scholarly journals statacons: An SCons-Based Build Tool for Stata

2022 ◽  
Author(s):  
Raymond Guiteras ◽  
Ahnjeong Kim ◽  
Brian Quistorff ◽  
Clayson Shumway
Keyword(s):  
External Shell

This paper presents statacons, an SCons-based build tool for Stata. Because of the integration of Stata and Python in recent versions of Stata, we are able to adapt SCons for Stata workflows without the use of an external shell or extensive configuration. We discuss the usefulness of build tools generally, provide examples of the use of statacons in Stata workflows, present key elements of the syntax of statacons, and discuss extensions, alternatives, and limitations. Appendices provide installation instructions and recommendations for collaborative workflows.

scholarly journals Effect of reduced pH on physiology and shell integrity of juvenile Haliotis iris (pāua) from New Zealand

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7670
Author(s):  
Vonda J. Cummings ◽  
Abigail M. Smith ◽  
Peter M. Marriott ◽  
Bryce A. Peebles ◽  
N. Jane Halliday
Keyword(s):  
New Zealand ◽  
Ambient Conditions ◽  
X Ray Diffraction ◽  
Shell Quality ◽  
External Shell ◽  
Seawater Ph ◽  
Mollusc Species ◽  
Higher Temperature ◽  
Combination Of Methods ◽  
Carbonate Composition

The New Zealand pāua or black footed abalone, Haliotis iris, is one of many mollusc species at potential risk from ocean acidification and warming. To investigate possible impacts, juvenile pāua (~24 mm shell length) were grown for 4 months in seawater pH/pCO2 conditions projected for 2100. End of century seawater projections (pHT 7.66/pCO2 ~1,000 μatm) were contrasted with local ambient conditions (pHT 8.00/pCO2 ~400 μatm) at two typical temperatures (13 and 15 °C). We used a combination of methods (morphometric, scanning electron microscopy, X-ray diffraction) to investigate effects on juvenile survival and growth, as well as shell mineralogy and integrity. Lowered pH did not affect survival, growth rate or condition, but animals grew significantly faster at the higher temperature. Juvenile pāua were able to biomineralise their inner nacreous aragonite layer and their outer prismatic calcite layer under end-of-century pH conditions, at both temperatures, and carbonate composition was not affected. There was some thickening of the nacre layer in the newly deposited shell with reduced pH and also at the higher temperature. Most obvious was post-depositional alteration of the shell under lowered pH: the prismatic calcite layer was thinner, and there was greater etching of the external shell surface; this dissolution was greater at the higher temperature. These results demonstrate the importance of even a small (2 °C) difference in temperature on growth and shell characteristics, and on modifying the effects at lowered pH. Projected CO2-related changes may affect shell quality of this iconic New Zealand mollusc through etching (dissolution) and thinning, with potential implications for resilience to physical stresses such as predation and wave action.

scholarly journals Morphometric and phylogenetic analyses of the Paleozoic Subulitoidea (Gastropoda)

1992 ◽  
Vol 6 ◽  
pp. 93-93
Author(s):  
Douglas H. Erwin
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Temporal Trends ◽  
Thin Sections ◽  
Middle Ordovician ◽  
Shell Form ◽  
External Shell ◽  
Morphometric Analyses ◽  
Angular Measurements ◽  
Permian Mass Extinction

