Morisita-Horn Index Research Articles

Abstract 905: ML quantification of tumor-Infiltrating lymphocytes distinguishes immune-phenotypes and reveals phenotypic heterogeneity

Abstract Immune phenotypes (IP), defined by the tumor-infiltrating lymphocyte (TIL) distribution within the tumor microenvironment (TME), is prognostic and predictive of treatment response. Here, machine learning (ML) models that characterize the TME were deployed in non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC) to exhaustively label TILs directly from hematoxylin and eosin (H&E)-stained whole slide images (WSI), compute IP and quantify TIL distribution, tasks which are manually untenable. ML-powered TME models (PathAI, Boston, MA; commercially available as PathExplore™) for NSCLC and HNSCC that quantify tissue regions (e.g. tumor, epithelium, and stroma) and cells (e.g. lymphocytes) in H&E-stained WSI were deployed on 126 NSCLC and 103 HNSCC commercial samples. Ground truth CD3 and CD8 scores were obtained from paired immunohistochemically-stained WSI (HALO, Indica Labs, Albuquerque, NM). Inflamed, desert, or excluded IPs (based on data-driven cutoffs) were inferred from the mean TIL density in epithelium and stroma (slide-level IP, sIP), and from the fraction of “hot” patches in all 100um x 100um patches tiling the tumor and stroma areas (patch-level IP, pIP). TIL spatial distribution was measured by the Morisita-Horn index that computes the patch-wise overlap between TILs and cancer cells (MHI, ranging from 0 to 1), and epithelial-stromal interface distance index (EDI) indicating the hot stromal patch bias toward the epithelium (-EDI) or stroma (+EDI). ML-predicted TIL densities highly correlated with ground truth CD3+ and CD8+ cell densities (NSCLC/HNSCC CD3, CD8: tumor Pearson r= 0.88/0.85, 0.74/0.74; epithelium r= 0.76/0.71, 0.88/0.62; stroma r= 0.74/0.87, 0.61/0.76). High s- and pIP agreement was seen (NSCLC 93% and HNSCC 83%); 6/26 discordant cases were driven by TIL hotspots with high density (116%-310% of the cutoff) but few (median = 26%) hot patches in the epithelium. MHI was higher for the inflamed vs excluded IP (p < 0.0001 for NSCLC and HNSCC) and intra-group variability was high (NSCLC/HNSCC inflamed: 0.66±0.11/0.31±0.14, excluded: 0.51±0.12/0.26±0.17, desert: 0.48±0.09/0.28±0.17; mean±std). EDI was lowest and negative in inflamed IP but near zero in desert and excluded IP (NSCLC/HNSCC inflamed: -43±4um/-184±19um, excluded: 1.6±4um/-41±13um, desert: 18±4um/-14±13; mean±sem). Excluded and desert IPs had roughly equal + and - EDI cases (NSCLC +/-: 57/46; HNSCC +/-: 39/29). ML-powered IP prediction using TIL distribution enables accurate and rapid profiling of the TME using routine histopathology. pIPs were concordant with sIPs and highlight TIL heterogeneity. Spatial markers (MHI and EDI) reveal differences between IP classes and intra-group heterogeneity relevant for drug discovery and patient stratification. Investigating prognostic associations of these markers is a promising direction for future studies. Citation Format: Nhat Le, Bahar Rahsepar, Jennifer Hipp, Jake Conway, Ylaine Gerardin, Emma Krause, Ciyue Shen, Raymond Biju, Michael Nercessian, Nicholas Indorf, Sandrine Degryse, Miles Markey, Victoria Mountain, Pranjal Vaidya, William Wijaya, Aditee Shrotre, Patrick Caplazi, David Inzunza, Joann Palma, Erik Huntzicker, Catherine Tribouley, Diana Chen, Raluca Prediou, Francine Chen, Kevin Kolahi. ML quantification of tumor-Infiltrating lymphocytes distinguishes immune-phenotypes and reveals phenotypic heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 905.

How Poor Is Aphyllophoroid Fungi Diversity in the Boreal Urban Greenhouses of Eastern Europe?

