Rejoinder to Discussions on “Approval policies for modifications to machine learning‐based software as a medical device: A study of bio‐creep”

We thank the discussants for sharing their unique perspectives on the problem of designing automatic algorithm change protocols (aACPs) for machine learning‐based software as a medical device. Both Pennello et al. and Rose highlighted a number of challenges that arise in real‐world settings, and we whole‐heartedly agree that substantial extensions of our work are needed to understand if and how aACPs can be safely deployed in practice. Our work demonstrated that aACPs that appear to be harmless may allow for biocreep, even when the data distribution is assumed to be representative and stationary over time. While we investigated two solutions that protect against this specific issue, many more statistical and practical challenges remain and we look forward to future research on this topic.     

Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH.

A gel-stabilized gradient method that employed opposing gradients of Fe2+ and O2 was used to isolate and characterize two new Fe-oxidizing bacteria from a neutral pH, Fe(2+)-containing groundwater in Michigan. Two separate enrichment cultures were obtained, and in each the cells grew in a distinct, rust-colored band in the gel at the oxic-anoxic interface. The cells were tightly associated with the ferric hydroxides. Repeated serial dilutions of both enrichments resulted in the isolation of two axenic strains, ES-1 and ES-2. The cultures were judged pure based on (i) growth from single colonies in tubes at dilutions of 10(-7) (ES-2) (ES-2) and 10(-8) (ES-1); (ii) uniform cell morphologies, i.e., ES-1 was a motile long thin, bent, or S-shaped rod and ES-2 was a shorter curved rod; and (iii) no growth on a heterotrophic medium. Strain ES-1 grew to a density of 10(8) cells/ml on FeS with a doubling time of 8 h. Strain ES-2 grew to a density of 5 x 10(7) cells/ml with a doubling time of 12.5 h. Both strains also grew on FeCO3. Neither strain grew without Fe2+, nor did they grow with glucose, pyruvate, acetate, Mn, or H2S as an electron donor. Studies with an oxygen microelectrode revealed that both strains grew at the oxic-anoxic interface of the gradients and tracked the O2 minima when subjected to higher O2 concentrations, suggesting they are microaerobes. Phylogenetically the two strains formed a novel lineage within the gamma Proteobacteria. They were very closely related to each other and were equally closely related to PVB OTU 1, a phylotype obtained from an iron-rich hydrothermal vent system at the Loihi Seamount in the Pacific Ocean, and SPB OTU 1, a phylotype obtained from permafrost soil in Siberia. Their closest cultivated relative was Stenotrophomonas maltophilia. In total, this evidence suggests ES-1 and ES-2 are members of a previously untapped group of putatively lithotrophic, unicellular iron-oxidizing bacteria.     

Ultrastructure of the spermatozoa and eggs of the ocean pout (Macrozoarces americanus L.), an internally fertilizing marine fish

Ultrastructure of sperm and eggs of the ocean pout (Macrozoarces americanus L.), an internally fertilizing marine teleost, was examined by scanning and transmission electron microscopy. The results showed that the sperm do not have an acrosome but have a very long mid-piece (one to two times the sperm head length) containing numerous well-developed elongated mitochondria. The sperm also have two tails (is biflagellate) each consisting of nine peripheral and one central pair (9 ± 2) of microtubules. This long mid-piece and the biflagellate nature of the sperm appear to be associated with the long life-span of the sperm and with sperm dispersal in the ovary to fertilize the eggs internally. The ocean pout eggs are enveloped by a porous chorionic membrane similar to that found in other teleosts but have two micropyles, a condition likely related to a mechanism of egg fertilization which increases the egg fertlity in the presence of low sperm numbers. Following insemination, some biochemically undefined excretions appeared on the surface of fertilized eggs and led to the acquisition of adherent capability of the eggs which formed a tightly associated egg mass in sea water. © 1995 wiley-Liss, Inc.     

A stereological method for estimating fish fecundity

This paper describes the application and evaluation of a stereological method for counting fish oocytes. The method has been applied to herring, Clupea harengus L., Dover sole, Solea solea L., and mackerel, Scomber scombrus L., and compared with existing volumetric and/or automated particle counter methods. The stereological method has been shown to given similar results and to have a number of distinct advantages over the other methods.     

Characterization of a small cryptic plasmid from endophytic Pantoea agglomerans and its use in the construction of an expression vector

A circular cryptic plasmid named pPAGA (2,734 bp) was isolated from Pantoea agglomerans strain EGE6 (an endophytic bacterial isolate from eucalyptus). Sequence analysis revealed that the plasmid has a G+C content of 51% and contains four potential ORFs, 238(A), 250(B), 131(C), and 129(D) amino acids in length without homology to known proteins. The shuttle vector pLGM1 was constructed by combining the pPAGA plasmid with pGFPmut3.0 (which harbors a gene encoding green fluorescent protein, GFP), and the resulting construct was used to over-express GFP in E. coli and P. agglomerans cells. GFP production was used to monitor the colonization of strain EGE6gfp in various plant tissues by fluorescence microscopy. Analysis of EGE6gfp colonization showed that 14 days after inoculation, the strain occupied the inner tissue of Eucalyptus grandis roots, preferentially colonizing the xylem vessels of the host plants.     

Predominance of single paternity in the black spiny-tailed iguana: conservation genetic concerns for female-biased hunting

Because of female-biased illegal harvesting, knowledge about the genetic mating system of the black spiny-tailed iguana Ctenosaura pectinata is of primary interest for the conservation of this threatened species. Based on the high levels of multiple paternity found in clutches of many other reptiles, particularly in lizards, it is hypothesised that multiple paternity may also be common in black iguanas. This was investigated by using microsatellite DNA to estimate the number of males siring nine litters (9 mothers, 121 offspring genotyped at ten polymorphic loci) of black iguanas. Contrary to expectations, only 11% of sampled black iguana females produced litters consistent with being sired by multiple males. These data are the first evidence for the predominance of single paternity within an iguanid lizard, and suggest that black iguana may be more susceptible to loss of genetic variation in the face of gender-biased over-hunting pressure than previously thought.     

Combining contemporary and ancient DNA in population genetic and phylogeographical studies

The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed.     

A laboratory study on feeding plasticity of the shredder <Emphasis Type="Italic">Sericostoma vittatum</Emphasis> Rambur (Sericostomatidae)

Since litter input and availability of leaves in many streams is highly seasonal in Portugal, we investigated whether Sericostoma vittatum, a typical shredder, was able to grow using alternative food sources. To test this hypothesis we fed S. vittatum with Alnus glutinosa (alder, CPOM, coarse particulate organic matter), leaf powder from A. glutinosa and Acacia dealbata and FPOM (fine particulate organic matter) from a 5th and a >6th order river, the macrophyte Myriophyllum aquaticum and biofilm. Growth in S. vittatum was significantly influenced by the food item given (ANOVA, P = 0.0082). The food item promoting the highest growth was A. glutinosa, in the form of FPOM (6.48% day⁻¹) and CPOM (4.24% day⁻¹); all other forms of FPOM and biofilm provided relatively low growth rates (0.77–1.77% day⁻¹). The macrophyte M. aquaticum was also used as food source by S. vittatum and promoted intermediate growth (1.96% day⁻¹). Neither nitrogen, phosphorus nor caloric content was correlated with growth. However, since higher growth was achieved with alder, in the form of CPOM and FPOM, we concluded that the chemical content of food was more important for S. vittatum than the physical form of such food. This may partially explain why shredders are able to survive when leaves are scarce in streams. Handling editor: K. Martens