The gastropod superfamily Subulitoidea first appeared during the Early-Middle Ordovician gastropod radiation, seemingly from within the pleurotomarid family Lophospiridea, and persisted with low diversity and generally low abundance through the Paleozoic. One species survived the end-Permian mass extinction, but like many other Paleozoic remnants, the clade became extinct in the mid-Triassic. Many members of the clade are homeomorphic with later ‘neogastropods' and have frequently been fingered as the ancestors of these later, predatory gastropods. There is however, no direct evidence for an ancestor-descendent relationship. Addressing this possibility and understanding of the systematics and evolutionary history of the clade has been complicated by relatively simple shell form and apparent paucity of shell characters. The strength of the morphological and probable ecologic similarities between subulitids and ‘neogastropods' raises the question why this clade was unable to capitalize on their position as perhaps the only predatory gastropods during the Paleozoic. Such questions of evolutionary history are best addressed within the context of a combination of morphometric and phylogenetic analyses which may resolve the systematic questions and reveal something of the evolutionary relationships of the clade.Morphometric analyses were performed on some 40 specimens covering the 13 described genera (and several undescribed forms). Both linear and angular measurements of external shell form and internal structure from axial thin sections were measured and apertures were analyzed using elliptical Fourier analysis (EFA). The number of specimens analyzed was intentionally limited because of difficulties obtaining specimens with sufficient preservation of the aperture. The results demonstrate the necessity, for this clade at least, of including a more complex description of apertural morphology than simple maximum length and width. Principle component analyses of the EFA data distinguishes complexity of the columellar folds along the first axis and basal rounding along the second - both biologically meaningful aspects of apertural form. Moreover, the occupation of a taxon-specific apertural space defined by the PCA increases through the Paleozoic. Further, the analyses suggest that the two traditionally recognized subfamilies of the Subulitidae (Ordovician-Devonian and Devonian-Triassic) each exhibit increased variance in the occupation of morphologic space, but additional data is required to confirm this pattern and determine if any temporal trends exist.Analyzing patterns of occupation of morphologic space requires a rigorously constructed phylogeny. A cladistic (parsimony) analysis of the superfamily was performed using 16 taxa and over 30 discrete morphologic characters. The resulting cladograms were plotted within the taxon-specific morphospaces produced by the morphometric analyses.

Nitrogen isotope sclerochronology - insights into coastal environmental conditions and Pinna nobilis ecology

2021 ◽  
Author(s):  
Melita Peharda ◽  
David Gillikin ◽  
Bernd Schöne ◽  
Anouk Verheyden-Gillikin ◽  
Hana Uvanović ◽  
...  
Keyword(s):  
High Resolution ◽  
Shell Growth ◽  
Time Interval ◽  
Shell Surface ◽  
Growth Axis ◽  
Pinna Nobilis ◽  
External Shell ◽  
Isotopic Baseline ◽  
The Mediterranean ◽  
Shell Powder

<p><em>Pinna nobilis</em> is a large bivalve endemic to the Mediterranean Sea that lives in shallow coastal areas. Due to its size and relatively fast shell growth rates, it is an interesting taxon for high resolution geochemical and sclerochronological research. Subsequently to previous analyses of δ<sup>18</sup>O and δ<sup>13</sup>C in <em>P. nobilis</em> shells, here, we investigate nitrogen isotopes in the carbonate-bound organic matrix (δ<sup>15</sup>N<sub>CBOM</sub>) of this species. Our objectives were to test if <em>P. nobilis</em> shells (i) can be used as an indicator of the isotopic baseline of the system, and (ii) is a good candidate for obtaining high-resolution temporal data on environmental δ<sup>15</sup>N variability. Due to the multiple mass mortality events of <em>P. nobilis</em> spreading throughout the Mediterranean, including the Adriatic Sea, we also tested if (iii) <em>P. nobilis</em> geochemistry changes as a response to diseases.</p><p>Shells were opportunistically collected by skin diving from 4 shallow coastal localities in the eastern Adriatic, as a part of a project on mortality monitoring. Specimens from Lim channel (October 2019), Kaštela Bay (January 2020) and Mali Ston Bay (November 2019) were collected alive, while in Pag Bay, shells of three recently dead specimens were collected in September 2020. Tissue and epibionts were removed and shells carefully cleaned and air-dried. Shell powder was collected by milling sample swaths by hand using a DREMEL Fortiflex drill equipped with a 300 μm tungsten carbide drill bit. For δ<sup>15</sup>N<sub>CBOM</sub> analysis, three shells from each locality were processed and three replicas were collected from each of these shells by milling shallow lines parallel to the growth axis from the internal shell surface. In addition, high-resolution δ<sup>15</sup>N<sub>CBOM</sub> data were obtained for one shell from Kaštela by milling lines (N=40) perpendicular to the major growth axis from the external shell surface. From this shell we also collected shell powder for δ<sup>18</sup>O<sub>shell</sub> and δ<sup>13</sup>C<sub>shell</sub> analysis to enable placing δ<sup>15</sup>N<sub>CBOM</sub> into temporal context. Isotope samples were analyzed Union College on an elemental analyzer - isotope ratio mass spectrometer.</p><p>Results indicate significant differences in δ<sup>15</sup>N<sub>CBOM</sub> between sampling localities, with lowest values recorded for shells from Pag Bay (3.73±0.36‰), and highest for shells sampled in Lim channel (7.04±0.63‰). High-resolution δ<sup>15</sup>N<sub>CBOM</sub> data obtained from the shell collected from Kaštela Bay corresponded to a time interval from spring 2018 to spring 2019. These data showed relatively small variations (5.02±0.33‰). However, δ<sup>15</sup>N<sub>CBOM</sub> values increased to 8.65±1.61‰ closest to the shell margin, and were coupled with a decrease in δ<sup>13</sup>C<sub>shell</sub> values, indicating that this animal was experiencing stressful conditions several months prior to its death. According to our findings, δ<sup>15</sup>N<sub>CBOM</sub> values serve as an indicator of the isotopic baseline of the ecosystem as well as a potential powerful tool to study bivalve physiology.</p><p>Research was the supported by the Croatian Science Foundation, research project BivACME.</p>