It is generally accepted that mycobiota diversity in urban greenhouses is poorer than in natural ecosystems, but our knowledge on this field of research is fragmentary. Here, we present the results of a long-term study of aphyllophoroid macrofungi (Basidiomycota) forming fruitbodies on non-native sub/tropical woody and herbaceous plants in the greenhouses of Saint Petersburg, Moscow, and Ekaterinburg botanical gardens located in the hemiboreal vegetation subzone of Eastern Europe. Over 20 years of research, fruitbodies of 58 species of aphyllophoroid fungi have been identified. Fungal species that developed on the wooden structures of greenhouses and building materials made of local wood are discussed separately. The list of fungi on non-native substrates is dominated by saprobes (93.1% of total list) as well as mycorrhizal with basidiomata on plants (8.6%). Phytopathogens have the lowest number (7.0%), and ¾ of species are widespread locally. Non-native plants are dominated by native fungal species (78.9%), while the percentage of non-native species is low (21.1%). In the three surveyed cities, the area of the studied greenhouses is 2.8 ha, and not a single species of fungi has been found twice on the same substrate. Half of the identified species are characterized by a single specimen (29 species/50.9%). Hymenochaete rheicolor was discovered in Russia for the first time and its known distribution is discussed. Only six (Antrodia gossypium, Hyphodontia arguta, Lyomyces sambuci, Peniophora cinerea, Ramariopsis kunzei, and Trechispora farinacea) local species (10.5%) were collected in all the three cities. The α-diversity of mycobiota (mean number of species per site, Shannon Index, and Menhinick Index) in the Ekaterinburg's greenhouses is 1.2-3.0 times lower compared to suburban forest parks and old-growth natural forests, while β-diversity (Whittaker Index, Jaccard Index, and Morisita-Horn Index), on the contrary, is 2.1-7.7 times higher. With the plants' age, the probability of detecting fungi on them increases significantly. In greenhouses, phytopathogenic aphyllophoroid macrofungi are collected on woody plants only, but the probability of their development is not related to the plants' age.

Measures of spatial heterogeneity in the liver tissue micro-environment as predictive factors for fibrosis score

The organization and interaction between hepatocytes and other hepatic non-parenchymal cells plays a pivotal role in maintaining normal liver function and structure. Although spatial heterogeneity within the tumor micro-environment has been proven to be a fundamental feature in cancer progression, the role of liver tissue topology and micro-environmental factors in the context of liver damage in chronic infection has not been widely studied yet. We obtained images from 110 core needle biopsies from a cohort of chronic hepatitis B patients with different fibrosis stages according to METAVIR score. The tissue sections were immunofluorescently stained and imaged to determine the locations of CD45 positive immune cells and HBsAg-negative and HBsAg-positive hepatocytes within the tissue. We applied several descriptive techniques adopted from ecology, including Getis–Ord, the Shannon Index and the Morisita–Horn Index, to quantify the extent to which immune cells and different types of liver cells co-localize in the tissue biopsies. Additionally, we modeled the spatial distribution of the different cell types using a joint log-Gaussian Cox process and proposed several features to quantify spatial heterogeneity. We then related these measures to the patient fibrosis stage by using a linear discriminant analysis approach. Our analysis revealed that the co-localization of HBsAg-negative hepatocytes with immune cells and the co-localization of HBsAg-positive hepatocytes with immune cells are equally important factors for explaining the METAVIR score in chronic hepatitis B patients. Moreover, we found that if we allow for an error of 1 on the METAVIR score, we are able to reach an accuracy of around 80%. With this study we demonstrate how methods adopted from ecology and applied to the liver tissue micro-environment can be used to quantify heterogeneity and how these approaches can be valuable in biomarker analyses for liver topology.

An artificial intelligence-based ecological index for prognostic evaluation of colorectal cancer

Background and objectiveIn the tumor microenvironment (TME), the dynamic interaction between tumor cells and immune cells plays a critical role in predicting the prognosis of colorectal cancer. This study introduces a novel approach based on artificial intelligence (AI) and immunohistochemistry (IHC)-stained whole-slide images (WSIs) of colorectal cancer (CRC) patients to quantitatively assess the spatial associations between tumor cells and immune cells. To achieve this, we employ the Morisita-Horn ecological index (Mor-index), which allows for a comprehensive analysis of the spatial distribution patterns between tumor cells and immune cells within the TME.Materials and methodsIn this study, we employed a combination of deep learning technology and traditional computer segmentation methods to accurately segment the tumor nuclei, immune nuclei, and stroma nuclei within the tumor regions of IHC-stained WSIs. The Mor-index was used to assess the spatial association between tumor cells and immune cells in TME of CRC patients by obtaining the results of cell nuclei segmentation. A discovery cohort (N = 432) and validation cohort (N = 137) were used to evaluate the prognostic value of the Mor-index for overall survival (OS).ResultsThe efficacy of our method was demonstrated through experiments conducted on two datasets comprising a total of 569 patients. Compared to other studies, our method is not only superior to the QuPath tool but also produces better segmentation results with an accuracy of 0.85. Mor-index was quantified automatically by our method. Survival analysis indicated that the higher Mor-index correlated with better OS in the discovery cohorts (HR for high vs. low 0.49, 95% CI 0.27–0.77, P = 0.0014) and validation cohort (0.21, 0.10–0.46, < 0.0001).ConclusionThis study provided a novel AI-based approach to segmenting various nuclei in the TME. The Mor-index can reflect the immune status of CRC patients and is associated with favorable survival. Thus, Mor-index can potentially make a significant role in aiding clinical prognosis and decision-making.

Diet of the mona monkey Cercopithecus mona in the Gnanhouizounmè community forest in Southern Benin

The mona monkey Cercopithecus mona Schreber, 1774 is an arboreal and diurnal species occurring in some forests in Benin. The present study determined the feeding ecology of the species in the Gnanhouizounmè community forest, a forest fragment in Southern Benin. The ad libitum observation method was used to collect data during the minor wet and the major dry seasons. Descriptive statistics, proportion comparison tests, and diversity indices were used to analyse data. Results showed that the mona monkey foraged on 22 plant species in the study forest, with Ceiba pentandra, Dialium guineense, Elaeis guineensis and Spondia monbin constituting its major diet. Three species of leguminous plants were the most common food type. Fruits, both mature and immature, were the top food item in the diet, while other items were leaves, buds, tubers, stalks and flowers. Dietary diversity was low (H = 2.09 in the wet season, H = 1.74 in the dry season) with a low similarity between the two seasons (Morisita–Horn's index = 0.31). In forest fragments, the mona monkey has adapted to feed on few plant species and adjusts its diet to resources available each season. Plants consumed by this species should be taken into account in future tree-planting campaigns for the sustainable conservation of these monkeys in the study area.

Urban Green Spaces and Vector-Borne Disease Risk in Africa: The Case of an Unclean Forested Park in Libreville (Gabon, Central Africa).

In Africa, vector-borne diseases are a major public health issue, especially in cities. Urban greening is increasingly considered to promote inhabitants' well-being. However, the impact of urban green spaces on vector risk remains poorly investigated, particularly urban forests in poor hygienic conditions. Therefore, using larval sampling and human landing catches, this study investigated the mosquito diversity and the vector risk in a forest patch and its inhabited surroundings in Libreville, Gabon, central Africa. Among the 104 water containers explored, 94 (90.4%) were artificial (gutters, used tires, plastic bottles) and 10 (9.6%) were natural (puddles, streams, tree holes). In total, 770 mosquitoes belonging to 14 species were collected from such water containers (73.1% outside the forested area). The mosquito community was dominated by Aedes albopictus (33.5%), Culex quinquefasciatus (30.4%), and Lutzia tigripes (16.5%). Although mosquito diversity was almost double outside compared to inside the forest (Shannon diversity index: 1.3 vs. 0.7, respectively), the species relative abundance (Morisita-Horn index = 0.7) was similar. Ae. albopictus (86.1%) was the most aggressive species, putting people at risk of Aedes-borne viruses. This study highlights the importance of waste pollution in urban forested ecosystems as a potential driver of mosquito-borne diseases.

Host associations of biting midges (Diptera: Ceratopogonidae: Culicoides) at deer farms in Florida, USA.

Documenting the host use of vector species is important for understanding the transmission dynamics of vector-borne pathogens. Biting midges (Diptera: Ceratopogonidae: Culicoides) are vectors of epizootic hemorrhagic disease virus (EHDV) and bluetongue virus (BTV) worldwide. However, relative to mosquitoes and many other vector groups, host associations of this group are poorly documented. In this study, we used PCR-based bloodmeal analysis to determine species-level host associations of 3,603 blood-engorged specimens belonging to 18 Culicoides species at 8 deer farms in Florida, USA. We used a binomial mixed model with a Bayesian framework to compare the effect of host composition on the feeding patterns of Culicoides spp. and employed the Morisita-Horn Index to investigate the similarity of host use between farms for Culicoides stellifer and Culicoides insignis. Results show that the estimated probability of Culicoides spp. feeding upon white-tailed deer depends on the availability of cattle or exotic game and demonstrates differences in host-feeding selection among species. Culicoides insignis had high host similarity across farms suggesting that its host-use patterns are somewhat conserved. Culicoides stellifer had lower host similarity across farms suggesting that it is a more opportunistic feeder. White-tailed deer are fed upon by many Culicoides species on deer farms in Florida, and while most Culicoides species feed on white-tailed deer, the ratio of white-tailed deer bloodmeals to other bloodmeals is likely influenced by host availability. Culicoides spp. taking a majority of their bloodmeals from farmed white-tailed deer should be assessed for their vector competence for EHDV and BTV.

Digital Image Analysis of Ki67 Heterogeneity Improves the Diagnosis and Prognosis of Gastroenteropancreatic Neuroendocrine Neoplasms

Ki67 is a reliable grading and prognostic biomarker of gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs). The intratumor heterogeneity of Ki67, correlated with tumor progression, is a valuable factor that requires image analysis. The application of digital image analysis (DIA) enables new approaches for the assessment of Ki67 heterogeneity distribution. We investigated the diagnostic utility of Ki67 heterogeneity parameters in the classification and grading of GEP-NENs and explored their clinical values with regard to their prognostic relevance. The DIA algorithm was performed on whole-slide images of 102 resection samples with Ki67 staining. Good agreement was observed between the manual and DIA methods in the hotspot evaluation (R2 = 0.94, P < .01). Using the grid-based region of interest approach, score-based heat maps provided a distinctive overview of the intratumoral distribution of Ki67 between neuroendocrine carcinomas and neuroendocrine tumors. The computation of heterogeneity parameters related to DIA-determined Ki67 showed that the coefficient of variation and Morisita-Horn index were directly related to the classification and grading of GEP-NENs and provided insights into distinguishing high-grade neuroendocrine neoplasms (grade 3 neuroendocrine tumor vs neuroendocrine carcinoma, P < .01). Our study showed that a high Morisita-Horn index correlated with poor disease-free survival (multivariate analysis: hazard ratio, 56.69), which was found to be the only independent predictor of disease-free survival in patients with GEP-NEN. These spatial biomarkers have an impact on the classification and grading of tumors and highlight the prognostic associations of tumor heterogeneity. Digitization of Ki67 variations provides a direct and objective measurement of tumor heterogeneity and better predicts the biological behavior of GEP-NENs.

Mexico’s Forest Diversity: Common Tree Species and Proposed Forest-Vegetation Provinces

We report a relatively rare study of a national forest inventory in a megadiverse country with the systematic collection of herbarium specimens. The taxonomic identification of 22,659 herbarium collections from 6942 sites of Mexico’s national forest inventory resulted in 1464 native tree species (approximately half of Mexico’s estimated total), in 470 genera and 117 plant families. We compared visual tree-species identifications in the field by hired crews, with much more rigorous identification of submitted (mostly sterile) herbarium specimens by experienced taxonomists and specialists at the National Herbarium: for 40% of the 22,659 collections, the identification of species names from the field was confirmed, for 32% it was corrected at the herbarium, and 27% had been sent without any identification. The most commonly collected plant families were Fagaceae (oak family, 21.7% of all collections), Fabaceae (legumes, 17.7%), and Pinaceae (pine family, 13.3%). The most commonly collected tree species in six major forest-vegetation types were Pinus leiophylla in “coniferous forest”, Quercus magnoliifolia in “highland broadleaf forest”, Liquidambar styraciflua in “mountainous cloud forest”, Bursera simaruba in “lowland evergreen forest”, Lysiloma divaricatum in “lowland dry forest”, and Parkinsonia microphylla in “xerophilous scrub”. We overlapped the six major forest-vegetation types with Mexico’s 15 mainland floristic provinces, as circumscribed by Rzedowski. This resulted in 75 so-called forest-vegetation provinces, of which 35 had at least 20 collection sites. The similarity of species composition among these 35 forest-vegetation provinces was only 17–34% with the Jaccard community index, and 15–42% with the Morisita-Horn community index. The number of physically undetected species was estimated statistically for the 35 forest-vegetation provinces, which indicates that there are forest-vegetation provinces, where the number of species could be up to 8.8-fold higher than those detected in the present work. Finally, we suggest a method to distribute sites optimally among the country in future forest inventories, such as to minimize the average area represented by the sites in each forest-vegetation province.

GaWRDenMap: a quantitative framework to study the local variation in cell\u2013cell interactions in pancreatic disease subtypes

Spatial pattern modelling concepts are being increasingly used in capturing disease heterogeneity. Quantification of heterogeneity in the tumor microenvironment is extremely important in pancreatic ductal adenocarcinoma (PDAC), which has been shown to co-occur with other pancreatic diseases and neoplasms with certain attributes that make visual discrimination difficult. In this paper, we propose the GaWRDenMap framework, that utilizes the concepts of geographically weighted regression (GWR) and a density function-based classification model, and apply it to a cohort of multiplex immunofluorescence images from patients belonging to six different pancreatic diseases. We used an internal cohort of 228 patients comprised of 34 Chronic Pancreatitis (CP), 71 PDAC, 70 intraductal papillary mucinous neoplasm (IPMN), 16 mucinous cystic neoplasm (MCN), 29 pancreatic intraductal neoplasia (PanIN) and 8 IPMN-associated PDAC patients. We utilized GWR to model the relationship between epithelial cells and immune cells on a spatial grid. The GWR model estimates were used to generate density signatures which were used in subsequent pairwise classification models to distinguish between any two pairs of disease groups. Image-level, as well as subject-level analysis, were performed. When applied to this dataset, our classification model showed significant discrimination ability in multiple pairwise comparisons, in comparison to commonly used abundance-based metrics, like the Morisita-Horn index. The model was able to best discriminate between CP and PDAC at both the subject- and image-levels. It was also able to reasonably discriminate between PDAC and IPMN. These results point to a potential difference in the spatial arrangement of epithelial and immune cells between CP, PDAC and IPMN, that could be of high diagnostic significance. Further validation on a more comprehensive dataset would be warranted.

Consumption Patterns of a Generalist Omnivore: Eastern Box Turtle Diets in the Long Island Pine Barrens

Eastern Box Turtles (Terrapene carolina) are diet generalists and as such are predicted to have diverse diets in which familiar, low-quality foods are eaten consistently at low levels, and high-quality foods are rare but eaten whenever available. Previous work showed that they feed opportunistically on seasonally available plants (shoots, leaves, flowers, and fruit), invertebrates, mushrooms, and occasionally carrion. We used fecal samples to test optimal foraging predictions relevant to diet generalists and also whether the Eastern Box Turtle diets varied seasonally in a northeastern U.S. pine-oak habitat. We found that in-depth prey species consumption patterns of six different individuals were similar to those of the sampled population overall. Leaf and stem material was consumed by 100% of the turtles in all months despite being lower-quality than other prey available. Invertebrates were consumed by at least 80% of turtles in every study period; Coleopterans were found more commonly than other invertebrates. Snails were not eaten by more than 20% of the turtles in any study period, and mushroom consumption varied from 31–75% of samples in different study periods. Monthly diet overlap was measured using both Pianka’s Index of Overlap (PIO) and the Morisita–Horn Index (MH). The PIO method indicated that the prey consumption patterns were broadly similar from June–October, while the M–H method showed that only the July vs. August comparison was highly similar. The turtle diets changed only slightly between seasons, and they conform to predictions of diet generalist models usually applied to mammals.

Feeding Ecology of Invasive Three-Spined Stickleback (Gasterosteus aculeatus) in Relation to Native Juvenile Eurasian Perch (Perca fluviatilis) in the Pelagic Zone of Upper Lake Constance

The fish community of Lake Constance, a large, deep, oligotrophic lake has undergone drastic changes in recent years, with the sudden rise to dominance of invasive three-spined stickleback (Gasterosteus aculeatus) in the pelagic zone, a rather atypical habitat for this species in Central Europe. The core objective of this study was to compare the feeding ecology of stickleback and young Eurasian perch (Perca fluviatilis) in this unique situation to identify reasons for this unexpected dominance, a possible food niche and feeding time overlap, and to discuss consequences for the reshaped pelagic fish community. The diel feeding patterns and prey compositions of pelagic sticklebacks and juvenile (0+) perch sampled in October 2018 and March 2019 were studied analyzing stomach contents. The diets of both species mostly comprised zooplankton, with copepods appearing in the greatest numbers. Benthic and airborne insects were consumed occasionally, mostly by sticklebacks. Both species exhibited peaks of feeding activity early in the morning, afternoon and dusk, and in both species, stomachs were fullest at dusk. Stickleback stomachs contained about 20% more prey at night than perch, and mean estimated nocturnal stomach fullness values were almost 50% greater. Night feeding in sticklebacks was confirmed by digestive states, pointing to a possible competitive advantage over perch. Dietary composition varied over a 24-h cycle and the pattern of consumption of different prey varied between the species. Perch consumed more comparatively small cladocerans (Bosmina spp.), while larger Daphnia appeared more often in stickleback stomachs. In both species, seasonal variation in diet mirrored food availability, indicating some degree of opportunism. A Morisita-Horn index value of 0.95 confirmed dietary niche overlap between species, suggesting the large population of sticklebacks may exert a competitive effect on juvenile perch when resources are limited. Both the longer feeding periods and greater intake of nutritive high quality prey like daphnids can contribute to the rapid success of stickleback in dominating the pelagic zone of Lake Constance.

