Miracle-dz/UniFAR-FTUs huggingface dataset:
Neoamphitrite undevigintipes, a new terebellid species from South Korea (Annelida, Terebellida, Terebellidae)

Abstract A detailed description and illustrations of a new terebellid species are provided, and molecular information based on partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene are included. The new species, Neoamphitrite undevigintipessp. nov., is described from the deep sea off the eastern coast of South Korea. It is similar to Neoamphitrite groenlandica (Malmgren, 1866) in that the thorax has 19 notopodial chaetigers. However, Neoamphitrite undevigintipessp. nov. is clearly distinguishable from N. groenlandica in having the uncini of the first abdominal chaetiger arranged in a single row and in having 12 ventral shields. A taxonomic key to all known Neoamphitrite species is also included.
Modelling Oxygen Transfer and Aerobic Growth in Shake Flasks and Well‐Mixed Bioreactors

Oxygen transfer is an important aspect of aerobic metabolism. In this work, microbial growth on glucose (fast metabolism) and phenol (slow metabolism) have been studied using Pseudomonas putida in shake flasks and a mixed bioreactor considering both substrate and oxygen depletion. Under typical operating conditions, the highest mass transfer coefficient (KLa) for the aerated well-mixed bioreactor was found to be 50.8 h−1, while the maximum non-aerated shake flask KLa was 21.1 h−1. The presence of media and/or dead cells did not have significant effect on measured values of KLa. A new equation for prediction of KLa in shake flasks with an absolute average deviation of 11.1% is introduced, and a combined model for oxygen mass transfer and microbial growth is shown to fit experimental data during growth on glucose and phenol in both shake flasks and the mixed bioreactor with an absolute average deviation of 19.3%. Le transfert d'oxygene est un aspect important du metabolisme aerobique. Dans ce travail, on a etudie la croissance microbienne du glucose (metabolisme rapide) et du phenol ( metabolisme lent) a l'aide de Pseudomonas putida dans des flasques vibrantes et un bioreacteur mixte considerant la depletion a la fois du substrat et de l'oxygene. Dans des conditions operatoires typiques, on a trouve que le coefficient de transfert de matiere (KLa) le plus eleve pour le bioreacteur bien melange aere etait de 50.8 h−1, tandis que le KLa maximum de la flasque vibrante non aeree etait de 21,1 h−1. La presence de cellules du milieu et/ou de cellules mortes n'a pas eu d'effet significatif sur les valeurs mesurees de KLa. Une nouvelle equation pour la prediction de KLa dans les flasques vibrantes avec un ecart type moyen absolu de 11,1% est introduite, et on montre qu'un modele combine pour le transfert de matiere et la croissance microbienne de l'oxygene cale les donnees experimentales pendant la croissance sur le glucose et le phenol a la fois dans les flasques vibrantes et le bioreacteur melange avec un ecart type moyen absolu de 19,3%.
General results concerning the trade-off between gaining energy and avoiding predation

When animals can choose from a range of feeding options, often those options with a higher energetic gain carry a higher risk of predation. This paper analyses the optimal trade-off between food and predation. We are primarily interested in how an animal’s decisions and its state change over time. Our models are very general. They can be applied to growth decisions, such as choice of habitat, in which case we might consider how the state variable size changes over an animal’s lifetime. Equally our models are applicable to short-term foraging decisions, such as vigilance level, in which case we might consider how energy reserves vary over a day. We concentrate on two cases: (i) the animal must reach a fixed state, its fitness depending on when this is attained; (ii) the animal must survive to a fixed time, its fitness depending on its final state. In case (i) minimization of m ortality per unit increase of state is optimal under certain baseline conditions. In case (ii) behaviour is constant over time under baseline conditions (the 9Risk-spreading Theorem’). We analyse how these patterns are modified by complicating factors, e.g. time penalties, premature termination of the food supply, stochasticity in food supply or in metabolic expenditure, and state-dependence in the ability to obtain food, in metabolic expenditure and in predation risk. From this analysis we obtain a variety of possible explanations for why an animal should reduce its intake rate over time (i.e. show satiation). We show how earlier work can be viewed as special cases of our results.
“It’s Not that it Will Kill Me”: Living with Electromagnetic Hypersensitivity

While the future visions of Internet of Things are slowly being implemented, the wireless and networked infrastructures that enable these connections already intervene and matter in people’s everyday lives in powerful ways. In this paper, we present a case study of a woman living with electromagnetic hypersensitivity; the heightened sensitivity of electromagnetic fields. We describe how her daily activities and everyday habits are both enabled and constrained by digital technologies. Through this narrative, we reflect on how this case has impact for design research regarding how the objects we design matter in people’s everyday life in unpredictable and uncomfortable ways - also those that are not wirelessly connected.
Effects of cold stress on mRNA level of uncoupling protein 2 in liver of chicks.

