Multiple Specimens Research Articles

A study on the effect of different Paris constants in mixed mode (I/II) fatigue life prediction in Al 7075-T6 alloy

Mixed-mode (I/II) fatigue crack growth experiments in Al 7075-T6 alloy have been performed using a newly proposed single edge cracked circular (SECC) specimen. An equivalent stress intensify factor (ΔKeq) model based on the generalized MTS criterion (GMTS) has been tested for the first time for mixed-mode fatigue crack growth rate correlation and prediction of the fatigue life. Along with this proposed model, other widely used ΔKeq models have also been considered to study the effect of Paris constants on the fatigue life prediction. Three different mode mixity configurations (30°, 45°, and 60°) have been considered for experiments with multiple specimens to study the reproducibility aspect. With the help of detailed fatigue crack growth finite element simulations and experimental results, the performance of the various ΔKeq models has been tested in terms of correlation with the fatigue crack growth rate and prediction of the fatigue life. The results of the present investigation show that using the mixed-mode Paris constants along with Tanaka’s and Richard’s ΔKeq models accurately and consistently predicts the fatigue life compared to other Paris constants. The GMTS criterion has been shown to exhibit excellent performance in the prediction of crack growth path and thus signifies the importance of T- stress under mixed-mode fatigue loading. Additionally, the results of the present investigation establish the potential application of the SECC specimen for mixed-mode fatigue crack growth studies of metallic materials. Furthermore, fractographic studies also confirm the experimental observations in Al 7075-T6 alloy.

P29 Catheter-associated urinary tract infections, potential for diagnostic and antimicrobial stewardship

Abstract Background and Objectives Catheter-associated urinary tract infections (CAUTIs) are one of the most common healthcare-associated infections.1 Microbiological investigation of catheter specimens of urine (CSUs) results in a significant workload for microbiology laboratories. As bacteria cultured from CSUs often reflect colonization rather than infection, we must prudently interpret these culture results and judiciously prescribe antimicrobials in this setting. For these reasons, we felt it was important to assess if CAUTIs are being appropriately investigated and managed in our hospital. Methods We identified all the CSUs received in the microbiology laboratory from inpatients over a 7 day period in an 820-bed adult tertiary referral hospital. Once identified, a retrospective review of each patient’s clinical and drug charts was undertaken. The CDC definition of CAUTI was applied for the purpose of this audit.2 Results A total of 126 CSUs from 101 patients were included. The majority of patients (n=79, 78%) had a urinary catheter introduced during their hospital admission. At the time of CSU sampling, suspicion of infection was documented in only 47 patients. Only 9% of patients who had a CSU processed met the criteria for a CAUTI.2 Fifty-six percent of patients were commenced on antibiotics, despite only 31% returning a culture positive CSU sample. CSU results were documented in only 10% of patient charts. In cases where a CAUTI was suspected, it took an average of 6.75 days for the urinary catheter to be exchanged or removed. Four patients continued to receive an antibiotic despite the organism isolated being reported as resistant. Conclusions Overall, we noted that there was poor documentation of both urinary catheter status and of CSU results. Our audit revealed that several patients had multiple specimens processed within the 7 day period. Most patients had no clear indication for CSU sampling. From an antimicrobial stewardship perspective, there was unnecessary and inappropriate prescribing of antimicrobials. The results of this audit show that there is potential for both diagnostic and antimicrobial stewardship in the management of CAUTIs.

Targeting TRIM24 promotes neuroblastoma differentiation and decreases tumorigenicity via LSD1/CoREST complex.

