Humic substances modulate bacterial communities and mitigate adverse effects of temperature stress in coral reef organisms.

Aims: In the present study, we tested if terrestrially-derived humic substances (HS) could mitigate the adverse effects of elevated temperature and UVB radiation on the bacterial communities of two hard corals (Montipora digitata and Montipora capricornis), one soft coral (Sarcophyton glaucum), sediment and water. We also examined the impact of temperature, UVB radiation and HS supplementation on coral photosynthetic activity, a proxy for coral bleaching.

Methods And Results: We performed a multifactorial experiment using a randomized-controlled microcosm setup.

Clinical utility of receptor status prediction in breast cancer and misdiagnosis identification using deep learning on hematoxylin and eosin-stained slides.

Background: Molecular profiling of estrogen receptor (ER), progesterone receptor (PR), and ERBB2 (also known as Her2) is essential for breast cancer diagnosis and treatment planning. Nevertheless, current methods rely on the qualitative interpretation of immunohistochemistry and fluorescence in situ hybridization (FISH), which can be costly, time-consuming, and inconsistent. Here we explore the clinical utility of predicting receptor status from digitized hematoxylin and eosin-stained (H&E) slides using machine learning trained and evaluated on a multi-institutional dataset.

Unravelling a Latent Pathobiome Across Coral Reef Biotopes.

Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis.

Using artificial intelligence to prioritize pathology samples: report of a test drive.

The digital transformation of pathology, through automation and computational tools, addresses current challenges in the field. This study evaluates Paige Pan Cancer, a novel artificial intelligence tool based on the Virchow foundation model, designed to flag invasive cancer in haematoxylin and eosin-stained slides from 16 primary tissue types. Using 62 cases from the Ipatimup Pathology Laboratory, we found the tool had a sensitivity of 93.

Development and validation of an experimental life support system to study coral reef microbial communities.

In the present study, we developed and validated an experimental life support system (ELSS) designed to investigate coral reef associated bacterial communities. The microcosms in the ELSS consisted of coral reef sediment, synthetic seawater, and specimens of five benthic reef species. These included two hard corals Montipora digitata and Montipora capricornis, a soft coral Sarcophyton glaucum, a zoanthid Zoanthus sp.

Image analysis for bright-field HER2 in situ hybridization: validation for clinical use.

The aim of the present study was to develop and validate a quantitative image analysis (IA) algorithm to aid pathologists in assessing bright-field HER2 in situ hybridization (ISH) tests in solid cancers. A cohort of 80 sequential cases (40 HER2-negative and 40 HER2-positive) were evaluated for HER2 gene amplification with bright-field ISH. We developed an IA algorithm using the ISH Module from HALO software to automatically quantify HER2 and CEP17 copy numbers per cell as well as the HER2/CEP17 ratio.

Evaluation of Artificial Intelligence-Based Gleason Grading Algorithms "in the Wild".

The biopsy Gleason score is an important prognostic marker for prostate cancer patients. It is, however, subject to substantial variability among pathologists. Artificial intelligence (AI)-based algorithms employing deep learning have shown their ability to match pathologists' performance in assigning Gleason scores, with the potential to enhance pathologists' grading accuracy.

Somatic Mutations in KEAP1-NRF2 Complex in Breast Cancer.

Breast cancer remains the leading cause of cancer deaths for women. Long-term estrogen exposure is considered carcinogenic due to semiquinone production and to compromised detoxification. Metabolic regulator polymorphisms, such as (rs1048290) and (rs35652124, rs6721961, rs6706649), can be valuable in understanding the individual cytoprotection profile.

The 1000 Mitoses Project: A Consensus-Based International Collaborative Study on Mitotic Figures Classification.

The identification of mitotic figures is essential for the diagnosis, grading, and classification of various different tumors. Despite its importance, there is a paucity of literature reporting the consistency in interpreting mitotic figures among pathologists. This study leverages publicly accessible datasets and social media to recruit an international group of pathologists to score an image database of more than 1000 mitotic figures collectively.

HER2 and PD-L1 Expression in Gastric and Gastroesophageal Junction Cancer: Insights for Combinatorial Targeting Approaches.

Gastric and gastroesophageal junction adenocarcinomas (GA/GEJA) are associated with a poor prognosis, primarily due to late disease diagnosis. Human Epidermal Growth Factor Receptor 2 (HER2) overexpression and programmed death-ligand 1 (PD-L1) expression are important biomarkers for treatment selection in locally advanced unresectable and metastatic GA/GEJA, and there is increasing interest in their role in earlier stages of disease. In this study, we aimed to evaluate HER2 and PD-L1 expression in a curative-intent GA/GEJA cohort to describe their expression patterns and analyze the association between HER2 expression and clinicopathological features.

Tsunami deposits in Tunisia contemporaneous of the large 365 CE Crete earthquake and Mediterranean Sea catastrophic event.

New field investigations along the East Tunisian coastline reveal sedimentary deposits and damaged localities that may account for a catastrophic event during the late Holocene. North of Sfax city, ~ 3.4 m high cliff coastal marine and alluvial terraces show 20 to 50-cm-thick chaotic layer with sandy coarse gravels mixed with reworked pebbles, broken shells of gastropods and molluscs, organic matter and Roman pottery.

Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp.

Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems.

Optimizing the management of thyroid specimens to efficiently generate whole slide images for diagnosis.

Transition from optical to digital observation requires an additional procedure in the pathology laboratory, the scanning of glass slides, leading to increased time and digital archive consumption. Thyroid surgical samples often carry the need to collect several tissue fragments that generate many slides to be scanned. This study evaluated the impact of using different inking colours for the surgical margin, section thickness, and glass slide type, in the consumption of time and archive.

One nodule-one punction-one slide: Optimizing thyroid fine-needle aspiration for a digital workflow.

Objective: Interventional pathologists have expanded their expertise by acquiring proficiency in ultrasound-guided thyroid fine-needle aspiration biopsy (FNAB) and are now required to optimize punction procedures due to low resources and digital workflows. The aim of this study is to compare FNAB sample adequacy in two series with one versus two slides available for cytopathological analysis and its influence on diagnosis categorization, time taken to reach a final diagnosis, scanning time and size of the digital files produced.

Methods: Patients were retrospectively selected based on the sampling of thyroid nodules using either two glass slides (two-slide group) or one slide only (one-slide group) and cytological diagnosis was performed using the second edition of the Bethesda system.

Inking cell blocks improves scanner detection for diagnosis in pathology.

Cell blocks may be hard to be totally automatically detected by the scanner (ADS), generating incomplete whole slide images (WSIs), with areas that are not scanned, leading to possible false negative diagnosis. The aim of this study is to test if inking the cell blocks helps increasing ADS. Test 1: 15 cell blocks were sectioned, one half inked black (1HB) and the other inked green (1HG).

A Study of Sponge Symbionts from Different Light Habitats.

The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C.

Exploring Prokaryotic Communities in the Guts and Mucus of Nudibranchs, and Their Similarity to Sediment and Seawater Microbiomes.

In the present study, we compared mucus and gut-associated prokaryotic communities from seven nudibranch species with sediment and seawater from Thai coral reefs using high-throughput 16S rRNA gene sequencing. The nudibranch species were identified as Doriprismatica atromarginata (family Chromodorididae), Jorunna funebris (family Discodorididae), Phyllidiella nigra, Phyllidiella pustulosa, Phyllidia carlsonhoffi, Phyllidia elegans, and Phyllidia picta (all family Phyllidiidae). The most abundant bacterial phyla in the dataset were Proteobacteria, Tenericutes, Chloroflexi, Thaumarchaeota, and Cyanobacteria.

Demonstrating the interference of tissue processing in the evaluation of tissue biomarkers: The case of PD-L1.

The immunohistochemical (IHC) expression of PD-L1 in cancer models is used as a predictive biomarker of response to immunotherapy. We aimed to evaluate the impact of the usage of 3 different tissue processors in the IHC expression of PD-L1 antibody clones: 22C3 and SP142. Three different topographies of samples (n = 73) were selected at the macroscopy room: 39 uterine leiomyomas, 17 placentas and 17 palatine tonsils.

Syndecan-4 is a maestro of gastric cancer cell invasion and communication that underscores poor survival.

Gastric cancer is a dominating cause of cancer-associated mortality with limited therapeutic options. Here, we show that syndecan-4 (SDC4), a transmembrane proteoglycan, is highly expressed in intestinal subtype gastric tumors and that this signature associates with patient poor survival. Further, we mechanistically demonstrate that SDC4 is a master regulator of gastric cancer cell motility and invasion.

Metastatic solid tumours to the penis: a clinicopathologic evaluation of 109 cases from an international collaboration.

Aims: To elucidate the spectrum of metastatic tumours to the penis and their clinicopathologic features.

Methods: The databases and files of 22 pathology departments from eight countries on three continents were queried to identify metastatic solid tumours of the penis and to characterize their clinical and pathologic features.

Results: We compiled a series of 109 cases of metastatic solid tumours that secondarily involved the penis.

Artificial intelligence-assisted cancer diagnosis improves the efficiency of pathologists in prostatic biopsies.

Paige Prostate is a clinical-grade artificial intelligence tool designed to assist the pathologist in detecting, grading, and quantifying prostate cancer. In this work, a cohort of 105 prostate core needle biopsies (CNBs) was evaluated through digital pathology. Then, we compared the diagnostic performance of four pathologists diagnosing prostatic CNB unaided and, in a second phase, assisted by Paige Prostate.

Decline of case reports in pathology and their renewal in the digital age: an analysis of publication trends over four decades.

Aims: We investigated the trend in case reports (CRs) publication in a sample of pathology journals. Furthermore, we proposed an alternative publishing route through new digital communication platforms, represented by the 'social media case report'.

Methods: 28 pathology journals were selected from SCImago database and searched in PubMed to identify the number of published CRs.

Dataset of analyzes performed to determine the level and timing of selected organic pollutants' inputs in sediments of the Lake of Cavazzo (Italy).

This data article presents the dataset collected for selected organic pollutants in the framework of a larger research project aimed at assessing the effects of different environmental stressors (natural and anthropogenic) in sediments of the Lake of Cavazzo, a basin of glacial origin located in a seismically active region of the Italian Eastern Alps. Information relative to sampling strategy and operations, location of sampling sites, sedimentary chronological benchmarks, and profiles of RGB (Red-Green-Blue) color code determined from high resolution photos taken at cores CAV-04 and CAV-06 are reported, together with analytical data for 15 polycyclic aromatic hydrocarbons, 21 polychlorinated biphenyls' congeners (including the non-Aroclor CB-11), 14 polybrominated diphenyl ethers' congeners, and 22 organochlorine pesticides, whose concentrations were determined by Gas Chromatography coupled both to Low-Resolution and High-Resolution Mass Spectrometry. Interpretation of this dataset is fully discussed in the companion article by Pizzini et al.

Deep learning for fully-automated nuclear pleomorphism scoring in breast cancer.

To guide the choice of treatment, every new breast cancer is assessed for aggressiveness (i.e., graded) by an experienced histopathologist.