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Manually delineating upper abdominal organs at risk (OARs) is a time-consuming task. To develop a deep-learning-based tool for accurate and robust auto-segmentation of these OARs, forty pancreatic cancer patients with contrast-enhanced breath-hold computed tomographic (CT) images were selected. We trained a three-dimensional (3D) U-Net ensemble that automatically segments all organ contours concurrently with the self-configuring nnU-Net framework. Our tool's performance was assessed on a held-out test set of 30 patients quantitatively. Five radiation oncologists from three different institutions assessed the performance of the tool using a 5-point Likert scale on an additional 75 randomly selected test patients. The mean (± std. dev.) Dice similarity coefficient values between the automatic segmentation and the ground truth on contrast-enhanced CT images were 0.80 ± 0.08, 0.89 ± 0.05, 0.90 ± 0.06, 0.92 ± 0.03, 0.96 ± 0.01, 0.97 ± 0.01, 0.96 ± 0.01, and 0.96 ± 0.01 for the duodenum, small bowel, large bowel, stomach, liver, spleen, right kidney, and left kidney, respectively. 89.3% (contrast-enhanced) and 85.3% (non-contrast-enhanced) of duodenum contours were scored as a 3 or above, which required only minor edits. More than 90% of the other organs' contours were scored as a 3 or above. Our tool achieved a high level of clinical acceptability with a small training dataset and provides accurate contours for treatment planning.

Abstract Approximately 8100 km2 of Alaska are leased to the oil and gas industry for exploration and extraction. According to industry estimates, subsurface expansion from these leases could cover up to 130.2 km2 per pad. As industrial oil extraction activities increase across the thawing Alaskan permafrost, impacts on the permafrost environment will include rapid thaw, increased hydrological flux, and the release of climate warming greenhouse gases. Here, we use remote sensing and field observations to provide a first-order comparison of the direct impacts to the permafrost tundra from oil well pads, and the long-term consequences of a legacy oil pads on the warming North Slope of Alaska. We find that oil well pads on the permafrost accelerate permafrost degradation and persist despite remediation.

Abstract The future of organ and tissue biofabrication strongly relies on 3D bioprinting technologies. However, maintaining sterility remains a critical issue regardless of the technology used. This challenge becomes even more pronounced when the volume of bioprinted objects approaches organ dimensions. Here, we introduce a novel device called the Flexible Unique Generator Unit (FUGU), which is a unique combination of flexible silicone membranes and solid components made of stainless steel. Alternatively, the solid components can also be made of 3D printed medical-grade polycarbonate. The FUGU is designed to support micro-extrusion needle insertion and removal, internal volume adjustment, and fluid management. The FUGU was assessed in various environments, ranging from custom-built basic cartesian to sophisticated 6-axis robotic arm bioprinters, demonstrating its compatibility, flexibility, and universality across different bioprinting platforms. Sterility assays conducted under various infection scenarios highlight the FUGU’s ability to physically protect the internal volume against contaminations, thereby ensuring the integrity of the bioprinted constructs. The FUGU also enabled bioprinting and cultivation of a 14.5 cm3 human colorectal cancer tissue model within a completely confined and sterile environment, while allowing for the exchange of gases with the external environment. This FUGU system represents a significant advancement in 3D bioprinting and biofabrication, paving the path toward the sterile production of implantable tissues and organs.