High-risk neuroblastoma (NB) still has an unfavorable prognosis and inducing NB differentiation is a potential strategy in clinical treatment, yet underlying mechanisms are still elusive. Here we identify TRIM24 as an important regulator of NB differentiation. Multiple datasets and clinical specimens were analyzed to define the role of TRIM24 in NB. The effects of TRIM24 on differentiation and growth of NB were determined by cell morphology, spheres formation, soft agar assay, and subcutaneous xenograft in nude mice. RNA-Seq and qRT-PCR were used to identify genes and pathways involved. Mass spectrometry and co-immunoprecipitation were used to explore the interaction of proteins. Trim24 is highly expressed in spontaneous NB in TH-MYCN transgenic mice and clinical NB specimens. It is associated with poor NB differentiation and unfavorable prognostic. Knockout of TRIM24 in neuroblastoma cells promotes cell differentiation, reduces cell stemness, and inhibits colony formation in soft agar and subcutaneous xenograft tumor growth in nude mice. Mechanistically, TRIM24 knockout alters genes and pathways related to neural differentiation and development by suppressing LSD1/CoREST complex formation. Besides, TRIM24 knockout activates the retinoic acid pathway. Targeting TRIM24 in combination with retinoic acid (RA) synergistically promotes NB cell differentiation and inhibits cell viability. Our findings demonstrate that TRIM24 is critical for NB differentiation and suggest that TRIM24 is a promising therapeutic target in combination with RA in NB differentiation therapy.

Detection of Bartonella DNA in Yellow Flies, Lone Star Ticks, and a Human Patient with Concurrent Evidence of Borrelia burgdorferi Infection in Northeast Florida, USA.

Background: Bartonella species and Borrelia burgdorferi sensu lato (Bbsl) are emerging zoonotic pathogens. The vectors and frequency of infections with both pathogen groups in the southern United States is understudied. This study describes an investigation of Bartonella and Bbsl in yellow flies collected at a residence in northeast Florida, USA, that led to subsequent discoveries of both organisms in lone star ticks (Amblyomma americanum) and a human patient. Materials and Methods: DNA samples from flies, ticks, and human patient blood specimens were tested via polymerase chain reaction assays for Bartonella or Bbsl species. DNA sequences were compared to reference strains for identification and characterization. Results: An exploratory investigation of arthropod-borne pathogens in yellow flies collected at a residence in northeast Florida revealed the presence of uncharacterized Bartonella species DNA sequences similar to ones previously detected in two lone star ticks from Virginia. Subsequent testing of several lone star ticks from the area detected similar sequences of Bartonella in three ticks. Testing of stored blood samples from a resident of the site, who had experienced chronic relapsing and remitting symptoms for over a decade, identified nearly identical Bartonella DNA sequences in multiple samples collected over a 10-year period. Two lone star ticks and several samples from the same patient and time period also tested positive for Bo. burgdorferi DNA, suggesting possible long-term coinfection of the patient with both organisms. Conclusion: This investigation identified highly similar Bartonella DNA sequences in yellow flies, lone star ticks, and a human patient in northeast Florida. Similarly, Bo. burgdorferi DNA was detected in two lone star ticks and multiple specimens from the patient. Positive PCR results from archived patient blood samples documented the presence of both organisms at multiple time points over more than a decade. More studies on human patients with chronic undefined illness and on the presence of Bartonella and Bbsl in hematophagous arthropods and animal hosts in the southeastern United States are needed.

DP12 Painful oral keratosis and skin lesions: a paraneoplastic diagnostic conundrum

