Distribution, Hybridization, and Taxonomic Status of Two-lined Salamanders (\u3ci\u3eEurycea bislineata\u3c/i\u3e complex) in Virginia and West Virginia

We used three diagnostic protein markers to examine salamanders of the Eurycea bislineata complex at 80 localities in Virginia and West Virginia. Two groups were strongly differentiated and met at a narrow contact zone. Rare hybridization was observed as well as limited introgression up to 5 km north and 10 km south of the contact zone. At the contact zone, 1% F1, 2% F2, 32% backcross, and 66% parental genotypes were observed. This pattern of parapatric distribution with limited hybridization and introgression argues for the recognition of Eurycea bislineata and E. cirrigera as separate species

Stitching of near-nulled subaperture measurements

A metrology system for measuring aspheric test objects by subaperture stitching. A wavefront-measuring gauge having a limited capture range of wavefront shapes collects partially overlapping subaperture measurements over the test object. A variable optical aberrator reshapes the measurement wavefront with between a limited number of the measurements to maintain the measurement wavefront within the capture range of the wavefront-measuring gauge. Various error compensators are incorporated into a stitching operation to manage residual errors associated with the use of the variable optical aberrator

PromptSet: A Programmer's Prompting Dataset

The rise of capabilities expressed by large language models has been quickly followed by the integration of the same complex systems into application level logic. Algorithms, programs, systems, and companies are built around structured prompting to black box models where the majority of the design and implementation lies in capturing and quantifying the `agent mode'. The standard way to shape a closed language model is to prime it for a specific task with a tailored prompt, often initially handwritten by a human. The textual prompts co-evolve with the codebase, taking shape over the course of project life as artifacts which must be reviewed and maintained, just as the traditional code files might be. Unlike traditional code, we find that prompts do not receive effective static testing and linting to prevent runtime issues. In this work, we present a novel dataset called PromptSet, with more than 61,000 unique developer prompts used in open source Python programs. We perform analysis on this dataset and introduce the notion of a static linter for prompts. Released with this publication is a HuggingFace dataset and a Github repository to recreate collection and processing efforts, both under the name \texttt{pisterlabs/promptset}.Comment: 8 pages, ICSE '24 LLM4Code Worksho

Book Reviews

GREAT COURT-MARTIAL CASES. By Joseph DiMona. New York: Grosset & Dunlap Publishers, 1972. Pp. xi, 291. $6.95. THE CONCEPT OF REPRESENTATION. By Hanna Fenichel Pitkin. Berkeley: University of Califorina [sic] Press, 1972. Pp. 323.$3.65. THE NEW URBAN POLITICS: CITIES AND THE FEDERAL GOVERNMENT. Edited by Douglas M. Fox. Pacific Palisades: Goodyear Publishing Company, Inc., 1972. Pp. xiv, 303. $4.95

Measurement Via Optical Near-Nulling and Subaperture Stitching

A subaperture stitching interferometer system provides near-nulling of a subaperture wavefront reflected from an object of interest over a portion of a surface of the object. A variable optical element located in the radiation path adjustably provides near-nulling to facilitate stitching of subaperture interferograms, creating an interferogram representative of the entire surface of interest. This enables testing of aspheric surfaces without null optics customized for each surface prescription. The surface shapes of objects such as lenses and other precision components are often measured with interferometry. However, interferometers have a limited capture range, and thus the test wavefront cannot be too different from the reference or the interference cannot be analyzed. Furthermore, the performance of the interferometer is usually best when the test and reference wavefronts are nearly identical (referred to as a null condition). Thus, it is necessary when performing such measurements to correct for known variations in shape to ensure that unintended variations are within the capture range of the interferometer and accurately measured. This invention is a system for nearnulling within a subaperture stitching interferometer, although in principle, the concept can be employed by wavefront measuring gauges other than interferometers. The system employs a light source for providing coherent radiation of a subaperture extent. An object of interest is placed to modify the radiation (e.g., to reflect or pass the radiation), and a variable optical element is located to interact with, and nearly null, the affected radiation. A detector or imaging device is situated to obtain interference patterns in the modified radiation. Multiple subaperture interferograms are taken and are stitched, or joined, to provide an interferogram representative of the entire surface of the object of interest. The primary aspect of the invention is the use of adjustable corrective optics in the context of subaperture stitching near-nulling interferometry, wherein a complex surface is analyzed via multiple, separate, overlapping interferograms. For complex surfaces, the problem of managing the identification and placement of corrective optics becomes even more pronounced, to the extent that in most cases the null corrector optics are specific to the particular asphere prescription and no others (i.e. another asphere requires completely different null correction optics). In principle, the near-nulling technique does not require subaperture stitching at all. Building a near-null system that is practically useful relies on two key features: simplicity and universality. If the system is too complex, it will be difficult to calibrate and model its manufacturing errors, rendering it useless as a precision metrology tool and/or prohibitively expensive. If the system is not applicable to a wide range of test parts, then it does not provide significant value over conventional null-correction technology. Subaperture stitching enables simpler and more universal near-null systems to be effective, because a fraction of a surface is necessarily less complex than the whole surface (excepting the extreme case of a fractal surface description). The technique of near-nulling can significantly enhance aspheric subaperture stitching capability by allowing the interferometer to capture a wider range of aspheres. More over, subaperture stitching is essential to a truly effective near-nulling system, since looking at a fraction of the surface keeps the wavefront complexity within the capability of a relatively simple nearnull apparatus. Furthermore, by reducing the subaperture size, the complexity of the measured wavefront can be reduced until it is within the capability of the near-null design