Growth Increments and Geochemical Variations in the Molluscan Shell

1985 ◽  
Vol 13 ◽  
pp. 72-87 ◽  
Author(s):  
Douglas S. Jones
Keyword(s):  
Shell Growth ◽  
Maximum Growth ◽  
Growth Increment ◽  
Growth Patterns ◽  
Random Disturbance ◽  
Growth Increments ◽  
Molluscan Shell ◽  
External Shell ◽  
Periodic Growth ◽  
Geochemical Variations

Perhaps the one structural feature of the molluscan shell which has historically attracted the most attention from biologists and paleobiologists alike is the banding or growth increment variation associated with so many molluscan species. Such growth patterns are often prominently displayed on the external surfaces of shells and have long been the focus of serious biological and paleontological research (see reviews by Clark, 1974; Lutz and Rhoads, 1980). The usefulness of external shell growth patterns in ecological or paleoecological contexts is limited, however, by both the inability to distinguish true periodic features from random disturbance marks and by the extreme crowding of growth lines near the margins of mature shells. In the last two decades these problems have been surmounted with the recognition of periodic growth patterns within molluscan shells. Internal shell growth patterns are known from all classes of mollusks, but those in the Bivalvia have been studied most extensively. This is a result of the relative ease with which a complete ontogenetic growth record can be obtained by sectioning a shell along the axis of maximum growth (Rhoads and Pannella, 1970). Analogous ontogenetic records are very difficult, if not impossible, to obtain from coiled or spiral shells (e.g., gastropods) using current techniques (Lutz and Rhoads, 1980). This chapter, then, aims to review the major types of internal shell growth patterns described within molluscan shells (mainly bivalves) and to discuss their origin and applications in ecology and paleoecology. Also taken up in this chapter is a brief consideration of geochemical variations (stable oxygen and carbon isotopes and trace and minor elements) within molluscan shells. Physical-chemical, environmental, and physiological influences on shell chemistry are discussed in relation to how biogeochemical variations in the shell may be used to reconstruct paleoenvironmental conditions.

