Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make

Matrix representation with parsimony (MRP) can be used to combine trees in the supertree or the consensus settings. However, despite its popularity, it is still unclear whether MRP is really a consensus method or whether it behaves more like the total evidence approach. Previous simulations have shown that it approximates total evidence trees, whereas other studies have depicted similarities with average consensus trees. In this paper, we assess the hypothesis that MRP is equally related to both approaches. We conducted a simulation study to evaluate the accuracy of total evidence with that or various consensus methods, including MRP. Our results show that the total evidence trees are not significantly more accurate than average consensus trees that accounts for branch lengths, but that both perform better than MRP trees in the consensus setting. The accuracy rate of all methods was similarly affected by the number of taxa, the number of partitions, and the heterogeneity of the data

Impact of feedback dimensions on police officers’ performance in crime reduction and security system in the province of Laguna, Philippines: The case of Laguna Provincial Police Office

This quantitative study sought to determine the impact of feedback dimensions on police officers’ performance in crime reduction and security system in Laguna, Philippines.Survey questionnaire served as the primary research instrument.Data were analyzed using descriptive statistics such as frequency counts and percentages, regression using dummy variables, and supplementary details from KII. Findings of this research could provide guidelines for the LPPO in planning the organization's program for crime reduction and enhancement of security system. The consistent practice of feedback exchange among police officers to increase crime solution efficiency in Laguna is recommended

Managing and measuring sustainability performance of supply chains

Sustainable development from an industrial perspective has extended beyond organisational boundaries to incorporate a supply chain approach. This paper provides a framework which can assist focal companies in development of sustainable supply chains. The literature related to sustainable supply chain evaluation is reviewed incorporating concepts from four organisational theories including the resource based, institutional, stakeholder and social network perspectives to illustrate key drivers and enablers of sustainability initiatives in the supply chain. A conceptual multidimensional framework is then developed which can serve as a tool for research scholars and supply chain practitioners in identifying and assessing various economic, environmental and social performance indicators

Opportunistic Infections and Associated Factors among HIV-Infected Adult Persons on Antiretroviral Therapy at Ruhengeri Referral Hospital, Rwanda: A cross-sectional study

Background Human Immunodeficiency Virus (HIV) is among the highest health crises that humanity ever confronted and it causes progressive weakening of the immune system leading to opportunistic infections (OIs) or malignancies during the natural course of the disease. This study aimed at assessing the prevalence and factors associated with the occurrence of OIs among adult PLWHIV on antiretroviral therapy (ART) at Ruhengeri referral hospital. Methodology A cross-sectional study was performed by reviewing records of HIV-positive adult (≥ 15 years) on ART enrolled at Ruhengeri referral hospital from 1st January 2007 to 31st December 2017. Opportunistic infections were reported based on clinical diagnosis and the prevalence of OIs was determined. Results The study reviewed records from 423 PLWHIV. Thirty-nine (9.2%) PLWHIV had been diagnosed with OIs; and frequent OIs were tuberculosis (20%), oral candidiasis, pneumonia and STI (15.6% each). The independent risk factors for developing OIs were being jobless (AOR = 5.03, 95% CI = 2.13, 32.99), spending more than five years on ART (AOR = 4.34, 95% CI = 1.12-16.78) and starting ART at WHO clinical stage III (AOR = 4.88, 95% CI = 1.65-16.78). Conclusion There is a need to strengthen the management of opportunistic infections despite the use of ART at Ruhengeri referral hospital. Rwanda J Med Health Sci 2022;5(3):323-33

War and peace in phylogenetics: a rejoinder on total evidence and consensus

Abstract.-For more than 10 years, systematists have been debating the superiority of character or taxonomic congruence in phylogenetic analysis. In this paper, we demonstrate that the competing approaches can converge to the same solution when a consensus method that accounts for branch lengths is selected. Thus, we propose to use both methods in combination, as a way to corroborate the results of combined and separate analyses. We could engage in this debate by opting for character congruence, taxonomic congruence, or the conditional combination approach. Rather, we prefer to suggest using combined and separate analyses jointly, as proposed by de Queiroz (1993; see also Larson, 1994). Interestingly, a distance-based procedure relying on the average consensus has been applied successfully by Lapointe et al. (1999) to combine either trees or data matrices in a coherent fashion. This hybrid procedure is defined as a global congruence approach (see Lapointe, 1998b) because it assesses neither the congruence among characters nor that among individual phylogenies; rather, it evaluates the congruence between total evidence and consensus trees. This approach can thus be used to cross-corroborate the trees obtained by combined and separate analyses. In the present paper, we apply the socalled global congruence approach to a wide variety of published datasets sampled from the systematic literature, using a uniform 88

