map has been reduced from several weeks using traditional manual techniques to a few days. The increased signal/noise provided has allowed for the extraction of additional layer lines not previously identified by manual techniques.

We continually see reports on high profile industrial failures and the impact these have on people and our environment, not least the operating companies involved. These failures are often attributed to the failure of the organisations to manage the risks, ineffective leadership and failure to follow prescribed standards. In the case of maintenance and reliability standards, there is wide-spread acceptance and knowledge of what is known to be best practices. So why is it that we regularly see incidents where companies have failed to “adhere to the rules”? All too often, many organisations attempt to adopt best practices and industry standards, with a view of “being seen to be doing something” or selecting the elements of best practices that are seen as “the key”. This paper explores, through a case study, where elements of good practice were in place, but still resulted in an unforeseen catastrophic failure, impacting on operations and performance. This case study demonstrates that even when efforts and investment are made, organisations still experience costly failures, which also impact on the credibility of the investment in maintenance and reliability efforts. Therefore, without considering the fundamental elements of maintenance and reliability (asset management) best practice, i.e. management information systems, foundational data, work flows, fault recording, planning and scheduling, incident / failure investigation, etc, together with the absolute need in addressing organisational change (structures, culture and practices), then hard work and best efforts will not be enough. (5 pages)

Muscle contraction consists of a cyclical interaction between myosin and actin driven by the concomitant hydrolysis of adenosine triphosphate (ATP). A model for the rigor complex of F actin and the myosin head was obtained by combining the molecular structures of the individual proteins with the low-resolution electron density maps of the complex derived by cryo-electron microscopy and image analysis. The spatial relation between the ATP binding pocket on myosin and the major contact area on actin suggests a working hypothesis for the crossbridge cycle that is consistent with previous independent structural and biochemical studies.

Three-dimensional data representing biological structures can be derived using several methods, including serial section reconstruction, optical sectioning, and tomography. The investigation, comprehension, and communication of structural relationships to others is greatly facilitated by computer-based visualization procedures. We describe SYNU, a suite of programs developed for interactive investigation of three-dimensional structure and for the production of high-quality three-dimensional images and animations. We illustrate the capabilities of SYNU in applications to biological data obtained by confocal light microscopy, serial section, and high-resolution electron microscopy from investigations at the cellular, subcellular, and molecular levels.

The isolation of human DNA sequences that encode immunoglobulin genes, T cell receptor genes, and protooncogenes involved in the pathogenesis of lymphoid neoplasms has provided highly sensitive molecular probes to determine clonality and lineage in lymphopro-liferative lesions. The application of these probes to diagnostic problems in pathology has enhanced greatly the ability of the pathologist to determine clonality and lineage in lymphoid neoplasms, distinguish lymphoid from non-lymphoid tumors, monitor minimal residual disease, and identify early relapse.

Rates of ketone body (β-hydroxybutyrate plus acetoacetate) production by perfused livers from starved rats were decreased about 60% from 39 ± 2 to 17 ± 3 μmol/g/hr by 2-ethylhexanol (200,μM), a primary metabolite of the plasticizer diethylhexyl phthalate. Inhibition of ketogenesis by ethylhexanol was dose dependent (half-maximal inhibition occurred with 25 μM) in the presence or absence of 4-methylpyrazole, an inhibitor of alcohol dehydrogenase. Concentrations of β-hydroxbutyrate relative to acetoacetate (B/A) increased in a step-wise manner from 0.32 to 0.75 in the effluent perfusate when ethylhexanol was infused. In contrast, the B/A ratio decreased in parallel with inhibition of ketone body production when alcohol dehydrogenase was inhibited. Pretreatment of rats with phenobarbital, an inducer of ω and ω-1 hydroxylases, diminished inhibition of ketone body production by low ( 50 μM) of ethylhexanol. Thus, ethylhexanol is oxidized via phenobarbitalinducible pathways to metabolites which do not inhibit ketogenesis. Studies were conducted to determine the site of inhibition of fatty acid oxidation by ethylhexanol. Rates of ketone body production in the presence of oleate (250 μM), which requires transport of the corresponding CoA compound into mitochondria, were reduced from 80 ± 6 to 58 ± 8 μmol/g/hr by ethylhexanol. In contrast, ketone body production from hexanoate, which is activated in the mitochondria, was not affected by ethylhexanol. Basal and oleate-stimulated rates of H2O2 production were not affected by ethylhexanol, indicating that peroxisomal β-oxidation was not altered by the compound. Based on these data it is concluded that 2-ethylhexanol inhibits β-oxidation of fatty acids in mitochondria but not in peroxisomes. Treatment of rats with ethylhexanol (0.32 g/kg, i.p.) decreased plasma ketone bodies from 1.6 to 0.8 mM, increased hepatic triglycerides and increased lipid predominantly in periportal regions of the liver lobule. These data indicate that alterations in hepatic fatty acid metabolism in periportal regions of the liver lobule may be early events in peroxisome proliferation.

