Measurements over distributed high performance computing and storage systems

A strawman proposal is given for a framework for presenting a common set of metrics for supercomputers, workstations, file servers, mass storage systems, and the networks that interconnect them. Production control and database systems are also included. Though other applications and third part software systems are not addressed, it is important to measure them as well

Banner News

https://openspace.dmacc.edu/banner_news/1342/thumbnail.jp

The Nature Press, Vol. 3

Nature News was a newsletter publication about activities at the Cheadle Center for Biodiveristy and Ecological Restoration

A Tour of Gallifrey, a Language for Geodistributed Programming

Programming efficient distributed, concurrent systems requires new abstractions that go beyond traditional sequential programming. But programmers already have trouble getting sequential code right, so simplicity is essential. The core problem is that low-latency, high-availability access to data requires replication of mutable state. Keeping replicas fully consistent is expensive, so the question is how to expose asynchronously replicated objects to programmers in a way that allows them to reason simply about their code. We propose an answer to this question in our ongoing work designing a new language, Gallifrey, which provides orthogonal replication through _restrictions_ with _merge strategies_, _contingencies_ for conflicts arising from concurrency, and _branches_, a novel concurrency control construct inspired by version control, to contain provisional behavior

In Stories We Trust: Studies of the Validity of Autobiographies

There is a dearth of research addressing the validity of life stories, or autobiographies. In part, this is because it is unclear how such data sources might be validated. This article recommends two differ-ent perspectives for obtaining evidence relevant to the validity of autobiographical data. A study is conducted from each of these perspectives, and multiple validity estimates are obtained in each in-vestigation. The construct validity of standard psychological constructs (e.g., assertiveness, trustwor-thiness) obtained in Study 1 from autobiographies was equal to that of standard instruments designed to assess these constructs. Evidence for the validity of life themes, extracted from autobi-ographies in Study 2, was also apparent. Because life histories, autobiographies, and case studies are relied on heavily in the practice of counseling psychology and are rapidly regaining popularity in scientific studies, these positive findings suggest the wisdom in this increasing use of life history data

In Stories We Trust: Studies of the Validity of Autobiographies

There is a dearth of research addressing the validity of life stories, or autobiographies. In part, this is because it is unclear how such data sources might be validated. This article recommends two differ-ent perspectives for obtaining evidence relevant to the validity of autobiographical data. A study is conducted from each of these perspectives, and multiple validity estimates are obtained in each in-vestigation. The construct validity of standard psychological constructs (e.g., assertiveness, trustwor-thiness) obtained in Study 1 from autobiographies was equal to that of standard instruments designed to assess these constructs. Evidence for the validity of life themes, extracted from autobi-ographies in Study 2, was also apparent. Because life histories, autobiographies, and case studies are relied on heavily in the practice of counseling psychology and are rapidly regaining popularity in scientific studies, these positive findings suggest the wisdom in this increasing use of life history data

Detecting and tracing farmed salmon with natural geo-element otolith ‘fingerprint’ tags: developing and validating tag delivery techniques