Genome-wide analysis of intraspecific transposon diversity in yeast

BACKGROUND: In the model organism Saccharomyces cerevisiae, the transposable elements (TEs) consist of LTR (Long Terminal Repeat) retrotransposons called Ty elements belonging to five families, Ty1 to Ty5. They take the form of either full-length coding elements or non-coding solo-LTRs corresponding to remnants of former transposition events. Although the biological features of Ty elements have been studied in detail in S. cerevisiae and the Ty content of the reference strain (S288c) was accurately annotated, the Ty-related intra-specific diversity has not been closely investigated so far. RESULTS: In this study, we investigated the Ty contents of 41 available genomes of isolated S. cerevisiae strains of diverse geographical and ecological origins. The strains were compared in terms of the number of Ty copies, the content of the potential transpositionally active elements and the genomic insertion maps. The strain repertoires were also investigated in the closely related Ty1 and Ty2 families and subfamilies. CONCLUSIONS: This is the first genome-wide analysis of the diversity associated to the Ty elements, carried out for a large set of S. cerevisiae strains. The results of the present analyses suggest that the current Ty-related polymorphism has resulted from multiple causes such as differences between strains, between Ty families and over time, in the recent transpositional activity of Ty elements. Some new Ty1 variants were also identified, and we have established that Ty1 variants have different patterns of distribution among strains, which further contributes to the strain diversity

Influence of genetic background on the occurrence of chromosomal rearrangements in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Chromosomal rearrangements such as duplications and deletions are key factors in evolutionary processes because they promote genomic plasticity. Although the genetic variations in the <it>Saccharomyces cerevisiae </it>species have been well documented, there is little known to date about the impact of the genetic background on the appearance of rearrangements.</p> <p>Results</p> <p>Using the same genetic screening, the type of rearrangements and the mutation rates observed in the S288c <it>S. cerevisiae </it>strain were compared to previous findings obtained in the FL100 background. Transposon-associated rearrangements, a major chromosomal rearrangement event selected in FL100, were not detected in S288c. The mechanisms involved in the occurrence of deletions and duplications in the S288c strain were also tackled, using strains deleted for genes implicated in homologous recombination (HR) or non-homologous end joining (NHEJ). Our results indicate that an Yku80p-independent NHEJ pathway is involved in the occurrence of these rearrangements in the S288c background.</p> <p>Conclusion</p> <p>The comparison of two different <it>S</it>. <it>cerevisiae </it>strains, FL100 and S288c, allowed us to conclude that intra-species genomic variations have an important impact on the occurrence of chromosomal rearrangement and that this variability can partly be explained by differences in Ty1 retrotransposon activity.</p

Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals

Phenol-Explorer, launched in 2009, is the only comprehensive web-based database on the content in foods of polyphenols, a major class of food bioactives that receive considerable attention due to their role in the prevention of diseases. Polyphenols are rarely absorbed and excreted in their ingested forms, but extensively metabolized in the body, and until now, no database has allowed the recall of identities and concentrations of polyphenol metabolites in biofluids after the consumption of polyphenol-rich sources. Knowledge of these metabolites is essential in the planning of experiments whose aim is to elucidate the effects of polyphenols on health. Release 2.0 is the first major update of the database, allowing the rapid retrieval of data on the biotransformations and pharmacokinetics of dietary polyphenols. Data on 375 polyphenol metabolites identified in urine and plasma were collected from 236 peer-reviewed publications on polyphenol metabolism in humans and experimental animals and added to the database by means of an extended relational design. Pharmacokinetic parameters have been collected and can be retrieved in both tabular and graphical form. The web interface has been enhanced and now allows the filtering of information according to various criteria. Phenol-Explorer 2.0, which will be periodically updated, should prove to be an even more useful and capable resource for polyphenol scientists because bioactivities and health effects of polyphenols are dependent on the nature and concentrations of metabolites reaching the target tissues. The Phenol-Explorer database is publicly available and can be found online at http://www.phenol-explorer.eu. Database URL: http://www.phenol-explorer.eu

