Igneous Rock Associations 22. Experimental Petrology: Methods, Examples, and Applications

Experiments are an important source of basic information in petrology, from thermodynamic data used to develop predictive models to physical property data used to understand magma ascent and eruption. Since we all use experimental data in our work as geoscientists, it is important that we have a basic understanding of the methods used to prepare and perform experiments on rocks and minerals and their synthetic analogues. In this review I examine how the observational science of geology changed in the late 1800’s with the development of the interdisciplinary science of physical chemistry. The second part of the paper discusses what factors need to be considered in designing an experimental study; it focuses particularly on the problems of reaching equilibrium on the short timescales available in the laboratory. In the final section, I give four examples of geological problems that have been solved using experimental methods and make some suggestions about the directions that future experimental campaigns might take.RÉSUMÉL’expérimentation est une source importante d’information de base en pétrologie, qu’il s’agisse de données thermodynamiques pour développer des modèles prédictifs, ou des propriétés physiques utilisés pour comprendre la montée et l’éruption d’un magma. Puisque nous utilisons tous des données expérimentales dans notre travail de géoscientifique, il est important que nous ayons une compréhension minimale des méthodes utilisées pour préparer et réaliser des expériences sur les roches, les minéraux et leurs analogues de synthèse. Dans la présente étude, je me suis penché sur les changements survenus en science d’observation qu’est la géologie, à la fin des années 1800, avec le développement de la science interdisciplinaire de la chimie physique. La deuxième partie de l’article traite des facteurs à prendre en compte dans la conception d’une étude expérimentale; elle porte en particulier sur les problèmes d’atteinte d’un équilibre sur les temps courts du laboratoire. Dans la dernière section, je donne quatre exemples de problèmes géologiques qui ont été résolus à l’aide de méthodes expérimentales, et je fais des suggestions sur des orientations qui pourraient être adoptées lors de campagnes expérimentales à venir

Individual surgeon mortality rates: can outliers be detected? A national utility analysis

Objectives: There is controversy on the proposed benefits of publishing mortality rates for individual surgeons. In some procedures, analysis at the level of an individual surgeon may lack statistical power. The aim was to determine the likelihood that variation in surgeon performance will be detected using published outcome data. Design: A national analysis surgeon-level mortality rates to calculate the level of power for the reported mortality rate across multiple surgical procedures. Setting: The UK from 2010 to 2014. Participants: Surgeons who performed colon cancer resection, oesophagectomy or gastrectomy, elective aortic aneurysm repair, hip replacement, bariatric surgery or thyroidectomy. Outcomes: The likelihood of detecting an individual with a 30-day, 90-day or in-patient mortality rate of up to 5 times the national mean or median (as available). This was represented using a novel heat-map approach. Results: Overall mortality rates for the procedures ranged from 0.07% to 4.5% and mean/median surgeon volume was between 23 and 75 cases. The national median case volume for colorectal (n=55) and upper gastrointestinal (n=23) cancer resections provides around 20% power to detect a mortality rate of 3 times the national median, while, for hip replacement, this is a rate 5 times the national average. At the mortality rates reported for thyroid (0.08%) and bariatric (0.07%) procedures, it is unlikely a surgeon would perform a sufficient number of procedures in his/her entire career to stand a good chance of detecting a mortality rate 5 times the national average. Conclusions: At present, surgeons with increased mortality rates are unlikely to be detected. Performance within an expected mortality rate range cannot be considered reliable evidence of acceptable performance. Alternative approaches should focus on commonly occurring meaningful outcome measures, with infrequent events analysed predominately at the hospital level

Human Exonuclease 1 Threads 5'-Flap Substrates Through its Helical Arch

Human exonuclease 1 (hEXO1) is a member of the 5'-nuclease superfamily and plays important roles in DNA repair. Alongside acting as a 5'-exonuclease on blunt, gapped, nicked and 3'-overhang DNAs, hEXO1 can also act as an endonuclease removing protruding 5'-single-stranded flaps from duplex ends. How hEXO1 and related 5'-nuclease human flap endonuclease 1 (hFEN1) are specific for discontinuous DNA substrates like 5'-flaps has been controversial. Here we report the first functional data that implies that hEXO1 threads the 5'-flap through a hole in the protein known as the helical arch, thereby excluding reactions of continuous single-strands. Conjugation of bulky 5'-streptavidin that would "block" threading through the arch drastically slowed the hEXO1 reaction. In contrast, addition of streptavidin to a pre-formed hEXO1 5'-biotin flap DNA complex trapped a portion of the substrate in a highly-reactive threaded conformation. However, another fraction behaves as if "blocked" and decayed very slowly implying there were both threaded and unthreaded forms of the substrate present. The reaction of an unmodified hEXO1-flap DNA complex did not exhibit marked biphasic kinetics, suggesting a fast re-equilibration occurs that produces more threaded substrate when some decays. The finding that a threading mechanism like that used by hFEN1 is also used by hEXO1, unifies the mode of operation for members of the 5'-nuclease superfamily that act on discontinuous substrates. As with hFEN1, intrinsic disorder of the arch region of the protein may explain how flaps can be threaded without a need for a coupled energy source

