The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard

The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics

Undergraduate Education Students’ Perceptions of Effective and Ineffective Course Experiences: What Counts as an Effective Experience?

Pre-service teachers’ conceptions of effective and ineffective instruction stand to inform their personal views of what constitutes effective and ineffective instruction, yet few qualitative studies have examined both conceptions of effective and ineffective instruction. The purpose of this study was to determine whether pre-service teachers described what happens in university courses primarily in terms of teacher characteristics, teaching practices, or instructional context. There were two research questions guiding the study. First, how are the dimensions of effective and ineffective instruction alike and different? Second, how do results correspond to similar qualitative studies? Nine distinct themes were inductively derived through open coding of 34 pre-service teachers’ essays: (a) motivation, (b) student autonomy, (c) meaningful learning, (d) comfortable learning environment, (e) classroom management, (f) student-teacher relationship, (g) teacher’s personal characteristics and manner, (h) lesson organization, and (i) teacher impact/student development. The results of this study support previous findings and add to the small number of studies that have examined pre-service teachers' descriptions of effective and ineffective instruction. Findings have also contributed a new category that has not appeared in previous literature: teacher impact/student development. Pre-service teachers’ descriptions in this study confirm that the theoretical conception of what happens in classrooms must include the teacher’s characteristics, teaching, and the context of instruction. Keywords: education theory and practice, educational psychology, higher education, teacher education, pre-service teacher beliefs, pre-service teacher conceptions, effective instruction, effective teaching. Les conceptions qu’ont les enseignants en formation de l’enseignement efficace et inefficace informent naturellement leurs points de vue personnels de ce qui constitue l’enseignement efficace et inefficace; pourtant, peu d’études qualitatives se sont penchées sur les conceptions de l’enseignement efficace ainsi que sur celles de l’enseignement inefficace. L’objectif de cette étude était de déterminer dans quelle mesure les enseignants en formation décrivent ce qui se passe dans les cours à l’université, notamment en fonction des caractéristiques des enseignants, des pratiques d’enseignement ou du contexte pédagogique. Deux questions ont guidé la recherche. D’abord, qu’est-ce que l’enseignement efficace et l’enseignement inefficace ont en commun et qu’est-ce qui les distingue? Deuxièmement, comment les résultats correspondent-ils à ceux d’études qualitatives similaires? Un codage ouvert de 34 dissertations écrites par des enseignants en formation a permis de recueillir, par induction, neuf thèmes distincts: (a) motivation, (b) autonomie des étudiants, (c) apprentissage significatif, (d) milieu d’apprentissage confortable, (e) gestion de la classe, (f) rapport étudiant-enseignant, (g) caractéristiques et manières personnelles de l’enseignant, (h) organisation des leçons, et (i) impact de l’enseignant/progression des étudiants. Les résultats de cette étude appuient ceux des études antérieures. Cette étude élargit le nombre restreint d’études qui ont porté sur les descriptions par des enseignants en formation de l’enseignement efficace et l’enseignement inefficace. Les résultats contribuent également à une nouvelle catégorie qui n’apparait pas dans les travaux antérieurs : impact de l’enseignant/progression des étudiants. Les descriptions par les enseignants en formation qui ont participé à cette étude confirment la conception théorique selon laquelle ce qui arrive dans la salle de classe doit tenir compte des caractéristiques personnelles de l’enseignant, de l’enseignement et du contexte pédagogique. Mots clés : théorie et pratique en éducation, psychologie de l’éducation; études supérieures, formation des enseignants; croyances des enseignants en formation, conceptions des enseignants en formation, enseignement efficac

Electroconvulsive Therapy Increases Plasma Levels of Interleukin-6 a

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74956/1/j.1749-6632.1990.tb40529.x.pd

The effects of pentoxifylline on lipopolysaccharide (LPS) fever, plasma interleukin 6 (IL 6), and tumor necrosis factor (TNF) in the rat

The purpose of these studies was to test whether pentoxifylline, a drug that can inhibit the production and action of cytokines hypothesized to be endogenous pyrogens (for example, interleukin 1 and tumor necrosis factor [TNF]), is antipyretic. We also tested the effects of pentoxifylline on plasma activities of interleukin 6 (IL 6) and TNF in response to an injection of a fever-inducing dose of lipopolysaccharide (LPS). Our results showed that a high dose of pentoxifylline (200 mg/kg) caused hypothermia in control rats and blocked LPS fever, while a low dose (50 mg/kg) did not have these effects. Injection of the high dose of pentoxifylline in control rats caused a rise in plasma IL 6 but not in plasma TNF. However, the peak levels of plasma IL 6 and TNF activities following an injection of LPS were significantly reduced by pretreatment with pentoxifylline. Overall, the data are consistent with the hypothesis that pentoxifylline is an antipyretic drug, which may act at least in part by inhibiting the secretion of pyrogenic cytokines.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/28504/1/0000301.pd