Abstract A 70-year-old man was referred to oral medicine with extensive, painful oral hyperkeratosis affecting the tongue, buccal mucosa and palate. Medical history included a previous diagnosis of prostate cancer. Histology from multiple oral biopsy specimens showed only hyperparakeratosis and acanthosis, with no fungi or dysplasia. Owing to the absence of oral inflammation, the pain was treated as neuropathic. The patient then developed skin lesions and dermatology review was requested. Skin examination revealed marked hyperkeratotic, verrucous plaques affecting the extensor surfaces of the limbs and dorsal hands, as well as the plantar feet bilaterally. The nails were unaffected. There was violaceous discolouration of the pinnae. Given the history of prostate cancer, a paraneoplastic process was suspected. Two incisional biopsies were taken, which showed epidermal acanthosis with necrotic and dyskeratotic keratinocytes throughout the epidermis. There was a dense eosinophilic inflammatory infiltrate. Direct and indirect immunofluorescence was negative. The appearances were suggestive of a paraneoplastic phenomenon, including acrokeratosis paraneoplastica. Haematological investigations identified an IgG monoclonal paraproteinaemia with raised kappa:lambda ratio. Following further investigation, including bone marrow biopsy and positron emission tomography computed tomography, a diagnosis of monoclonal gammopathy of undetermined significance was made by haematology. A repeat bone marrow biopsy 7 months later confirmed evolution to myeloma. As CRAB criteria (hypercalcaemia, renal insufficiency, anaemia and bone lesions) were absent, a period of observation followed. A trial of oral steroids improved the cutaneous eruption, but he developed significant side-effects. Oral mycophenolate, methotrexate and acitretin were used as steroid-sparing agents, with a poor clinical response. The skin lesions progressed to a widespread psoriasiform eruption on the trunk and lower limbs with the formation of bullae. Further biopsies showed an eosinophil-rich infiltrate with negative immunofluorescence, raising the possibility of an eosinophilic dermatosis of haematological malignancy. After 2 years, given the worsening skin symptoms, it was decided to commence bortezomib, cyclophosphamide and dexamethasone (VCD) chemotherapy. Despite four cycles of VCD treatment, the skin lesions worsened and as the paraprotein levels did not reduce, treatment was stopped. Subsequently, further elevations in serum free light chains prompted treatment with lenalidomide. This resulted in a marked improvement in the skin and reduced pain from the oral lesions, as well as a reduction in serum free light chains. Acrokeratosis paraneoplastica (Bazex syndrome) is characterized by digital hyperkeratosis and paronychia, which may progress to involve the limbs and trunk. Eosinophilic dermatosis of haematological malignancy is characterized by a pruritic, papular skin eruption with a vesiculobullous component. This case presents a diagnostic conundrum, with evolving features of two different paraneoplastic conditions.

Genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) in South Florida, United States using physical features and de novo genome assembly.

The distribution of octopuses within the Octopus vulgaris species complex remains inadequately understood. Species determination can be complex and involves characterizing a specimen's physical features and comparing its genetic makeup to other populations. In this study, we present the first genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) inhabiting the coastal waters of the Florida Keys, United States. We employed visual observations to identify species-specific body patterns of three wild-caught octopuses and used de novo genome assembly to confirm their species. All three specimens exhibited a red/white reticulated pattern on their ventral arm surface. Two specimens displayed body pattern components of deimatic display (white eye encircled by a light ring, with darkening around the eye). All visual observations were consistent with distinguishing features of O. insularis. We then compared mitochondrial subunits COI, COIII, and 16S in these specimens across all available annotated octopod sequences, including Sepia apama (Hotaling et al., 2021) as a control outgroup taxon. For species exhibiting intraspecific genomic variation, we included multiple sequences from geographically distinct populations. Laboratory specimens consistently clustered into a single taxonomic node with O. insularis. These findings confirm O. insularis presence in South Florida and suggest a more extensive northern distribution than previously assumed. Whole genome Illumina sequencing of multiple specimens enabled taxonomic identification with well-established DNA barcodes while also generating the first de novo full assembly of O. insularis. Furthermore, constructing and comparing phylogenetic trees for multiple conserved genes is essential for confirming the presence and delineation of cryptic species in the Caribbean.

MicroRNA-1179 targets Epiregulin (EREG) regulates the proliferation and metastasis of human multiple myeloma cells.

MicroRNA-1179 (miRNA-1179) is an extensively studied tumor suppressor. however, the significance of miR-1179 in multiple myeloma has not been investigated previously. So, there is a need for research to find out about the significance of miR-1179 in multiple myeloma. However, current investigations have examined the significance of miRNA-1179 in multiple myeloma for the first time by targeting epiregulin (EREG). In this study, 26 multiple myeloma specimens and 16 healthy donor specimens were examined. Multiple myeloma cell lines (U266, RPMI-8226, KMS-11, JJN-3, and IM-9) were used. In this study, expression analysis, cell viability, colony formation assay, and transwell assay were carried out by standard methods. The outcomes revealed the downregulation of miRNA-1179 in multiple myeloma. Overexpression of miRNA-1179 promotes, while its inhibition suppresses, the survival ability and colony formation of the U266 multiple myeloma cells. Investigation of underlying mechanisms revealed apoptosis to be responsible for the tumour-suppressive effects of miRNA-1179. The proportion of apoptosis in U266 cells rose from 5.32% to 34.86% when miRNA-1179 was overexpressed. Additionally, it was discovered that miRNA-1179 directs its tumor-inhabiting activities toward EREG at the molecular level. While EREG knockdown was found to halt the proliferation of U266 cells, its overexpression could overcome the suppressive effects of miRNA-1179 on the survival ability, mobility, and invasion of the U266 cells. This research proves that miRNA-1179 can be used as a new treatment or drug for multiple myeloma.

