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Research experience provides critical training for new biomedical research scientists. Students from underrepresented populations studying science, technology, engineering, and mathematics (STEM) are increasingly recruited into research pathways to diversify STEM fields. However, support structures outside of research settings designed to help these students navigate biomedical research pathways are not always available; nor are program support components outside the context of laboratory technical skills training and formal mentorship well understood. This study leveraged a multi-institutional research training program, Enhancing Cross-Disciplinary Infrastructure and Training at Oregon (EXITO), to explore how nine institutions designed a new curricular structure (Enrichment) to meet a common goal of enhancing undergraduate research training and student success. EXITO undergraduates participated in a comprehensive, 3-year research training program with the Enrichment component offered across nine sites: three universities and six community colleges, highly diverse in size, demographics, and location. Sites' approaches to supporting students in the training program were studied over a 30-month period. All sites independently created their own nonformal curricular structures, implemented interprofessionally via facilitated peer groups. Site data describing design and implementation were thematically coded to identify essential programmatic components across sites, with student feedback used to triangulate findings. Enrichment offered students time to critically reflect on their interests, experiences, and identities in research; network with peers and professionals; and support negotiation of hidden and implicit curricula. Students reported the low-pressure setting and student-centered curriculum balanced the high demands associated with academics and research. Core curricular themes described Enrichment as fostering a sense of community among students, exposing students to career paths and skills, and supporting development of students' professional identities. The non-formal, interprofessional curricula enabled students to model diverse biomedical identities and pathways for each other while informing institutional structures to improve diverse undergraduate students' success in academia and research.

A partial mitochondrial DNA Cytochrome Oxidase subunit I (mtCOI) gene haplotype variant of the coconut rhinoceros beetle (CRB) Oryctes rhinoceros, classed as 'CRB-G (clade I)', has been the focus of much research since 2007, with reports of invasions into new Pacific Island locations (e.g., Guam, Hawaii, Solomons Islands). For numerous invasive species, inference of invasion biology via whole genome is superior to assessments via the partial mtCOI gene. Here, we explore CRB draft mitochondrial genomes (mitogenomes) from historical and recent collections, with assessment focused on individuals associated within the CRB-G (clade I) classification. We found that all Guam CRB individuals possessed the same mitogenome across all 13 protein-coding genes and differed from individuals collected elsewhere, including 'non-Guam' individuals designated as CRB-G (clade I) by partial mtCOI assessment. Two alternative ATP6 and COIII partial gene primer sets were developed to enable distinction between CRB individuals from Guam that classed within the CRB-G (clade I) haplotype grouping and CRB-G (Clade I) individuals collected elsewhere. Phylogenetic analyses based on concatenated ATP6–COIII genes showed that only Guam CRB-G (clade I) individuals clustered together, and therefore Guam was not the source of the CRB that invaded the other locations in the Pacific assessed in this study. The use of the mtCOI and/or mtCOIII genes for initial molecular diagnosis of CRB remained crucial, and assessment of more native CRB populations will further advance our ability to identify the provenance of CRB invasions being reported within the Pacific and elsewhere. [ABSTRACT FROM AUTHOR]

We report biosecurity interceptions of Oryctes rhinoceros in Australia, New Zealand, Guam, United States, and other jurisdictions to provide the first such published assessment for this highly invasive species. Between 2003 and July 2023 New Zealand found O. rhinoceros 13 times. Between 2002 and July 2023 Australia found Oryctes rhinoceros 14 times. Since 2017 inspections in Guam detected individuals twice. Between 2003 and 2014, beetles were found eight times at ports in the United States. No credible interceptions were made in the European Union. Four other intercepts were reported from two other jurisdictions. There were very little commonalities among the intercept data. All but one detection were of adults, and of the 14 adults that were sexed, eight were female and six were male. From the Australian data, which included month of detection, there was no seasonality associated with detections. Detections were associated with a broad array of commodities or situations. Oryctes rhinoceros appears to be a generalist passenger, being accidentally transported by a wide variety of means at any time. This finding indicates that there is little possibility of focusing on any specific commodity, packaging, vessel, or season to detect accidental transport of this species. Instead, biosecurity vigilance is required on all goods and vessels arriving at, or leaving, destinations. [ABSTRACT FROM AUTHOR]

