Research collection

SEPS:PRISM methods for specimen linked parasite morphology

We specify a reproducible route from specimen images to defensible morphological claims. SEPS:PRISM separates acquisition, boundary review, diagnostic measurement, candidate comparison and expert interpretation. We define the mathematical quantities that support conventional measurements, polygon descriptors, elliptic Fourier analysis and landmark shape analysis, then connect each quantity to calibration, tracing and sampling assumptions. The accompanying empirical analyses use recovered host counts, two photographed nematode profiles and published pentastome landmarks. They demonstrate specific computations rather than validated automated identification. We treat image readability, measurement accuracy and taxonomic adequacy as separate outcomes. This distinction allows useful observations to survive incomplete records while preventing a polished derivative from supplying evidence that the specimen never provided.

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SEPS FUZZARIA Evidence and Claim Limits Final · PDF

SEPS HookFuse Morphometric Methods Final · PDF

SEPS PRISM Research Architecture Final · PDF

SEPS TEGUMENT Source and Boundary Review Final · PDF

Source linked morphometry of two nematode image profiles

We recover two visible rim profiles from one brightfield nematode photograph and compute measurements from saved source-coordinate polygons. The profiles have areas of 2856.2 and 3292.88 squared source pixels, maximum Feret diameters of 68.84 and 73.54 pixels, and circularities of 0.9631 and 0.9766. We then calculate elliptic Fourier coefficients directly from the actual traces and quantify reconstruction error over 512 perimeter positions. At eight harmonics, root mean squared reconstruction error reaches approximately 0.097 and 0.116 source pixels. These small errors describe the selected polygons rather than anatomical accuracy. We retain neutral region labels, explicit tracing provenance and missing physical calibration. The study supplies a reproducible geometric replacement for ambiguous legacy figures while reserving taxonomic and biological comparisons for independently reviewed, comparable specimens.

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Host grouped reanalysis of published pentastome landmarks

We reanalyze published Raillietiella orientalis landmark configurations while preserving host grouping and an unresolved repeated specimen identifier. The source contains 39 ten-landmark configurations, 38 printed specimen identifiers and 14 host groups across five host species. Our primary analysis excludes both configurations with the ambiguous identifier and retains 37 configurations. Generalized Procrustes alignment and PCA assign 35.08% and 20.21% of shape variance to the first two components. An exploratory comparison of equally weighted host means gives a host-label permutation p value of 0.2387. Alternative repeated-identifier decisions change that value to 0.1192, 0.1203 or 0.0993. These results concern a specifically defined secondary analysis and do not reproduce all estimands in the original publication. The study demonstrates how identity and sampling hierarchy affect a reproducible reference comparison.

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Source linked scanning electron microscopy: comparative morphology and calibration corrections

We reconcile two visually similar but biologically distinct scanning electron microscopy sources. The multipanel montage depicts Linguatula serrata from Shamsi and colleagues, whereas the three-panel image depicts Raillietiella orientalis from Sapion-Miranda and colleagues. We retain their identities and source attributions. A recorded endpoint pair and a 100 micrometer scale bar in the Linguatula montage yield a projected separation of 137.18 micrometers. A selected endpoint and bar perturbation produces a sensitivity range of 131.02 to 143.52 micrometers, which we do not interpret as a confidence interval. The source comparison supports careful character documentation and illustrates why a measurement can be reproducible while its anatomical interpretation still requires review. We also identify conflicting scale overlays in three legacy SEM figures, retire the unsupported dimensions, and recover an overview that retains its original 500 micrometer instrument bar.

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Parasite burden records and ecological inference in South Florida

We reconstruct a 33-row host-count transcription and distinguish the questions it can answer from those that require examination-level evidence. The archive contains 28 cottonmouth records with 178 recorded parasites and five banded watersnake records with two. Sixteen cottonmouth rows and one watersnake row contain positive values. Two cottonmouth rows account for 57.3% of the cottonmouth count. We recalculate denominator-specific summaries, conditional uncertainty, count concentration and leave-one-record-out influence. We also reconcile the separate 26-row county summary and the positive lizard series without pooling their observational units. We develop a specimen-linked ecological analysis that separates detection, burden, coinfection and transmission. The resulting data and figures provide reproducible descriptive findings while leaving population prevalence, taxon-specific interaction and geographic risk unresolved.

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SEPS South Florida Parasite Research Final · PDF

Microscopy evidence and inference in Cyclospora research

We examine how a microscopy reference can support recognition without implying viability, infectivity or validated automated diagnosis. We reconstruct the five-reader comparison reported by Ma and colleagues and pair it with authenticated CDC DPDx images. Across five readers, ultraviolet fluorescence agreement ranges from 74% to 94%, whereas modified acid-fast agreement ranges from 80% to 90% on the same 50-specimen set. Reader dependence, shared specimens and differences among biological endpoints prevent a single accuracy value from summarizing the problem. We specify source-linked image records and a prospective paired evaluation within SEPS:PRISM. The resulting gallery and reader comparison support education and study design; they do not establish clinical performance of SEPS.

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SEPS Cyclospora Comparative Microscopy Final · PDF

SEPS PARAPLEX analysis of recorded reptile parasite assemblages

We apply the PARAPLEX ecological layer of SEPS:PRISM to 194 reptile observation rows in the recovered necropsy master workbook. The rows identify 81 hosts. Seventy-three hosts have positive parasite-group records and eight have explicit none entries. Forty-seven hosts have records in at least two broad groups. We retain unknown group cells and do not estimate population prevalence. The pentastome subtotal comprises 33 recorded organisms across 20 Basiliscus vittatus hosts, two across two Anolis equestris hosts and three in one Thamnophis sauritus. The first two components reconcile the 35-organism positive lizard summary at aggregate level. We preserve five repeated sample keys and separate 12 follow-up identification rows from new examinations. Five follow-up rows have candidates with agreeing host labels and counts; two have host-label conflicts, three have count mismatches and two lack a sample-key match. The resulting figures and tables support reproducible descriptions of the archive while identifying exactly which links and observation fields constrain ecological inference.

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SEPS PARAPLEX Recorded Assemblages Final · PDF