Several organophosphates including diisopropylfluorophosphonate (DPF) and a variety of compounds used as chemical warfare agents produced dose- and time-dependent increases in phosphorylase-a, the phosphorylated form of glycogen phosphorylase in rat pheochromocytoma cells, PC12, and isolated hepatocytes. Increases in phosphorylase-a did not occur in cells exposed to the carbamates, physostigmine or pyridostigmine, or to O-ethyl S-2-diisopropylaminoethylmethyl-phosphonathiolate (VX), an organophosphate which is protonated at physiological pH. When extracellular pH was increased to pH 8, VX acted like the other organophosphates and increased phosphorylase-a activity. The possibility that organophosphates increase phosphorylase-a in intact cells by releasing Ca2+ from intracellular binding sites is supported by the following findings: organophosphate-induced increases in phosphorylase-a did not correlate with changes in cyclic AMP in the two cell types studied; in PC12 cells, increases in this activity occurred in the absence of extracellular calcium and were not inhibited by the calcium channel blocker, verapamil; fluorescence of the calcium sensitive dye, Quin-2, in PC12 cells preloaded with the acetoxymethyl ester of the dye was increased by soman; finally, addition of the calcium ionophore, A23187, to PC12 cells maintained in calcium-free medium caused sarin-stimulated phosphorylase-a activity to return rapidly to basal levels. Collectively, these data argue strongly that organophosphates increase phosphorylase-a activity in intact cells via a novel mechanism involving release of calcium from intracellular binding sites.

Kinesin motors power many motile processes by converting ATP energy into unidirectional motion along microtubules. The force-generating and enzymatic properties of conventional kinesin have been extensively studied; however, the structural basis of movement is unknown. Here we have detected and visualized a large conformational change of an approximately 15-amino-acid region (the neck linker) in kinesin using electron paramagnetic resonance, fluorescence resonance energy transfer, pre-steady state kinetics and cryo-electron microscopy. This region becomes immobilized and extended towards the microtubule 'plus' end when kinesin binds microtubules and ATP, and reverts to a more mobile conformation when gamma-phosphate is released after nucleotide hydrolysis. This conformational change explains both the direction of kinesin motion and processive movement by the kinesin dimer.

Brush border myosin-I (BBMI) is a single-headed unconventional myosin found in the microvilli of intestinal epithelial cells, where it links the core bundle of actin filaments to the plasma membrane. An association of BBMI with anionic phospholipids has been shown to be mediated by a carboxy-terminal domain which is rich in basic amino acids. We have exploited this natural affinity of BBMI for negatively charged lipids to form two-dimensional (2D) crystals of this protein which are suitable for structural analysis by electron crystallographic techniques. The 2D crystals which we have obtained belong to one of two space groups, p22121 or p2. We present here projection maps calculated from images of negatively stained crystals for each of these crystal types to a resolution of 20 A and show that the asymmetric unit is the same in both crystal types.

We describe here a set of procedures and algorithms for helical processing that we refer to as the PHOELIX package. The package was developed to provide a time-efficient and semiautomated method for determining a three-dimensional density map from a specimen with helical symmetry. The procedures which are part of PHOELIX are drawn from the original MRC helical processing suite with extensions principally developed using the SUPRIM image processing package. The package in its current form has been optimized for the processing of actomyosin filaments but has been modified and applied to other helical structures.

