Masked Autoencoders are Scalable Learners of Cellular Morphology

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how self-supervised deep learning approaches scale when training larger models on larger microscopy datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised baselines. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 93-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised baseline at inferring known biological relationships curated from public databases. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.Comment: Spotlight at NeurIPS 2023 Generative AI and Biology (GenBio) Worksho

Cytogenetic Biomonitoring of Carpet Fabric Workers Using Micronucleus Frequency, Nuclear Changes, and the Calculation of Risk Assessment by Repair Index in Exfoliated Mucosa Cells

WOS: 000295396900009PubMed ID: 21495858The micronucleus (MN) assay in exfoliated buccal cells is a minimally invasive method for monitoring genetic damage in human populations and is used as an indicator of genotoxic exposition, as it is associated with chromosome aberrations. In this study, we evaluated MN frequencies and other nuclear changes (NCs), such as karyorrhexis (KR), karyolysis (KL), broken egg (BE), and binucleus in buccal mucosa cells of 50 carpet fabric workers (25 smokers and 25 nonsmokers) and 50 healthy control subjects (25 smokers and 25 nonsmokers). Microscopic observation of 2000 cells per individual was performed in both workers and control subjects. In both the control group and the exposed group, for each person a repair index (RI) was calculated via the following formula: (KR+KL)/(BE+MN). The results showed a statistically significant increase in the frequency of MN in buccal epithelial cells of exposed group compared with control group. There is a significant difference between worker and control groups (p<0.001) for RI. We believe that the calculation of RI values, in addition to nuclear changes, presents a new approach in risk assessment in relation to occupational exposure

Assessment of Genetic Damage in Buccal Epithelium Cells of Painters: Micronucleus, Nuclear Changes, and Repair Index

WOS: 000278871500002PubMed ID: 20218900The micronucleus (MN) assay in exfoliated buccal cells is a useful and minimally invasive method for monitoring genetic damage in humans exposed to occupational and environmental agents. The MN test is used as an indicator of genotoxic exposition, since it is associated with chromosome aberrations. An increased mutation rate in oral squamous cells, which is indicated by an increased MN frequency, is also related to the development of oral mucosa diseases, such as carcinomas. We evaluated MN frequencies and other nuclear changes (NCs), karyorrhexis (KR), karyolysis (KL), broken egg (BE), and binucleus in buccal mucosa cells of 60 painters (30 smokers and 30 nonsmokers) and 60 healthy control subjects (30 smoker and 30 nonsmoker). Microscopic observation of 3000 cells per individual was performed in both painters and control subjects. In the control group and the exposed group, for each person repair index (RI) was calculated via the following formula: (KR+KL)/(BE+MN). The results showed a statistically significant increase in the frequency of MN in buccal epithelial cells of the exposed group compared with the control group (p<0.05). Smokers and nonsmokers differed with respect to the incidence of MN and NCs in all groups. In painters, RI was less than that in the control group. There was a significant difference between painters and the control group (p<0.01) for RI. We believe that determination of RI in addition to NCs and the MN will present a new approach to genotoxicity studies of a population

When to start secukinumab treatment in patients with axial spondyloarthropathy: Before or after anti-TNFot treatment?

Introduction and objectives: This study aimed to evaluate the efficacy of secukinumab (SEC) in axial spondyloarthropathy (axSpA) in anti-TNFot naive and anti-TNFot experienced patients. It also focused on the duration of SEC treatment and its side effects.Patients and methods: The patients with axSpA treated with SEC and followed up in our outpatient clinic from May 2018 through October 2021 were included in this study. All patients in the study also fulfilled the ASAS classification criteria for axSpA. Patients were separated into two groups according to whether they received prior anti-TNFot therapy. While anti-TNFot naive patients comprised group 1, anti-TNFot experienced patients were included in group 2. Pre-and post-treatment BASDAI scores were reported and compared.Results: Eighty-four axSpA patients (42 men; duration of the disease: 86.86 +/- 65.35 months in group 1 and 160.65 +/- 97.4 months in group 2) were treated with SEC. 45.5% of anti-TNFot naive patients and 56.5% of anti-TNFot experienced patients were still on SEC therapy in October 2021. Duration of SEC treatment was 12.5 +/- 7.9 months in group 1 and 17.19 +/- 12 months in group 2 (p = 0.098). The differences between pre-and post-treatment BASDAI scores were statistically significant in both groups (p < 0.001). While patients in group 1 did not develop any adverse effects, three patients in group 2 experienced alopecia, uveitis, and recurrent pneumonia after SEC treatment.Conclusion: Our study's efficacy and safety data on the use of SEC were reassuring in both anti-TNFot naive and anti-TNFot experienced patients. However, further studies are still needed to determine the appropriate timing to begin SEC treatment.(c) 2022 Elsevier Espan similar to a, S.L.U. and Sociedad Espan similar to ola de Reumatologi ' a y Colegio Mexicano de Reumatologi ' a. All rights reserved