Microstructure characterization and elastic-plastic self-consistent simulation studies of anisotropic deformation of [formula omitted]-tin

Uniaxial compression tests of 99.9% pure polycrystalline β-tin (Sn) were conducted at various strain rates (10−3/s, 10−1/s and 1/s) and temperatures (294 K and 193 K) to understand the effects of these variables on the stress–strain response, microstructure evolution, and stress relaxation behavior. Multiple Sn specimens were subjected to complex compressive loading/unloading/reloading paths at different strain rates. Specimens initially compressed at higher strain rates showed strain rate-dependent texture evolution and more pronounced relaxation upon reloading, as compared to those pre-strained at lower rates at room temperature (RT). Compression tests conducted at low temperature (193 K) revealed increased strength, similar to the enhanced strength observed when the strain rate was increased at RT. Neutron diffraction was employed to characterize the initial and final bulk textures of the RT specimens. Electron backscatter diffraction was utilized to examine the crystallographic grain orientation and morphology, thereby identifying the signatures of dislocation-mediated deformation, grain refinement, recrystallization, and twinning behaviors. Elastic-plastic self-consistent simulations were performed to investigate the deformation modes responsible for the strain rate-dependent macroscopic stress–strain response and texture evolution. Effects of crystallographic orientation on stress relaxation behavior was also examined. The model predictions are in reasonable agreement with experimental observations.

Pediatric Respiratory Syncytial Virus Diagnostic Testing Performance: A Systematic Review and Meta-analysis.

Adding additional specimen types (eg, serology or sputum) to nasopharyngeal swab (NPS) reverse transcription polymerase chain reaction (RT-PCR) increases respiratory syncytial virus (RSV) detection among adults. We assessed if a similar increase occurs in children and quantified underascertainment associated with diagnostic testing. We searched databases for studies involving RSV detection in persons <18 years using ≥2 specimen types or tests. We assessed study quality using a validated checklist. We pooled detection rates by specimen and diagnostic tests and quantified performance. We included 157 studies. Added testing of additional specimens to NP aspirate (NPA), NPS, and/or nasal swab (NS) RT-PCR resulted in statistically nonsignificant increases in RSV detection. Adding paired serology testing increased RSV detection by 10%, NS by 8%, oropharyngeal swabs by 5%, and NPS by 1%. Compared to RT-PCR, direct fluorescence antibody tests, viral culture, and rapid antigen tests were 87%, 76%, and 74% sensitive, respectively (pooled specificities all ≥98%). Pooled sensitivity of multiplex versus singleplex RT-PCR was 96%. RT-PCR was the most sensitive pediatric RSV diagnostic test. Adding multiple specimens did not substantially increase RSV detection, but even small proportional increases could result in meaningful changes in burden estimates. The synergistic effect of adding multiple specimens should be evaluated.

RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.

The RaggedExperiment R / Bioconductor package provides lossless representation of disparate genomic ranges across multiple specimens or cells, in conjunction with efficient and flexible calculations of rectangular-shaped summaries for downstream analysis. Applications include statistical analysis of somatic mutations, copy number, methylation, and open chromatin data. RaggedExperiment is compatible with multimodal data analysis as a component of MultiAssayExperiment data objects, and simplifies data representation and transformation for software developers and analysts. Measurement of copy number, mutation, single nucleotide polymorphism, and other genomic attributes that may be stored as VCF files produce "ragged" genomic ranges data: i.e. across different genomic coordinates in each sample. Ragged data are not rectangular or matrix-like, presenting informatics challenges for downstream statistical analyses. We present the RaggedExperiment R/Bioconductor data structure for lossless representation of ragged genomic data, with associated reshaping tools for flexible and efficient calculation of tabular representations to support a wide range of downstream statistical analyses. We demonstrate its applicability to copy number and somatic mutation data across 33 TCGA cancer datasets.