Abstract Planning for palliative radiotherapy is performed without the advantage of MR or PET imaging in many clinics. Here, we investigated CT-only GTV delineation for palliative treatment of head and neck cancer. Two multi-institutional datasets of palliative-intent treatment plans were retrospectively acquired: a set of 102 non-contrast-enhanced CTs and a set of 96 contrast-enhanced CTs. The nnU-Net auto-segmentation network was chosen for its strength in medical image segmentation, and five approaches separately trained: (1) heuristic-cropped, non-contrast images with a single GTV channel, (2) cropping around a manually-placed point in the tumor center for non-contrast images with a single GTV channel, (3) contrast-enhanced images with a single GTV channel, (4) contrast-enhanced images with separate primary and nodal GTV channels, and (5) contrast-enhanced images along with synthetic MR images with separate primary and nodal GTV channels. Median Dice similarity coefficient ranged from 0.6 to 0.7, surface Dice from 0.30 to 0.56, and 95th Hausdorff distance from 14.7 to 19.7 mm across the five approaches. Only surface Dice exhibited statistically-significant difference across these five approaches using a two-tailed Wilcoxon Rank-Sum test (p ≤ 0.05). Our CT-only results met or exceeded published values for head and neck GTV autocontouring using multi-modality images. However, significant edits would be necessary before clinical use in palliative radiotherapy.

Abstract Studies showed that Brazilian Amazon indigenous territories (ITs) are efficient models for preserving forests by reducing deforestation, fires, and related carbon emissions. Considering the importance of ITs for conserving socio-environmental and cultural diversity and the recent climb in the Brazilian Amazon deforestation, we used official remote sensing datasets to analyze deforestation inside and outside indigenous territories within Brazil's Amazon biome during the 2013–2021 period. Deforestation has increased by 129% inside ITs since 2013, followed by an increase in illegal mining areas. In 2019–2021, deforestation was 195% higher and 30% farther from the borders towards the interior of indigenous territories than in previous years (2013–2018). Furthermore, about 59% of carbon dioxide (CO2) emissions within ITs in 2013–2021 (96 million tons) occurred in the last three years of analyzed years, revealing the magnitude of increasing deforestation to climate impacts. Therefore, curbing deforestation in indigenous territories must be a priority for the Brazilian government to secure these peoples' land rights, ensure the forests' protection and regulate the global climate.

Abstract A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489–422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.

Abstract Face masks obscure a significant portion of the face, reducing the amount of information available to gauge the mental states of others—that is, to exercise the Theory of Mind (ToM) capacity. In three experiments, we assessed the effect of face masks on ToM judgements, measuring recognition accuracy, perceived valence, and perceived arousal in various sets of facial expressions comprising 45 different mental states. Significant effects of face masks were found in all three variables. Judgements of all expressions are less accurate when masked, but, while judgements of negative expressions do not show consistent changes in valence or arousal, positive expressions are perceived to be less positive and less intense. In addition, we identified face muscles associated with changes in perceived valence and arousal, shedding light on the mechanisms through which masks impact ToM judgements, which might be relevant for mitigation strategies. We discuss the implications of these findings in the context of the recent pandemic.

Abstract Fragile X syndrome (FXS) is a neurodevelopmental disorder that is caused by the loss of Fragile X-linked mental retardation protein (FMRP), an RNA binding protein that can bind and recognize different RNA structures and regulate the target mRNAs’ translation involved in neuronal synaptic plasticity. Perturbations of this gene expression network have been related to abnormal behavioral symptoms such as hyperactivity, and impulsivity. Considering the roles of FMRP in the modulation of mRNA translation, we investigated the differentially expressed genes which might be targeted to revert to normal and ameliorate behavioral symptoms. Gene expression data was analyzed and used the connectivity map (CMap) to understand the changes in gene expression in FXS and predict the effective drug candidates. We analyzed the GSE7329 dataset that had 15 control and 8 FXS patients’ lymphoblastoid samples. Among 924 genes, 42 genes were selected as signatures for CMap analysis, and 24 associated drugs were found. Pirenperone was selected as a potential drug candidate for FXS for its possible antipsychotic effect. Treatment of pirenperone increased the expression level of Fmr1 gene. Moreover, pirenperone rescued the behavioral deficits in Fmr1 KO mice including hyperactivity, spatial memory, and impulsivity. These results suggest that pirenperone is a new drug candidate for FXS, which should be verified in future studies.