Monitoring of nuclear abnormalities in peripheral erythrocytes of three fish species from the Goksu Delta (Turkey): genotoxic damage in relation to water pollution

Goksu Delta is a specially protected area in the Mediterranean region of Turkey. The delta is classified as a Wetland of International Importance according to the RAMSAR Convention on Wetlands of International Importance. Increases in population have recently taken place in this region due to heavy agricultural activities and discharges of anthropogenic wastes. In the present study, frequencies of erythrocytic nuclear abnormalities such as, micronuclei (MN) and nuclear buds (NB) were investigated in peripheral blood of three fish species; Clarias gariepinus (Catfish), Alburnus orontis (Bleak), and Mugil cephalus (Mullet) from Akgol (AG) and Paradeniz (PD) lagoons of Goksu Delta. Concentrations of heavy metals (Cu, Cd, Ni, Pb) were also measured in the water, sediment samples. MN and NA frequencies were elevated in fish from AG and PD lagoons in comparison with those from upstream regions. The results of this study indicate that the lagoons of Goksu Delta contaminated with genotoxic pollutants and that the genotoxicity is related to the agricultural activities and to the discharge of anthropogenic waste waters

Suicidal hanging in Istanbul, Turkey: 1979-2012 Autopsy results

WOS: 000355681900010PubMed ID: 26048496A retrospective study was carried out on 4549 which is the total number of hanging cases autopsied at Forensic Medicine Institute in Istanbul, Turkey. 4502 hanging cases of suicidal origin were detected and evaluated in terms of demographic features, the type of hanging material used for ligature, internal findings in neck organs, toxicological findings and microscopic findings. Of these suicides, 3295 (73.2%) were males and 1207 (26.8%) were females. The average age of the victims was 37.8 (SD 1.6). Crude suicidal hanging rate is approximately two-fold increase in women, while it is about five-to six-fold increase in men during 33 years. 1424 of the victims committed suicide by hanging themselves at home, and 441 of them in prison and indoor areas. The alcohol in the blood of all autopsy victims was tested and results were positive for 687 people. A drug active agent was detected in 108 (2.4%) victims: 70 (1.5%) of them were antidepressants, 20 (0.5%) of them were analgesic/anti-inflammatory/anti-histaminic and 18 (0.4%) of them were antipsychotic. In the examination of the psychoactive substances in blood and urine, any of such substances was not detected in 4146 of the victims. However, victims' blood and urine contained a sedative-hypnotic-anxiolytic with 74 (1.6%), a cannabinoid with 16 (0.4%) and an opioid with 12 (0.3%). Psychoactive substance examination was not carried out for 243 victims. Of these cases, 4060 (90.2%), ecchymosis in soft tissues and 2800 (62.1%) fracture in neck organs was found. (C) 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved

Strength-Based Design Analysis of a Damaged Engine Mounting Bracket Designed for a Commercial Electric Vehicle

This study describes a strength-based design analysis protocol by means of finite element analysis (FEA) for a damaged engine mounting bracket in a converted electric vehicle. The mounting bracket considered in the study is a product specifically designed and manufactured for a converted electric vehicle and failed during conventional operation of the vehicle. Thus, design improvement/revision (redesign) on the bracket geometry was investigated. In this context, to prevent such undesired failures, strength-based design features such as deformation behaviour and stress distribution under projected loads on the bracket should be properly described; however, an accurate description of these features of the bracket may become a complex experimental problem to be solved by designers. This study described redesign of the strength-based design features of the engine mounting bracket through finite element analysis under torsional loading generated by the electric engine that was determined to be the reason for the failure and thus the motivation to realise a safer design. Visual and numerical results obtained from the simulation revealed a clear understanding of the failure behaviour of the bracket and therefore enabled an informed approach to the redesign stage. The initial FEA of the part design mapped the damage regions on the part geometry and indicated the stress magnitudes that were more than the material’s stress limits. The comparison of the failure plots and numerical data obtained from this initial FEA and physically damaged part was consistent. This concluded that the FEA satisfactorily exhibited the deformation behaviour and the main reason for the failure was insufficient geometry thickness and notch effect against predefined loading conditions. Therefore, the main design improvement was realised on these geometric features. Subsequently, the final FEA highlighted that the redesign would enable safe operation. This work contributes to further research into usage of numerical method-based deformation simulation studies for the mounting elements used in customised electric vehicles

