On the Greenlees-May Duality and the Matlis-Greenlees-May Equivalence

Let A be a commutative unital ring and a an ideal in it. We define and study a-reduced complexes and a-coreduced complexes in both the category of chain complexes of A-modules as well as in the derived category of A-modules. We show that these two types of complexes give rise to variants of the well known Greenlees-May duality and the Matlis-Greenlees-May equivalence in the aforementioned categories.Comment: 23 page

Short- and long-term effects of 56Fe irradiation on cognition and hippocampal DNA methylation and gene expression.

BackgroundAstronauts are exposed to 56Fe ions that may pose a significant health hazard during and following prolonged missions in deep space. We showed previously that object recognition requiring the hippocampus, a structure critical for cognitive function, is affected in 2-month-old mice irradiated with 56Fe ions. Here we examined object recognition in 6-month-old mice irradiated with 56Fe ions, a biological age more relevant to the typical ages of astronauts. Moreover, because the mechanisms mediating the detrimental effects of 56Fe ions on hippocampal function are unclear, we examined changes in hippocampal networks involved in synaptic plasticity and memory, gene expression, and epigenetic changes in cytosine methylation (5mC) and hydroxymethylation (5hmC) that could accompany changes in gene expression. We assessed the effects of whole body 56Fe ion irradiation at early (2 weeks) and late (20 weeks) time points on hippocampus-dependent memory and hippocampal network stability, and whether these effects are associated with epigenetic changes in hippocampal DNA methylation (both 5mC and 5hmC) and gene expression.ResultsAt the two-week time point, object recognition and network stability were impaired following irradiation at the 0.1 and 0.4 Gy dose, but not following irradiation at the 0.2 Gy dose. No impairments in object recognition or network stability were seen at the 20-week time point at any irradiation dose used. Consistent with this pattern, the significance of pathways for gene categories for 5hmC was lower, though not eliminated, at the 20-week time point compared to the 2-week time point. Similarly, significant changes were observed for 5mC gene pathways at the 2-week time point, but no significant gene categories were observed at the 20-week time point. Only the 5hmC changes tracked with gene expression changes.ConclusionsDose- and time-dependent epigenomic remodeling in the hippocampus following 56Fe ion exposure correlates with behavioral changes

Bi-directional and shared epigenomic signatures following proton and 56Fe irradiation.

The brain's response to radiation exposure is an important concern for patients undergoing cancer therapy and astronauts on long missions in deep space. We assessed whether this response is specific and prolonged and is linked to epigenetic mechanisms. We focused on the response of the hippocampus at early (2-weeks) and late (20-week) time points following whole body proton irradiation. We examined two forms of DNA methylation, cytosine methylation (5mC) and hydroxymethylation (5hmC). Impairments in object recognition, spatial memory retention, and network stability following proton irradiation were observed at the two-week time point and correlated with altered gene expression and 5hmC profiles that mapped to specific gene ontology pathways. Significant overlap was observed between DNA methylation changes at the 2 and 20-week time points demonstrating specificity and retention of changes in response to radiation. Moreover, a novel class of DNA methylation change was observed following an environmental challenge (i.e. space irradiation), characterized by both increased and decreased 5hmC levels along the entire gene body. These changes were mapped to genes encoding neuronal functions including postsynaptic gene ontology categories. Thus, the brain's response to proton irradiation is both specific and prolonged and involves novel remodeling of non-random regions of the epigenome

Effects of interpregnancy interval on pregnancy complications: protocol for systematic review and meta-analysis

Introduction: Interpregnancy interval (IPI) is the length of time between a birth and conception of the next pregnancy. Evidence suggests that both short and long IPIs are at increased risk of adverse pregnancy and perinatal outcomes. Relatively less attention has been directed towards investigating the effect of IPI on pregnancy complications, and the studies that have been conducted have shown mixed results. This systematic review will aim to provide an update to the most recent available evidence on the effect of IPI on pregnancy complications. Method and Analysis: We will search electronic databases such as Ovid/MEDLINE, EMBASE, CINAHL, Scopus, Web of Science and PubMed to identify peer-reviewed articles on the effects of IPI on pregnancy complications. We will include articles published from start of indexing until 12 February 2018 without any restriction to geographic setting. We will limit the search to literature published in English language and human subjects. Two independent reviewers will screen titles and abstracts and select full-text articles that meet the eligibility criteria. The Newcastle-Ottawa tool will be used to assess quality of observational studies. Where data permit, meta-analyses will be performed for individual pregnancy complications. A subgroup analyses by country categories (high-income vs low and middle-income countries) based on World Bank income group will be performed. Where meta-analysis is not possible, we will provide a description of data without further attempt to quantitatively pool results. Ethics and Dissemination: Formal ethical approval is not required as primary data will not be collected. The results will be published in peer-reviewed journals and presented at national and international conferences. Prospero Registration Number: CRD42018088578