Anomalous Chromomagnetic Moments of Quarks and Large Transverse Energy Jets

We consider the jet cross sections for gluons coupling to quarks with an anomalous chromomagnetic moment. We then apply this to the deviation and bounds from QCD found in the CDF and D0 Fermilab data, respectively, to find a range of possible values for the anomalous moments. The quadratic and quartic terms in the anomalous moments can fit to the rise of a deviation with transverse energy. Since previous analyses have been done on the top quark total cross section, here we assume the same moment on all quarks except the top and find the range $|\kappa'| \equiv |\kappa/(2 m_q)| = 1.0\pm 0.3$ TeV$^{-1}$ for the CDF data. Assuming the anomalous moment is present only on a charm or bottom quark which is pair produced results in a range $|\kappa'_{b,c}| = 3.5 \pm 1.0$ TeV$^{-1}$. The magnitudes here are compared with anomalous magnetic moments that could account for $R_b$ and found to be in the same general range, as well as not inconsistent with LEP and SLD bounds on $\Delta \Gamma_{\text{had}}$.Comment: REVTeX, 11 pages, 2 postscript figure

From Analysis Model to Software Architecture: a PIM2PIM Mapping.

To our knowledge, no current software development methodology explicitly describes how to transit from the analysis model to the software architecture of the application. This paper presents a method to derive the software architecture of a system from its analysis model. To do this, we are going to use MDA. Both the analysis model and the architectural model are PIMs described with UML 2. The model type mapping designed consists of several rules (expressed using OCL and natural language) that, when applied to the analysis artifacts, generate the software architecture of the application. Specifically the rules act on elements of the UML 2 metamodel (metamodel mapping). We have developed a tool (using Smalltalk) that permits the automatic application of these rules to an analysis model defined in RoseTM to generate the application architecture expressed in the architectural style C2

Unusual morphologies and the occurrence of pseudomorphs after ikaite (CaCO3•6H2O) in fast growing, hyperalkaline speleothem

Unusual speleothem, associated with hyperalkaline (pH>12) groundwaters have formed within a shallow, abandoned railway tunnel at Peak Dale, Derbyshire, UK. The hyperalkaline groundwaters are produced by the leaching of a thin layer (<2 m) of old lime kiln waste above the soil-bedrock surface above the tunnel by rainwater. This results in a different reaction and chemical process to that more commonly associated with the formation of calcium carbonate speleothems from Ca-HCO3-type groundwaters and degassing of CO2. Stalagmites within the Peak Dale tunnel have grown rapidly (averaging 33 mm y-1), following the closure of the tunnel 70 years ago. They have an unusual morphology comprising a central sub-horizontally-laminated column of micro- to nano-crystalline calcium carbonate encompassed by an outer sub-vertical assymetric ripple laminated layer. The stalagmites are largely composed of secondary calcite forming pseudomorphs (<1 mm) which we believe to be predominantly after the ‘cold climate’ calcium carbonate polymorph, ikaite (calcium carbonate hexahydrate: CaCO3•6H2O), with minor volumes of small (<5 μm) pseudomorphs after vaterite. The tunnel has a near constant temperature of 8-9°C which is slightly above the previously published crystallisation temperatures for ikaite (<6°C). Analysis of a stalagmite actively growing at the time of sampling, and preserved immediately within a dry nitrogen cryogenic vessel, indicates that following crystallisation of ikaite, decomposition to calcite occurs rapidly, if not instantaneously. We believe this is the first occurrence of this calcium carbonate polymorph observed within speleothem

Isolation and analysis of genes specifically expressed during basidiomatal development in Antrodia cinnamomea by subtractive PCR and cDNA microarray

cDNAs specifically expressed at the basidiome stage were isolated by using PCR-selected cDNA subtraction in order to study gene regulation during porous-hymenium basidiomatal formation in Antrodia cinnamomea. BLASTX results suggested that most of the expressed sequence tags (52.4-69.5%) had no significant protein homology to genes from other published living things. cDNAs particularly expressed at different growing conditions were identified using cDNA microarray analysis. Reverse transcriptase PCR analyses confirmed that the clone putative to P-type ATPase, various cytochrome P450s and some unknown genes were abundant at natural basidiomes while endoglucanase was abundant at the tissue from artificial medium

