1,705 research outputs found
Data and Statistical Methods To Analyze the Human Microbiome
No full textThe Waldron lab for computational biostatistics bridges the areas of cancer genomics and microbiome studies for public health, developing methods to exploit publicly available data resources and to integrate -omics studies.</jats:p
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
No full textBackgroundThe correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.ResultsWe compare methods developed for single-cell and bulk RNA-seq, and specifically for microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, concordance, power, and correct identification of differentially abundant genera. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing.ConclusionsThe multivariate and compositional methods developed specifically for microbiome analysis did not outperform univariate methods developed for differential expression analysis of RNA-seq data. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner
Primo Levi: the educational resources of a polyhedric writing. Didactic proposals for primary schools
No full textreservedPrimo Levi è principalmente conosciuto per essere sopravvissuto ad Auschwitz e per aver scritto delle opere di testimonianza su questa terribile esperienza. In realtà, egli è un autore fortemente poliedrico, la cui produzione abbraccia ambiti, temi e generi molto diversi e non solo legati alla Shoah. Questa grande varietà costituisce una risorsa importante per gli insegnanti, in quanto all’interno dell’opera leviana è possibile individuare tanti testi potenzialmente utilizzabili con gli alunni, anche della scuola primaria. Sulla base di tale considerazione, è stata progettata e condotta la ricerca in questa sede riportata, avente lo scopo di trarre evidenze che potessero confermare o smentire l’ipotesi secondo cui Primo Levi può essere proposto, con i dovuti accorgimenti pedagogico-didattici, anche a bambini frequentanti la scuola primaria. Tale ricerca è stata articolata in due fasi principali. La prima si è basata sulla somministrazione di un questionario rivolto a persone attive in ambito educativo e/o letterario, volto a rilevare le loro opinioni rispetto alla domanda di ricerca: dalle risposte dei partecipanti è emerso che la maggioranza di essi conosceva Levi a un livello piuttosto superficiale e lo riteneva un autore adeguato ad alunni dalla scuola secondaria in poi. La seconda fase ha previsto invece una sperimentazione presso la scuola primaria “Manzoni” di Limena (PD), nella quale due testi scritti da Levi sono stati proposti agli alunni di una classe quarta: i dati raccolti attraverso conversazioni, osservazioni, questionari e analisi dei prodotti realizzati dai bambini hanno nel complesso confermato l’ipotesi di ricerca formulata.Primo Levi is primarily known for surviving Auschwitz and for writing testimonial works about this terrible experience. Actually, he is a highly versatile author, whose work encompasses various fields, themes, and genres not only related to the Shoah. This great variety is an important resource for teachers, as within Levi’s body of work, many texts can be found that are potentially suitable for students, even in primary school. Based on this consideration, the research presented here was designed and conducted with the aim of gathering evidence to confirm or refute the hypothesis that Primo Levi can be introduced, with appropriate pedagogical and didactic adjustments, to children attending primary school. This research was divided into two main phases. The first was based on a questionnaire administered to individuals active in the educational and/or literary fields, aimed at investigating their opinions on the research question: the participants’ responses showed that the majority had only a rather superficial knowledge of Levi and considered him suitable for students from secondary school onwards. The second phase involved an experiment conducted at the “Manzoni” primary school in Limena (PD), in which two texts written by Levi were presented to a fourth-grade class: the data collected through conversations, observations, questionnaires, and analysis of the children's works overall confirmed the research hypothesis
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.
No full textShotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the "healthy" microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml
Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites.
No full textTranscript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5' untranslated regions was strongly associated with improvement in predictive accuracy. On the basis of these observations, we propose that the recently discovered widespread uTISs in the human genome can be a previously unappreciated substrate of translational control mediated by RBPs
Weekly Guides for Daily Prayer with the Readings from the Roman Catholic Lectionary.
No full textThe LORD, a merciful and gracious God, slow to anger and rich in kindness and fidelity, continuing his kindness for a thousand generations, and forgiving wickedness and crime and sin... Exodus 33Seventeenth Week of Ordinary Time|The Seventeenth Sunday in Ordinary Time begins five weeks of Sunday reflections on Chapter 6 of John's Gospel on Jesus as the Bread of Life. This Sunday is the miracle of the five barley loaves and two fishes.|Wednesday is the Memorial of Saint Martha with its own special readings. Friday is a celebration at Creighton University and other Jesuit ministries around the world as we remember the Memorial of Saint Ignatius of Loyola, founder of the Society of Jesus. Saturday is the Memorial of Saint Alphonsus Liguori, bishop and doctor of the Church.|This is the third and final week from the Book of Exodus. Moses carries down the Ten Commandments from God but breaks them in a fury when he sees the people worshipping a golden calf. He meets face to face with God in a tent in the desert and invites God to come with them on their journey. Moses' face is so radiant after meeting with God, it is covered with a veil. Moses builds a movable meeting tent for their journey, and puts the arc of the commandments in it, and in a cloud by day and with fire by night, God was with them. On Friday and Saturday we have two days of readings from the Book of Leviticus which is the third book of the set of five books that begin the scriptures, called the Pentateuch. It is a book of liturgical practices governing the ministry of the priestly descendants of Levi. Here we read about the great Jewish festivals and Jubilee years.