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Enhanced protein domain discovery by using language modeling techniques from speech recognition.

Most modern speech recognition uses probabilistic models to interpret a sequence of sounds. Hidden Markov models, in particular, are used to recognize words. The same techniques have been adapted to find domains in protein sequences of amino acids. To increase word accuracy in speech recognition, language models are used to capture the information that certain word combinations are more likely than others, thus improving detection based on context. However, to date, these context techniques have not been applied to protein domain discovery. Here we show that the application of statistical language modeling methods can significantly enhance domain recognition in protein sequences. As an example, we discover an unannotated Tf_Otx Pfam domain on the cone rod homeobox protein, which suggests a possible mechanism for how the V242M mutation on this protein causes cone-rod dystrophy.

Algorithms↗

Understanding economic outcomes in critical care.

PURPOSE OF REVIEW: The high costs of critical illness make economic outcomes important adjuncts to clinical outcomes in intensive care unit research. Costs are markedly different than other clinical outcomes, both in their measurement and their interpretation. RECENT FINDINGS: Although not necessarily patient-centered, economic outcomes are important to society. Costs are also useful summary measures of less-meaningful surrogates such as organ failures and lengths of stay. Limitations of economic outcomes, however, are numerous. Accurate measurement of costs in the ICU requires a thorough consideration of both direct and indirect costs, an understanding of the fixed and variable components of critical care expenditures, and knowledge that reducing resource use saves only the marginal, versus average, cost of ICU resources. Costs must also be interpreted alongside measures of effectiveness using proper modeling techniques. Interpretation can vary based on choice of effectiveness measure, perspective of the analysis, and societal and cultural norms. SUMMARY: When correctly measured and interpreted alongside measures of effectiveness, costs are a useful and important outcome in critical care research.

Cost-Benefit Analysis↗

The spleen colony technique. I. Correction for the overlap effect and sources of error in CFU-s determination.

A linear model for the errors of the 'spleen colony' assay for haemopoietic stem cells has been derived. The components emerging from the model are interpreted and practical recommendations given for interpreting measurements made with this assay. The model permits correction for the effect of overlapping colonies and gives average errors for single measurements of the number of CFU-s. More reliable and more precise information can be obtained using this model. The spleen colony technique detects a population of immature precursor cells designated as CFU-s (Till & McCulloch, 1961). The relative error of measurement is often large when compared with the changes in the phenomena studied. Consequently a better knowledge of the errors of this technique is highly desirable. This paper should be regarded as an extension of the previous analysis of Till (1972). The theory for the errors of the spleen colony technique was applied to 905 determinations of the CFU-s numbers performed on random-bred mice. Data from random-bred mice rather than those from inbred mice have been used because the error components can be expected to be larger and, consequently, more easily detectable. The model of errors has also been validated using data published by Till (1972) and has subsequently been applied to data from several inbred mice strains (Znojil & Necas, 1988).

Animals↗

Improving the design and analysis of high-throughput screening technology comparison experiments using statistical modeling.

Contemporary small-molecule drug discovery frequently involves the screening of large compound files as a core activity. Subsequently cost, speed, and safety become critical issues. In order to meet this need, numerous technologies have been developed to allow mix and measure approaches, facilitate miniaturization, and to increase speed and to minimize the use of potentially hazardous reagents such as radioactive materials. However, despite the on-paper advantages of these new technologies, risks can remain undefined. For example, the question of whether the novel method will facilitate identification of active chemical series in a way that is comparable with conventional methods arises. In order to address this question, we have taken the approach of carrying out experiments to directly compare the output of high-throughput screens using a given novel approach and a traditional method. The concordance between the screening methods can then be determined via comparison of the numbers and structures of the active molecules identified. This article describes the approach taken in our laboratory to minimize variability in such experiments and shows data that exemplifies the general result of lower than expected concordance. Statistical modeling was subsequently used to facilitate this interpretation. The model used beta-distribution function to generate a real-activity frequency relationship with added normal random error and occasional outliers to represent assay variability. Hence, the effect of assay parameters such as the threshold, the number of real actives, and the number of outliers and the standard deviation could readily be explored. The model was found to describe the data reasonably and moreover was found to be of great utility when it came to planning further optimal experiments. A key conclusion from the model was that concordance between screening methods could appear poor even when one approach is compared with itself. This occurs simply because the result is a function of assay threshold, standard deviation and the true compound % activity. In response to this finding we have adopted alternative experimental designs that more reliably measure the concordance between screening methods.