Calmodulin disruption impacts growth and motility in juvenile liver fluke

BACKGROUND: Deficiencies in effective flukicide options and growing issues with drug resistance make current strategies for liver fluke control unsustainable, thereby promoting the need to identify and validate new control targets in Fasciola spp. parasites. Calmodulins (CaMs) are small calcium-sensing proteins with ubiquitous expression in all eukaryotic organisms and generally use fluctuations in intracellular calcium levels to modulate cell signalling events. CaMs are essential for fundamental processes including the phosphorylation of protein kinases, gene transcription, calcium transport and smooth muscle contraction. In the blood fluke Schistosoma mansoni, calmodulins have been implicated in egg hatching, miracidial transformation and larval development. Previously, CaMs have been identified amongst liver fluke excretory-secretory products and three CaM-like proteins have been characterised biochemically from adult Fasciola hepatica, although their functions remain unknown. METHODS: In this study, we set out to investigate the biological function and control target potential of F. hepatica CaMs (FhCaMs) using RNAi methodology alongside novel in vitro bioassays. RESULTS: Our results reveal that: (i) FhCaMs are widely expressed in parenchymal cells throughout the forebody region of juvenile fluke; (ii) significant transcriptional knockdown of FhCaM1-3 was inducible by exposure to either long (~200 nt) double stranded (ds) RNAs or 27 nt short interfering (si) RNAs, although siRNAs were less effective than long dsRNAs; (iii) transient long dsRNA exposure-induced RNA interference (RNAi) of FhCaMs triggered transcript knockdown that persisted for ≥ 21 days, and led to detectable suppression of FhCaM proteins; (iv) FhCaM RNAi significantly reduced the growth of juvenile flukes maintained in vitro; (v) FhCaM RNAi juveniles also displayed hyperactivity encompassing significantly increased migration; (vi) both the reduced growth and increased motility phenotypes were recapitulated in juvenile fluke using the CaM inhibitor trifluoperazine hydrochloride, supporting phenotype specificity. CONCLUSIONS: These data indicate that the Ca(2+)-modulating functions of FhCaMs are important for juvenile fluke growth and movement and provide the first functional genomics-based example of a growth-defect resulting from gene silencing in liver fluke. Whilst the phenotypic impacts of FhCaM silencing on fluke behaviour do not strongly support their candidature as new flukicide targets, the growth impacts encourage further consideration, especially in light of the speed of juvenile fluke growth in vivo. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-016-1324-9) contains supplementary material, which is available to authorized users

Proteomic profiling and protein identification by MALDI-TOF mass spectrometry in unsequenced parasitic nematodes.

Lack of genomic sequence data and the relatively high cost of tandem mass spectrometry have hampered proteomic investigations into helminths, such as resolving the mechanism underpinning globally reported anthelmintic resistance. Whilst detailed mechanisms of resistance remain unknown for the majority of drug-parasite interactions, gene mutations and changes in gene and protein expression are proposed key aspects of resistance. Comparative proteomic analysis of drug-resistant and -susceptible nematodes may reveal protein profiles reflecting drug-related phenotypes. Using the gastro-intestinal nematode, Haemonchus contortus as case study, we report the application of freely available expressed sequence tag (EST) datasets to support proteomic studies in unsequenced nematodes. EST datasets were translated to theoretical protein sequences to generate a searchable database. In conjunction with matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), Peptide Mass Fingerprint (PMF) searching of databases enabled a cost-effective protein identification strategy. The effectiveness of this approach was verified in comparison with MS/MS de novo sequencing with searching of the same EST protein database and subsequent searches of the NCBInr protein database using the Basic Local Alignment Search Tool (BLAST) to provide protein annotation. Of 100 proteins from 2-DE gel spots, 62 were identified by MALDI-TOF-MS and PMF searching of the EST database. Twenty randomly selected spots were analysed by electrospray MS/MS and MASCOT Ion Searches of the same database. The resulting sequences were subjected to BLAST searches of the NCBI protein database to provide annotation of the proteins and confirm concordance in protein identity from both approaches. Further confirmation of protein identifications from the MS/MS data were obtained by de novo sequencing of peptides, followed by FASTS algorithm searches of the EST putative protein database. This study demonstrates the cost-effective use of available EST databases and inexpensive, accessible MALDI-TOF MS in conjunction with PMF for reliable protein identification in unsequenced organisms