MSIreg: an R package for unsupervised coregistration of mass spectrometry and H&E images.

Summary: Joint analysis of mass spectrometry images (MS images) and microscopy images of hematoxylin and eosin (H&E) stained tissues assists pathologists in characterizing the morphological structure of the tissues, and in performing diagnosis. Unfortunately, the analysis is undermined by substantial differences between these modalities in terms of aspect ratios, spatial resolution, number of channels in each image, as well as by large global or small local elastic spatial deformations of one image with respect to the other. Therefore, accurate coregistration of the images is a critical pre-requisite for their joint interpretation.

Evolutionary innovation accelerates morphological diversification in pufferfishes and their relatives.

Evolutionary innovations have played an important role in shaping the diversity of life on Earth. However, how these innovations arise and their downstream effects on patterns of morphological diversification remain poorly understood. Here, we examine the impact of evolutionary innovation on trait diversification in tetraodontiform fishes (pufferfishes, boxfishes, ocean sunfishes, and allies).

New species of redbait from the Philippines (Teleostei, Emmelichthyidae, ).

We describe a new species of redbait in the genus collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs.

Correlation of wastewater surveillance data with traditional influenza surveillance measures in Cook County, Illinois, October 2022-April 2023.

Influenza is a respiratory illness that can result in serious outcomes, particularly among persons who are immunocompromised, aged <5 years or aged >65 years. Traditional influenza surveillance approaches rely upon syndromic surveillance of emergency departments and public health reporting from clinicians and laboratories. Wastewater surveillance infrastructure developed to monitor SARS-CoV-2 is being used for influenza surveillance in the Chicago area.

Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis.

Cardinal v.3 is an open-source software for reproducible analysis of mass spectrometry imaging experiments. A major update from its previous versions, Cardinal v.

The mitochondrial genome of the endangered Spiny Butterfly Ray (Linnaeus 1758) (Myliobatiformes: Gymnuridae) provides insights into cryptic lineages.

The Spiny Butterfly Ray, , is found in tropical and temperate coastal waters with a discontinuous distribution: it occurs along the east coast of the United States of America, Brazil, and Uruguay in the western Atlantic Ocean, from Portugal to Angola in the eastern Atlantic, and also in the Mediterranean Sea. Globally, is considered endangered by the International Union for Conservation of Nature (IUCN). Our study analyzed the complete mitochondrial genome of sequenced from an individual captured in the western Atlantic and compared it with a mitochondrial genome from a conspecific collected in the Mediterranean to explore if comprises cryptic species.

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens.

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g.

Cardinal v3 - a versatile open source software for mass spectrometry imaging analysis.

Cardinal v3 is an open source software for reproducible analysis of mass spectrometry imaging experiments. A major update from its previous versions, Cardinal v3 supports most mass spectrometry imaging workflows. Its analytical capabilities include advanced data processing such as mass re-calibration, advanced statistical analyses such as single-ion segmentation and rough annotation-based classification, and memory-efficient analyses of large-scale multi-tissue experiments.

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

Motivation: Mass Spectrometry Imaging (MSI) analyzes complex biological samples such as tissues. It simultaneously characterizes the ions present in the tissue in the form of mass spectra, and the spatial distribution of the ions across the tissue in the form of ion images. Unsupervised clustering of ion images facilitates the interpretation in the spectral domain, by identifying groups of ions with similar spatial distributions.

Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes.

Background: Ray-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) coding for olfactory receptors in 185 species of ray-finned fishes.

Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing.

DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens.

Evolutionary Dynamics of the OR Gene Repertoire in Teleost Fishes: Evidence of an Association with Changes in Olfactory Epithelium Shape.

Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. Richness of the olfactory repertoire depends on the diversity of receptors coded by homologous genes classified into four families: OR, TAAR, VR1, and VR2. Herein, we focus on the OR gene repertoire.

Review of the Indian Ocean spikefish genus Mephisto (Tetraodontiformes: Triacanthodidae).

We redescribe the triacanthodid spikefish Mephisto fraserbrunneri Tyler 1966 based upon eight specimens (five newly reported herein) and the first color photographs of freshly collected specimens; these data are compared with that of the single specimen of the recently described M. albomaculosus Matsuura, Psomadakis, and Mya Than Tun 2018. Both species are found in the Indian Ocean, with M.

Inappropriate Administration of Rabies Postexposure Prophylaxis, Cook County, Illinois, USA.