Biological Assay↗

Avian GIS models signal human risk for West Nile virus in Mississippi.

BACKGROUND: West Nile virus (WNV) poses a significant health risk for residents of Mississippi. Physicians and state health officials are interested in new and efficient methods for monitoring disease spread and predicting future outbreaks. Geographic Information Systems (GIS) models have the potential to support these efforts. Environmental conditions favorable for mosquito habitat were modeled using GIS to derive WNV risk maps for Mississippi. Variables important to WNV dissemination were selected and classified as static and dynamic. The static variables included road density, stream density, slope, and vegetation. The dynamic variable represented seasonal water budget and was calculated using precipitation and evaporation estimates. Significance tests provided deterministic evidence of variable importance to the models. RESULTS: Several models were developed to estimate WNV risk including a landscape-base model and seasonal climatic sub-models. P-values from t-tests guided variable importance ranking. Variables were ranked and weights assigned as follows: road density (0.4), stream density (0.3), slope (0.2) and vegetation (0.1). This landscape-base model was modified by climatic conditions to assess the importance of climate to WNV risk. Human case data at the zip code level were used to validate modeling results. All models were summarized by zip codes for interpretation and model validation. For all models, estimated risk was higher for zip codes with at least one human case than for zip codes where no human cases were recorded. Overall median measure of risk by zip code indicated that 67% of human cases occurred in the high-risk category. CONCLUSION: Modeling results indicated that dead bird occurrences are correlated with human WNV risk and can facilitate the assessment of environmental variables that contribute to that risk. Each variable's importance in GIS-based risk predictions was assigned deterministically. Our models indicated non-uniform distribution of risk across the state and showed elevated risk in urban and as well as rural areas. Model limitations include resolution of human data, zip code aggregation issues, and quality/availability of vegetation and stream density layers. Our approach verified that WNV risk can be modeled at the state level and can be modified for risk predictions of other vector-borne diseases in varied ecological regions.

Animals↗

Anticoagulation therapy advisor: a decision-support system for heparin therapy during ECMO.

We present a case study describing our development of a mathematical model to control a clinical parameter in a patient--in this case, the degree of anticoagulation during extracorporeal membrane oxygenation (ECMO) support. During ECMO therapy, an anticoagulant agent (heparin) is administered to prevent thrombosis. Under- or over-coagulation can have grave consequences. To improve control of anticoagulation, we developed a pharmacokinetic-pharmacodynamic (PK-PD) model that predicts activated clotting times (ACT) using the NONMEM program. We then integrated this model into a decision-support system, and validated it with an independent data set. The population model had a mean absolute error of prediction for ACT values of 33.5 seconds, with a mean bias in estimation of -14.3 seconds. Individualization of model-parameter estimates using nonlinear regression improved the absolute error prediction to 25.5 seconds, and lowered the mean bias to -3.1 seconds. The PK-PD model is coupled with software for heuristic interpretation of model results to provide a complete environment for the management of anticoagulation.

Blood Coagulation Disorders↗

Modeling EEG signals and interpreting measures of relationship during temporal-lobe seizures: an approach to the study of epileptogenic networks.