Abstract Manually delineating upper abdominal organs at risk (OARs) is a time-consuming task. To develop a deep-learning-based tool for accurate and robust auto-segmentation of these OARs, forty pancreatic cancer patients with contrast-enhanced breath-hold computed tomographic (CT) images were selected. We trained a three-dimensional (3D) U-Net ensemble that automatically segments all organ contours concurrently with the self-configuring nnU-Net framework. Our tool’s performance was assessed on a held-out test set of 30 patients quantitatively. Five radiation oncologists from three different institutions assessed the performance of the tool using a 5-point Likert scale on an additional 75 randomly selected test patients. The mean (± std. dev.) Dice similarity coefficient values between the automatic segmentation and the ground truth on contrast-enhanced CT images were 0.80 ± 0.08, 0.89 ± 0.05, 0.90 ± 0.06, 0.92 ± 0.03, 0.96 ± 0.01, 0.97 ± 0.01, 0.96 ± 0.01, and 0.96 ± 0.01 for the duodenum, small bowel, large bowel, stomach, liver, spleen, right kidney, and left kidney, respectively. 89.3% (contrast-enhanced) and 85.3% (non-contrast-enhanced) of duodenum contours were scored as a 3 or above, which required only minor edits. More than 90% of the other organs’ contours were scored as a 3 or above. Our tool achieved a high level of clinical acceptability with a small training dataset and provides accurate contours for treatment planning.

Abstract Implantoplasty is a mechanical decontamination technique that consists of removing the threads and polishing and smoothing the dental implant surface. During implantoplasty there is a large release of titanium metal particles that might provoke a proinflammatory response and reduce the viability of osteogenic cells. We analyze the inflammatory and osteogenic response induced by Ti6Al4V particles released during implantoplasty and by as-received commercially pure Ti particles. Macrophages stimulated with metal particles obtained by implantoplasty and with as-received Ti particles showed an increased proinflammatory expression of TNF-α and a decreased expression of TGF-β and CD206. Regarding cytokine release, there was an increase in IL-1β, while IL-10 decreased. The osteogenic response of Ti6Al4V extracts showed a significant decrease in Runx2 and OC expression compared to the controls and commercially pure Ti extracts. There were no relevant changes in ALP activity. Thus, implantoplasty releases metal particles that seems to induce a pro-inflammatory response and reduce the expression of osteogenic markers.

Abstract Interleukin (IL) 1, and its family member, IL-1 receptor antagonist (IL-1ra), are involved in the pathogenesis and inflammation perpetuation of patients with rheumatoid arthritis (RA). Besides, IL-1 has been linked to an increased risk and greater severity of cardiovascular (CV) disease. We aimed to study if IL-1ra is related to the CV manifestations—including lipid pattern and insulin resistance or subclinical atherosclerosis—that accompanies the disease in a large series of patients with RA. Cross-sectional study that encompassed 430 patients with RA. Serum IL-1ra levels were assessed. A multivariable analysis was performed to analyze the relation of IL-1ra to subclinical carotid atherosclerosis, and to traditional CV factors including a complete lipid molecules profile and insulin resistance or beta cell function indices. Body mass index, abdominal circumference, and the presence of obesity were significantly and positively associated with circulating IL-1ra. Similarly, erythrocyte sedimentation rate, and disease activity scores were significantly related to higher IL-1ra serum levels after adjustment for confounders. Neither carotid intima-media thickness nor the presence of carotid plaque were associated with serum levels of IL-1ra. However, after multivariable analysis circulating IL-1ra was independently and positively associated with higher serum levels of total cholesterol, triglycerides, and apolipoproteins B and C-III. Similarly, IL-1ra was related to higher levels of beta-cell function in the univariable analysis, although, in this case, significance was lost after adjustment. Among patients with RA, IL-1ra is associated with both disease activity and several traditional CV risk factors such as obesity and the presence of higher lipid levels. Our findings suggest that IL-1ra can represent a link between the inflammation and the CV disease risk that are present in patients with RA.