Grokking-like effects in counterfactual inference

We show that a typical neural network, which ignores any covariate/feature re-balancing, can be as effective as any explicit counterfactual method. We adopt the architecture of TARNet—a simple neural network with two heads (one for treatment, one for control) which is trained with a relatively high batch size. Combined with ensemble methods, this produces competitive results in four counterfactual inference benchmarks: IHDP, NEWS, JOBS, and TWINS. Our results indicate that relatively simple methods might be good enough for counterfactual prediction, with quality constraints coming from hyperparameter tuning. Our analysis indicates that the reason behind the observed phenomenon might be “grokking”, a recently developed theory

The effects of physical training without equipment on pain perception and balance in the elderly: a randomized controlled trials

Background: Research supports a link between exercise and falls prevention in the older population. Objectives: Our aims were to evaluate pain perception and balance skills in a group of elderly subjects and to examine the consequences of a standardized equipment-free exercise program intervention on these variables. The study utilized a randomized controlled trial method. Methods: 92 subjects were recruited from a rural Sicilian village (Resuttano, Sicily, Italy). Subjects were randomly split into two groups, an experimental group (EG; n= 49) and a control group (CG; n =43). Qualified fitness instructors delivered the standardized physical exercise program for the EG whilst the CG did not receive this exercise intervention. The Berg Balance Scale and the Oswestry Disability Index were administered in both groups before (T0) and after the intervention (T1). Results: At T1, the EG group significantly improvement in balance (p<0.0001) and pain perception (p<0.0001). No significant differences were found within the CG both in BBS and ODI, respectively. Conclusions: Our findings suggest that a 13-weeks standardized exercise equipment-free program is effective in improving balance and perception of pain in the elderly. This type of intervention can consequently provide a low cost strategy to counteract the rate of disability in elderly

The ocular albinism type 1 protein, an intracellular G protein-coupled receptor, regulates melanosome transport in pigment cells

The protein product of the ocular albinism type 1 gene, named OA1, is a pigment cell-specific G protein-coupled receptor exclusively localized to intracellular organelles, namely lysosomes and melanosomes. Loss of OA1 function leads to the formation of macromelanosomes, suggesting that this receptor is implicated in organelle biogenesis, however the mechanism involved in the pathogenesis of the disease remains obscure. We report here the identification of an unexpected abnormality in melanosome distribution both in retinal pigment epithelium (RPE) and skin melanocytes of Oa1-knock-out (KO) mice, consisting in a displacement of the organelles from the central cytoplasm towards the cell periphery. Despite their depletion from the microtubule (MT)-enriched perinuclear region, Oa1-KO melanosomes were able to aggregate at the centrosome upon disruption of the actin cytoskeleton or expression of a dominant-negative construct of myosin Va. Consistently, quantification of organelle transport in living cells revealed that Oa1-KO melanosomes displayed a severe reduction in MT-based motility; however, this defect was rescued to normal following inhibition of actin-dependent capture at the cell periphery. Together, these data point to a defective regulation of organelle transport in the absence of OA1 and imply that the cytoskeleton might represent a downstream effector of this receptor. Furthermore, our results enlighten a novel function for OA1 in pigment cells and suggest that ocular albinism type 1 might result from a different pathogenetic mechanism than previously thought, based on an organelle-autonomous signalling pathway implicated in the regulation of both membrane traffic and transport

Insight into ER quality control mechanisms : novel characterization of the E3 ubiquitin ligase gp78/autocrine motility factor receptor and the G<alpha>s subunit in the ER