This work is focused on the study of the epileptogenic zone organization (EZ) in humans, based on the analysis of stereoelectroencephalographic (SEEG) signals with signal processing methods, and more specially those dedicated to the estimation of signal interdependencies. In order to evaluate quantities provided by these methods and in order to relate them to the notion of functional coupling between cerebral structures, we developed a neurophysiologically relevant model able to generate EEG signals from organized networks of neural populations. We showed [2, 3] that the model can produce realistic multichannel epileptiform signals (when compared to real SEEG signals) under certain conditions (excitation/inhibition ratio within populations, uni/bi-directional coupling between populations). In this paper, the model framework is used to evaluate the performance of nonlinear regression analysis as a method to characterize couplings between cerebral structures from SEEG signals they produce. Two quantities, a nonlinear correlation coefficient and a direction index, respectively related to coupling parameters in the model (degree/direction) are presented. These two quantities are measured on real SEEG signals recorded in patients suffering from temporal lobe epilepsy and candidate for surgical treatment. Results show that the characterization of functional couplings leads to the identification of networks referred to as "epileptogenic networks" and that might be responsible for the triggering of seizures. These results also corroborate our previous results on the classification of temporal lobe epilepsies [4, 5] showing that a recurrent seizure pattern exists that can be classified on the basis of interactions between medial and lateral neocortical structures. From the identified networks, it is also possible to describe "propagation networks" with a different organization is different and which play a major role in the clinical expression of seizures.

Journal Article↗

Factors influencing the enhancement of the new iron triangle in healthcare organisations.

PURPOSE: A new paradigm, "healthcare's new iron triangle," has been developed to emphasise the technological perspective of healthcare delivery, focusing on automation, value and empathy. The study aims to build a conceptual model and to identify factors for the enhancement of the new iron triangle in healthcare organisations. DESIGN/METHODOLOGY/APPROACH: The healthcare organisation is the primary focus point of the current study. To determine the factors, a survey of the literature and healthcare experts' opinions was conducted. The healthcare professionals validated the identified factors. Data for this study were gathered using a closed-ended questionnaire and scheduled interviews. The study employed "Total Interpretive Structural Modeling methodology and Matriced' Impacts Croise´s Multiplication Appliqué´ a UN Classement/Cross-Impact Matrix Multiplication Applied to a Classification (MICMAC) analysis" to address the "why" and "how" the factors interact and prioritise the identified factors. FINDINGS: The study found that organisational structure (F8), artificial intelligence (F1), innovation (F2) and human resources (F5) are the driving or key factors of the study. RESEARCH LIMITATIONS/IMPLICATIONS: The study primarily focused on identifying factors for the enhancement of a new iron triangle in healthcare organisations. The scope could eventually be expanded to explore more areas. PRACTICAL IMPLICATIONS: Academics and other stakeholders will have a better understanding of the key drivers for the enhancement of the new iron triangle in healthcare organisations. ORIGINALITY/VALUE: In this study, total interpretive structural modeling and cross-impact MICMAC analysis are proposed as an innovative approach to address the new iron triangle in healthcare organisations.

Humans↗

Interpretation of injection-withdrawal tracer experiments conducted between two wells in a large single fracture.

Tracer experiments conducted using a flow field established by injecting water into one borehole and withdrawing water from another are often used to establish connections and investigate dispersion in fractured rock. As a result of uncertainty in the uniqueness of existing models used for interpretation, this method has not been widely used to investigate more general transport processes including matrix diffusion or advective solute exchange between mobile and immobile zones of fluid. To explore the utility of the injection-withdrawal method as a general investigative tool and with the intent to resolve the transport processes in a discrete fracture, two tracer experiments were conducted using the injection-withdrawal configuration. The experiments were conducted in a fracture which has a large aperture (>500 microm) and horizontally pervades a dolostone formation. One experiment was conducted in the direction of the hydraulic gradient and the other in the direction opposite to the natural gradient. Two tracers having significantly different values of the free-water diffusion coefficient were used. To interpret the experiments, a hybrid numerical-analytical model was developed which accounts for the arcuate shape of the flow field, advection-dispersion in the fracture, diffusion into the matrix adjacent to the fracture, and the presence of natural flow in the fracture. The model was verified by comparison to a fully analytical solution and to a well-known finite-element model. Interpretation of the tracer experiments showed that when only one tracer, advection-dispersion, and matrix diffusion are considered, non-unique results were obtained. However, by using multiple tracers and by accounting for the presence of natural flow in the fracture, unique interpretations were obtained in which a single value of matrix porosity was estimated from the results of both experiments. The estimate of porosity agrees well with independent measurements of porosity obtained from core samples. This suggests that: (i) the injection-withdrawal method is a viable tool for the investigation of general transport processes provided all relevant experimental conditions are considered and multiple conservative tracers are used; and (ii) for the conditions of the experiments conducted in this study, the dominant mechanism for exchange of solute between the fracture and surrounding medium is matrix diffusion.