Mosquitos (Diptera: Culicidae) en trampas de oviposición puestas en fragmentos de selva estacional semidecidua de dominancia Atlántica, Estado de Rio Grande do Sul, Brasil

This study aimed to compare the mosquito fauna found in three remnant forest fragments of a semideciduous seasonal forest by using oviposition traps in the northwestern region of the state of Rio Grande do Sul, Brazil. Between 2018 and 2019, larvae were collected quarterly in three forest fragments, one situated in an urban area, another in a rural area close to the city and a third formed by an extensive area of native forest far from the urban environment. Four species were caught: Aedes terrens (Walker, 1856) (282), Limatus durhamii Theobald, 1901 (30), Aedes aegypti (Linnaeus, 1762) (23) and Toxorhynchites theobaldi (Dyar and Knab, 1906) (6). The Morisita-Horn index indicated a high similarity between the fragments studied (&gt;80%). The mean number of mosquitoes collected in the rural area was significantly higher than in the other areas (F = 6.073; d.f. = 17; p &lt;0.05). The calculation of the phi coefficient to assess the co-occurrence of two species in the same trap did not indicate significant values (p&gt; 0.05). Aedes terrens demonstrated a good ability to colonize and inhabit the different types of forest fragments studied. In addition, the forest fragment located in a rural area close to the urban area offered conditions for the survival of species of wild and urban mosquitoes, such as Ae. aegypti.

Pulmonary Microbiome of Patients Receiving Mechanical Ventilation: Changes Over Time.

Interest in the pulmonary microbiome is growing, particularly in patients undergoing mechanical ventilation. To explore the pulmonary microbiome over time in patients undergoing prolonged mechanical ventilation and to evaluate the effect of an oral suctioning intervention on the microbiome. This descriptive subanalysis from a clinical trial involved a random sample of 16 participants (7 intervention, 9 control) who received mechanical ventilation for at least 5 days. Five paired oral and tracheal specimens were evaluated for each participant over time. Bacterial DNA from the paired specimens was evaluated using 16S rRNA gene sequencing. Bacterial taxonomy composition, α-diversity (Shannon index), and β-diversity (Morisita-Horn index) were calculated and compared within and between participants. Participants were predominantly male (69%) and White (63%), with a mean age of 58 years, and underwent mechanical ventilation for a mean of 9.36 days. Abundant bacterial taxa included Prevotella, Staphylococcus, Streptococcus, Stenotrophomonas, and Veillonella. Mean tracheal α-diversity decreased over time for the total group (P = .002) and the control group (P = .02). β-Diversity was lower (P = .04) in the control group (1.905) than in the intervention group (2.607). Prolonged mechanical ventilation was associated with changes in the pulmonary microbiome, with the control group having less diversity. The oral suctioning intervention may have reduced oral-tracheal bacterial transmission.

Feeding habits of the fishes Euthynnus lineatus and Scomberomorus sierra (Perciformes: Scombridae) in the Eastern Tropical Pacific

ABSTRACT. Introduction: Black skipjack, Euthynnus lineatus, and Pacific sierra, Scomberomorus sierra, are of great economic importance in the small-scale fishery of the Tropical Eastern Pacific and in particular in the study area. Objectives: The objectives of the present study were to assess the diet components of E. lineatus and S. sierra, as well as to evaluate the niche width, trophic level, and trophic overlap between the two species, by size and season. Methods: Biological samples were obtained weekly from small-scale fishery catches in Bahía de Acapulco, Mexico. The E. lineatus sampling period occurred from October 2016 to October 2017, whereas S. sierra was sampled from October 2016 to June 2018. The Prey-specific Index of Relative Importance (% PSIRI) was used to evaluate the importance of each prey item in the diet of the predator. Levin´s index (Bi) was used as a measure of niche width. The Morisita-Horn index was used to evaluate diet overlap by size (juveniles or adults), by season (dry or wet), and between the two species. The trophic level (TL) of predators was calculated using the Cortés´ method. Results: A total of 262 E. lineatus stomachs were analyzed (42 % were empty and 58 % contained food) and a total of 209 S. sierra stomachs were analyzed (74.6 % were empty and 25.3 % contained food). Of the total E. lineatus specimens sampled, 107 were juveniles and 155 were adults. Black skipjack juveniles fed on five food items and adults fed on 13 food items. Of the total S. sierra specimens sampled, 75 were juveniles and 134 were adults. Pacific sierra juveniles and adults fed on five food items. The diet of the two species comprised fish, mollusks, and crustaceans. The two species showed narrow niche width. The diet of juvenile and adult E. lineatus presented differences with growth, contrary to what was observed for juveniles and adults of S. sierra. There were no significant differences in diet by season for both species. The trophic overlap obtained between the two species was low. The trophic level calculated for both species indicated that are tertiary consumers. Conclusions: Black skipjack and Pacific sierra are tertiary predators and present a specialist behavior, feeding mainly on fish from the families Engraulidae and Clupeidae. Although a degree of similarity in the dietary food components of these species was observed, there was not a high degree of interspecific competition for food.

