The Influence of Mathematical Definitions on Patellar Kinematics Representations.
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ABSTRACT:
SUBMITTER: Sauer A
PROVIDER: S-EPMC8709478 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must include structural representation as an indispensable component. Mathematical representations that simplify the biomolecular structural complexity and reduce ML dimensionality have emerged as a prime winner in D3R Grand Challenges. This review is devoted to the recent advances in developing low-dimensional and scalable mathematical representations of biomolecules in our laboratory. We discuss three classes of mathematical approaches, including algebraic topology, differential geometry, and graph theory. We elucidate how the physical and biological challenges have guided the evolution and development of these mathematical apparatuses for massive and diverse biomolecular data. We focus the performance analysis on protein-ligand binding predictions in this review although these methods have had tremendous success in many other applications, such as protein classification, virtual screening, and the predictions of solubility, solvation free energies, toxicity, partition coefficients, protein folding stability changes upon mutation, etc.
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Project description:BACKGROUND:Sexual mixing between heterogeneous population subgroups is an integral component of mathematical models of sexually transmitted infections (STIs). This study compares the fit of different mixing representations to survey data and the impact of different mixing assumptions on the predicted benefits of hypothetical human papillomavirus (HPV) vaccine strategies. METHODS:We compared novel empirical (data-driven) age mixing structures with the more commonly-used assortative-proportionate (A-P) mixing structure. The A-P mixing structure assumes that a proportion of sexual contacts - known as the assortativity constant, typically estimated from survey data or calibrated - occur exclusively within one's own age group and the remainder mixes proportionately among all age groups. The empirical age mixing structure was estimated from the National Survey on Sexual Attitudes and Lifestyles 3 (Natsal-3) using regression methods, and the assortativity constant was estimated from Natsal-3 as well. Using a simplified HPV transmission model under each mixing assumption, we calibrated the model to British HPV16 prevalence data, then estimated the reduction in steady-state prevalence and the number of infections averted due to expanding HPV vaccination from 12- through 26-year-old females alone to 12-year-old males or 27- to 39-year-old females. RESULTS:Empirical mixing provided a better fit to the Natsal-3 data than the best-fitting A-P structure. Using the model with empirical mixing as a reference, the model using the A-P structure often under- or over-estimated the benefits of vaccination, in one case overestimating by 2-fold the number of infections prevented due to extended female catch-up in a high vaccine uptake setting. CONCLUSIONS:An empirical mixing structure more accurately represents sexual mixing survey data, and using the less accurate, yet commonly-used A-P structure has a notable effect on estimates of HPV vaccination benefits. This underscores the need for mixing structures that are less dependent on unverified assumptions and are directly informed by sexual behavior data.
| S-EPMC6367925 | biostudies-literature
Project description:BackgroundPrior research has inconsistently operationalized Science, Technology, Engineering, and Math (STEM) fields, presenting an interpretation challenge. A content analysis of 51 quantitative, gender-focused, higher education-oriented, STEM-related studies in the ERIC database published between January 2010 and July 2018 revealed that only 13 articles used an existing STEM definition. In 15, STEM was not explicitly defined, and others defined STEM independently. This wide range of definitions may lead to confusion or misrepresentation of findings for interventions and practices to support women in STEM. To illustrate the issue and prompt recommendations for future research, this study uses data from the United States National Center for Education Statistics' Education Longitudinal Study (ELS:2002/12) to investigate the connection between STEM definition and the outcome of college degree completion, comparing results by gender for five ways of operationalizing STEM fields.ResultsWe found the size, direction, and significance of the gender gap depended on STEM operationalization. When STEM was defined as high paradigm fields, the odds of women attaining a non-STEM degree were higher than otherwise. When social science fields were included in STEM, there was no statistically significant difference by gender. When looking specifically at fields considered related to science and engineering, the direction of the relationship was reversed.ConclusionWhile our findings follow expectations about social science fields and gender, it is noteworthy that results regarding STEM degree completion by gender for science and engineering-related fields were opposite those of high paradigm STEM fields. This result highlights that the definition of STEM matters, and inconsistent operationalization in the literature presents an interpretation challenge. We argue the field should strive to find common categorizations of STEM that retain the legitimate variation in how STEM can and should be defined, while providing a basis for consistent comparison. We recommend researchers and practitioners developing research-based practices: 1) interpret research findings understanding potential inconsistency from different STEM operationalizations, 2) explicitly describe STEM operational definitions to enable comparing findings, 3) routinely analyze sensitivity to alternate STEM definitions, and 4) find common STEM categorizations that retain legitimate variation while providing a basis for consistent comparison.