Diffusion↗

Effects of oxazepam on anxiety: implications for Fowles' psychophysiological interpretation of Gray's model.

The present dose-response study investigated the effects of the benzodiazepine oxazepam (Serax) on anxiety as measured by autonomic and self-report indices in a nonclinical sample. Given Fowles' (1980, 1988) theory that electrodermal activity primarily reflects the activity of the behavioral inhibition system (BIS) while heart rate primarily reflects the activity of the behavioral activation system (BAS), we predicted that electrodermal indices of anxiety would be more affected by oxazepam than heart rate. Psychophysiological and self-report measures were recorded prior to and following a speech stressor in subjects given placebo (n = 17), 15 mg oxazepam (n = 19), and 30 mg oxazepam (n = 17). Anxiolytic effects were found during stressed state as measured by skin conductance level but not heart rate or self-reported anxiety. Furthermore, the anxiolytic effects of oxazepam were noted only during the stressful phases of the experiment. The results are viewed as supportive of Fowles' motivational interpretation of the distinction between heart rate and electrodermal responding.

Adolescent↗

Improved computer analysis of solid phase gastric emptying scans.

OBJECTIVES: The solid phase gastric emptying scan (GES) is used to confirm the clinical impression of abnormal gastric emptying. There is variability in the interpretation of GES. Determination of initial lag phase of the GES and the emptying half-time (t1/2) is generally performed by curve inspection and thus may suffer from lack of objectivity. The purpose of this study was to develop a physiological model for interpretation of the GES using nonlinear curve fitting. This model resulted in computer-generated best fits for lag time and t1/2, which were analyzed in a group of patients with suspected gastroparesis. METHODS: All gastric emptying scans performed at our institution over a 3.5-yr period were studied. Raw data from these studies were analyzed by nonlinear curve fitting. Using the equation: If (x < xo, plateau, plateau * exp( - K * (x - xo))) data were best fit to a function describing a lag followed by a log linear decay. This model generated four parameters; lag, K, t1/2, and T50%. Forty patients with less than 50% emptying at 1 h (group II) were compared with 31 patients with normal emptying (group I). RESULTS: The nonlinear model resulted in better curve fitting (higher r2) in 59 of 71 studies (81%) when compared with a monoexponential decay after a lag of 0 min. Mean lag for patients in group I was 8.5 +/- 1.2 min and was 25.9 +/- 3.1 min in group II (p < 0.0005). Mean t1/2 was 31.7 +/- 1.8 min in group I and 69.7 +/- 5.0 min in group II (p < 0.007). By adding 2 SD to lag and t1/2 in group I, normal values for these parameters were 21.9 and 52.2 min, respectively. Eleven patients in group II had a prolonged lag alone, 13 had a prolonged t1/2, and 13 had prolongation of both parameters. CONCLUSIONS: A new physiological model for the interpretation of GES is presented. Individual patients with delayed gastric emptying may have increased lag times, a decreased rate of antral emptying, or both abnormalities.

Gastric Emptying↗

Interpretation of surface-tension isotherms of n-alkanoic (fatty) acids by means of the van der Waals model.

