Integration of feature vectors from raw laboratory, medication and procedure names improves the precision and recall of models to predict postoperative mortality and acute kidney injury
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ABSTRACT:
SUBMITTER: Hofer I
PROVIDER: S-EPMC9205878 | biostudies-literature | 2022 Jan
REPOSITORIES: biostudies-literature
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Project description:BackgroundActive participation in patients' own care is essential for success after Lapidus procedure. Poor health literacy, comprehension, and retention of patient instructions may be correlated with patient participation. Currently, there is no objective measure of how well patients internalize and retain instructions before and after a Lapidus procedure. We performed this study to assess how much of the information given to patients preoperatively was able to be recalled at the first postoperative visit.MethodsAll patients between ages 18 and 88 years undergoing a Lapidus procedure for hallux valgus by the senior author between June 2016 and July 2018 were considered eligible for inclusion. Patients were excluded if they had a history of previous bunion surgery or if the procedure was part of a flatfoot reconstruction. Patients were given written and verbal instructions at the preoperative visit. Demographic and comprehension surveys were administered at their first visit approximately 2 weeks postoperatively. A total of 50 patients, of which 42 (84%) were female and 43 (86%) had a bachelor's degree or higher, were enrolled.ResultsMean overall score on the comprehension survey was 6.2/8 (±1.2), mean procedure subscore was 1.8/3 (±0.64), and mean postoperative protocol subscore was 4.4/5 (±0.8). The most frequently missed question asked patients to identify the joint fused in the procedure.ConclusionAlthough comprehension and retention of instructions given preoperatively was quite high in our well-educated cohort, our findings highlight the importance of delivering clear instructions preoperatively and reinforcing these instructions often.Level of evidenceLevel II, prospective cohort study.
| S-EPMC8697229 | biostudies-literature
Project description:Over the last several years, the study of working memory (WM) for simple visual features (e.g., colors, orientations) has been dominated by perspectives that assume items in WM are stored independently of one another. Evidence has revealed, however, systematic biases in WM recall which suggest that items in WM interact during active maintenance. In the present study, we report two experiments that replicate a repulsion bias between metrically similar colors during active storage in WM. We also observed that metrically similar colors were stored with lower resolution than a unique color held actively in mind at the same time. To account for these effects, we report quantitative simulations of two novel neurodynamical models of WM. In both models, the unique behavioral signatures reported here emerge directly from laterally-inhibitory neural interactions that serve to maintain multiple, distinct neural representations throughout the WM delay period. Simulation results show that the full pattern of empirical findings was only obtained with a model that included an elaborated spatial pathway with sequential encoding of memory display items. We discuss implications of our findings for theories of visual working memory more generally.
| S-EPMC9588047 | biostudies-literature
Project description:Memory formation involves binding of contextual features into a unitary representation1-4, whereas memory recall can occur using partial combinations of these contextual features. The neural basis underlying the relationship between a contextual memory and its constituent features is not well understood; in particular, where features are represented in the brain and how they drive recall. Here, to gain insight into this question, we developed a behavioural task in which mice use features to recall an associated contextual memory. We performed longitudinal imaging in hippocampus as mice performed this task and identified robust representations of global context but not of individual features. To identify putative brain regions that provide feature inputs to hippocampus, we inhibited cortical afferents while imaging hippocampus during behaviour. We found that whereas inhibition of entorhinal cortex led to broad silencing of hippocampus, inhibition of prefrontal anterior cingulate led to a highly specific silencing of context neurons and deficits in feature-based recall. We next developed a preparation for simultaneous imaging of anterior cingulate and hippocampus during behaviour, which revealed robust population-level representation of features in anterior cingulate, that lag hippocampus context representations during training but dynamically reorganize to lead and target recruitment of context ensembles in hippocampus during recall. Together, we provide the first mechanistic insights into where contextual features are represented in the brain, how they emerge, and how they access long-range episodic representations to drive memory recall.