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Project description:Language can be viewed as a set of cues that modulate the comprehender's thought processes. It is a very subtle instrument. For example, the literature suggests that people perceive direct speech (e.g., Joanne said: 'I went out for dinner last night') as more vivid and perceptually engaging than indirect speech (e.g., Joanne said that she went out for dinner last night). But how is this alleged vividness evident in comprehenders' mental representations? We sought to address this question in a series of experiments. Our results do not support the idea that, compared to indirect speech, direct speech enhances the accessibility of information from the communicative or the referential situation during comprehension. Neither do our results support the idea that the hypothesized more vivid experience of direct speech is caused by a switch from the visual to the auditory modality. However, our results do show that direct speech leads to a stronger mental representation of the exact wording of a sentence than does indirect speech. These results show that language has a more subtle influence on memory representations than was previously suggested.
| S-EPMC3680483 | biostudies-literature
Project description:Background/objectiveCurrent cycling pedals constrain the pedaling motion to the sagittal plane. This study aimed to evaluate novel pedal systems that allow lateral translation through the pedal stroke via frontal plane kinematics and muscle recruitment.MethodsSixteen cyclists were recruited to pedal on three pedal systems: standard pedals (STD), free lateral translation (LAT), and a guided lateral translation pedal (VL). Frontal plane kinematics were measured via markers on the hip, knee, and foot. EMG recordings were collected from 8 leg muscles and expressed as a percentage of functional threshold power activation levels.ResultsKnee and ankle range of movement was significantly more highly correlated in the VL pedals compared to STD (r?=?.46?±?.08, vs. .23?±?.05; p?=?.028). The rectus femoris was recruited significantly less in the VL vs. STD pedals (23.6?±?7.7% lower, p?=?.008). The hip abductors were more highly recruited in VL vs. STD: gluteus medius (16.9?±?7.2% higher, p?=?.033) and the tensor fascia latae (30.9?±?8.5% lower, p?=?.003).ConclusionVL pedals may improve knee-to-ankle tracking through the pedal stroke and may allow cyclists to increase power output through the additional recruitment of hip abductors.
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Project description:Cytotoxic lymphocytes (CTL) have been reported to show a range of motility patterns from rapid long-range tracking to complete arrest, but how and whether these kinematics affect their ability to kill target cells is not known. Many in vitro killing assays utilize cell lines and tumour-derived cells as targets, which may be of limited relevance to the kinetics of CTL-mediated killing of somatic cells. Here, live-cell microscopy is used to examine the interactions of CTL and primary murine skin cells presenting antigens. We developed a qualitative and quantitative killing assay using extended-duration fluorescence time-lapse microscopy coupled with large-volume objective software-based data analysis to obtain population data of cell-to-cell interactions, motility and apoptosis. In vivo and ex vivo activated antigen-specific cytotoxic lymphocytes were added to primary keratinocyte targets in culture with fluorometric detection of caspase-3 activation in targets as an objective determinant of apoptosis. We found that activated CTL achieved contact-dependent apoptosis of non-tumour targets after a period of prolonged attachment - on average 21 hours - which was determined by target cell type, amount of antigen, and activation status of CTL. Activation of CTL even without engagement of the T cell receptor was sufficient to mobilise cells significantly above baseline, while the addition of cognate antigen further enhanced their motility. Highly activated CTL showed markedly increased vector displacement, and velocity, and lead to increased antigen-specific target cell death. These data show that the inherent kinematics of CTL correlate directly with their ability to kill non-tumour cells presenting cognate antigen.
