Contribution of Somatic Ras/Raf/Mitogen-Activated Protein Kinase Variants in the Hippocampus in Drug-Resistant Mesial Temporal Lobe Epilepsy

Importance: Mesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy subtype and is often refractory to antiseizure medications. While most patients with MTLE do not have pathogenic germline genetic variants, the contribution of postzygotic (ie, somatic) variants in the brain is unknown. Objective: To test the association between pathogenic somatic variants in the hippocampus and MTLE. Design, Setting, and Participants: This case-control genetic association study analyzed the DNA derived from hippocampal tissue of neurosurgically treated patients with MTLE and age-matched and sex-matched neurotypical controls. Participants treated at level 4 epilepsy centers were enrolled from 1988 through 2019, and clinical data were collected retrospectively. Whole-exome and gene-panel sequencing (each genomic region sequenced more than 500 times on average) were used to identify candidate pathogenic somatic variants. A subset of novel variants was functionally evaluated using cellular and molecular assays. Patients with nonlesional and lesional (mesial temporal sclerosis, focal cortical dysplasia, and low-grade epilepsy-associated tumors) drug-resistant MTLE who underwent anterior medial temporal lobectomy were eligible. All patients with available frozen tissue and appropriate consents were included. Control brain tissue was obtained from neurotypical donors at brain banks. Data were analyzed from June 2020 to August 2022. Exposures: Drug-resistant MTLE. Main Outcomes and Measures: Presence and abundance of pathogenic somatic variants in the hippocampus vs the unaffected temporal neocortex. Results: Of 105 included patients with MTLE, 53 (50.5%) were female, and the median (IQR) age was 32 (26-44) years; of 30 neurotypical controls, 11 (36.7%) were female, and the median (IQR) age was 37 (18-53) years. Eleven pathogenic somatic variants enriched in the hippocampus relative to the unaffected temporal neocortex (median [IQR] variant allele frequency, 1.92 [1.5-2.7] vs 0.3 [0-0.9]; P =.01) were detected in patients with MTLE but not in controls. Ten of these variants were in PTPN11, SOS1, KRAS, BRAF, and NF1, all predicted to constitutively activate Ras/Raf/mitogen-activated protein kinase (MAPK) signaling. Immunohistochemical studies of variant-positive hippocampal tissue demonstrated increased Erk1/2 phosphorylation, indicative of Ras/Raf/MAPK activation, predominantly in glial cells. Molecular assays showed abnormal liquid-liquid phase separation for the PTPN11 variants as a possible dominant gain-of-function mechanism. Conclusions and Relevance: Hippocampal somatic variants, particularly those activating Ras/Raf/MAPK signaling, may contribute to the pathogenesis of sporadic, drug-resistant MTLE. These findings may provide a novel genetic mechanism and highlight new therapeutic targets for this common indication for epilepsy surgery

Proceedings - Asia-Pacific Software Engineering Conference, APSEC

CONTEXT: Several studies in effort estimation havefound that it can be effective to use only recent project data for building an effort estimation model. The generality of this timeaware approach has been explored across a variety of effort estimation model approaches, organizations and definitions of recency. However, other studies have shown that it is not alwayshelpful. A question arises: how can one tell whether the approachwould be effective for a given target project? OBJECTIVE: Toinvestigate a potential method to decide between selecting recentor all project data. METHOD: Using a single-company ISBSGdata set1 studied previously in similar research, we propose andevaluate a selection method. The method utilizes a variant ofcross-validation based on recent projects to make the decision.RESULTS: There are significant differences in the estimation accuracybetween using the proposed method and using the growingportfolio (always using all available data). The method could alsoselect the better approach on average. However, the differencein estimation accuracy between using the proposed method andalways using moving windows was not statistically significant.CONCLUSIONS: The selection method could select the betterapproach on average. The results contribute to developing amethod for suggesting a better approach for practitioners

Empirical Software Engineering in Practice (IWESEP), 2014 6th International Workshop on

BACKGROUND: Several studies in software effortestimation have found that it can be effective to use a window ofrecent projects as training data for building an effort estimationmodel. The previous studies evaluated the use of a windowwith popular estimation models: linear regression (LR) andestimation by analogy (EbA). Many effort estimation models havebeen proposed, and the generality of windowing approach stillremains uncertain for other effort estimation models, especiallyfor those based on different theory. OBJECTIVE: This studyinvestigates the effect of using a window on estimation accuracywith Classification and regression trees (CART). CART wasrecently found as a good performance method, and is based ona different theory from LR and EbA. METHOD: We comparedthe estimation accuracy of a windowing approach and growingapproach with the same data set and procedure as the past stud-ies. RESULTS: There is a difference in the estimation accuracybetween using a window and not using a window. However, theeffctive range of using windows on CART is narrower than thaton LR. CONCLUSIONS: Windowing is also effective with CART.However, the range of effectiveness is narrower. The resultscontribute to the generality of the effectiveness of windowingapproach