This manuscript looks at ER Quality Control (ERQC) mechanisms and in particular, focuses on two cellular pathways: (1) the ER-associated degradation (ERAD) pathway and (2) the ER stress response. ERQC represents a complex assembly of pathways that are vital in maintaining proper cellular function and homeostasis, by helping the cell adapt to ER stress, prevent chronic imbalance in the ER and avoid many protein conformational diseases. Here, we investigate (1) a regulatory role for palmitoylation of the E3 ubiquitin ligase gp78/AMFR in the ERAD pathway; (2) the implication of G proteins in gp78/AMFR functions; and (3) the involvement of ER-localized Gαs in both substrate polyubiquitylation and ER stress. The dynamic posttranslational modification, palmitoylation, is important for receptor stability and intracellular trafficking. Using metabolic radiolabeling and Acyl-Biotinyl Exchange Chemistry, in chapter 2, we show that the E3 ubiquitin ligase gp78/AMFR is palmitoylated within the catalytic RING finger motif, a domain that is responsible for its ubiquitin ligase activity. We also discuss the modulatory implication of gp78/AMFR palmitoylation, showing that palmitoylation disrupts the RING finger motif, regulates its ER distribution and enhances its turnover. Whether palmitoylation of E3 ubiquitin ligases is gp78/AMFR-specific or a general mechanism to control the activity of RING finger ubiquitin ligases remains to be determined. Next, we look at the Gα subunit, a known component of the G protein-coupled receptor (GPCR) signal transduction pathway. In chapter 3, using immunoprecipitation and immunocytochemistry experiments, we report that the E3 ubiquitin ligase gp78/AMFR interacts with and recruits several G proteins to the ER, namely Gαi1 and Gαs. Thus, we reintroduce the possibility that gp78/AMFR is a novel ER-localized GPCR. The Gαs subunit is further discussed in chapter 4 where we characterize in detail its ER localization and its association with ERAD components, as well as we show a novel intracellular function, demonstrating the ability of Gαs to induce substrate polyubiquitylation and protect against ER stress. Together, these findings mark the beginning in understanding the physiological significance of (1) E3 ubiquitin ligase palmitoylation; (2) G protein binding to gp78/AMFR; (3) Gαs-mediated substrate polyubiquitylation and protection against ER stress, in ERQC mechanisms.Medicine, Faculty ofGraduat

RING finger palmitoylation of the endoplasmic reticulum Gp78 E3 ubiquitin ligase

AbstractGp78 is an E3 ubiquitin ligase within the endoplasmic reticulum-associated degradation pathway. We show that Flag-tagged gp78 undergoes sulfhydryl cysteine palmitoylation (S-palmitoylation) within the RING finger motif, responsible for its ubiquitin ligase activity. Screening of 19 palmitoyl acyl transferases (PATs) identified five that increased gp78 RING finger palmitoylation. Endoplasmic reticulum (ER)-localized Myc-DHHC6 overexpression promoted the peripheral ER distribution of Flag-gp78 while RING finger mutation and the palmitoylation inhibitor 2-bromopalmitate restricted gp78 to the central ER. Palmitoylation of RING finger cysteines therefore regulates gp78 distribution to the peripheral ER

Differential Impact of Caveolae and Caveolin-1 Scaffolds on The Membrane Raft Proteome*

Caveolae, a class of cholesterol-rich lipid rafts, are smooth invaginations of the plasma membrane whose formation in nonmuscle cells requires caveolin-1 (Cav1). The recent demonstration that Cav1-associated cavin proteins, in particular PTRF/cavin-1, are also required for caveolae formation supports a functional role for Cav1 independently of caveolae. In tumor cells deficient for Golgi β-1,6N-acetylglucosaminyltransferase V (Mgat5), reduced Cav1 expression is associated not with caveolae but with oligomerized Cav1 domains, or scaffolds, that functionally regulate receptor signaling and raft-dependent endocytosis. Using subdiffraction-limit microscopy, we show that Cav1 scaffolds are homogenous subdiffraction-limit sized structures whose size distribution differs from that of Cav1 in caveolae expressing cells. These cell lines displaying differing Cav1/caveolae phenotypes are effective tools for probing the structure and composition of caveolae. Using stable isotope labeling by amino acids in cell culture, we are able to quantitatively distinguish the composition of caveolae from the background of detergent-resistant membrane proteins and show that the presence of caveolae enriches the protein composition of detergent-resistant membrane, including the recruitment of multiple heterotrimeric G-protein subunits. These data were further supported by analysis of immuno-isolated Cav1 domains and of methyl-β-cyclodextrin-disrupted detergent-resistant membrane. Our data show that loss of caveolae results in a dramatic change to the membrane raft proteome and that this change is independent of Cav1 expression. The proteomics data, in combination with subdiffraction-limit microscopy, indicates that noncaveolar Cav1 domains, or scaffolds are structurally and functionally distinct from caveolae and differentially impact on the molecular composition of lipid rafts