A generalized framework to predict continuous scores from medical ordinal labels

Many variables of interest in clinical medicine, like disease severity, are recorded using discrete ordinal categories such as normal/mild/moderate/severe. These labels are used to train and evaluate disease severity prediction models. However, ordinal categories represent a simplification of an underlying continuous severity spectrum. Using continuous scores instead of ordinal categories is more sensitive to detecting small changes in disease severity over time. Here, we present a generalized framework that accurately predicts continuously valued variables using only discrete ordinal labels during model development. We found that for three clinical prediction tasks, models that take the ordinal relationship of the training labels into account outperformed conventional multi-class classification models. Particularly the continuous scores generated by ordinal classification and regression models showed a significantly higher correlation with expert rankings of disease severity and lower mean squared errors compared to the multi-class classification models. Furthermore, the use of MC dropout significantly improved the ability of all evaluated deep learning approaches to predict continuously valued scores that truthfully reflect the underlying continuous target variable. We showed that accurate continuously valued predictions can be generated even if the model development only involves discrete ordinal labels. The novel framework has been validated on three different clinical prediction tasks and has proven to bridge the gap between discrete ordinal labels and the underlying continuously valued variables

Biodiversity of protists and nematodes in the wild nonhuman primate gut

Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.Fil: Mann, Allison E.. University of British Columbia; CanadáFil: Mazel, Florent. University of British Columbia; CanadáFil: Lemay, Matthew A.. University of British Columbia; CanadáFil: Morien, Evan. University of British Columbia; CanadáFil: Billy, Vincent. University of British Columbia; CanadáFil: Kowalewski, Miguel Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia". Estación Biológica de Usos Múltiples (Sede Corrientes); ArgentinaFil: Di Fiore, Anthony. University of Texas at Austin; Estados UnidosFil: Link, Andrés. Universidad de los Andes; ColombiaFil: Goldberg, Tony L.. University of Wisconsin; Estados UnidosFil: Tecot, Stacey. University of Arizona; Estados UnidosFil: Baden, Andrea L.. City University Of New York. Hunter College; Estados UnidosFil: Gomez, Andres. University of Minnesota; Estados UnidosFil: Sauther, Michelle L.. State University of Colorado at Boulder; Estados UnidosFil: Cuozzo, Frank P.. Lajuma Research Centre; SudáfricaFil: Rice, Gillian A. O.. Dartmouth College; Estados UnidosFil: Dominy, Nathaniel J.. Dartmouth College; Estados UnidosFil: Stumpf, Rebecca. University of Illinois at Urbana; Estados UnidosFil: Lewis, Rebecca J.. University of Texas at Austin; Estados UnidosFil: Swedell, Larissa. University of Cape Town; Sudáfrica. City University of New York; Estados UnidosFil: Amato, Katherine. Northwestern University; Estados UnidosFil: Wegener Parfrey, Laura. University of British Columbia; Canad

Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

An (Awassi × Merino) × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P < 0.01) and additional 25 suggestive (P < 0.05) QTL were detected across both single QTL methods and all traits. In preparation of a meta-analysis, all QTL results were compared with a meta-assembly of QTL for milk production traits in dairy ewes from various public domain sources and can be found on the ReproGen ovine gbrowser http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep

Wild-type and mutant SOD1 share an aberrant conformation and a common pathogenic pathway in ALS.

Many mutations confer one or more toxic function(s) on copper/zinc superoxide dismutase 1 (SOD1) that impair motor neuron viability and cause familial amyotrophic lateral sclerosis (FALS). Using a conformation-specific antibody that detects misfolded SOD1 (C4F6), we found that oxidized wild-type SOD1 and mutant SOD1 share a conformational epitope that is not present in normal wild-type SOD1. In a subset of human sporadic ALS (SALS) cases, motor neurons in the lumbosacral spinal cord were markedly C4F6 immunoreactive, indicating that an aberrant wild-type SOD1 species was present. Recombinant, oxidized wild-type SOD1 and wild-type SOD1 immunopurified from SALS tissues inhibited kinesin-based fast axonal transport in a manner similar to that of FALS-linked mutant SOD1. Our findings suggest that wild-type SOD1 can be pathogenic in SALS and identify an SOD1-dependent pathogenic mechanism common to FALS and SALS