On the effectiveness of weighted moving windows: Experiment on linear regression based software effort estimation

In construction of an effort estimation model, it seems effective to use a window of training data so that the model is trained with only recent projects. Considering the chronological order of projects within the window, and weighting projects according to their order within the window, may also affect estimation accuracy. In this study, we examined the effects of weighted moving windows on effort estimation accuracy. We compared weighted and non-weighted moving windows under the same experimental settings. We confirmed that weighting methods significantly improved estimation accuracy in larger windows, although the methods also significantly worsened accuracy in smaller windows. This result contributes to understanding properties of moving windows. Copyright © 2014 John Wiley & Sons, Ltd

Accidental fatalities among heroin users in South Australia, 1994-1997: Toxicological findings and circumstances of death

A total of 101 accidental deaths were identified among heroin users in South Australia for the period 1994-1997. Mean age at death was 29.9 years. Cases typically involved a single, unemployed, Caucasian male in his late twenties with a history of heroin and other drug use. Two or more drug types were detected in 80% of cases. The total number of substance types identified increased significantly with age. In comparison to younger fatalities, alcohol and benzodiazepines were identified in more of those 27 years of age and over. Thirteen deaths occurred within four weeks of release from prison and in nine cases tricyclic anti-depressants were found. The majority of deaths occurred in a private home and in the presence (or near proximity) of others. Identified risk factors included: being male; being a long-term heroin user; recent release from prison; use of tricyclic antidepressants and/or other central nervous system depressants

Bacterial degradation of risperidone and paliperidone in decomposing blood

The stability of two benzisoxazole antipsychotics was determined in vitro in decomposing porcine blood inoculated with bacteria, utilizing a high-performance liquid chromatography with ultraviolet and fluorescence detection method for drug quantitation. Stability experiments for risperidone and paliperidone were conducted at 7, 20 and 37°C for 4 days using sterile and bacterially inoculated porcine blood. The drugs were stable in sterile blood at each temperature and in inoculated blood at 7°C, but degraded significantly in inoculated blood at 20 and 37°C. Complete loss occurred within 2 days when incubated at 37°C. The benzisoxazole-cleaved degradation products for both drugs were identified as 2-hydroxybenzoyl-risperidone and 2-hydroxybenzoyl-paliperidone utilizing liquid chromatography quadrupole-time-of-flight mass spectrometry and accurate mass measurements. The degradation products have been found in postmortem case studies, including one case where risperidone and paliperidone were not detected, indicating complete conversion can occur in situ.Danielle M. Butzbach, Peter C. Stockham, Hilton J. Kobus, D. Noel Sims, Roger W. Byard, Robert J. Lokan, and George Stewart Walke

Stability of serotonin-selective antidepressants in sterile and decomposing liver tissue

It is well established that bacteria are capable of degrading selected drugs during decomposition. The aim of this study was to investigate the stability of several serotonin-selective reuptake inhibitor antidepressants and venlafaxine during putrefaction in porcine liver macerate inoculated with porcine cecal contents rich in bacteria. Blank liver matrices, sterile liver macerates, and sterile aqueous controls were included with the experiment performed for 57 days at 20°C under anaerobic conditions. A liquid chromatography/mass spectrometry method was developed for quantitative determination of the drugs investigated in both sterile and decomposed liver matrices. The method was found to encounter matrix effects not detected during the validation stage. Citalopram, paroxetine, sertraline, venlafaxine, and fluoxetine were found to be stable under the experimental conditions; however, fluvoxamine was found to be decreased by c. 50% over 57 days in bacterially inoculated liver macerate. This study suggests that fluvoxamine concentrations in cases with evidence of decomposition/putrefaction should be interpreted with extra caution.Danielle M. Butzbach, Peter C. Stockham, Hilton J. Kobus, Noel Sims, Roger W. Byard, Robert J. Lokan, and G. Stewart Walke

Australian Indigenous students: addressing equity issues in assessment

This article provides the background and context to the important issue of assessment and equity in relation to Indigenous students in Australia. Questions about the validity and fairness of assessment are raised and ways forward are suggested by attending to assessment questions in relation to equity and culture-fair assessment. Patterns of under-achievement by Indigenous students are reflected in national benchmark data and international testing programmes like the Trends in International Mathematics and Science Sstudy and the Program for International Student Assessment. The argument developed views equity, in relation to assessment, as more of a sociocultural issue than a technical matter. It highlights how teachers need to distinguish the "funds of knowledge" that Indigenous students draw on and how teachers need to adopt culturally responsive pedagogy to open up the curriculum and assessment practice to allow for different ways of knowing and being