Myosin II crossbridges interact with F-actin producing powerstrokes of around 100 A (refs 1, 2), during which the products of ATP hydrolysis are released. This has been postulated to involve an articulation of the myosin head (S1) on actin, or substantial conformational changes in S1 itself. Small movements of the regulatory light chain have been detected (see, for example, refs 9, 10), but most data suggest that the bulk of S1 does not move on actin during crossbridge cycling. Here we present three-dimensional maps of S1-decorated F-actin in the presence and absence of MgADP. The myosin motor domain is similar in both states but there are major orientational differences in the light-chain-binding domain. This domain acts as a rigid level arm pivoting about the end of the motor domain and swinging approximately 23 degrees, resulting in a approximately 35-A step. Small, nucleotide-mediated conformational changes in the motor domain may thus be converted by the light-chain domain into large movement steps.

Comparisons of three-dimensional maps of vertebrate muscle thin filaments obtained by cryo-electron microscopy and image analysis, reveal the molecular structure of F-actin, the location of the C terminus of the monomer and the positions of the binding sites of tropomyosin, the myosin head and the N-terminal portion of the myosin A1 light chain on the filament. These data provide strong constraints for evaluating models built from the atomic structure of the monomer and the subsequent identification of molecular contacts.

1. 1. Glycogen phosphorylase- α , a commonly used index of cytosolic free calcium, was compared in various preparations of rat liver in the absence and presence of 0.1 μM epinephrine. 2. 2. Total phosphorylase in isolated perfused livers and freshly-isolated hepatocytes were the same as that observed in liver in situ ; however, phosphorylase- α was 50% higher in perfused liver and 80% higher in hepatocytes than activies measured in situ . Total phosphorylase was reduced approximately 50% in hepatocytes maintained in primary culture for 24 hr. 3. 3. Epinephrine increased phosphorylase- a approximately 2-fold in livers perfused for 30 min but only about 20% in hepatocytes incubated for 30 min. After 90 min of perfusion or incubation, epinephrine increased phosphorylase- α nearly 4-fold in perfused livers and only 30% in isolated hepatocytes. The results suggest that amounts of free calcium and calcium-dependent coupling of adrenergic receptors to phosphorylase- α differ markedly between the intact liver and isolated hepatocytes.

Rates of hydrolysis of 3-hydroxybenzo[a]pyrenyl glucuronide by microsomal beta-glucuronidase from rat liver were 397 +/- 17 nmol/min per g protein and were half-maximal with about 100 microM substrate. Treatment of rats with phenobarbital or 3-methylcholanthrene, which elevates activities of glucuronosyltransferase(s), lowered rates of hydrolysis of benzo[a]pyrene glucuronide by 25%. Hydrolysis of the glucuronide by microsomal beta-glucuronidase was stimulated by micromolar concentrations of calcium in the range existing in cytosol of hepatocytes (apparent Km approximately 0.2 microM). Thus, humoral factors that change intracellular concentrations of free calcium may alter the production and export of glucuronides of benzo[a]pyrene metabolites from the liver.

A high-resolution model of the microtubule has been obtained by docking the crystal structure of tubulin into a 20 A map of the microtubule. The excellent fit indicates the similarity of the tubulin conformation in both polymers and defines the orientation of the tubulin structure within the microtubule. Long C-terminal helices form the crest on the outside of the protofilament, while long loops define the microtubule lumen. The exchangeable nucleotide in β -tubulin is exposed at the plus end of the microtubule, while the proposed catalytic residue in α -tubulin is exposed at the minus end. Extensive longitudinal interfaces between monomers have polar and hydrophobic components. At the lateral contacts, a nucleotide-sensitive helix interacts with a loop that contributes to the binding site of taxol in β -tubulin.

Recently developed non-invasive optical and polarographic techniques along with ultramicrobiochemical methods were used to study the actions of allyl alcohol, a classic periportal toxin, on biochemical events in sublobular zones of the isolated perfused liver. Anterograde infusion of allyl alcohol (350 μM) for 60 minutes selectively injured periportal hepatocytes as indexed by uptake of trypan blue and by decreases in ATP/ADP ratios. Zone-specific decreases in ATP/ADP ratios were accompanied by impaired rates of oxygen uptake. Potassium cyanide (2 mM), an inhibitor of cytochrome oxidase, decreased ATP/ADP ratios but did not increase trypan blue uptake. Thus, disruption of ATP generation is a consequence rather than a cause of cellular injury due to allyl alcohol. Rates of oxidation of allyl alcohol to acrolein via alcohol dehydrogenase and depletion of cellular glutathione occurred equally in both zones of livers exposed to allyl alcohol indicating that zonal toxicity due to allyl alcohol was not due to differences in rates of metabolism of this compound.