| S-EPMC9577479 | biostudies-literature
Project description:IntroductionFree recall tends to be better for names of animate concepts such as animals than for names of inanimate objects. In Popp and Serra's 2016 article, the authors replicated this "animacy effect" in free recall but when participants studied words in pairs (animate-animate pairs intermixed with inanimate-inanimate pairs) and were tested with cued recall, performance was better for inanimate-inanimate pairs than for animate-animate pairs ("reverse animacy"). We tested the replicability of this surprising effect and one possible explanation for the effect (semantic similarity).MethodsOur Experiment 1 was a preregistered direct replication (N = 101) of Popp and Serra's Experiment 1 (mixed-lists condition). In a second preregistered experiment conducted in four different samples (undergraduate N = 153, undergraduate N = 143, online Prolific N = 101, online Prolific/English-as-a-first-language N = 150), we manipulated the within-category semantic similarity of animal and object wordlists.ResultsAIn Experiment 1, just as in Popp and Serra, we observed an animacy effect for free recall and a reverse animacy effect for cued recall. Unlike Popp and Serra, we found that controlling for interference effects rendered the reverse animacy effect non-significant. We took this as evidence that characteristics of the stimulus sets (e.g., category structure, within-category similarity) may play a role in animacy and reverse animacy effects. In Experiment 2, in three out of our four samples, we observed reverse animacy effects when within-category similarity was higher for animals and when within-category similarity was equated for animals and objects.DiscussionOur results suggest that the reverse animacy effect observed in Popp and Serra's 2016 article is a robust and replicable effect, but that semantic similarity alone cannot explain the effect.
| S-EPMC10232972 | biostudies-literature
Project description:MotivationYeast two-hybrid screens are an important method to map pairwise protein interactions. This method can generate spurious interactions (false discoveries), and true interactions can be missed (false negatives). Previously, we reported a capture-recapture estimator for bait-specific precision and recall. Here, we present an improved method that better accounts for heterogeneity in bait-specific error rates.ResultFor yeast, worm and fly screens, we estimate the overall false discovery rates (FDRs) to be 9.9%, 13.2% and 17.0% and the false negative rates (FNRs) to be 51%, 42% and 28%. Bait-specific FDRs and the estimated protein degrees are then used to identify protein categories that yield more (or fewer) false positive interactions and more (or fewer) interaction partners. While membrane proteins have been suggested to have elevated FDRs, the current analysis suggests that intrinsic membrane proteins may actually have reduced FDRs. Hydrophobicity is positively correlated with decreased error rates and fewer interaction partners. These methods will be useful for future two-hybrid screens, which could use ultra-high-throughput sequencing for deeper sampling of interacting bait-prey pairs.AvailabilityAll software (C source) and datasets are available as supplemental files and at http://www.baderzone.org under the Lesser GPL v. 3 license.
| S-EPMC2639075 | biostudies-literature
Project description:There is enduring interest in why some of us have clearer memories than others, given the substantial individual variation that exists in retrieval ability and the precision with which we can differentiate past experiences. Here we report novel evidence showing that variation in the size of human hippocampal subfield CA3 predicted the amount of neural interference between episodic memories within CA3, which in turn predicted how much retrieval confusion occurred between past memories. This effect was not apparent in other hippocampal subfields. This shows that subtle individual differences in subjective mnemonic experience can be accurately gauged from measurable variations in the anatomy and neural coding of hippocampal region CA3. Moreover, this mechanism may be relevant for understanding memory muddles in aging and pathological states.