Performances de reproduction du poisson chat endogène du Cameroun Clarias jaensis (Boulenger, 1909) en milieu contrôlé

Les performances de reproduction de Clarias jaensis ont été évaluées entre mai et octobre 2014 à Batié (Ouest-Cameroun). A cet effet, 30 femelles de poids moyen 199, 52 ± 34,85 g ont été réparties en 5 lots comparables. Chaque lot choisi au hasard a été soumis à l’Hormone Chorionique Gonadotrophine (HCG) aux doses de 3500, 4000 et 4500 Unités Internationales (UI) / kg et aux extraits hypophysaires des mâles et des femelles. Le poids et le diamètre des ovocytes, les taux de fécondation et d’éclosion ont été évalués. Les principaux résultats ont montré que: le poids des ovocytes a été le plus élevé (p &lt; 0, 05) avec l’extrait hypophysaire femelle (39,33±17,08g) ; le diamètre des ovocytes a été comparable entre les traitements. Le taux de fécondation a été le plus élevé pour la dose de 4000 UI / kg de HCG (87, 50 ± 12,45%) suivi de l’extrait hypophysaire femelle (85,08 ± 14,29%). Cependant aucune différence significative (p ˃ 0,05) n’a été obtenue. Le taux d’éclosion a été plus élevé avec l’extrait hypophysaire femelle (19, 38 ± 6,58%). La reproduction artificielle chez Clarias jaensis est possible avec l’hormone HCG à 4000 UI / kg ou des extraits hypophysaires femelles.© 2016 International Formulae Group. All rights reserved.Mots clés: Clarias jaensis, espèce endogène, performances de reproduction, captivité, CamerounEnglish Title:  Reproductive performances of indigenous catfish of Cameroon Clarias jaensis (Boulenger, 1909) in captivityEnglish AbstractIn order to improve local biodiversity and number of fishes in aquaculture in Cameroon, reproductive performances in captivity of Clarias jaensis have been studied between Mai and October 2014 in Batié (West Cameroon). In fact, 30 females with 199, 52 ± 34, 85 g were divided randomly into five comparable treatments. Each was submitted to a Human Chorionic Gonatropin Hormon at 3500, 4000 and 4500 Internationals Units (UI) / kg of body weight, males and female’s pituitary extracts. The main results obtained were: The oocyte weight was significantly higher (p &lt; 0, 05) with females’ pituitary extracts (39, 33 ± 17,08g), the oocyte diameter mean was comparable within the treatments. The higher fecundity rate was obtained with the Human Chorionic Gonadotropin Hormon at 4000 UI / kg of body weight (85, 08 ± 14, 29%). However, no significant differences (p ˃ 0, 05) were found. The hatching rate was significantly higher (p &lt; 0, 05) with the pituitary extracts of females (19, 38 ± 6, 58%). Clarias jaensis can be reproduced artificially using Human Chorionic Gonadotropin Hormon at 4000 UI / kg of body weight or female’s pituitary extracts.© 2016 International Formulae Group. All rights reserved.Keywords: Clarias jaensis, reproductive performances, indigenous species, captivity, Cameroo

Systematic analysis of the polyphenol metabolome using the Phenol-Explorer database

SCOPE: The Phenol-Explorer web database details 383 polyphenol metabolites identified in human and animal biofluids from 221 publications. Here we exploit these data to characterize and visualize the polyphenol metabolome, the set of all metabolites derived from phenolic food components. METHODS AND RESULTS: Qualitative and quantitative data on 383 polyphenol metabolites as described in 424 human and animal intervention studies were systematically analyzed. Of these metabolites, 301 were identified without prior enzymatic hydrolysis of biofluids, and included glucuronide and sulfate esters, glycosides, aglycones, and O-methyl ethers. Around one third of these compounds are also known as food constituents and corresponded to polyphenols absorbed without further metabolism. Many ring-cleavage metabolites formed by gut microbiota were noted, mostly derived from hydroxycinnamates, flavanols and flavonols. Median maximum plasma concentrations (Cmax ) of all human metabolites were 0.09 μM and 0.32 μM when consumed from foods or dietary supplements respectively. Median time to reach maximum plasma concentration in humans (Tmax ) was 2.18 h. CONCLUSION: These data show the complexity of the polyphenol metabolome and the need to take into account biotransformations to understand in vivo bioactivities and the role of dietary polyphenols in health and disease. This article is protected by copyright. All rights reserved