Administration of rabies postexposure prophylaxis (PEP) is expensive and time-consuming. In suburban Cook County, Illinois, USA, administration of 55.5% of PEP treatments did not follow Advisory Committee on Immunization Practices guidelines.

Visualizing Acoustic Imaging of Hydrothermal Plumes on the Seafloor.

Hydrothermal plumes are ongoing venting of hot solutions, on a time scale of months to years, relating to volcanic activities on the seafloor. Recent developments in acoustical observational techniques have produced images to support the scientific investigation of such plumes. However, understanding the complex behavior of plumes in a long-time series poses a challenge to the existing analysis approaches.

Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020.

From January 21 through February 23, 2020, public health agencies detected 14 U.S. cases of coronavirus disease 2019 (COVID-19), all related to travel from China (1,2).

Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues.

Motivation: Mass spectrometry imaging (MSI) characterizes the spatial distribution of ions in complex biological samples such as tissues. Since many tissues have complex morphology, treatments and conditions often affect the spatial distribution of the ions in morphology-specific ways. Evaluating the selectivity and the specificity of ion localization and regulation across morphology types is biologically important.

Tooth and consequences: Heterodonty and dental replacement in piranhas and pacus (Serrasalmidae).

Tooth replacement in piranhas is unusual: all teeth on one side of the head are lost as a unit, then replaced simultaneously. We used histology and microCT to examine tooth-replacement modes across carnivorous piranhas and their herbivorous pacu cousins (Serrasalmidae) and then mapped replacement patterns onto a molecular phylogeny. Pacu teeth develop and are replaced in a manner like piranhas.

Life history, distribution and molecular phylogenetics of the Upward-Mouth Spikefish Atrophacanthus japonicus (Teleostei: Tetraodontiformes: Triacanthodidae).

Ninety-six juvenile specimens (37-54 mm standard length; L ) of the rarely collected Upward-Mouth Spikefish Atrophacanthus japonicus (Triacanthodidae) were obtained from the stomachs of three Yellowfin Tuna Thunnus albacares collected off Guam in the Mariana Islands in the central Pacific Ocean. These specimens extend the range of A. japonicus eastward into Oceania.

Tooth development and replacement in the Atlantic Cutlassfish, Trichiurus lepturus, with comparisons to other Scombroidei.

Atlantic Cutlassfish, Trichiurus lepturus, have large, barbed, premaxillary and dentary fangs, and sharp dagger-shaped teeth in their oral jaws. Functional teeth firmly ankylose to the dentigerous bones. We used dry skeletons, histology, SEM, and micro-CT scanning to study 92 specimens of T.

Application-Driven Design: Help Students Understand Employment and See the "Big Picture".

Few tools for career exploration utilize visualizations despite their potential to help students understand the intangible relationships between jobs and majors. Our application-driven design combines the intuitiveness of node-link diagrams and the scalability of aggregation-based techniques to combine an overview of a job database with the option for individualized exploration.

Spatial clusters of latent tuberculous infection, Connecticut, 2010-2014.

Setting: In the United States, tuberculosis (TB) control is increasingly focusing on the identification of persons with latent tuberculous infection (LTBI).

Objective: To characterize the local epidemiology of LTBI in Connecticut, USA.

Methods: We used spatial analyses 1) to identify census tract-level clusters of reported LTBI and TB disease in Connecticut, 2) to compare persons and populations in clusters with those not in clusters, and 3) to compare persons with LTBI to those with TB disease.

Using an Emergency Department Syndromic Surveillance System to Evaluate Reporting of Potential Rabies Exposures, Illinois, 2013-2015.

Objectives: Mandatory reporting of potential rabies exposures and initiation of postexposure prophylaxis (PEP) allow local health authorities to monitor PEP administration for errors. Our objectives were to use an emergency department (ED) syndromic surveillance system to (1) estimate reporting compliance for exposure to rabies in suburban Cook County, Illinois, and (2) initiate interventions to improve reporting and reassess compliance.

Methods: We queried ED records from 45 acute care hospitals in Cook County and surrounding areas from January 1, 2013, through June 30, 2015, for chief complaints or discharge diagnoses pertaining to rabies, PEP, or contact with a wild mammal (eg, bat, raccoon, skunk, fox, or coyote).

matter: an R package for rapid prototyping with larger-than-memory datasets on disk.

Summary: We introduce matter , an R package for direct interactions with larger-than-memory datasets, stored in an arbitrary number of files of any size. matter is primarily designed for datasets in new and rapidly evolving file formats, which may lack extensive software support. matter enables a wide variety of data exploration and manipulation steps, and is extensible to many bioinformatics applications.