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At least 613 records · Page 34Linked to original sources
arXiv2022

COVID 19: Open source model for rapid reduction of R to below 1 in high R0 scenarios

We present an open source model that allows quantitative prediction of the effects of testing on the rate of spread of COVID-19 described by R, the reproduction number, and on the degree of quarantine, isolation and lockdown required to limit it. The paper uses the model to quantify the outcomes of different test types and regimes, and to identify strategies and tests that can reduce the rate of spread and R value by a factor of between 1.67 and 33.3, reducing it to between 60% and 3% of the initial value.

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arXiv2021

Electric Field Models of Transcranial Magnetic Stimulation Coils with Arbitrary Geometries: Reconstruction from Incomplete Magnetic Field Measurements

Background: Calculation of the electric field induced by transcranial magnetic stimulation (TMS) in the brain requires accurate models of the stimulation coils. Reconstructing models from the measured magnetic fields of coils so far worked only for flat coil geometries and required data of their full magnetic field distribution. Objective: To reconstruct models of coils with arbitrary winding geometries from spatially incomplete magnetic field measurements. Methods: Dipole approximation via minimum norm estimation with a cross validation procedure simultaneously assessing predictability and reproducibility of the field approximation. The methods were validated on both simulated and acquired magnetic flux density data. Furthermore, reconstruction of coil models from sparsely sampled data is investigated and a procedure for obtaining sparse dipole coil models based on orthogonal matching pursuit is suggested. Results: Given that measured data from regions around the coil are available, the magnetic vector potential can accurately be represented by fitted dipole models even from sparsely sampled data. Considerable sparsification of dipole models is possible while retaining accurate representation of the field also close to the coil. Conclusion: Our versatile approach removes an important hurdle for constructing coil models from measurement data and enables a flexible trade-off between the accuracy and computational efficiency of the reconstructed dipole models.

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arXiv2022

Effect of a mixture of amoxicillin and norfloxacin in piglets feeding on productive performance and clinical signs

An experiment was conducted to evaluate the effect of feeding post-weaned piglets different levels of a commercial amoxicillin plus norfloxacin formula (Respirend) on the performance, clinical evidence of sickness, and the cost:benefit ratio. 454 PIC x Camborough female and castrated male, weaned at 21 d of age, with an average initial weight of 6.19 kg, were used in this experiment. Treatment 1 consisted in feeding a basal diet supplemented with 1000 g of a commercial tilmicosin product (Pulmotil) per metric tonne of feed (control group, from 21 to 35 d of age) and Treatments 2), 3) and 4) consisted in feeding the basal diet supplement with 500, 300 y 100 g of Respirend per metric tonne of feed, respectively, from 21 to 42 d of age. The results did not show significant differences (P<0.05) in mortality nor in parenteral medicine administration cost in none of the periods. Nevertheless, 500 g of Respirend per metric tonne of feed improved significantly (P<0.05) the general health status in the period between 21 and 35 d of age. For the whole evaluation period (21 to 42 d of age), this level improved significantly (P<0.05) the final body weight, the average daily weight gain, the average daily feed intake, the feed:gain ratio and optimized the cost:benefit ratio.

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arXiv2022

Effect of an antimicrobial association (Respirend-M) on productive performance of broilers

The objective of this study was to determine the effect of feeding an antimicrobial association to males broiler chickens from 0 to 14 days of age on the performance and clinical signs of bacterial processes. Two treatments were tested: a control treatment without Respirend-M, and a treatment with the antimicrobial (300 g/t Respirend-M, 0-14 d). 398 male Cobb 500 chicks were randomly assigned to two treatments and four replications per treatment. Body weight at 14 d, body weight gain, feed intake, feed conversion ratio, and health status were evaluated. The results showed feeding 300 g/t Respirend-M significantly (P<0.05) improved the final body weight, the body weight gain and the feed intake. No statistically significant (P>0.05) effect was detected on the feed conversion ratio.