Damage detection with ultrasonic guided waves using machine learning and aggregated baselines

In guided wave (GW)-based structural health monitoring (SHM), ultrasonic elastic waves are used to detect damages in structures by comparing the acquired signals with those acquired before defect formation. Making the SHM system automatic, especially for similar structures, such as turbine blades, is rather challenging. The high sensitivity of GWs to environmental and operational conditions, the variabilities due to sensor positioning, sensor coupling, and material variability in composites limit the baseline application. This work presents a machine learning (ML)-based damage detection method using aggregated baselines independent of their damaged states to enhance the generalization capability of ML algorithms by considering similar structures’ variabilities. The methodology relies on feature extraction from raw GW signals and training classification algorithms (e.g., kernel machines, ensemble methods, and neural networks). Two experimental data sets on composite panels are used. The first experimental data set of 45 composite panels is used to validate the approach by considering the aforementioned inter-specimen variabilities. Half of the 45 panels provide pristine data, and the rest provide damaged data so that the same sample is present in the training or test set but never in both. High classification performance is obtained, demonstrating that the classifier has successfully learned to recognize defect signatures despite the influence of the variabilities linked to the multiple instrumented specimens. The second experimental data set of 1 composite panel with temperature variation is used. Good classification performance is obtained without using baseline correction methods.

Editorial: Optimizing the success of cold snare polypectomy in colonoscopy practice

Editorial: Optimizing the success of cold snare polypectomy in colonoscopy practice

Acute necrotic hepatotoxicity caused by Melanthera latifolia (Asteraceae) in cattle

This study aims to report a spontaneous and experimental intoxication in cattle by Melanthera latifolia (Asteraceae) for the first time, and to describe its epidemiological, clinical, and pathological findings. An outbreak of acute toxic hepatopathy in cattle occurred from December of 2021 to January of 2022 in a beef cattle farm from Rio Grande do Sul state, Southern Brazil, and resulted in 94 deaths from a herd of 430 animals. At necropsy, lesions consisted of enhanced lobular pattern of the liver, transmural gallbladder edema, and hemorrhages on the surface of multiple organs. The main microscopic lesion was marked hepatocellular necrosis in the centrilobular region associated with hemorrhage and infiltration of neutrophils. During the outbreak, multiple specimens of M. latifolia were noted in the paddocks where affected cattle were grazing and many showed signs of consumption. No other known acute hepatotoxic plants were found. Two 12-month-old steers were experimentally intoxicated with a single oral dose of the fresh plant (flowers, leaves, and less fibrous stalks). One bovine ingested a dose of 10 g/kg and was euthanized after 48 h, and the other ingested 15 g/kg and was euthanized 17 h later. Clinical signs, macroscopic, and microscopic lesions in both animals were similar to those observed in the spontaneous cases. Thus, this study demonstrates that M. latifolia was the cause of the outbreak of acute toxic hepatopathy with significant mortality in cattle. M. latifolia nor any plant of the genus Melantherahad ever been reported as toxic.

Abstract 2289: Predicting tumor somatic versus clonal hematopoiesis origin for short variants in liquid assay

