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Does Personhood Begin at Conception?
Published in Christopher Kaczor, The Ethics of Abortion, 2023
There are really two different, opposing standards at work here, each with its own difficulty. McMahan summarizes the two different theses in the following sentences: “We continue to exist as long as those areas of the brain in which consciousness is realized retain the capacity for consciousness. When the capacity is irreversibly lost, we cease to exist” (2005, pp. 1–2). The first sentence claims that actual capacity for consciousness is needed for our identity. A difficulty with this view is the possibility of our brains losing neural capacity and gaining it back. For centuries, serious damage to the hip meant an end to a person's capacity to walk. Now, we have full or partial hip replacement reenabling those who had lost the capacity to walk. We cannot currently perform surgery to repair injured parts of the brain, but it is, in principle, possible that lack of neural capacity could be restored for the victim of an accident or disease. If this takes place, and if the actual capacity for consciousness is necessary for our identity, then we could come into existence and leave existence many times over, as often as we were injured and had brain surgery to restore neural capacity. This is not a mere theoretical difficulty because brain swelling can cause a loss of neural capacity, which is only regained after the brain swelling ceases. We have the episodic problem in spades.
The Video Examination: What We Learnt
Published in Peter Tate, Francesca Frame, Bedside Matters, 2020
Well, with some notable exceptions, trainees did not convincingly demonstrate what they professed to believe in. In the MRCGP oral viva examination examiners were taught not just to expose the attitudes of the candidate, for or against termination for example, but to seek the justification of that attitude. The argument being that you can't really mark attitudes out of 10, but you can have a stab at rank-ordering the justifications. This is not easy, and one person's justification is another's bigotry. Justifications tend, of course, to be post hoc, cortical intellectualisations of inherently mid-brain feelings. In the oral examination all candidates, without exception, claimed they believed in, and practiced, the patient-centred method, and most could describe several consulting models and the concepts behind them to the satisfaction of the examiners. But in their videos, effective patient-centred communication was rare. It rapidly became clear that candidates’ attitudes were not necessarily what they claimed. We can say this with absolute certainty, because we watched so many consultations from so many doctors, and we found that only around 10% of doctors could demonstrate the behaviour of actually involving patients regularly in consultations which they themselves had selected to demonstrate just that. In 1985 Tuckett found the same, as had Byrne and Long a decade before us. We confirmed their findings, in spades as they say.
An Introduction to Statistics and Proposition Setting
Published in Jo-Anne Bright, Michael D. Coble, Forensic DNA Profiling, 2019
Jo-Anne Bright, Michael D. Coble
If event S is drawing a spade from a deck of cards, Pr(S) = 13/52, and event K is drawing a king from a deck of cards, Pr(K) = 4/52, then Pr(S or K) = 13/52 + 4/52 − 1/52. This is the probability of drawing a spade plus the probability of drawing a king minus the probability of drawing a king of spades.
Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis
Published in Gut Microbes, 2022
Maximilian Baumgartner, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, Olga Bochkareva, Vera Emelianenko, Harald Vogelsang, Michaela Lang, Anton Klotz, Birgit Moik, Athanasios Makristathis, David Berry, Stefanie Dabsch, Vineeta Khare, Christoph Gasche
Bacterial DNA was extracted using a phenol chloroform-based method. Whole-genome sequencing was performed using HiSeqV4 PE125 methodology. For genome assembly, the spades pipeline was used. Assemblies were submitted to NCBI for annotation. The CFSAN SNP pipeline was used with the E. coli reference genome O103:H2 12009 to construct an SNP matrix with the 57 strains from this study and 348 publicly available AEEC genomes of diverse pathotypes and one E. albertii genome. For phylogenomic maximum likelihood inference, IQ-TREE was applied with the best-fit model automatically selected by ModelFinder.41 For pangenome analysis, the Roary pipeline was used with standard parameters, followed by Scoary for the identification of associations between all genes in the accessory genome and EspG2 and EspV positivity.42 Pangenome composition was visualized with Phandango. To investigate the presence of known virulence factors, the VFDB database was used. For the detection of novel hypothetical secreted proteins and additional secretion systems, the EffectiveDB was applied. Pairwise comparison between EspG2-pos and EspV-pos genomes was performed with the Mann–Whitney U test, prevalences were compared using Fisher’s exact test, with Bonferroni correction for multiple comparisons. Sequencing data and assemblies are publicly accessible at NCBI under the project number PRJNA528578. Additional information on bioinformatic analysis can be found in the supplementary method section.
Contribution of biofilm formation genetic locus, pgaABCD, to antibiotic resistance development in gut microbiome
Published in Gut Microbes, 2020
Dachuan Lin, Kaichao Chen, Jiubiao Guo, Lianwei Ye, Ruichao Li, Edward Wai Chi Chan, Sheng Chen
Genomic DNA of representative E. coli isolates was extracted using the Invitrogen PureLink genomic DNA mini kit, following the manufacturer’s instructions. Genomic libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®(NEB) to obtain 2 × 150 bp paired-end reads for NextSeq 500 Illumina sequencing. After de novo assembly by SOAPdenovo2,24 the contigs were uploaded to CSI Phylogeny 1.2 (https://cge.cbs.dtu.dk/services/CSIPhylogeny/) for phylogenetic analysis. E. coli strain K-12 strain MG1655(NC_000913.3) was chosen as the reference genome.25 The SNP profile was obtained using iTOL to construct the Phylogenetic tree (http://itol.embl.de/index.shtml).26 To obtain the completed genome of strains E3 and E62, PacBio RSII single-molecule, real-time (SMRT) sequencing was performed at the Wuhan Institute of Biotechnology, Wuhan, China to create libraries of 20 kb. SPAdes was utilized to perform hybrid-assembly to obtain the complete sequence of these two isolates.27 The subsystem categories of the predicted ORFs were obtained from the SEED viewer.28 The complete genome sequences of the E. coli strains in this study were as follows: E. coli E62 (CP022393), E. coli E2 (NJIS00000000), E. coli E3 (NJIR00000000), E. coli E15 (NJIQ00000000), E. coli E21(NJIP00000000), and E. coli E27 (NJIO00000000).
The autoimmune susceptibility gene, PTPN2, restricts expansion of a novel mouse adherent-invasive E. coli
Published in Gut Microbes, 2020
Ali Shawki, Rocio Ramirez, Marianne R. Spalinger, Paul M. Ruegger, Anica Sayoc-Becerra, Alina N. Santos, Pritha Chatterjee, Vinicius Canale, Jonathan D. Mitchell, John C. Macbeth, Casey M. Gries, Michel L. Tremblay, Ansel Hsiao, James Borneman, Declan F. McCole
– Genome sequences of our mAIEC (strain UCR-PP2) and E. coli K12 (ATCC 25404) were obtained using shotgun DNA sequencing (Novogene, Sacramento, CA). Genomes were assembled using Spades 3.11.1 and annotated using Prokka 1.13.3.61,62 The genome of mAIEC was compared with the genome sequence of the human LF82 isolate.37 Putative virulence genes found in E. coli’s and other AIECs including LF82 were identified by comparing the known sequence of each gene from K12. Putative virulence genes common between mAIEC; another opportunistic mouse E. coli with some AIEC features, NC101; and the human LF82 AIEC; or genes unique to each isolate, were compared and the percent identity of each gene and predicted protein between the isolates was determined using EMBOSS Water.63,64