Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk of Immune-related Adverse Events in Melanoma Patients With Preexisting Autoimmune Disease Treated With Immune Checkpoint Inhibitors

Supplemental Digital Content is available in the text. Objective: The objective of this study was to examine the risk of immune-related adverse events (irAEs) in patients with a preexisting autoimmune disease (pAID) presenting with a cutaneous melanoma receiving an immune checkpoint inhibitor (ICI) therapy. Methods: Data from the Surveillance, Epidemiology, and End Results cancer registries and linked Medicare claims between January 2010 and December 2015 was used to identify patients diagnosed with cutaneous melanoma who had pAID or received ICI or both. Patients were then stratified into 3 groups: ICI+pAID, non-ICI+pAID, and ICI+non-pAID. Inverse probability of treatment weighted Cox proportional hazards regression models were fitted to assess the risk of cardiac, pulmonary, endocrine, and neurological irAE. Results: In total, 3704 individuals were included in the analysis. The majority of patients consisted of non-ICI+pAID patients (N=2706/73.1%), while 106 (2.9%) patients and 892 (24.1%) were classified as ICI+pAID and ICI+non-pAID, respectively. The risk of irAE was higher in the ICI+pAID group compared with the non-ICI+pAID and ICI+non-pAID, respectively (non-ICI: cardiac: hazard ratio [HR]=3.59, 95% confidence interval [CI]: 2.83-4.55; pulmonary: HR=3.94, 95% CI: 3.23-4.81; endocrine: HR=1.72, 95% CI: 1.53-1.93; neurological: HR=3.88, 95% CI: 2.30-6.57/non-pAID: cardiac: HR=3.83, 95% CI: 3.39-4.32; pulmonary: HR=2.08, 95% CI: 1.87-2.32; endocrine: HR=1.23, 95% CI: 1.14-1.32; neurological: HR=3.77, 95% CI: 2.75-5.18). Conclusions: Patients with a pAID face a significantly higher risk of irAEs. Further research examining the clinical impact of these events on the patients’ oncological outcome and quality of life is urgently needed given our findings of significantly worse rates of adverse events.
U-Net Deep-Learning-Based 3D Cell Counter for the Quality Control of 3D Cell-Based Assays through Seed Cell Measurement

Conventional cell-counting software uses contour or watershed segmentations and focuses on identifying two-dimensional (2D) cells attached on the bottom of plastic plates. Recently developed software has been useful tools for the quality control of 2D cell-based assays by measuring initial seed cell numbers. These algorithms do not, however, quantitatively test in three-dimensional (3D) cell-based assays using extracellular matrix (ECM), because cells are aggregated and overlapped in the 3D structure of the ECM such as Matrigel, collagen, and alginate. Such overlapped and aggregated cells make it difficult to segment cells and to count the number of cells accurately. It is important, however, to determine the number of cells to standardize experiments and ensure the reproducibility of 3D cell-based assays. In this study, we apply a 3D cell-counting method using U-net deep learning to high-density aggregated cells in ECM to identify initial seed cell numbers. The proposed method showed a 10% counting error in high-density aggregated cells, while the contour and watershed segmentations showed 30% and 40% counting errors, respectively. Thus, the proposed method can reduce the seed cell-counting error in 3D cell-based assays by providing the exact number of cells to researchers, thereby enabling the acquisition of quality control in 3D cell-based assays.
Mechanism underlying long non-coding RNA ILF3-AS1-mediated inhibition of cervical cancer cell proliferation, invasion and migration, and promotion of apoptosis

Long non-coding RNA ILF3 divergent transcript (ILF3-AS1) displays a tumor-suppressing effect. StarBase predicted that the potential target microRNA (miR) of ILF3-AS1 was miR-454-3p; therefore, the present study investigated the effect of ILF3-AS1 and its target miR-454-3p on cervical cancer (CC). Gene Expression Profiling Interactive Analysis was used to predict the expression of ILF3-AS1 in CC and the overall survival rate of patients. The present study demonstrated that ILF3-AS1 expression was significantly downregulated in human CC tissues and cells compared with adjacent tissues (ANTs) and normal cervical epithelial cells (NCEs), respectively. Patients with CC with high ILF3-AS1 expression displayed higher survival rates compared with patients with low ILF3-AS1 expression. Cell viability, apoptosis, migration and invasion were detected by performing Cell Counting Kit-8, flow cytometry, wound healing and Transwell assays, respectively. Compared with the negative control (NC) group, ILF3-AS1 overexpression significantly inhibited CC cell viability and migration, but significantly increased CC cell apoptosis. Moreover, ILF3-AS1 overexpression significantly upregulated E-Cadherin expression levels, but significantly downregulated N-Cadherin and snail family transcriptional repressor 1 expression levels compared with the NC group. miR-454-3p expression was negatively correlated with ILF3-AS1, and highly expressed in CC tissues and cells compared with ANTs and NCEs, respectively. PTEN, which was predicted and verified as the target gene for miR-454-3p, was significantly downregulated in CC tissues and cells compared with ANTs and NCEs, respectively. ILF3-AS1 expression was positively correlated with PTEN expression, and ILF3-AS1 overexpression partially reversed the inhibitory effect of miR-454-3p on PTEN expression. In conclusion, the present study indicated that ILF3-AS1 inhibited CC cell proliferation and migration, and promoted CC cell apoptosis by inhibiting epithelial-mesenchymal transition, and ILF3-AS1 overexpression partially reversed the inhibitory effect of miR-454-3p on PTEN expression.
Phenological and intrinsic predictors of mite and haemacoccidian infection dynamics in a Mediterranean community of lizards

Abstract Abstract Ectotherms are vulnerable to environmental changes and their parasites are biological health indicators. Thus, parasite load in ectotherms is expected to show a marked phenology. This study investigates temporal host–parasite dynamics in a lizard community in Eastern Spain during an entire annual activity period. The hosts investigated were Acanthodactylus erythrurus, Psammodromus algirus and Psammodromus edwardsianus, three lizard species coexisting in a mixed habitat of forests and dunes, providing a range of body sizes, ecological requirements and life history traits. Habitat and climate were considered as potential environmental predictors of parasite abundance, while size, body condition and sex as intrinsic predictors. Linear models based on robust estimates were fitted to analyse parasite abundance and prevalence. Ectoparasitic mites and blood parasites from two haemococcidian genera were found: Lankesterella spp. and Schellackia spp. Habitat type was the only predictor explaining the abundance of all parasites, being mostly higher in the forest than in the dunes. The results suggest that particularities in each host–parasite relationship should be accounted even when parasites infect close-related hosts under the same environmental pressures. They also support that lizard parasites can be biomarkers of environmental perturbation, but the relationships need to be carefully interpreted for each host–parasite assemblage.
Localized Induced Defenses Limit Gall Formation by Eriophyid Mite Against Invasive Lygodium microphyllum (Schizaeales: Lygodiaceae)

Abstract A potential barrier to the establishment of weed biological control agents is interference from other management tactics that induce plant defenses. Methods that suppress the weed such as feeding by other biological control agents or mechanical removal are especially disposed to inducing plant defenses and potentially limiting agent establishment. Here, we focused on the invasive weed Lygodium microphyllum (Cav.) R. Br. (Schizaeales: Lygodiaceae, Old World climbing fern) and one of its biological control agents, the mite Floracarus perrepae Knihinicki and Boczek (Acariformes: Eriophyidae). We experimentally induced plant defenses in potted plants via damage or application of jasmonic acid, a hormone typically involved in plant defenses, and measured the responses of the mite in a screenhouse. Localized damage to the pinnae (e.g., leaflets) via cutting or larval feeding from a second biological control agent, Neomusotima conspurcatalis (Warren) (Lepidoptera; Crambidae), reduced F. perrepae gall formation, but not the number of mites per gall. In contrast, damage to rachises (e.g., stems) did not affect galling, likely because plant defense responses were not systemic. Application of jasmonic acid reduced gall formation but not the numbers of mites within galls. Taken together, we found that localized damage interfered with gall formation but not within-gall reproduction. However, these effects on the mite from induced plant defenses are likely short-lived, and therefore interference between management tactics is unlikely to affect F. perrepae establishment and performance.
Bioturbation by black soldier fly larvae—Rapid soil formation with burial of ceramic artifacts

Bioturbation involves the incorporation of residues from the surface soil into the subsoil; however, common small soil ‘bioengineers’, such as earthworms or termites, are unlikely to transport human artifacts to deeper soil horizons. However, such artifacts occur in the deeper soil horizons within Amazonian Anthrosols (Terra Preta). Here we test the assumption that such tasks could be carried out by fly larvae, which could thus play a crucial role in waste decomposition and associated soil mixing under tropical conditions. We performed two greenhouse experiments with sandy substrate covered with layers of organic waste, ceramic fragments, and black soldier fly larvae (BSFL) (Hermetia illucens (L.) (Dipt.: Stratiomyidae)). We used in-situ images to assess the rate of bioturbation by BSFL, and then designed our main study to observe waste dissipation (reduction of organic carbon and phosphorus contents from waste model trials with and without charcoal) as related to larval-induced changes in soil properties. We found that the bioturbation of macroinvertebrates like BSFL was able to bury even large (> 5 cm) ceramic fragments within hours, which coincided with high soil growth rates (0.5 cm h-1). The sandy soil was subsequently heavily enriched with organic matter and phosphorus originating from organic waste. We conclude that BSFL, and possibly other fly species, are important, previously overlooked soil ‘bioengineers’, which may even contribute to the burial of artifacts in Anthrosols and other terrestrial waste dumps.
Path planning for the Platonic solids on prescribed grids by edge-rolling

The five Platonic solids—tetrahedron, cube, octahedron, dodecahedron, and icosahedron—have found many applications in mathematics, science, and art. Path planning for the Platonic solids had been suggested, but not validated, except for solving the rolling-cube puzzles for a cubic dice. We developed a path-planning algorithm based on the breadth-first-search algorithm that generates a shortest path for each Platonic solid to reach a desired pose, including position and orientation, from an initial one on prescribed grids by edge-rolling. While it is straightforward to generate triangular and square grids, various methods exist for regular-pentagon tiling. We chose the Penrose tiling because it has five-fold symmetry. We discovered that a tetrahedron could achieve only one orientation for a particular position.
Two Immersive Virtual Reality Tasks for the Assessment of Spatial Orientation in Older Adults with and Without Cognitive Impairment: Concurrent Validity, Group Comparison, and Accuracy Results

Abstract Objective: Spatial disorientation is common in Alzheimer’s disease (AD), Mild Cognitive Impairment (MCI), and preclinical individuals with AD biomarkers. However, traditional neuropsychological tests lack ecological validity for the assessment of spatial orientation and to date, there is still no gold standard. The current study aimed to determine the validity and accuracy of two virtual reality tasks for the assessment of spatial orientation. Methods: We adapted two spatial orientation tasks to immersive virtual environments: a “survey to route” task in which participants had to transfer information from a map to their body position within a maze [Spatial Orientation in Immersive Virtual Environment Test (SOIVET) Maze], and an allocentric-type, route learning task, with well-established topographic landmarks (SOIVET Route). A total of 19 MCI patients and 29 cognitively healthy older adults aged 61–92 participated in this study. Regular neuropsychological assessments were used for correlation analysis and participant performances were compared between groups. Receiver Operating Characteristic (ROC) curve analysis was performed for accuracy. Results: The SOIVET Maze correlated with measures of visuoperception, mental rotation, and planning, and was not related to age, educational level, or technology use profile. The SOIVET Route immediate correlated with measures of mental rotation, memory, and visuoconstruction, and was influenced only by education. Both tasks significantly differentiated MCI and control groups, and demonstrated moderate accuracy for the MCI diagnosis. Conclusion: Traditional neuropsychological assessment presents limitations and immersive environments allow for the reproduction of complex cognitive processes. The two immersive virtual reality tasks are valid tools for the assessment of spatial orientation and should be considered for cognitive assessments of older adults.
Circulating microRNA-122, microRNA-126-3p and microRNA-146a are associated with inflammation in patients with pre-diabetes and type 2 diabetes mellitus: A case control study