The spatial localization of CD163+ tumor-associated macrophages predicts prognosis and response to therapy in inflammatory breast cancer.

3086 Background: The mechanisms contributing to the aggressive biology of inflammatory breast cancer (IBC) are under investigation. A specific immune response seems to be an important driver, but the functional role of infiltrating immune cells in IBC remains unclear. Tumor-associated macrophages (TAMs) are associated with worse outcome, while CD8+ cytotoxic T cells demonstrate anti-tumor properties in breast cancer. In this study, we assessed spatial associations between CD163+ TAMs, CD8+ cells and cancer cells in IBC, using deep-learning and ecological statistics. Methods: We collected clinicopathological variables, evaluated PDL1-positivity (SP142, Ventana) and scored TILs according to the TIL working group guidelines on H&amp;E slides for 144 IBC patients. Immunostainings for CD8 and CD163 (Hematoxylin-DAB) were done according to validated protocols. All slides were digitized, underwent virtual multiplexing and were evaluated in Visiopharm to quantify the number of DAB+ immune cells. Each immune cell was located using XY coordinates and spatial interactions were examined using a Morisita Horn Index (MHI). Tumor cell coordinates were collected using a deep-learning algorithm applied to the CD8-stained slide. This algorithm was trained in 18 images with more than 150.000 iterations (Deeplabv3+). Results: Complete pathological response (pCR) after neo-adjuvant chemotherapy was achieved by 30.6% (n= 30/98) of the patients with initially localized disease. Besides PDL1-postivity ( P= .03), infiltration with CD8+ T cells ( P= .02) and TAMs ( P= .01) also predicted pCR. However, a likelihood ratio test showed no difference between a model using CD8+ cells, TAMs or TILs. Interestingly, the colocalization of CD163+ and CD8+ cells (MHI &gt;0.83) was associated with pCR (P= .01) and remained significant in a multivariate model (OR: 3.18; 95% CI: 1.04 – 10.6; P= .05) including TIL score, PDL1-positivity and hormone receptor (HR) status. Furthermore, a shorter disease-free survival (DFS) was associated with HR- status, no pCR and the colocalization of TAMs near tumor cells (HR: 3.3; 95% CI: 1.6 – 7.1; P= .002) in a multivariate model. The density of TAMs was not associated with outcome. Conclusions: The impact of TAMs on clinical outcome appears to depend on the spatial arrangement. The number of TAMs solely was not associated with outcome, but patients with more TAMs in proximity of the tumor cells had a worse DFS. Surprisingly, the clustering of TAMs near CD8+ cells was associated with pCR independent of the number of TAMs or TILs.

Palynological analysis of the outer parts of camelid coprolites: implications for vegetation reconstruction

The aim of this study was to analyze pollen from the outer parts of camelid coprolites and contemporaneous sediments to evaluate the potential of coprolites for the reconstruction of the vegetation history of Patagonia during the Holocene. The pollen composition of camelid coprolites coming from archeological layers between 10,920 yrs. cal BP and 2823 yrs. cal BP found in the sites Cerro Casa de Piedra 5 and 7 (Perito Moreno National Park, Santa Cruz, Argentina) were analyzed. Coprolites were divided into outer and inner subsamples. Outer subsample pollen extraction was performed through acetolysis and determination and counting under optical microscope. Morisita-Horn index and Wilcoxon test were performed to evaluate similarities between pollen spectra of outer subsamples of coprolites and contemporaneous sediments. The dominant pollen types were: Nothofagus (Nothofagaceae), Empetrum (Ericaceae), Asteraceae subf. Asteroideae, Nassauvia (Asteraceae subf. Mutisioideae), Poaceae and Caryophyllaceae. The similarities found between outer subsamples of coprolites and contemporaneous sediments reflected the dominant pollen types of the vegetation and forest development, whereas significant differences could be attributed to coprolite pollen spectra that may be biased by season of coprolite deposition, selectivity of the diet and/or higher temporal resolution. Also, the presence of pollen types in outer subsamples of coprolites absent in sediments could give information for paleoenvironmental reconstructions by enriching information of the past flora. This study demonstrates that coprolites can be a valuable tool for paleoenvironmental reconstructions in arid and semiarid areas where depositional environments that support pollen preservation are typically rare.