A high-density genetic linkage map of papaya, previously developed using an [F.sub.2] mapping population derived from the intraspecific cross AU9 x SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents ~71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution. Key words: Cacica papaya, DNA marker, genetic mapping, linkage groups, microsatellite. Une carte genetique a haute densite produite precedemment chez la papaye au moyen dune population [F.sub.2] issue d'un croisement intraspecifique AU9 x SunUp a ete bonifiee par l'ajout de marqueurs AFLP. La carte genetique exhaustive decrite dans ce travail s'etend sur 945,2 cM et couvre neuf grouper de liaison majeurs et cinq groupes mineurs qui totalisent 712 SSR, 277 AFLP et un marqueur morphologique. La densite moyenne des marqueurs pour les neuf groupes majeurs est de 0,9 cM entre marqueurs adjacents et le nombre de breches >5 cM a ete reduit de 48 a 27 dans cette nouvelle carte. Les AFLP generes au moyen de combinaisons d'amorces EcoRI/MseI etaient distribues sur l'ensemble des 14 groupes de liaison et ont entraine plusieurs rearrangements importants de l'ordre des locus au rein des neuf groupes de liaison majeurs. L'integration des marqueurs AFLP a entraine une liaison genetique accrue entre locus et a ainsi reduit la taille des groupes de liaison LG1, 2 et 4, laquelle etait surestimee sur la carte precedente, et a permis de corriger l'ordre des marqueurs sur LG8. La suppression de la recombinaison au sein de la region Y specifique aux males (MSY) sur LG1 est davantage confirmee par l'addition de 27 marqueurs AFLP affichant une co-segregation avec le sexe. Un grand segment entourant la region MSY et presentant une distorsion de la segregation s'etend sur 54,4 cM et represente ~71 % du groupe de liaison. Cette carte genetique exhaustive a haute densite fournit un cadre pour la cartographie de caracteres quantitatifs, la cartographie fine ainsi quo des etudes de genomique comparee du developpement et de l'evolution des especes cultivees. Mots-cles : Cacica papaya, marqueur de l'ADN, cartographie genetique, groupes de liaison, microsatellite. [Traduit par la Redaction], Introduction Papaya (Cacica papaya L.) is grown throughout the tropics and subtropics primarily for fresh market fruit and to some extent for latex production for use in a wide range [...]

The UCSC Kestrel could be considered as a single-board parallel processor able to perform its target applications as fast as a single-purpose accelerator and also to be intuitively programmed. It was found that Kestrel was not a programmable sequence analysis engine, but a small-scale massively parallel processor.

We describe an approach to optimization based on a multiple-restart quasi-Hopfield network where the only problem-specific knowledge is embedded in the energy function that the algorithm tries to minimize. We apply this method to three different variants of the graph coloring problem: the minimum coloring problem, the spanning subgraph k-coloring problem, and the induced subgraph k-coloring problem. Though Hopfield networks have been applied in the past to the minimum coloring problem, our encoding is more natural and compact than almost all previous ones. In particular, we use k-state neurons while almost all previous approaches use binary neurons. This reduces the number of connections in the network from [(Nk).sup.2] to [N.sup.2] asymptotically and also circumvents a problem in earlier approaches, that of multiple colors being assigned to a single vertex. Experimental results show that our approach compares favorably with other algorithms, even nonneural ones specifically developed for the graph coloring problem. Index Terms--Energy functions, energy minimization, graph coloring, Hopfield neural networks, optimization, simulated annealing.

The architectural landscape of high-performance computing stretches from superscalar uniprocessor to explicitly parallel systems to dedicated hardware implementations of algorithms. Single-purpose hardware can achieve the highest performance and uniprocessors can be the most programmable. Between these extremes, programmable and reconfigurable architectures provide a wide range of choice in flexibility, programmability, computational density, and performance. The UCSC Kestrel parallel processor strives to attain single-purpose performance while maintaining user programmability. Kestrel is a single-instruction stream, multiple- data stream (SIMD) parallel processor with a 512-element linear array of 8-bit processing elements. The system design focuses on efficient high-throughput DNA and protein sequence analysis, but its programmability enables high performance on computational chemistry, image processing, machine learning, and other applications. The Kestrel system has had unexpected longevity in its utility due to a careful design and analysis process. Experience with the system leads to the conclusion that programmable SIMD architectures can excel in both programmability and performance. This paper presents the architecture, implementation, applications, and observations of the Kestrel project at the University of California at Santa Cruz. [ABSTRACT FROM AUTHOR]

Carotenoid pigments in fruits are indicative of the ripening process and potential nutritional value. Papaya (Carica papaya) fruit flesh color is caused by the accumulation of lycopene or beta-carotenoids in chromoplasts. It is a distinct feature affecting nutritional composition, fruit quality, shelf life, and consumer preference. To uncover the molecular basis of papaya flesh color, we took map-based cloning and candidate gene approaches using integrated genetic and physical maps. A DNA marker tightly linked to flesh color colocalized on a contig of the physical map with a cDNA probe of the tomato (Solanum lycopersicum) chromoplast-specific lycopene beta-cyclase, CYC-b. Candidate gene sequences were obtained from amplified fragments and verified by sequencing two bacterial artificial chromosomes containing the two alleles. Sequence comparison revealed a 2-bp insertion in the coding region of the recessive red flesh allele resulting in a frame-shift mutation and a premature stop codon. A color complementation test in bacteria confirmed that the papaya CpCYC-b is the gene controlling fruit flesh color. Sequence analysis of wild and cultivated papaya accessions showed the presence of this frame-shift mutation in all red flesh accessions examined. Evaluation of DNA markers near CpCYC-b revealed a recombination hot spot, showing that CpCYC-b is located in a gene-rich region with a recombination rate at 3.7 kb per centimorgan, more than 100-fold higher than the genome average at 400 kb per centimorgan. Conserved microsynteny of the CpCYC-b region is indicated by colinearity of two to four genes between papaya, Arabidopsis (Arabidopsis thaliana), grape (Vitis vinifera), and tomato. Our results enhanced our understanding of papaya flesh color inheritance and generated new tools for papaya improvement.