The prevalence of type 2 diabetes mellitus (T2DM) is increasing dramatically worldwide. Dysregulation of microRNA (miRNA) as key regulators of gene expression, has been reported in numerous diseases including diabetes. The aim of this study was to investigate the expression levels of miRNA-122, miRNA-126-3p and miRNA-146a in diabetic and pre-diabetic patients and in healthy individuals, and to determine whether the changes in the level of these miRNAs are reliable biomarkers in diagnosis, prognosis, and pathogenesis of T2DM. Additionally, we examined the relationship between miRNA levels and plasma concentrations of inflammatory factors including tumor necrosis factor alpha (TNF-α) and interleukin 6 (Il-6) as well as insulin resistance. In this case-control study, participants (n = 90) were allocated to three groups (n = 30/group): T2DM, pre-diabetes and healthy individuals as control (males and females, age: 25–65, body mass index: 25–35). Expression of miRNA was determined by real-time polymerase chain reaction (RT-PCR). Furthermore, plasma concentrations of TNF-α, IL-6 and fasting insulin were measured by enzyme-linked immunosorbent assay. Homeostatic model assessment for insulin resistance (HOMA-IR) was calculated as an indicator of insulin resistance. MiRNA-122 levels were higher while miRNA-126-3p and miRNA-146a levels were lower in T2DM and pre-diabetic patients compared to control (p<0.05). Furthermore, a positive correlation was found between miRNA-122 expression and TNF-α (r = 0.82), IL-6 (r = 0.83) and insulin resistance (r = 0.8). Conversely, negative correlations were observed between miRNA-126-3p and miRNA-146a levels and TNF-α (r = -0.7 and r = -0.82 respectively), IL-6 (r = -0.65 and r = -0.78 respectively) as well as insulin resistance (r = -0.67 and r = -0.78 respectively) (all p<0.05). Findings of this study suggest the miRNAs can potentially contribute to the pathogenesis of T2DM. Further studies are required to examine the reproducibility of these findings.
Age and growth of the bull shark (Carcharhinus leucas) around Reunion Island, South West Indian Ocean.

Sharks exhibit varied demographic strategies depending on both the species and the population location, which make them more or less vulnerable to fishing. Accurate evaluation of local age and growth parameters is therefore fundamental for the sustainable management of their stocks. Although demographic parameters have been assessed for bull shark (Carcharhinus leucas) populations in several locations of the world, this information was missing so far around the Reunion Island, in the South West Indian Ocean. To fill this gap of knowledge, age and growth data was gathered from the vertebrae of 140 individuals of C. leucas (77 females and 63 males, mostly adults) fished around the island between 2012 and 2019. After verification of the annual deposition of growth band pairs on these structures using relative marginal increment analysis on 40 individuals, band pairs were counted along the vertebral centrum for each individual. Thanks to this approach, growth was shown to significantly differ between male and female C. leucas around the reunion island, with respective von Bertalanffy growth model equations of Lt = 314 1 - e - 0.0814 t + 5.45 and Lt = 321.5 1 - e - 0.0999 t + 3.420 . Indeed, the females of the species fished in this area were significantly (p < 0.001) larger than local males, with an estimated difference in size of ~ 16.1 cm at 20 years old. They also apparently reach older ages, with an estimated maximum age of 33.50 years, against 29.75 years only for the males. The estimated size at birth around the island is larger than elsewhere in the world, varying from 92.30 to 100.00 cm depending on the method used. These results confirm that the population of C. leucas around the Reunion Island exhibits a K-selected strategy, which makes it highly vulnerable to fishing pressure. This article is protected by copyright. All rights reserved.
An X-ray Diffraction and Small Angle X-ray Scattering Study of Solvated Li-Graphite Intercalation Compounds

Stage I C 6 Li and stage II C 12 Li were prepared using a low temperature liquid lithium route. Small angle X-ray scattering measurements of both pristine binary compounds indicated that the surfaces are highly dissected. As a result using a mixed layered graphite precursor containing pre- graphitic, chemically distinct lamellar domains, both C 6 Li and C 12 Li produced an additional suite of ternary structures after successive intercalation with Li and THF. The use of a THF- Li-graphite ternary compound to entrap LiBH 4 for hydride storage is explored. Lithium insertion compounds based on graphite anode are attractive anodes for reversible Li storage in the anode material in high energy density batteries in terms of safety and cycle life compared with lithium metal. (1) For other energy- based applications, e.g., hydrogen storage, the phase instability of the hydrogenated compounds presents significant challenges for a rechargeable system. (2), (3) At liquid nitrogen temperature, Li- doped carbons are reported to physisorb only 2-3 wt% H 2 , less than that demonstrated by the carbon used to prepare the intercalation compound.
Pygmy Marmoset Exudate Feeding Stimulates Exudate Production