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arXiv2022

In vitro evaluation of the effect of Ceftiofur Sodium and of a new Gentamycin Sulfate formulation on the viability of Marek disease virus

The present study evaluated In vitro effect of gentamicin sulfate and ceftiofur sodium on the viability of the Marek's disease virus. The titer of cell associated turkey herpesvirus (HVT) vaccine was not appreciably reduced when incubated with 50 mg/ml of gentamicin sulfate or ceftiofur sodium. Statistic difference was not found between the number of plaqueforming units (PFU) of reconstituted vaccine associated with both antibiotics 0, 15, 30 and 60 minutes after reconstitution of vaccine. The antibiotics did not considerably alter the pH values. There was a significative decrease of the titer of all vaccinal solutions when they were inoculated 30 and 60 minutes after the reconstitution of the vaccine. Nevertheless, these titers are higher than the required titers to protectect against the Marek disease.

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arXiv2022

Meta-analysis for Discovering Which Genes are Differentially Expressed in Neuroinflammation

Neuroinflammation is a significant aspect of many neurological diseases of Homo sapiens, and the genes that are differentially expressed in this process should be well understood to gather the nature of such diseases. We have conducted a meta-analysis (based on a combined adjusted P value and logFC scheme) of 6 multi-species (Homo sapiens, Mus musculus) datasets (available on GEO, short for Gene Expression Omnibus) obtained through microarray technology. Our analysis shows that the genes coding pleckstrin homology domain and galectin-9 proteins take part in neuroinflammation in microglia.

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arXiv2021

On the origins of the Omicron variant of the SARS-CoV-2 virus

A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise allows SARS-CoV-2 greater latitude to explore its own mutational space. This latitude is not withoutr estriction, and a specific biophysical constraint is explored. Specifically, a nearly two- to five-fold discrepancy in backbone hydrogen bonding is observed between sub-molecules in Protein Data Bank files of the spike glycoprotein yielding two conclusions: mutagenic residues in the receptor-binding subunit of the spike much more frequently do not participate in backbone hydrogen bonds; and a technique of viral escape is therefore to remove such bonds within physico-chemical and functional constraints. Earlier work, from which the previous discussion is entirely independent, explains these phenomena from general principles of free energy, namely, the metastability of the glycoprotein. The conclusions therefore likely hold more generally as principles in virology.

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arXiv2022

Influence of different factors on survival of patients with colorectal cancer

Colorectal cancer refers to the cancer from the dentate line to the junction of rectosigmoid colon, which is one of the most common malignant tumors of the digestive tract. The treatment of colorectal cancer is controversial, so understanding the risk factors and survival factors of colorectal cancer is of great significance for the diagnosis of patients. This study sampled patients with colorectal cancer from the SEER database. The factors affecting the survival of colorectal cancer patients were analysed by combining principal component analysis and competitive risk model, and the survival time of patients was analysed by combining principal component analysis and linear regression. Finally, the data were predicted. The results show that principal component analysis can effectively reduce the number of variables, and the combination of competitive risk model and linear regression model can effectively analyse and predict the data.

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arXiv2022

Recommendations for extending the GFF3 specification for improved interoperability of genomic data

The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common software packages that export annotations in GFF3 format model the same data and metadata in different notations, which puts the burden on end-users to interpret the data model. The AgBioData consortium is a group of genomics, genetics and breeding databases and partners working towards shared practices and standards. Providing concrete guidelines for generating GFF3, and creating a standard representation of the most common biological data types would provide a major increase in efficiency for AgBioData databases and the genomics research community that use the GFF3 format in their daily operations. The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome further discussion of these recommendations. We request the genomics and bioinformatics community to utilize the github repository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) to provide feedback via issues or pull requests.

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arXiv2022

Evolution and Mutations of Beta 2 Microglobulin

Here we examine the evolution of beta-2 microglobulin in terms of its hydropathic shapes, a theoretical construct that has revealed important trends. The dynamics of many proteins are largely driven by interactions between the protein itself and the thin water film that covers it. \b{eta}2m constitutes the basic building unit of the immunoglobulin superfamily; the evolution of its amino acid sequences from chickens to mice to humans provides new information about its multiple functions. Our hydrodynamic method involves concepts of topological shape evolution towards a critical point for optimized functions. The results are in excellent agreement with experiment for the details of the mouse-human evolution, as well as both the dangerous natural amyloid aggregation mutation D76N, and six other DN test mutations.

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arXiv2023

Translational Quantum Machine Intelligence for Modeling Tumor Dynamics in Oncology

Quantifying the dynamics of tumor burden reveals useful information about cancer evolution concerning treatment effects and drug resistance, which play a crucial role in advancing model-informed drug developments (MIDD) towards personalized medicine and precision oncology. The emergence of Quantum Machine Intelligence offers unparalleled insights into tumor dynamics via a quantum mechanics perspective. This paper introduces a novel hybrid quantum-classical neural architecture named $η-$Net that enables quantifying quantum dynamics of tumor burden concerning treatment effects. We evaluate our proposed neural solution on two major use cases, including cohort-specific and patient-specific modeling. In silico numerical results show a high capacity and expressivity of $η-$Net to the quantified biological problem. Moreover, the close connection to representation learning - the foundation for successes of modern AI, enables efficient transferability of empirical knowledge from relevant cohorts to targeted patients. Finally, we leverage Bayesian optimization to quantify the epistemic uncertainty of model predictions, paving the way for $η-$Net towards reliable AI in decision-making for clinical usages.

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arXiv2022

Assessing Phenotype Definitions for Algorithmic Fairness

Disease identification is a core, routine activity in observational health research. Cohorts impact downstream analyses, such as how a condition is characterized, how patient risk is defined, and what treatments are studied. It is thus critical to ensure that selected cohorts are representative of all patients, independently of their demographics or social determinants of health. While there are multiple potential sources of bias when constructing phenotype definitions which may affect their fairness, it is not standard in the field of phenotyping to consider the impact of different definitions across subgroups of patients. In this paper, we propose a set of best practices to assess the fairness of phenotype definitions. We leverage established fairness metrics commonly used in predictive models and relate them to commonly used epidemiological cohort description metrics. We describe an empirical study for Crohn's disease and diabetes type 2, each with multiple phenotype definitions taken from the literature across two sets of patient subgroups (gender and race). We show that the different phenotype definitions exhibit widely varying and disparate performance according to the different fairness metrics and subgroups. We hope that the proposed best practices can help in constructing fair and inclusive phenotype definitions.

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arXiv2022

Modeling-informed policy, policy evaluated by modeling: Evolution of mathematical epidemiology in the context of society and economy

The COronaVIrus Disease 2019 (COVID-19) pandemic that has had the world in its grip from the beginning of 2020, has resulted in an unprecedented level of public interest and media attention on the field of mathematical epidemiology. Ever since the disease came to worldwide attention, numerous models with varying levels of sophistication have been proposed; many of these have tried to predict the course of the disease over different time-scales. Other models have examined the efficacy of various policy measures that have been adopted (including the unparalleled use of "lockdowns") to contain and combat the disease. This multiplicity of models may have led to bewilderment in many quarters about the true capabilities and utility of mathematical modeling. Here we provide a brief guide to epidemiological modeling, focusing on how it has emerged as a tool for informed public-health policy-making and has in turn, influenced the design of interventions aimed at preventing disease outbreaks from turning into raging epidemics. We show that the diversity of models is somewhat illusory, as the bulk of them are rooted in the compartmental modeling framework that we describe here. While their basic structure may appear to be a highly idealized description of the processes at work, we show that features that provide more realism, such as the community organization of populations or strategic decision-making by individuals, can be incorporated into such models. We conclude with the argument that the true value of models lies in their ability to test in silico the consequences of different policy choices in the course of an epidemic, a much superior alternative to trial-and-error approaches that are highly costly in terms of both lives and socio-economic disruption.

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arXiv2022

Cryopreservation of seeds of blue waterlily (Nymphaea caerulea) using glutathione adding plant vitrification solution, PVS+

Nymphaea caerulea is a valuable freshwater aquatic plant, not only because of its ornamental value but also its extractions for chemical and medical uses. It is necessary to store its seeds as backup resources. Cryopreservation is the reliable, cost-effective method for long-term preservation of botanical genetic banks, especially for recalcitrant plants. In this study, we demonstrated that due to unable to tolerate desiccation and low-temperature, N. caerulea is recalcitrant. Since viability was lost before 6 months storage, N. caerulea seeds were not appropriate to long-term store by traditional storage method. The only way to long-term store N. caerulea seeds is cryopreservation. However, Plant Vitrification Solution 3 (PVS3; 50% w/v sucrose, 50% w/v glycerol), a commonly used plant vitrification solution, was ineffective on N. caerulea seeds cryopreservation. The maximum survival rate of cryopreserved seeds treated by PVS3 was only 23%. Oxidative stress induced by reactive oxygen species (ROS) accumulation within seeds was the reason to cause inefficiency of PVS3 treated seeds cryopreservation. We developed a new plant vitrification solution (PVS+), by adding glutathione (GSH) into PVS3. PVS+ rescued the inefficiency by decreasing ROS accumulation and elevated survival rate of cryopreserved seeds to 97%. Our results showed some inefficiencies of plant tissue cryopreservation may be caused by ROS-induced oxidative stress. Antioxidants can reduce ROS-induced oxidative stress and improve seeds survival after cryopreservation. In conclusion, N. caerulea seeds were identified as recalcitrant and successfully cryopreserved. Suppressing ROS accumulation during cryopreservation may be a potential strategy to improve survival rate of recalcitrant seeds after cryopreservation.

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arXiv2022

A decade of molecular cell atlases

The recent opinion article "A decade of molecular cell atlases" by Stephen Quake narrates the incredible single-cell genomics technology advances that have taken place over the last decade, and how they have translated to increasingly resolved cell atlases. However the sequence of events described is inaccurate and contains several omissions and errors. The errors are corrected in this note.

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arXiv2022

Embedding of Functional Human Brain Networks on a Sphere

Human brain activity is often measured using the blood-oxygen-level dependent (BOLD) signals obtained through functional magnetic resonance imaging (fMRI). The strength of connectivity between brain regions is then measured as a Pearson correlation matrix. As the number of brain regions increases, the dimension of matrix increases. It becomes extremely cumbersome to even visualize and quantify such weighted complete networks. To remedy the problem, we propose to embed brain networks onto a sphere, which is a Riemannian manifold with constant positive curvature. The Matlab code for the spherical embedding is given in https://github.com/laplcebeltrami/sphericalMDS.

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arXiv2022

Evaluacion de un producto a base de aceite esencial de oregano sobre la integridad intestinal, la capacidad de absorcion de nutrientes y el comportamiento productivo de pollos de carne

Eight experiments were conducted to test an oregano-essential-oil-based product (PRO) on performance, gut health, and nutrient absorption capacity in broilers. The first three, up to 14d and without specific challenges, tested the effects on intestinal histology, skeletal integrity, and growth. Other two experiments, up to 28d birds were challenged to induce feed passage syndrome (STR) and test the effect on the antioxidant status and performance, contrasting later the results under a natural challenge in commercial conditions. Finally, in two other experiments, up to 21 d, birds challenged with coccidia were tested to determine the effects on coccidiosis, nutrient digestibility, and feed efficiency (FCR). Corn-soybean-fish meal diets were used. Under healthy conditions, PRO effects were observed on intestinal villus height and surface area, mucosa density and structure, villus to crypt ratio, goblet cells density, mucus production, body weight gain, and FCR (P<0.04), and carcass yield and bone density (P<0.08). Birds affected by STR showed effects (P<0.05) on superoxide dismutase activity, bodyweight gain, FCRE, non-normal feces frequency, bursal diameter, and dysbacteriosis. Birds affected by coccidia showed effects on cocci-positive ratio, cocci microscopic score, oocysts count, bursal diameter, body weight gain, FCR, apparent digestibility of dry matter and crude protein, protein and energy efficiencies (P<0.01), and nitrogen apparent retention (P<0.07). Results showed PRO added value to the diet favoring feed efficiency and performance.

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