Farmed fish escape and enter the environment with possible effects on wild populations. Attempts to reduce the incidence of escape could be assisted if individuals can be traced back to the point of escape, so that escape causes can be identified and technical standards improved. We tested if permanent marks could be created on the otoliths of salmon that could be detected throughout the lives of the fish. Marks were created by altering the natural ratios of the natural elements barium (Ba) and strontium (Sr) in the otolith. By combining several natural geo-elements, unique fingerprints can be created, which can act as codes that enable tracing of fish back to the point of escape. The marks are detected by laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS). We delivered marks to salmon in 4 different ways: 1) injecting female broodstock with geo-element markers prior to spawning so that the marks can be passed from the mother to all eggs in a clutch, with all larvae receiving a mark in the core of their otolith; 2) incorporating small amounts of geo-element markers into the vaccination serum for co-delivery of the marks into the fish along with the vaccine; 3) bathing eggs of salmon in geo-element solution immediately after fertilisation; and 4) bathing late stage yolk-sac larvae in an geo-element solution. All methods were successful in creating unique, permanent marks on the otoliths of salmon that could be detected throughout the lifetime of the fish. For all four delivery techniques, marking was 100% successful with Ba at concentrations as low as 0.001 μg. g-1 fish and for Sr at 1 μg. g-1 fish. Detection limits with the laser were set at 99.94%, so the techniques delivered a very high degree of accuracy. In all methods, we developed procedures that minimized marking and analysis costs, so that methods could be implemented at full-scale commercial application. After marking, fish were ongrown under standard commercial conditions to harvest size (approx. 4 kg). Marking methods had no effect on all standard production parameters, such as survival, growth, and the incidence of larval deformities compared to unmarked control fish. Further, the amounts of natural 2 strontium and barium used to create the marks are so small that they pose no problem for food safety, as they represent less than 0.1–1% of the amounts that naturally occur in salmon tissues. Our results indicate single marking with one of the techniques can create up to 63 unique fingerprint marks at low cost using Ba (0.0002–0.02 $US per mark) and Sr (0.46–0.82$US per mark). Double marking in different parts of the otolith using two of the different code delivery methods was also successful (e.g. maternal transfer and vaccination combined). This means 63 x 15 unique codes, or 1023 codes are possible, which is sufficient to provide a unique code for every site in the sea in Norway. We conclude that fingerprinting with natural geo-elements is feasible for commercial application. 94% of the salmon in Norway could be marked for as little as 0.02 $US per fish with a single marking method with traceability back to the top 63 producing companies. Double marking would enable more detailed tracing of every fish back to its site in the sea.Oppdrettslaks rømmer og kan påvirke de ville populasjonene. Antallet rømminger kunne vært redusert hvis den rømte fisken kunne vært sporet tilbake til rømningsstedet slik at årsaken til rømning kunne blitt identifisert. Vi testet om det er mulig å lage kjemiske merker på laksens ørestein som kan identifiseres gjennom hele livssyklusen. Disse merkene ble laget ved å endre forholdet mellom naturlige geoelementer (stabile isotoper av barium (Ba) og strontium (Sr)) i øresteinen. Ved å kombinere flere av disse naturlige geoelementene kan en lage unike ’fingeravtrykk/strekkoder’ som kan brukes for å spore en fisk tilbake til rømningsstedet. Merkene leses ved en teknikk hvor en brenner hull i øresteinen med laser og måler sammensetningen ved hjelp av massespektrometri. Merkene i øresteinen ble etablert ved hjelp av fire metoder: 1) ved å injisere morfisken med geoelementer i forkant av gytingen slik at disse kan overføres til alle eggene og at merket blir avsatt i øresteinens kjerne; 2) ved å tilsette små mengder av geoelementene i fiskens vaksine slik at fisken merkes ved vaksineringen; 3) ved å tilsette geoelementer i svellevannet som tilsettes rett etter befruktningen av eggene; 4) ved å bade plommesekkyngelen i en løsning med geoelementer. Ved alle metodene klarte vi å lage unike, permanente merker i øresteinen som kunne finnes og kjennes igjen gjennom hele fiskens livssyklus. Alle metodene ga 100 Etter merking ble fisken oppdrettet under standard oppdrettsbetingelser til slaktestørrelse (ca. 4 kg). Merkemetodene påvirket ingen produksjonsparametre som overlevelse, vekst eller innslag av deformiteter. Mengden naturlig strontium og barium som ble brukt er mindre enn 1 Våre resultater viser at en ved enkel merking med en av teknikkene kan lage opptil 63 unike ‘fingeravtrykk’ til en lav kostnad ved bruk av Ba (0,0002–0,02$US per merke) og Sr (0,46–0,82 $US per 3 merke). Dobbelmerking; dvs. å merke i ulike deler av øresteinen ved hjelp av to av metodene, var også mulig (for eksempel injeksjon av morfisk og vaksinering på parrstadiet). Dette betyr at en kan lage 63 x 15 = 1023 unike koder, nok til å gi hver lokalitet i Norge en unik kode. Vi konkluderer med at merking med naturlige geoelementer er en mulig løsning for å merke oppdrettsfisk. 94$US per fisk og med mulighet til å spore den tilbake til de 63 største produsentene. Dobbelmerking gir mulighet for sporing tilbake til lokalitet

Aligned macroporous monoliths with intrinsic microporosity via a frozen-solvent-templating approachd

Aligned macroporous monoliths of an organic cage, a polymer of intrinsic microporosity (PIM-1), and a metal–organic framework (HKUST-1) are prepared by a controlled freezing approach. In addition to macropores, all the monoliths contain the intrinsic micropores.</p

Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV–vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV–vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate