Wheaton College - Massachusetts

Abstract Haplotype networks are widely used in population genetics and phylogeography to visualize genealogical relationships among DNA sequences and to infer population structure, historical connectivity, and demographic processes. Existing software for haplotype network construction relies primarily on interactive graphical interfaces, which limits reproducibility, automation, and integration into modern bioinformatic workflows. Here, I introduce HapNet, an open-source Python package that enables automated construction, visualization, and summarization of haplotype networks directly from aligned FASTA files. HapNet is the first Python-native package designed specifically for automated, population-aware haplotype network construction and visualization from aligned FASTA files. HapNet implements a minimum-spanning-tree approach based on Hamming distances among haplotypes and incorporates population metadata encoded in sequence headers to produce population-aware network visualizations in which shared haplotypes are represented as pie charts and node sizes scale with haplotype frequency. In addition to a publication-ready network, HapNet generates machine-readable tabular output describing haplotype composition, population membership, and shared versus private haplotypes, facilitating downstream statistical analysis and reproducibility. Here, HapNet’s utility is demonstrated using mitochondrial DNA sequences from the shell-boring polychaete worm Polydora neocaeca , illustrating how the software reveals patterns of population connectivity and haplotype sharing. HapNet provides a reproducible, scriptable alternative to existing graphical tools and is freely available via the Python Package Index and GitHub.

Intimate partner violence (IPV) and mental health (MH) issues among women in Nepal are deeply influenced by complex intergenerational family dynamics and power hierarchies. The traditional power hierarchies often place mothers-in-law (MILs) in authoritative roles over daughters-in-law (DILs), limiting the latter's autonomy and decision-making power. We designed a multi-component family intervention called MILAP to lower depression and address intimate partner violence by improving communication, promoting gender equity, and improving family relationships. This paper explores the perceptions and experiences of DILs who received the MILAP intervention. A total of 61 families participated in a pilot study of the MILAP intervention. Of these, 8 families (comprising triads of daughter-in-law, mother-in-law, and husband) were purposively selected for in-depth interviews (IDIs). All interviews were conducted immediately after the intervention and at the 6-month follow-up to assess MILAP's sustainability and impact. A thematic approach was used to analyze the data, utilizing Dedoose data management software. Four major themes were identified: (1) Enhanced communication within the family, (2) Strengthened DIL's empowerment, (3) Improved relationship quality, and (4) Increased DIL's freedom of movement. Participants reported improvement in communication among family members, particularly by using active listening skills which in turn contributed to conflict reduction and a more harmonious family environment. DILs experienced increased empowerment. They were more involved in family decision-making as the family unit adopted more equitable gender norms. The intervention strengthened spousal relationship improved MIL-DIL interactions, facilitated mutual understanding, and reduced household stress. Additionally, MILAP enabled DILs to move more freely outside the home. This increased mobility expanded their social networks, as DILs participated in community events, visited natal families, and accessed health services. However, some participants expressed concerns about the long-term sustainability of these changes, highlighting the need for continued reinforcement. Our study underscores the importance of a family-based intervention in improving relationship quality and promoting autonomy among DILs experiencing IPV. The positive shifts perceived within families suggest promise for MILAP to strengthen support structures and address factors that may influence DIL's mental health. However, ongoing follow-up and reinforcement strategies are recommended to maintain the gains achieved from the intervention.

Metalloestrogens, metals and metalloids capable of mimicking or interfering with estrogen signaling, are emerging environmental contributors to breast cancer risk and endocrine therapy resistance. Compounds such as cadmium, arsenic, aluminum, and chromium bind to estrogen receptors or activate non-genomic pathways such as G protein-coupled estrogen receptor and epidermal growth factor receptor signaling, leading to aberrant proliferation, survival, and oxidative stress. These mechanisms promote epithelial–mesenchymal transition, genomic instability, and therapy resistance in estrogen receptor-positive breast cancer. Cadmium and arsenic can sustain estrogenic signaling and activate MAPK/ERK and PI3K/Akt pathways even under tamoxifen treatment, while arsenic-mediated BRCA1 methylation further reduces drug responsiveness. Limited studies suggest metalloestrogens may also attenuate the efficacy of aromatase inhibitors and selective estrogen receptor degraders by maintaining G protein-coupled estrogen receptor and oxidative stress signaling. Epidemiological evidence correlates elevated cadmium, nickel, and aluminum exposure with increased estrogen receptor-positive breast cancer incidence, yet clinical translation remains incomplete. Understanding metalloestrogen-mediated crosstalk between estrogen receptor-dependent and estrogen receptor-independent pathways will be essential for designing effective combination therapies and integrating environmental toxicology into precision breast cancer management.

The digenetic trematode Proctoeces maculatus is a cosmopolitan parasite that infects various invertebrates and fish hosts, including the blue mussel, Mytilus edulis, along the northeastern U.S. coast. Despite its impact on mussel fitness and the region's aquaculture, little is known about the genetic diversity and connectivity of P. maculatus in this region. This study provides the first genetic characterization of P. maculatus populations in New England using the D1-D3 region of the 28S ribosomal RNA gene. Bayesian phylogenetic analysis and a haplotype network were used to assess genetic variation and connectivity across six localities in Maine, New York, and southern New England, and to compare these populations to global samples. Our results revealed distinct geographic structuring of P. maculatus haplotypes. The ME1 haplotype, unique to Maine, reflects either recent range expansion or isolation driven by environmental and biogeographic factors, such as Cape Cod's role as a phylogeographic barrier. The most common haplotype, US1, was shared by populations in southern New England, New York, and a single specimen from Tunisia, indicating possible historical or anthropogenic connectivity. Two divergent haplotypes from Mississippi and Chile likely represent misidentifications or cryptic species. These findings support the hypothesis that P. maculatus is likely a cryptic species complex. Molecular evidence suggests connectivity across distant regions, emphasizing the role of host movement in parasite dispersal. Continued genetic studies, particularly from under-sampled regions, are needed to unravel the diversity and biogeography of P. maculatus and its potential impact on declining mussel populations.

Oral reading assessments provide teachers with valuable information about children’s reading abilities, which can then inform instruction. However, the structure of some oral reading assessments (e.g., running records) have been critiqued, especially when they are used to provide students with a prescribed “reading level”. The purpose of the current study was to support in-service teachers (ISTs) and pre-service teachers (PSTs) in implementing a highly supportive oral reading assessment, the Listening to Reading–Watching While Writing Protocol (LTR—WWWP), which guides teachers towards specific instructional targets for individual children instead of a score or level. We were curious about the ISTs’ and PSTs’ perceptions of the protocol, including its affordances and limitations. Data sources were the ISTs’ feedback responses and the researcher fieldnotes after five professional learning sessions, as well as the PSTs’ survey responses after learning about the protocol during literacy method courses. Results revealed that both the ISTs and PSTs found the protocol to be useful, and they appreciated the concrete information it provides regarding multiple components of literacy (e.g., decoding, comprehension monitoring). However, they also noted logistical concerns regarding assessment implementation and selecting authentic texts. Results also revealed misconceptions about the assessment, which subsequently informed revisions of the LTR-WWWP and the related professional learning.