|The gospels are from Matthew"s Gospel, with wonderful stories worth pondering and reflecting on. We hear of the tiny mustard seed which grows into a towering bush, the explanation of the parable of the weeds in the field. Then we again hear how the Kingdom is like a treasure or a pearl a merchant makes great sacrifices to obtain. With the story of the fishing net tossed into the sea, we consider how everyone is gathered by God at the end of time to be judged. Jesus comes to his hometown to teach but took offense at him. "A prophet is not without honor except in his native place and in his own house." We end the week with the sad story of Herod, not wanting to be embarrassed in front of his guests, ordering John the Baptist beheaded.|On the 18th Sunday in Ordinary Time, we are in the second of three Sunday gospels from the 6th chapter of John's gospel and the Bread of Life readings. Jesus tells the crowd, "Do not work for food that perishes but for the food that endures for eternal life, which the Son of Man will give you."Daily Prayer This Week|This whole week could be a time for each of us to grow in a sense of what we most deeply desire. If we let Sunday's gospel open our hearts we might find ourselves asking, begging God for what we need.|And we can let the daily gospels renew our hope. Have we become cynical and jaded a bit? The world does seem to be like a field someone sowed weeds into. The growth of God's reign in this world doesn't seem to be growing, and the seeds seem so small. This is a good week to get in touch with what is discouraged in our hearts and to let the courage the Lord is offering us renew us. He promises that even small seeds work and that even a little yeast allows dough to grow. The process is sometimes imperceptible, but that's why Jesus reminds us to place our trust in him. Our own hearts might be full of weeds, but the Lord doesn't want us ripping ourselves apart. He is full of mercy and healing reconciliation. Jesus does not want us to be scandalized by the evil we see in the world. God is patient. And, God alone will judge.|So every day this week, we can begin our day, establishing a focus. This might be while standing next to our bed for a brief minute, or while pouring ourselves a cup of coffee, or while in the shower or getting dressed. This is the time that can transform any busy day into a more focused time of connection with our Lord. Using all sorts of background times throughout the day will take no "extra" time for prayer, but will make it possible to let these powerful scriptures interact with the daily events and relationships with which we are involved.|One morning we might begin our day, simply by saying, "Lord, thank you for this day. Help me to pay attention to what and who I'm treasuring today." Or, "Lord, be with me this day and help me check my need to judge others. Help me place my trust in you today." While in the shower or driving to work I might talk with the Lord about the day ahead, asking for particular help, focus, or a new way of valuing during that difficult 10 a.m. meeting or with the clients or students or patients I will see. While doing the wash or shopping or preparing meals or while taking time with my family or friends in the evening, I can let myself have these 30 second friend-to-friend conversations with the Lord. The readings provide a compass for our daily journey, but it is the continual practice at connecting with our Lord that carries us through the day. Looking back and saying "thank you" every night, if even for 30 seconds, will gradually transform us and give us more courage and hope
Geodesic structure of generalized Levi-Civita solutions
No full textTitle: Geodesic structure of generalized Levi-Civita solutions Author: Adam Tyc Institute: Institute of Theoretical Physics Supervisor: doc. RNDr. Martin Žofka, Ph.D., Institute of Theoretical Physics Abstract: We study the geodesic structure of the generalized Levi-Civita spacetime, a cylindrically symmetric solution to the Einstein field equations. By analyzing the geodesic motion, we investigate how the parameters of the metric influence the dynamics and physical interpretation of the spacetime
Geodesic structure of generalized Levi-Civita solutions
No full textTitle: Geodesic structure of generalized Levi-Civita solutions Author: Adam Tyc Institute: Institute of Theoretical Physics Supervisor: doc. RNDr. Martin Žofka, Ph.D., Institute of Theoretical Physics Abstract: We study the geodesic structure of the generalized Levi-Civita spacetime, a cylindrically symmetric solution to the Einstein field equations. By analyzing the geodesic motion, we investigate how the parameters of the metric influence the dynamics and physical interpretation of the spacetime.Název práce: Geodetická struktura zobecněných Levi-Civitových řešení Autor: Adam Tyc Ústav: Ústav teoretické fyziky Vedoucí bakalářské práce: doc. RNDr. Martin Žofka, Ph.D., Ústav teoretické fyziky Abstrakt: Zabýváme se geodetickou strukturou zobecněného Levi-Civitova prostoročasu, cylindricky symetrického řešení Einsteinovo rovnic. Zkoumáním geodetického pohybu zjišťujeme, jak parametry této metriky ovlivňují dynamiku a fyzikální interpretaci tohoto prostoročasu.Ústav teoretické fyzikyInstitute of Theoretical PhysicsFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult
Interpreting Primo Levi: Interdisciplinary Perspectives
No full textThis collection contains new and innovative research into the work of the Italian antifascist partisan, concentration camp survivor, author and thinker Primo Levi (1919-1987). It features original essays by many of the world's foremost Levi scholars and by specialists in fields as varied as education, theology, and fine art. Levi's legacy continues to drive a vibrant, continually evolving body of interdisciplinary scholarship, as the contributions to this intellectually rich, tightly organized volume confirm. The essays gathered here demonstrate a remarkable breadth across five distinct yet interrelated areas: ethics, communication, and education; humanity, animality, and science; the camps: memory and space; literature and intertext; and media, publishing, and illustration
Remarks on the Levi conditions for differential systems
No full textIn this paper we prove two results on the Levi conditions for weakly hyperbolic systems with characteristics of constant multiplicities.
A first result concerns scalar operators: we prove that Levi conditions defined by the second author in (C. R. Acad. Sc. Paris 1991) are equivalent to the usual Levi conditions for scalar operator.
A second result concerns systems whose principal symbol has a Jordan form made of a large number of 2x2 blocks. For these systems we express the first Levi condition via an invariant constructed from the sub-characteristic matrix. Moreover we show that this condition is necessary for the C-infinity well-posedness
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