Tumour PD-L1 expression in small-cell lung cancer: A systematic review and meta-analysis

: Antibodies against programmed death-1 (PD-1), and its ligand, (PD-L1) have been approved recently for the treatment of small-cell lung cancer (SCLC). Although there are previous reports that addressed PD-L1 detection on tumour cells in SCLC, there is no comprehensive meta-analysis on the prevalence of PD-L1 expression in SCLC. We performed a systematic search of the PubMed, Cochrane Library and EMBASE databases to assess reports on the prevalence of PD-L1 expression and the association between PD-L1 expression and overall survival (OS). This meta-analysis included 27 studies enrolling a total of 2792 patients. The pooled estimate of PD-L1 expression was 26.0% (95% CI 17.0-37.0), (22.0% after removing outlying studies). The effect size was significantly heterogeneous (I2 = 97.4, 95% CI: 95.5-98.5, p \u3c 0.0001).Positive PD-L1 expression was a favourable prognostic factor for SCLC but not statistically significant (HR = 0.86 (95% CI (0.49-1.50), p = 0.5880; I2 = 88.7%, p \u3c 0.0001). Begg\u27s funnel plots and Egger\u27s tests indicated no publication bias across included studies (p \u3e 0.05). Overall, there is heterogeneity in the prevalence of PD-L1 expression in SCLC tumour cells across studies. This is significantly moderated by factors such as immunohistochemistry (IHC) evaluation cut-off values, and assessment of PD-L1 staining patterns as membranous and/or cytoplasmic. There is the need for large size, prospective and multicentre studies with well-defined protocols and endpoints to advance the clinical value of PD-L1 expression in SCLC

A Review of Von Hippel-Lindau Syndrome

Von Hippel-Lindau syndrome (VHL) is a familial neoplastic condition seen in approximately 1 in 36,000 live births. It is caused by germline mutations of the tumor suppressor gene VHL, located on the short arm of chromosome 3. While the majority of the affected individuals have a positive family history, up to 20% of cases arise from de novo mutations. VHL syndrome is characterized by the presence of benign and malignant tumors affecting the central nervous system, kidneys, adrenals, pancreas, and reproductive organs. Common manifestations include hemangioblastomas of the brain, spinal cord, and retina; pheochromocytoma and paraganglioma; renal cell carcinoma; pancreatic cysts and neuroendocrine tumors; and endolymphatic sac tumors. Diagnosis of VHL is prompted by clinical suspicion and confirmed by molecular testing. Management of VHL patients is complex and multidisciplinary. Routine genetic testing and surveillance using various diagnostic techniques are used to help monitor disease progression and implement treatment options. Despite recent advances in clinical diagnosis and management, life expectancy for VHL patients remains low at 40–52 years. This article provides an overview of the major clinical, histological, and radiological findings, as well as treatment modalities

RPL24: a potential therapeutic target whose depletion or acetylation inhibits polysome assembly and cancer cell growth.

Partial loss of large ribosomal subunit protein 24 (RPL24) function is known to protect mice against Akt or Myc-driven cancers, in part via translational inhibition of a subset of cap(eIF4E)-dependently translated mRNAs. The role of RPL24 in human malignancies is unknown. By analyzing a public dataset of matched human breast cancers and normal mammary tissue, we found that breast cancers express significantly more RPL24 than matched normal breast samples. Depletion of RPL24 in breast cancer cells by \u3e70% reduced cell viability by 80% and decreased protein expression of the eIF4E-dependently translated proteins cyclin D1 (75%), survivin (46%) and NBS1 (30%) without altering GAPDH or beta-tubulin levels. RPL24 knockdown also reduced 80S subunit levels relative to 40S and 60S levels. These effects on expression of eIF4E-dependent proteins and ribosome assembly were mimicked by 2-24 h treatment with the pan-HDACi, trichostatin A (TSA), which induced acetylation of 15 different polysome-associated proteins including RPL24. Furthermore, HDAC6-selective inhibition or HDAC6 knockdown induced ribosomal protein acetylation. Via mass spectrometry, we found that 60S-associated, but not, polysome-associated, RPL24 undergoes HDACi-induced acetylation on K27. Thus, RPL24 K27 acetylation may play a role in ribosome assembly. These findings point toward a novel acetylation-dependent polysome assembly mechanism regulating tumorigenesis

Sensitive droplet digital PCR method for detection of TERT promoter mutations in cell free DNA from patients with metastatic melanoma