| S-EPMC4115494 | biostudies-literature
Project description:Microbial systems have been synthetically engineered to deploy therapeutic payloads in vivo. With emerging evidence that bacteria naturally home to tumors and modulate anti-tumor immunity one promising application is the development of bacterial vectors as precision cancer vaccines. In this study, we engineered probiotic E. coli Nissle 1917 (EcN) as an anti-tumor vaccination platform optimized for enhanced production and cytosolic delivery of neoepitope-containing peptide arrays, with increased susceptibility to blood clearance and phagocytosis. These features enhance both safety and immunogenicity, achieving a system which drives potent and specific T cell–mediated anti‑cancer immunity that effectively controls or eliminates tumor growth and extends survival in advanced murine primary and metastatic solid tumors. We demonstrate that the elicited anti-tumor immune response involves extensive priming and activation of neoantigen-specific CD4+ and CD8+ T cells, broader activation of both T and NK cells, and a reduction of tumor-infiltrating immunosuppressive myeloid and regulatory T and B cell populations. Taken together, this work leverages the advantages of living medicines to deliver arrays of tumor‑specific neoantigen–derived epitopes within the optimal context to induce specific, effective, and durable systemic anti-tumor immunity.
2024-07-21 | GSE244808 | GEO
Project description:Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain. Existing approaches, however, may involve a large number of features (100-400) or complicated mathematical operations. Finding fewer but more effective features is always desirable. In this paper, based on some key observations on DMs, we are able to decompose a DM image into four basic binary images, each representing the structural characteristics of a fundamental secondary structure element (SSE) or a motif in the domain. Using the concept of moments in image processing, we further derive 45 structural features based on the four binary images. Together with 4 features extracted from the basic images, we represent the structure of a domain using 49 features. We show that our feature vectors can represent domain structures effectively in terms of the following. (1) We show a higher accuracy for domain classification. (2) We show a clear and consistent distribution of domains using our proposed structural vector space. (3) We are able to cluster the domains according to our moment features and demonstrate a relationship between structural variation and functional diversity.
| S-EPMC3877117 | biostudies-literature
Project description:Precision-recall curves are highly informative about the performance of binary classifiers, and the area under these curves is a popular scalar performance measure for comparing different classifiers. However, for many applications class labels are not provided with absolute certainty, but with some degree of confidence, often reflected by weights or soft labels assigned to data points. Computing the area under the precision-recall curve requires interpolating between adjacent supporting points, but previous interpolation schemes are not directly applicable to weighted data. Hence, even in cases where weights were available, they had to be neglected for assessing classifiers using precision-recall curves. Here, we propose an interpolation for precision-recall curves that can also be used for weighted data, and we derive conditions for classification scores yielding the maximum and minimum area under the precision-recall curve. We investigate accordances and differences of the proposed interpolation and previous ones, and we demonstrate that taking into account existing weights of test data is important for the comparison of classifiers.
| S-EPMC3961324 | biostudies-literature
Project description:Current amyloid beta-targeting approaches for Alzheimer’s disease (AD) therapeutics only slow cognitive decline for small numbers of patients. This limited efficacy exists because AD is a multifactorial disease whose pathological mechanism(s) and diagnostic biomarkers are largely unknown. Here we report a new mechanism of AD pathogenesis in which the histone methyltransferase G9a noncanonically regulates translation of a hippocampal proteome that defines the proteopathic nature of AD. Accordingly, we developed a novel brain-penetrant inhibitor of G9a, MS1262, across the blood-brain barrier to block this G9a-regulated, proteopathologic mechanism. Intermittent MS1262 treatment of multiple AD mouse models consistently restored both cognitive and noncognitive functions to healthy levels. Comparison of proteomic/phosphoproteomic analyses of MS1262-treated AD mice with human AD patient data identified multiple pathological brain pathways that elaborate amyloid beta and neurofibrillary tangles as well as blood coagulation, from which biomarkers of early stage of AD including SMOC1 were found to be affected by MS1262 treatment. Notably, these results indicated that MS1262 treatment may reduce or avoid the risk of blood clot burst for brain bleeding or a stroke. This mouse-to-human conservation of G9a-translated AD proteopathology suggests that the global, multifaceted effects of MS1262 in mice could extend to relieve all symptoms of AD patients with minimum side effect. In addition, our mechanistically derived biomarkers can be used for stage-specific AD diagnosis and companion diagnosis of individualized drug effects.
2025-03-18 | GSE278032 | GEO