Evidence for an association between suicide and religion: a 33-year retrospective autopsy analysis of suicide by hanging during the month of Ramadan in Istanbul

WOS: 000371733000002This study was undertaken to examine the effect of the Islamic holy month of Ramadan on the number of suicides in order to assess whether religious faith is associated with a decreased number of suicides during that period. In this retrospective study, a total number of 82,871 autopsies have been performed in the Morgue Department of the Council of Forensic Medicine (Istanbul) of the Ministry of Justice between 1978 and 2012, 33years. For the study purposes, the earlier start of Islamic calendar months (i.e. 10 or 11days earlier each year) compared with the Gregorian calendar was taken into account and file details such as crime scene investigation reports, information obtained from the police, and autopsy results were assessed. Of the 4315 suicide cases, 267 were reported during Ramadan, while 4048 were recorded during other months. Of the 33years examined, only five Ramadan months exhibited a suicide rate above the annual average and there was a significantly lower (p = 0.042) incidence of suicides during Ramadan. Suicide by hanging is less frequent during Ramadan compared with non-Ramadan months, probably reflecting a positive spiritual influence of this period on Muslims

Characterization, antibacterial, anticarbonic anhydrase II isoenzyme, anticancer, electrochemical and computational studies of sulfonic acid hydrazide derivative and its Cu(II) complex

WOS: 000345116000022A new N'-acetyl butane sulfonic acid hydrazide, C4H9-SO2-NH-NH-COCH3 (Absh, an sulfonamide compound), and its Cu(II) complex [Cu(Absh)(2)(CH3COO)(2)], have been synthesized and characterized by elemental analysis, spectrometric methods (H-1-C-13 NMR, FT-IR, LC-MS), thermal analysis, magnetic susceptibility and conductivity measurements. In addition, molecular structure of the ligand, Absh was determined by single crystal X-ray diffraction technique and found that the compound crystallizes in monoclinic, space group P2(1)/c. To gain information about the structure of the ligand and its complex, we have performed computational studies using density functional theory (DFT) for optimized geometries of the compounds. Electrochemical studies showed that, the complex is electrochemically active and has one irreversible reduction and one irreversible oxidation potentials, and the half wave reduction potentials are -1.15 and 0.45 volt respectively, versus ferrocene/ferrocenium internal reference electrode. The antibacterial activities of synthesized compounds were studied against Gram positive bacteria; Staphylococcus aureus ATCC 6538, Bacillus subtilis ATCC 6633, Bacillus cereus NRRL-B-3711, Enterococcus faecalis ATCC 29212 and Gram negative bacteria; Escherichia coli ATCC 11230, Pseudomonas aeruginosa ATCC 15442, Klebsiella pneumonia ATCC 70063 by using the disc diffusion and micro dilution methods. The inhibition activities of these compounds on carbonic anhydrase II enzyme (hCA II) have been investigated by comparing IC50 and K-i values. The anticancer activities of these compounds on MCF-7 cell line investigated by comparing IC50 values. The biological activity screening showed that Cu(II) complex has more activity than ligand against the tested bacteria, hCA II enzyme and breast cancer cell lines MCF-7. (C) 2014 Elsevier B.V. All rights reserved.Gazi University Research FoundGazi University [05/2010-92]; TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [105T240]This research was supported by Gazi University Research Found under Project No. 05/2010-92 and TUBITAK Project No. 105T240. We thank Ankara University, Faculty of Pharmacy. Central Labs for allocation of time at the Mass Spectra and Elemental Analyses

Exploring Pre-Service Science Teacher Expectations on Learning Science

The purpose of this study was to examine the expectations of th