WOODY SPECIES STRUCTURE, DIVERSITY AND FLORISTIC AFFINITIES IN SEASONALLY DRY FOREST IN THE UXMAL ARCHAEOLOGICAL ZONE

&lt;p&gt;Archaeological zones in Mexico effectively preserve the vegetal diversity within them. An analysis and description were done of woody vegetation structure, diversity and floristic affinity in the Uxmal Archaeological Zone, in the Puuc region of Yucatan, Mexico. Twenty quadrants measuring 10 x 10 m (100 m&lt;sup&gt;2&lt;/sup&gt;) were placed throughout the zone to sample its diverse substrates. Height and diameter at breast height (DBH) of woody species with DBH &amp;gt;1cm were measured in each quadrant. Floristic affinities were analyzed with a dendrogram generated using the Morisita-Horn index. A total of 1,622 individuals were recorded which belonged to 101 species and 76 genera from 31 families. The richest families were Fabaceae, Rubiaceae, Malvaceae, Polygonaceae and Euphorbiaceae. The species with the highest relative importance values were &lt;em&gt;Bursera simaruba&lt;/em&gt;,&lt;em&gt; Piscidia piscipula&lt;/em&gt;,&lt;em&gt; Diospyros anisandra&lt;/em&gt;,&lt;em&gt; Thouinia paucidentata&lt;/em&gt;,&lt;em&gt; Gymnopodium floribundum &lt;/em&gt;and &lt;em&gt;Lonchocarpus xuul&lt;/em&gt;. The most frequent species were &lt;em&gt;B. simaruba&lt;/em&gt; and &lt;em&gt;D. anisandra&lt;/em&gt;, those with the greatest density were &lt;em&gt;D. anisandra&lt;/em&gt; and &lt;em&gt;L. xuul&lt;/em&gt;, and the most dominant were &lt;em&gt;G. floribundum&lt;/em&gt; and &lt;em&gt;P. piscipula&lt;/em&gt;. Floristic affinity analysis identified three floristic groups: dry tropical forest; mixed seasonally flooded forest; and semi-evergreen tropical forest. Although relatively small in area, Uxmal has highly diverse microclimates and substrate types which support a diverse woody species composition, structure and physiognomy within the same seasonally dry tropical forest.&lt;/p&gt;

Efectos de la calidad del agua y del sustrato blando sobre la macrofauna bentónica de la zona intermareal en la Playa Pochomil, San Rafael del Sur

Se realizó un estudio espacial y temporal de la macrofauna bentónica en la zona intermareal de la Playa Pochomil, Nicaragua, en tres sitios denominados S.A (sitio arenoso), SRR (sitio rocoso con río) y S.R (sitio rocoso), respectivamente. Al final del estudio se contabilizaron un total de 596 individuos pertenecientes a cuatro Filos (Molusca, Anélida, Artrópoda y Equinodermata). La diversidad de macrofauna bentónica calculada mediante el índice de Shannon-Weaver, refleja valores de diversidad muy bajos durante todas las épocas de muestreo. Mediante el índice de Jaccard y Morisita-Horn, se evidenció que hubo baja similitud de especies. Además, se comprobó que la temporalidad no tuvo efecto directo significativo sobre la abundancia y distribución de la macrofauna bentónica, sino que ésta fue influenciada principalmente por las características físicas de los sitios de muestreo

Distribución y correlación espacial de especies arbóreas por gradiente altitudinal en la Selva Lacandona, Chiapas

Se analizó el patrón de distribución y correlación espacial de las especies arbóreas a lo largo de un gradiente altitudinal en el Área Natural Protegida (ANP) Metzabok, Selva Lacandona, Chiapas. En cada estrato altitudinal (EA) se instaló una unidad de muestreo de 20 × 50 m, que fue dividida en 10 subunidades de muestreo (SUM) de 10 × 10 m, donde se registraron los fustales. En las SUM se delimitó un cuadro de 5 × 5 m para el registro de latizales, y en su interior se establecieron dos cuadros de 2 × 2 m para el reconocimiento de brinzales. La distribución espacial de fustales, latizales y brinzales se analizó con el índice de Morisita-Horn; mientras que, la distribución y correlación espacial de los fustales por categorías de altura (inferior, intermedia y superior) y EA se evaluó mediante la función univariada K(t) y bivariada K12 (t) de Ripley. El patrón espacial promedio de la clase fustal para las tres categorías de altura a lo largo del gradiente altitudinal fue agregado (), similar que en latizales y brinzales . La función K12 (t) indica que los EA 2, 3 y 5 de la categoría inferior-intermedia mostraron, tanto repulsión como atracción espacial, mientras las denominadas inferior-superior e intermedia-superior tuvieron un comportamiento de independencia y repulsión espacial, respectivamente. Estos hallazgos aportan bases para la implementación de estrategias silvícolas enfocadas a la conservación de las especies arbóreas presentes en el ANP Metzabok.