Here we apply the two-dimensional van der Waals model to interpret surface-tension isotherms of aqueous solutions of n-alkanoic (fatty) acids. We processed available experimental data for a homologous series of eight acids, from pentanoic to dodecanoic (lauric). Only three adjustable parameters have been varied to fit simultaneously all experimental curves. Excellent agreement between the theoretical model and the experiment has been obtained. The determined parameter values comply well with the molecular properties and allow one to calculate the surfactant adsorption, surface elasticity, and the surface pressure vs area isotherms. For the dodecanoic acid, the van der Waals model indicates the existence of a surface phase transition.

Journal Article↗

Neuro-fuzzy modeling: an accurate and interpretable method for predicting bladder cancer progression.

PURPOSE: New methods are required to improve the prediction of cancer progression as traditional statistical tests have limited accuracy. Accurate predictions would allow physicians to offer specific treatment according to individual patient risk. While predictive improvements are obtained using ANN, the hidden nature of these networks prevents insight and has hindered their widespread implementation. NFM is an alternate form of artificial intelligence using fuzzy logic (which is a multivalued logic which provides reasoning under uncertainty). By defuzzification the NFM rule base becomes transparent to overcome the black box nature of ANN. MATERIALS AND METHODS: Combinations of clinicopathological (tumor stage and grade, patient age, gender, and smoking status) and molecular (immunohistochemical expression of p53 and methylation status of 11 loci) data from 117 patients were used to develop and compare predictive models of tumor progression using NFM, ANN and LR. RESULTS: NFM (88% to 100% sensitivity, 97% to 100% specificity and 94% to 100% accuracy) predicted the presence and timing of cancer progression more accurately than ANN (81% to 87%, 95% to 100% and 89% to 90%, p = 0.002) and LR 3%, 61% to 72% and 47% to 53%, p = 0.00005). NFM was able to interrogate the clinicopathological and molecular data, and select the most important parameters (age, grade, stage, smoking, methylation) for progression prediction. CONCLUSIONS: Intelligent systems and molecular biomarkers improved the accuracy of cancer progression predictions. NFM appeared superior to ANN in terms of accuracy, sensitivity, specificity and transparency. The use of NFM in routine clinical practice warrants further validation.

Aged↗

Modeling intrinsic bioremediation for interpret observable biogeochemical footprints of BTEX biodegradation: the need for fermentation and abiotic chemical processes.

The intrinsic bioremediation of BTEX must be documented by the stoichiometric consumption and production of several other compounds, called 'footprints' of the biodegradation reaction. Although footprints of BTEX biodegradation are easy to identify from reaction stoichiometry, they can be confounded by the stepwise nature of the biodegradation reactions and by several abiotic chemical reactions that also produce or consume the footprints. In order to track the footprints for BTEX biodegradation, the following reactions need to be considered explicitly: (1) fermentation and methanogenesis as separate processes, (2) precipitation and dissolution of calcite, (3) precipitation and dissolution of amorphous iron monosulfide (FeS), (4) conversion of FeS into the thermodynamically stable pyrite (FeS2) with loss of sulfide and abiotic formation of H2, and (5) reductive dissolution of solid iron(III) by oxidation of sulfide. We critically review the research that underlies why these mechanisms must be included and how to describe them quantitatively. A companion manuscript develops and applies a mathematical model that includes these reactions.

Biodegradation, Environmental↗

Interpreting simple STR mixtures using allele peak areas.

Although existing statistical models can interpret mixtures qualitatively based upon the alleles present, the use of automated sequencers opens the opportunity to take account of quantitative aspects embodied by the peak area. One step in understanding simple mixtures consisting of just two donors is to estimate the mixture ratio. This is relatively easy to do when four-allele mixtures are evident at a given locus. However, if the mixture consists of three or fewer alleles, the process it is not straightforward. We demonstrate that mixture estimates are consistent across all loci in a multiplex system. Once the mixture ratio is known, then the expected peak areas for any given combination of alleles can be estimated using a simple spreadsheet analysis.