| S-EPMC4011687 | biostudies-literature
Project description:Researchers investigating relationships between the neighbourhood environment and health first need to decide on the spatial extent of the neighbourhood they are interested in. This decision is an important and ongoing methodological challenge since different methods of defining and delineating neighbourhood boundaries can produce different results. This paper explores this issue in the context of a New Zealand-based study of the relationship between the built environment and multiple measures of physical activity. Geographic information systems were used to measure three built environment attributes-dwelling density, street connectivity, and neighbourhood destination accessibility-using seven different neighbourhood definitions (three administrative unit boundaries, and 500, 800, 1000- and 1500-m road network buffers). The associations between the three built environment measures and five measures of physical activity (mean accelerometer counts per hour, percentage time in moderate-vigorous physical activity, self-reported walking for transport, self-reported walking for recreation and self-reported walking for all purposes) were modelled for each neighbourhood definition. The combination of the choice of neighbourhood definition, built environment measure, and physical activity measure determined whether evidence of an association was detected or not. Results demonstrated that, while there was no single ideal neighbourhood definition, the built environment was most consistently associated with a range of physical activity measures when the 800-m and 1000-m road network buffers were used. For the street connectivity and destination accessibility measures, associations with physical activity were less likely to be detected at smaller scales (less than 800 m). In line with some previous research, this study demonstrated that the choice of neighbourhood definition can influence whether or not an association between the built environment and adults' physical activity is detected or not. This study additionally highlighted the importance of the choice of built environment attribute and physical activity measures. While we identified the 800-m and 1000-m road network buffers as the neighbourhood definitions most consistently associated with a range of physical activity measures, it is important that researchers carefully consider the most appropriate type of neighbourhood definition and scale for the particular aim and participants, especially at smaller scales.
| S-EPMC6540146 | biostudies-literature
Project description:PurposeThe antiarrhythmic drug amiodarone has a long half-life of 60 days, which is often ignored in observational studies. This study aimed to investigate the impact of different exposure definitions on the association between amiodarone use and the risk of acute pancreatitis.MethodUsing data from the Dutch PHARMO Database Network, incident amiodarone users were compared to incident users of a different type of antiarrhythmic drug. Eighteen different definitions were applied to define amiodarone exposure, including dichotomized, continuous and categorized cumulative definitions with lagged effects to account for the half-life of amiodarone. For each exposure definition, a Cox proportional hazards model was used to estimate the hazard ratio (HR) of hospitalization for acute pancreatitis.ResultsThis study included 15,378 starters of amiodarone and 21,394 starters of other antiarrhythmic drugs. Adjusted HRs for acute pancreatitis ranged between 1.21-1.43 for dichotomized definitions of exposure to amiodarone, between 1.13-1.22 for dose definitions (per DDD) and between 0.52-1.72 for cumulative dose definitions, depending on the category. Accounting for lagged effects had little impact on estimated HRs.ConclusionsThis study demonstrates the relative insensitivity of the association between amiodarone and the risk of acute pancreatitis against a broad range of different exposure definitions. Accounting for possible lagged effects had little impact, possibly because treatment switching and discontinuation was uncommon in this population.
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Project description:The use of zebrafish larvae has aroused wide interest in the medical field for its potential role in the development of new therapies. The larvae grow extremely quickly and the embryos are nearly transparent which allows easy examination of its internal structures using fluorescent imaging techniques. Medical treatment of zebrafish larvae can directly influence its swimming behaviours. These behaviour changes are related to functional changes of central nervous system and transformations of the zebrafish body such as muscle mechanical power and force variation, which cannot be measured directly by pure experiment observation. To quantify the influence of drugs on zebrafish larvae swimming behaviours and energetics, we have developed a novel methodology to exploit intravital changes based on observed zebrafish locomotion. Specifically, by using an in-house MATLAB code to process the recorded live zebrafish swimming video, the kinematic locomotion equation of a 3D zebrafish larvae was obtained, and a customised Computational Fluid Dynamics tool was used to solve the fluid flow around the fish model which was geometrically the same as experimentally tested zebrafish. The developed methodology was firstly verified against experiment, and further applied to quantify the fish internal body force, torque and power consumption associated with a group of normal zebrafish larvae vs. those immersed in acetic acid and two neuroactive drugs. As indicated by our results, zebrafish larvae immersed in 0.01% acetic acid display approximately 30% higher hydrodynamic power and 10% higher cost of transport than control group. In addition, 500 μM diphenylhydantoin significantly decreases the locomotion activity for approximately 50% lower hydrodynamic power, whereas 100 mg/L yohimbine has not caused any significant influences on 5 dpf zebrafish larvae locomotion. The approach has potential to evaluate the influence of drugs on the aquatic animal's behaviour changes and thus support the development of new analgesic and neuroactive drugs.
| S-EPMC6954687 | biostudies-literature
Project description:Patellar luxation is an orthopaedic disorder in which the kneecap moves out of its normal location within the femoral trochlea. It can lead to osteoarthritis, lameness, and pain. In dogs it appears to be a heritable trait with a high incidence in some breeds. The prevalence of patellar luxation in the Dutch Flat-Coated Retriever population is 24%. We have performed a Genome Wide Association Analysis of the condition in this breed.
2014-11-01 | E-MTAB-2040 | biostudies-arrayexpress