Biosorption of thorium on the external shell surface of bivalve mollusks: The role of shell surface microtopography

Chemosphere ◽  
2012 ◽  
Vol 86 (6) ◽  
pp. 680-683 ◽  
Author(s):  
Michael Zuykov ◽  
Emilien Pelletier ◽  
Richard Saint-Louis ◽  
Antonio Checa ◽  
Serge Demers
Keyword(s):  
Bivalve Mollusks ◽  
Shell Surface ◽  
Surface Microtopography ◽  
External Shell

A Novel Radial Telescopic Tire Building Drum and its Kinematics Design

2012 ◽  
Vol 215-216 ◽  
pp. 207-211
Author(s):  
Yun Long Wang ◽  
Lei Zhang ◽  
Yu Hu Yang
Keyword(s):  
Design Method ◽  
Maximum Pressure ◽  
Interference Condition ◽  
Radial Tire ◽  
Mechanical Structure ◽  
Pressure Angle ◽  
External Shell ◽  
Contraction Ratio ◽  
Force Transfer ◽  
Tire Production

A novel radial telescopic tire building drum is proposed to meet the radial tire production requirements. After the discussion of the mechanical structure and transmission principle of this mechanism, the kinematics equations together with the formulas of contraction ratio and pressure angle are established. In order to optimize the characteristics of force-transfer, when taking the interference condition into consideration, a kinematics design method of this novel radial telescopic building drum is proposed, which can obtain the minimal value of mechanism maximum pressure angle and satisfy the demand of contraction ratio. The most important feature of this building drum is that the external shell is driven by the internal shell. Designer can derivative more design schemes by applying this transmission principle.

Versatile post-functionalization of the external shell of cowpea chlorotic mottle virus by using click chemistry

2014 ◽  
Vol 12 (24) ◽  
pp. 4065-4069 ◽  
Author(s):  
C. A. Hommersom ◽  
B. Matt ◽  
A. van der Ham ◽  
J. J. L. M. Cornelissen ◽  
N. Katsonis
Keyword(s):  
Click Chemistry ◽  
Mottle Virus ◽  
Cowpea Chlorotic Mottle Virus ◽  
External Shell ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle ◽  
Protein Shell ◽  
Post Functionalization

We present the modification of the outer protein shell of cowpea chlorotic mottle virus (CCMV) with linear and strained alkyne groups for post-functionalization by click chemistry.

A Method For Marking Small Juvenile Gastropods

1993 ◽  
Vol 73 (4) ◽  
pp. 963-966 ◽  
Author(s):  
Louis A. Gosselin
Keyword(s):  
Foraging Behaviour ◽  
Accurate Determination ◽  
Ecological Studies ◽  
Simple Method ◽  
Marine Gastropods ◽  
Small Juvenile ◽  
External Shell ◽  
Large Numbers ◽  
Invertebrate Larvae

Methods used to identify individual organisms consistently over time have been invaluable tools in ecological studies, enabling reliable assessments of time-dependent parameters such as growth and mortality, and an accurate determination of their variance. These methods have proved to be particularly amenable to gastropods owing to the presence of an external shell on which marks or tags can be applied with little or no adverse effects on the animal. Marking and tagging techniques have enabled the study of several ecological parameters in adult marine gastropods, including growth (Frank, 1965; Hughes, 1972; Palmer, 1983; Gosselin & Bourget, 1989), mortality (Frank, 1965; Hughes, 1972), movements (Frank, 1965; Chapman, 1986), and foraging behaviour (Menge, 1974; Hugheset al., 1992). Small organisms, however, can pose considerable problems for individual marking (Southwood, 1978). As a result, marking and tagging methods have seldom been applied to newly hatched or recently settled juvenile marine gastropods. Several methods have been developed for simultaneously labelling large numbers of invertebrate larvae (Levin, 1990), and some of these methods may be applicable to juvenile gastropods. The usefulness of these methods, however, is limited because all animals receive the same label and, consequently, individual animals cannot be recognized. To my knowledge, no method of individually marking very small juvenile marine gastropods has been documented. In fact, it is sometimes perceived that small juveniles cannot be individually marked due to their small size and sensitivity (Frank, 1965; Palmer, 1990). The object of this paper is to present a simple method of marking early juvenile gastropods, which consists of applying colour codes to the shells of individuals as small as 0·9 mm in length.

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