Alleles↗

Enterocutaneous Fistula-Associated Sepsis and Mortality: Development and Validation of a Multimodal Artificial Intelligence Prediction Model.

BACKGROUND: Predicting enterocutaneous fistula (ECF)-associated sepsis and mortality poses significant challenges in digital health care due to the disease's complexity and heterogeneous clinical manifestations. Current approaches that rely on single-modal data or traditional scoring systems often fail to capture the intricate immune-inflammatory dynamics and multisystem involvement in patients with ECF. OBJECTIVE: This study aims to develop an artificial intelligence (AI)-driven multimodal fusion model integrating clinical, imaging, and transcriptomic data for early prediction of ECF-associated sepsis and 28-day mortality, addressing the limitations of conventional single-dimensional models. METHODS: This study leveraged publicly available datasets (Medical Information Mart for Intensive Care III [MIMIC-III], electronic Intensive Care Unit [eICU], and The Cancer Genome Atlas) to construct a multimodal framework. Clinical parameters were processed using Extreme Gradient Boosting, abdominal imaging features were extracted via convolutional neural networks, and transcriptomic profiles were analyzed with variational autoencoders. A Transformer-based fusion network was employed for joint prediction and validated through cross-validation and external testing. Key features were identified using Shapley Additive Explanations and Local Interpretable Model-Agnostic Explanations interpretability algorithms, while immune regulatory mechanisms were explored via weighted gene co-expression network analysis. RESULTS: The multimodal model achieved an area under the curve (AUC) of 0.89 for predicting sepsis and 28-day mortality, outperforming unimodal models (clinical-only model, AUC 0.72, and imaging-only model, AUC 0.78). Critical predictors included Sequential Organ Failure Assessment score, lactate levels, intra-abdominal free fluid on imaging, and immunoregulatory genes (programmed death-ligand 1 [PD-L1] and indoleamine 2,3-dioxygenase 1 [IDO1]). Mechanistic analysis revealed distinct immune reprogramming in patients with sepsis, characterized by increased regulatory T cells and M2 macrophages, along with downregulated cluster of differentiation 8+ (CD8+) T cells. CONCLUSIONS: This multimodal AI model offers an innovative digital solution in medical informatics, enabling precise early risk stratification for ECF-associated sepsis. By integrating multisource data and providing interpretable insights into immune-inflammatory pathways, the model enhances health care quality for patients with ECF and paves the way for personalized intervention strategies.

Humans↗

Communication models, professionalization, and the work of medical interpreters.

A growing number of health institutions are employing medical interpreters, bilingual individuals who facilitate communication between health care providers and patients. Organizations working to establish the professional status of medical interpreting have articulated codes of ethics that prescribe a number of different roles for interpreters in their clinical work. Interviews obtained from 17 medical interpreters support the observation that the code of ethics, based primarily on a conduit model of interpreter communication, does not provide consistent guidance in clinical practice. I discuss the role of communication theory in developing improved models for interpreter practice.

Codes of Ethics↗

Derivation of the linear-logistic model and Cox's proportional hazard model from a canonical system description.

The linear-logistic regression model and Cox's proportional hazard model are widely used in epidemiology. Their successful application leaves no doubt that they are accurate reflections of observed disease processes and their associated risks or incidence rates. In spite of their prominence, it is not a priori evident why these models work. This article presents a derivation of the two models from the framework of canonical modeling. It begins with a general description of the dynamics between risk sources and disease development, formulates this description in the canonical representation of an S-system, and shows how the linear-logistic model and Cox's proportional hazard model follow naturally from this representation. The article interprets the model parameters in terms of epidemiological concepts as well as in terms of general systems theory and explains the assumptions and limitations generally accepted in the application of these epidemiological models.

Communicable Diseases↗