Exudates are an important renewable resource for many primates. Exudate renewability is based on observations of primates repeatedly depleting exudate sites and measures of exudate trees’ daily replenishment rates, but the role of the consumer in the renewal process is unclear. Trees’ exudate production may be independent of the consumer, remaining unchanged regardless of depletion frequency, but since trees produce exudates as a physiological response to fungal infection, they may produce more exudates with more frequent depletion. To test these competing hypotheses, we employed a within-subjects experimental design in which we exposed pygmy marmosets’ exudate holes to two treatment conditions: collecting exudates after 5 h and collecting exudates every hour for five consecutive hours. To compare production outputs between treatments, we used generalised linear mixed modelling in which log-transformed production data were a function of treatment with exudate holes nested within trees as a random effect. The model indicated that the cumulative production of hourly exudate removal was significantly greater than the amount accumulated after 5 h. Furthermore, the random effect of holes nested within trees had the greatest impact on variation in differences between treatments, but another unknown source also contributed to the observed variation. These results support the hypothesis that consumers partly drive exudate production, and although it is unknown what other factors, such as fungal load and healing trajectory, may influence variation between treatments, we conclude that pygmy marmosets can stimulate exudate production by consuming exudates.
Racial/Ethnic Disparities in Use of High-Quality Hospitals Among Thyroid Cancer Patients

Abstract This study examined racial/ethnic differences in the use of high-quality hospitals among thyroid cancer patients. The study included adult patients diagnosed between 2004 and 2015 identified in the California Cancer Registry linked with hospital discharge records. Hospital quality was defined using a composite thyroid cancer-specific hospital quality score. Black (risk ratio [RR] 0.75, 95% CI 0.70–0.80), Hispanic (RR 0.73, 95% CI 0.71–0.75), and Asian/Pacific Islander patients (RR 0.86, 95% CI 0.84–0.89) were less likely to be treated in high-quality hospitals than non-Hispanic White patients. This disparity persisted after adjusting for insurance status and socioeconomic status.
The Silk Vista Baby – The UK experience

Background The Silk Vista Baby (SVB) flow diverter (FDS) is the only FDS deliverable via a 0.017 inch microcatheter and is specifically designed for the distal vasculature. We sought to evaluate the safety and efficacy of the SVB. Materials and Methods We performed a retrospective review to identify SVB cases at 4 tertiary neurosurgical centres within the U.K. Clinical, procedural, angiographic and follow-up data were collected. Results We identified 60 patients (35 female, 58%) of average age 54 ± 10.5 (range 30–72) with 61 aneurysms, 50 (81.9%) located in the anterior circulation. The majority of the aneurysms treated were unruptured (46, 75.4%) and saccular (46, 75.4%). Dome size was 6.2 ± 6.2 mm (range 1–36mm) and parent vessel diameter was 2.3 ± 0.4 mm (range 1.2-3.3 mm). An average number of 1.07 devices were implanted. Coils or other devices were implanted in 14 aneurysms (23.3%). At last angiographic follow-up (n = 55), 7.5 ± 4.2 months post-procedure, 32 aneurysms (57.1%) were graded as RRC I, 7 (12.5%) RRC II, and 17 RRC III (30.4%). Clinical complications, excluding death, were seen in 4 patients (6.8%) including 1 delayed aneurysm rupture and 3 symptomatic ischaemic events. Only one patient had permanent morbidity (mRS 1). 3 patients died during follow-up (5.1%); 2 deaths were related to the aneurysms (3.4%) – one ruptured dissecting MCA aneurysm, and one giant partially thrombosed posterior circulation aneurysm. 93% of patients were mRS ≤ 2 at last follow-up. Conclusion The SVB has high rates of technical success and an acceptable safety profile. Distal aneurysms may occlude slower due to relative oversizing of the devices.