Background: Currently mainly BRAF mutant circulating tumor DNA (ctDNA) is utilized to monitor patients with melanoma. TERT promoter mutations are common in various cancers and found in up to 70% of melanomas, including half of BRAF wildtype cases. Therefore, a sensitive method for detection of TERT promoter mutations would increase the number of patients that could be monitored through ctDNA analysis. Methods: A droplet digital PCR (ddPCR) assay was designed for the concurrent detection of chr5:1,295,228 C \u3e T and chr5:1,295,250 C \u3e T TERT promoter mutations. The assay was validated using 39 melanoma cell lines and 22 matched plasma and tumor samples. In addition, plasma samples from 56 metastatic melanoma patients and 56 healthy controls were tested for TERT promoter mutations. Results: The established ddPCR assay detected TERT promoter mutations with a lower limit of detection (LOD) of 0.17%. Total concordance was demonstrated between ddPCR and Sanger sequencing in all cell lines except one, which carried a second mutation within the probe binding-site. Concordance between matched plasma and tumor tissue was 68% (15/22), with a sensitivity of 53% (95% CI, 27%- 79%) and a specificity of 100% (95% CI, 59%-100%). A significantly longer PFS (p=0.028) was evident in ctDNA negative patients. Importantly, our TERT promoter mutations ddPCR assay allowed detection of ctDNA in 11 BRAF wild-type cases. Conclusions: The TERT promoter mutation ddPCR assay offers a sensitive test for molecular analysis of melanoma tumors and ctDNA, with the potential to be applied to other cancers

The prognostic impact of circulating tumour dna in melanoma patients treated with systemic therapies—beyond braf mutant detection

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. In this study, we evaluated the predictive value of circulating tumour DNA (ctDNA) to inform therapeutic outcomes in metastatic melanoma patients receiving systemic therapies. We analysed 142 plasma samples from metastatic melanoma patients prior to commencement of systemic therapy: 70 were treated with BRAF/MEK inhibitors and 72 with immunotherapies. Patient-specific droplet digital polymerase chain reaction assays were designed for ctDNA detection. Plasma ctDNA was detected in 56% of patients prior to first-line anti-PD1 and/or anti-CTLA-4 treatment. The detection rate in the immunotherapy cohort was comparably lower than those with BRAF inhibitors (76%, p = 0.0149). Decreasing ctDNA levels within 12 weeks of treatment was strongly concordant with treatment response (Cohen’s k = 0.798, p \u3c 0.001) and predictive of longer progression free survival. Notably, a slower kinetic of ctDNA decline was observed in patients treated with immunotherapy compared to those on BRAF/MEK inhibitors. Whole exome sequencing of ctDNA was also conducted in 9 patients commencing anti-PD-1 therapy to derive tumour mutational burden (TMB) and neoepitope load measurements. The results showed a trend of high TMB and neoepitope load in responders compared to non-responders. Overall, our data suggest that changes in ctDNA can serve as an early indicator of outcomes in metastatic melanoma patients treated with systemic therapies and therefore may serve as a tool to guide treatment decisions

Knowledge-aware Assessment of Severity of Suicide Risk for Early Intervention

Mental health illness such as depression is a significant risk factor for suicide ideation, behaviors, and attempts. A report by Substance Abuse and Mental Health Services Administration (SAMHSA) shows that 80% of the patients suffering from Borderline Personality Disorder (BPD) have suicidal behavior, 5-10% of whom commit suicide. While multiple initiatives have been developed and implemented for suicide prevention, a key challenge has been the social stigma associated with mental disorders, which deters patients from seeking help or sharing their experiences directly with others including clinicians. This is particularly true for teenagers and younger adults where suicide is the second highest cause of death in the US. Prior research involving surveys and questionnaires (e.g. PHQ-9) for suicide risk prediction failed to provide a quantitative assessment of risk that informed timely clinical decision-making for intervention. Our interdisciplinary study concerns the use of Reddit as an unobtrusive data source for gleaning information about suicidal tendencies and other related mental health conditions afflicting depressed users. We provide details of our learning framework that incorporates domain-specific knowledge to predict the severity of suicide risk for an individual. Our approach involves developing a suicide risk severity lexicon using medical knowledge bases and suicide ontology to detect cues relevant to suicidal thoughts and actions. We also use language modeling, medical entity recognition and normalization and negation detection to create a dataset of 2181 redditors that have discussed or implied suicidal ideation, behavior, or attempt. Given the importance of clinical knowledge, our gold standard dataset of 500 redditors (out of 2181) was developed by four practicing psychiatrists following the guidelines outlined in Columbia Suicide Severity Rating Scale (C-SSRS), with the pairwise annotator agreement of 0.79 and group-wise agreement of 0.73. Compared to the existing four-label classification scheme (no risk, low risk, moderate risk, and high risk), our proposed C-SSRS-based 5-label classification scheme distinguishes people who are supportive, from those who show different severity of suicidal tendency. Our 5-label classification scheme outperforms the state-of-the-art schemes by improving the graded recall by 4.2% and reducing the perceived risk measure by 12.5%. Convolutional neural network (CNN) provided the best performance in our scheme due to the discriminative features and use of domain-specific knowledge resources, in comparison to SVM-L that has been used in the state-of-the-art tools over similar dataset