Abstract Introduction A common challenge presented by emerging liquid biopsy technology is to distinguish somatic variants originated in CH from those in tumor. While sequencing of genomic DNA from matched peripheral blood mononuclear cells (PBMC) can effectively identify CH variants, its wide application still remains prohibitively expensive. Computational-only solutions are challenging due to shared bioinformatic presentations in both CH and somatic variants such as low allele frequency. Development of such algorithm with clinically meaningful accuracy will have extensive utility in cancer care. Method We sequenced paired plasma-buffy coat samples from 754 pan-cancer patients using the FoundationOne® Liquid CDx (F1LCDx) assay. The samples were randomized into a training and a test set. Ground truth (tumor somatic vs. CH) for SV, including base substitutions and short indels, was determined by comparing variant calls in plasma vs in PBMC. A deep learning prediction model was developed in the training set. The model incorporates genomic and clinical features as input and returns a CH prediction score, which was dichotomized by a learned threshold. After the threshold and model parameters were finalized, we applied the model to the test set to evaluate performance. Results In the test set of 222 paired samples (523 CH and 904 tumor somatic variants), the model achieved 91% sensitivity (probability of predicting true CH variants as CH) and 88% specificity (probability of predicting true tumor somatic variants as tumor somatic). The model accurately identified CH variants in challenging genes such as TP53 (sensitivity = 94%, specificity = 90%, n = 144) and ATM (sensitivity = 93%, specificity = 95%, n = 49), which that are known to harbor both tumor somatic and CH variants. Performance was further evaluated by cancer types and variant allele frequency. CH variants were identified with 90% sensitivity and 89% specificity in non-small cell lung carcinoma (n = 384), and with 87% sensitivity and 100% specificity in pancreas cancer (n = 53). CH variants were identified with 92% sensitivity and 87% specificity in 1%-5% variant allele frequency (n = 645), and with 94% sensitivity and 94% specificity in 5%-10% variant allele frequency (n = 189). Of note, a well-known oncogenic mutation in ATM was predicted as CH in a prostate cancer patient, which would prevent ineffective administration of PARP inhibitors. Multiple plasma specimens also gained more accurate bTMB and tumor fraction estimation by filtering out CH variants. Conclusion For F1LCDx, we developed a computational method that distinguishes tumor somatic from CH variants from plasma cfDNA sequencing alone. The classifier exhibited high sensitivity and specificity in a pan-cancer cohort. Additional analytical validations are required in an external dataset. Clinical utility of this classifier will likely be further demonstrated in CH-corrected bTMB and tumor fraction. Citation Format: Daokun Sun, Zheng Kuang, Alexander D. Fine, Eliana Polisecki, Holley Gettler, Hawra Al-Rekabi, Dean Pavlick, Yanmei Huang, Lee A. Albacker, Brennan Decker, Chang Xu. Predicting tumor somatic versus clonal hematopoiesis origin for short variants in liquid assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2289.

Clinical, histopathological and molecular features of dedifferentiated melanomas: An EORTC Melanoma Group Retrospective Analysis

PurposeDedifferentiated melanoma (DedM) poses significant diagnostic challenges. We aimed to investigate the clinical, histopathological and molecular features of DedM. Methylation signature (MS) and copy number profiling (CNP) were carried out in a subgroup of cases. Patients and methodsA retrospective series of 78 DedM tissue samples from 61 patients retrieved from EORTC (European Organisation for Research and Treatment of Cancer) Melanoma Group centres were centrally reviewed. Clinical and histopathological features were retrieved. In a subgroup of patients, genotyping through Infinium Methylation microarray and CNP analysis was carried out. ResultsMost patients (60/61) had a metastatic DedM showing most frequently an unclassified pleomorphic, spindle cell, or small round cell morphology akin to undifferentiated soft tissue sarcoma, rarely associated with heterologous elements. Overall, among 20 successfully analysed tissue samples from 16 patients, we found retained melanoma-like MS in only 7 tissue samples while a non-melanoma-like MS was observed in 13 tissue samples. In two patients from whom multiple specimens were analysed, some of the samples had a preserved cutaneous melanoma MS while other specimens exhibited an epigenetic shift towards a mesenchymal/sarcoma-like profile, matching the histological features. In these two patients, CNP was largely identical across all analysed specimens, in line with their common clonal origin, despite significant modification of their epigenome. ConclusionsOur study further highlights that DedM represents a real diagnostic challenge. While MS and genomic CNP may help pathologists to diagnose DedM, we provide proof-of-concept that dedifferentiation in melanoma is frequently associated with epigenetic modifications.

