From Posterior Sampling to Meaningful Diversity in Image Restoration

Image restoration problems are typically ill-posed in the sense that each degraded image can be restored in infinitely many valid ways. To accommodate this, many works generate a diverse set of outputs by attempting to randomly sample from the posterior distribution of natural images given the degraded input. Here we argue that this strategy is commonly of limited practical value because of the heavy tail of the posterior distribution. Consider for example inpainting a missing region of the sky in an image. Since there is a high probability that the missing region contains no object but clouds, any set of samples from the posterior would be entirely dominated by (practically identical) completions of sky. However, arguably, presenting users with only one clear sky completion, along with several alternative solutions such as airships, birds, and balloons, would better outline the set of possibilities. In this paper, we initiate the study of meaningfully diverse image restoration. We explore several post-processing approaches that can be combined with any diverse image restoration method to yield semantically meaningful diversity. Moreover, we propose a practical approach for allowing diffusion based image restoration methods to generate meaningfully diverse outputs, while incurring only negligent computational overhead. We conduct extensive user studies to analyze the proposed techniques, and find the strategy of reducing similarity between outputs to be significantly favorable over posterior sampling. Code and examples are available in https://noa-cohen.github.io/MeaningfulDiversityInIRComment: Code and examples are available in https://noa-cohen.github.io/MeaningfulDiversityInI

Dog training alleviates PTSD symptomatology by emotional and attentional regulation

Background: Post-Traumatic Stress Disorder (PTSD) symptoms include re-experiencing, avoidance, hyperarousal, and cognitive deficits, reflecting both emotional and cognitive dysregulation. In recent years, non-pharmacological approaches and specifically animal-assisted therapy have been shown to be beneficial for a variety of disorders such as Attention-Deficit/Hyperactivity Disorder, Autism Spectrum Disorder, and PTSD. However, little is mentioned in the literature about the reciprocal effects of the animal–human interaction. Objective: To evaluate the effects of a one-year dog training programme on PTSD symptomatology in youngsters with PTSD and on dogs’ behaviour. Methods: Fifty-three adolescents, previously exposed to interpersonal trauma, were clinically diagnosed with PTSD and assigned to a dog-training programme group (n = 30) and a control group (n = 23) that engaged in other training programmes (e.g. cooking, hairstyling, etc.). Both groups were evaluated at baseline and following 12-months by The Clinician-Administered PTSD Scale for DSM-5 in Children and Adolescents (CAPS-CA-5) and Beck-Depression Inventory (BDI). Additionally, we physiologically measured both emotional and attention dysregulation. Results: Post-12-months training, a significant alleviation of PTSD symptomatology accompanied by lower depression severity was observed in the dog-training group, compared with a insignificant recovery in the control group. Furthermore, improved emotional and attentional regulation was observed in the dog-training group. Measuring the dogs’ behaviour revealed increased anxiety and decreased selective attention performance, which was inversely correlated with the beneficial effects observed in the dog-training programme group. Conclusions: Our findings emphasize the role of emotional and attentional regulations on the dog–handler interface, as evidence-based support for the beneficial effects of the dog-training programme, as either a non-pharmacological intervention or as complementary to anti-depressants treatment of PTSD. Though pharmacological treatments increase the patients’ well-being by treating certain PTSD symptoms, our suggested dog-training programme seems to influence the PTSD diagnostic status, thus may be implemented in civilians and veterans with PTSD

Lipid droplets in granulosa cells are correlated with reduced pregnancy rates

Abstract Background Lipids are an important source for energy production during oocyte maturation. The accumulation of intracellular lipids binds to proteins to form lipid droplets. This may lead to cellular lipotoxicity. The impact of lipotoxicity on cumulus and granulosa cells has been reported. This pilot study evaluated their correlation to oocyte and embryo quality. Design Prospective case-control study. Setting: Referral IVF unit. Patients: Women younger than age 40, undergoing IVF with intracytoplasmic sperm injection. Interventions: 15 women with BMI > 30 (high BMI) and 26 women with BMI < 25 (low BMI) were enrolled. IVF outcomes were compared between groups based on BMI. Lipid content in cumulus and granulosa cells was evaluated using quantitative and descriptive methods. Lipid profile, hormonal profile and C-reactive protein were evaluated in blood and follicular fluid samples. Demographic and treatment data, as well as pregnancy rates were collected from electronic medical records. Results Higher levels of LDL and CRP, slower cell division rate and lower embryo quality were found in the group with high BMI. There was no difference in pregnancy rates between groups. In light of these findings, treatment outcomes were reanalyzed according to patients who became pregnant and those who did not. We found that patients who conceived had significantly lower fat content in the granulosa cells, reflected by mean fluorescence intensity recorded by flow cytometry analysis (23,404 vs. 9370, P = 0.03). Conclusions BMI has no effect on lipid content in cumulus and granulosa cells, and does not affect likelihood of pregnancy. However, women who achieved pregnancy, regardless of their BMI, had lower lipid levels in their granulosa cells. This finding is important and further study is needed to evaluate lipid content in granulosa cells as a potential predictor of IVF treatment success

Global modulation in DNA epigenetics during pro-inflammatory macrophage activation

ISSN:1559-2294ISSN:1559-230

Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers

Abstract Background The DNA modification 5-hydroxymethylcytosine (5hmC) is now referred to as the sixth base of DNA with evidence of tissue-specific patterns and correlation with gene regulation and expression. This epigenetic mark was recently reported as a potential biomarker for multiple types of cancer, but its application in the clinic is limited by the utility of recent 5hmC quantification assays. We use a recently developed, ultra-sensitive, fluorescence-based single-molecule method for global quantification of 5hmC in genomic DNA. The high sensitivity of the method gives access to precise quantification of extremely low 5hmC levels common in many cancers. Methods We assessed 5hmC levels in DNA extracted from a set of colon and blood cancer samples and compared 5hmC levels with healthy controls, in a single-molecule approach. Results Using our method, we observed a significantly reduced level of 5hmC in blood and colon cancers and could distinguish between colon tumor and colon tissue adjacent to the tumor based on the global levels of this molecular biomarker. Conclusions Single-molecule detection of 5hmC allows distinguishing between malignant and healthy tissue in clinically relevant and accessible tissue such as blood and colon. The presented method outperforms current commercially available quantification kits and may potentially be developed into a widely used, 5hmC quantification assay for research and clinical diagnostics. Furthermore, using this method, we confirm that 5hmC is a good molecular biomarker for diagnosing colon and various types of blood cancer

Lighting Up Individual DNA Damage Sites by In Vitro Repair Synthesis

DNA damage and repair are linked to fundamental biological processes such as metabolism, disease, and aging. Single-strand lesions are the most abundant form of DNA damage; however, methods for characterizing these damage lesions are lacking. To avoid double-strand breaks and genomic instability, DNA damage is constantly repaired by efficient enzymatic machinery. We take advantage of this natural process and harness the repair capacity of a bacterial enzymatic cocktail to repair damaged DNA in vitro and incorporate fluorescent nucleotides into damage sites as part of the repair process. We use single-molecule imaging to detect individual damage sites in genomic DNA samples. When the labeled DNA is extended on a microscope slide, damage sites are visualized as fluorescent spots along the DNA contour, and the extent of damage is easily quantified. We demonstrate the ability to quantitatively follow the damage dose response to different damaging agents as well as repair dynamics in response to UV irradiation in several cell types. Finally, we show the modularity of this single-molecule approach by labeling DNA damage in conjunction with 5-hydroxymethylcytosine in genomic DNA extracted from mouse brain tissue