Dietary protein supplementation and its consequences for intake, digestion, and physical activity of a carnivorous marsupial, Sminthopsis crassicaudata

Diet regulation behavior can mediate the consequences of imbalanced diets for animal well‐being, particularly for captive species that have little dietary choice. Dasyurids (carnivorous marsupials) are of conservation concern in Australia, and many species are in captive breeding programmes. However, their nutrient targets and dietary regulation behaviors are poorly understood, a limitation that may decrease the breeding success and well‐being of captive animals. We tested how dietary protein content influenced the intake and utilization of nutrients, physical activity, and body mass of fat‐tailed dunnarts Sminthopsis crassicaudata. Twelve adult dunnarts from six sibling pairs (one female and one male per pair) were provided ad libitum access to three diets in a repeated measures design: cat food, cat food supplemented with raw lean beef (1:1), and cat food supplemented with cooked lean beef (1:1). Food intake, activity level, and fecal output were measured daily. Dunnarts significantly decreased food intake, increased protein digestion, and physical activity, but body mass was unchanged when on the high‐protein diet compared to the normal cat food diet. These observations suggest a capacity of dunnarts to maintain constant body mass using a dynamic balance of feeding, digestion, and activity. We also found a significant effect of family, with differences between families as large as the difference between the diet treatments, suggesting a genetic component to diet selection. The nutrient regulation responses of dunnarts to high‐protein diets and the strong family effects provide important messages for the management of populations of small carnivores, including the aspects of dietary manipulation and conservation of genetic diversity.Lihong Yuan, Shawn Wilder, David Raubenheimer, Stephen J. Simpson, Michelle Shaw, Bronwyn M. McAlla

Reflections on the Centenary of Sir William Osler: Science and Humanity are One, for Nursing and Medicine

Sir William Osler (1849-1991) was Regius Professor of Medicine at the University of Oxford in the UK and a founding professor at Johns Hopkins Hospital. The centenary of Osler’s death is a time for recognition in nursing, as well as medicine, of a pioneering and highly influential Oxford physician on both sides of the Atlantic, an influence that extended to nursing from the UK to the USA. This letter captures reflections and discussion on contemporary nursing issues from an Osler Seminar Series, held at the University of Oxford in 2019 to mark the Centenary of Sir William Osler’s death, focusing on his thinking and influence related to nursing. This extended letter illuminates issues on themes of science and humanity within a clinical and educational context, exploring a range of key contemporary nursing issues. These include the significance of interpersonal relations as they relate to care attitude and care technology; the therapeutic influence of the nurse; nursing education and clinical-academic development; the value of a life world perspective on nursing and wellbeing; and practice development within the context of person-centred workplace cultures. These issues are contextualised with examples from practice and include some from nursing developments and those illustrated in part by the clinical speciality of dermatological care. The letter concludes by considering the significance of the nursing service to promoting access to quality health care in the twenty-first century and its relevance to recognising the nursing contribution to universal health care through the WHO International Year(s) of the Nurse and Midwife in 2020-21

A prospective cohort study characterising patients declined emergency laparotomy: survival in the ‘NoLap’ population

Patients eligible for emergency laparotomy who do not proceed to surgery are not as well characterised as patients who do proceed to surgery. We studied patients eligible for laparotomy, as defined by National Emergency Laparotomy Audit criteria, from August 2015 to October 2016. We analysed the association of individual variables with survival and two composite scores: P‐POSSUM and a general survival model. Out of 314 patients, 214 (68%) underwent laparotomy and 100 (32%) did not. Median (IQR [range]) follow‐up was 1.3 (0.1–1.8 [0.0–2.5]) years for the cohort, 1.5 (1.1–2.0 [0.0–2.6]) years after laparotomy and 0.0 (0.0–1.1 [0.0–2.2]) years without laparotomy. There were 126/314 (40%) deaths in the follow‐up period, 52/214 (24%) deaths after laparotomy and 74/100 (74%) deaths without surgery. Ninety out of 126 deaths (71%) were within one month of hospital admission. Patient variables were different for the two groups, which when combined in the general survival model generated background median (IQR [range]) life expectancies of 12 (6–21 [0–49]) and 4 (2–6 [0–36]) years, respectively, p &lt; 0.0001. ‘Poor fitness’ precluded laparotomy in 74/100 (74%) patients. The decision to not operate involved a consultant less often than the decision to operate: 66/100 (66%) vs. 178/214 (83%), p = 0.001. Our study supports the contention that survival beyond 30 postoperative days could be predicted reasonably accurately. Survival in patients who did not have laparotomy was shorter than expected. Emergency laparotomy might have prolonged survival in some patients