Automatic Extraction of Specimens from Multi-specimen Herbaria

Since herbarium specimens are increasingly becoming digitized and accessible in online repositories, an important need has emerged to develop automated tools to process and enrich these collections to facilitate better access to the preserved archives. Particularly, automatic enrichment of multi-specimen herbaria sheets poses unique challenges and problems that have not been adequately addressed. The complexity of localization of species in a page increases exponentially when multiple specimens are present in the same page. This already challenges the performance of models that work accurately with single specimens. Therefore, in this work, we have performed experiments to identify the models that perform well for the plant specimen localization problem. The major bottleneck for performing such experiments was the lack of labeled data. We also address this problem by proposing tools and algorithms to semi-automatically generate annotations for herbarium images. Based on our experiments, segmentation models perform much better than detection models for the task of plant localization. Our binary segmentation model can accurately extract specimens from the background and achieves an F1 score of 0.977. The ablation experiments for multi-specimen instance segmentation show that our proposed augmentation method provides a 38% increase in performance (0.51 mAP@0.9 versus 0.37) on a dataset of 1,500 plant instances.

Broad snouted cladoselachian with sensory specialization at the base of modern chondrichthyans

Throughout the Silurian and Devonian, cartilaginous fish successively evolved their specialized skeletal and dental characteristics, and increasingly refined their sensory systems. The Late Devonian shark taxon Maghriboselache mohamezanei gen. et sp. n. from the eastern Anti-Atlas of Morocco is known from multiple specimens preserving most of its skeletal features, which in some instances are preserved in three dimensions. Key details of the dentition, jaws, and pectoral skeleton are shared with the iconic genus Cladoselache. Phylogenetic analyses place the family Cladoselachidae as the sister group of symmoriiforms and these groups as sister group of the holocephalans. Further phylogenetic results corroborate that the initial evolutionary radiation of crown chondrichthyans occurred within or before the Late Devonian. Remarkably, this new stem holocephalan is equipped with a wide snout and large laterally separated nasal capsules: the earliest known example of this condition in the chondrichthyan and (perhaps) gnathostome record. This suggests sensory specialization approaching that of extant broad-rostrum elasmobranchs and represents a significant addition to increasingly apparent ecomorphological diversity among early chondrichthyans.

Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition.

The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.

A New Maximum Length for the Bluebanded Ronquil, Rathbunella hypoplecta (Zoarcoidei: Bathymasteridae)

Throughout 2019, multiple large Rathbunella specimens were collected from recreational hook and line fishermen off San Diego County, California, USA. The individuals were larger than the previously reported maximum size for Rathbunella and exhibited a dark coloration known but not usually depicted for the genus. Herein, we provide morphological and molecular evidence that these specimens are Bluebanded Ronquils, Rathbunella hypoplecta, and we increase the maximum size of the species to 242 mm standard length. We provide descriptions of the specimens and the dark-phase coloration and demonstrate that dark and light-phase individuals are not genetically different.

Investigating the diversity of bioluminescent marine worm Polycirrus (Annelida), with description of three new species from the Western Pacific.

Bioluminescence, a phenomenon observed widely in organisms ranging from bacteria to metazoans, has a significant impact on the behaviour and ecology of organisms. Among bioluminescent organisms, Polycirrus, which has unique emission wavelengths, has received attention, and advanced studies such as RNA-Seq have been conducted, but they are limited to a few cases. In addition, accurate species identification is difficult due to lack of taxonomic organization. In this study, we conducted comprehensive taxonomic survey of Japanese Polycirrus based on multiple specimens from different locations and described as three new species: Polycirrus onibi sp. nov., P. ikeguchii sp. nov. and P. aoandon sp. nov. The three species can be distinguished from the known species based on the following characters: (i) arrangement of mid-ventral groove, (ii) arrangement of notochaetigerous segments, (iii) type of neurochaetae uncini, and (iv) arrangement of nephridial papillae. By linking the bioluminescence phenomenon with taxonomic knowledge, we established a foundation for future bioluminescent research development. We also provide a brief phylogenetic tree based on cytochrome c oxidase subunit I (COI) sequences to discuss the evolution of bioluminescence and the direction of future research.