Received: Revised: Accepted: February 18, 2013 December 10, 2013 December 25, 2013 The uncoupling protein 2 (UCP2) gene belong to the superfamily of electron transport carriers of the mitochondrial inner membrane which is involved in thermogenesis and determining the functional evolution of UCP2 gene is important to understand the evolution of thermo-regulation in chickens. The aim of this study was to investigate the effects of cold stress on the mRNA level of UCP2 in liver of chickens. In this study, 120 15-d-old male chickens were randomly allocated into 12 groups (10 each group) for exposure to acute (up to 24 h) and chronic (up to 20 days) cold stress (12±1°C). This study detected UCP2 mRNA levels in liver, glucagons (GLU) content in plasma, insulin (INS), blood glucose (BG) and free fatty acid (FFA) content in serum. The results showed that during acute cold stress, UCP2 mRNA levels gradually increased the INS and FFA content showed fluctuant change, GLU content gradually increased, and BG content first increased and then decreased. During chronic cold stress, UCP2 mRNA levels significantly increased compared with the control group, and the content of INS, GLU, BG and FFA were all gradually increased with the time lapsing. The results indicated that both acute and chronic cold stress could enhance the energy metabolism and the UCP2 mRNA levels in liver of chicks. ©2013 PVJ. All rights reserved
ANALYSIS OF IRREGULARLY SPACED TIME SERIES A DISSERTATION SUBMITTED TO THE DEPARTMENT OF STATISTICS OF THE UNIVERSIDAD CATÓLICA DE CHILE IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN STATISTICS

In this thesis, we propose novel stationary time series models that can be used when the observations are taken on irregularly spaced times. First, we present a model with a firstorder moving average structure, and then we generalized it to consider an autoregressive component. We called the first model irregularly spaced first-order moving average and the second one irregularly spaced first-order autoregressive moving average. Their definitions and properties are established. We present their state-space representations and their one-step linear predictors. The behavior of the maximum likelihood estimator is studied through Monte Carlo experiments. Illustrations are presented with real and simulated data.
Parasitismo de Trichogramma pretiosum em ovos da traça-das-crucíferas sob diferentes temperaturas

The parasitism capacity of Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) on eggs of Plutella xylostella (L.) (Lepidoptera: Plutellidae) was studied, under temperatures of 18; 20; 22; 25; 28; 30 and 32°C aiming to evaluate the number of days with parasitism, cumulated parasitism, total number of eggs parasitized per female and their longevity. Parasitism during the first 24 hours ranged from 1.6 to 16 eggs of P. xylostella per T. pretiosum female in the range of 18 to 32°C. Cumulated egg parasitism of P. xylostella by T. pretiosum reached 80% after 2; 16; 11; 3; 5; 4 and 7 days at 18; 20; 22; 25; 28; 30 and 32°C. Higher parasitism rates were recorded at 25; 28 and 30°C while longevity of T. pretiosum females varied from 2.3 to 13.3 days under temperatures of 18 to 32°C.
Immune response and protective potential following vaccination against Newcastle disease virus and fowl cholera in Naked neck chickens

Humoral immune responses to Newcastle Disease Virus (NDV) and Bangladesh Agricultural University (BAU) Fowl cholera (BAUFC) vaccines were evaluated in naked neck chickens (NNC). Ten birds were vaccinated with Baby Chick Ranikhet Disease Virus (BCRDV) at Day 7 through intra-ocular route and with Ranikhet Disease Virus (RDV) at day 35 of age through intramuscular route. Serum antibodies were measured by Haemagglutination Inhibition test. Two weeks after final immunization all birds were challenged with virulent field isolate of NDV where all vaccinated birds survived without illness during ten days, and all ten control birds died. Ten birds were vaccinated with BAUFC vaccine at Day 42 and 70 according to the Manufacturers instruction, which induced detectable levels of antibody titre as determined by Passive Haemagglutination Assay (PHA) test. Eight vaccinated birds survived following challenge with virulent fowl cholera isolate two weeks after final vaccination and all ten control birds died. DOI: http://dx.doi. org/10.3329/bvet.v29i2. 14342 Bangl. vet . 2012. Vol. 29, No. 2, 49-55
Nine Genes Mediate the Therapeutic Effects of Iodine-131 Radiotherapy in Thyroid Carcinoma Patients

Background Thyroid carcinoma (THCA) is one of the most common malignancies of the endocrine system, which is usually treated by surgery combined with iodine-131 (I131) radiotherapy. Aims This study is aimed at exploring the potential targets of I131 radiotherapy in THCA. Methods The RNA-sequencing data of THCA in The Cancer Genome Atlas database (including 568 THCA samples) was downloaded. The differentially expressed genes (DEGs) between the tumour samples whether or not subjected to I131 radiotherapy were identified using edgeR package. Using the WGCNA package, the module that was relevant with I131 radiotherapy was selected. The intersection genes of the hub module nodes and the DEGs were obtained as hub genes, followed by the function and pathway enrichment analyses using the clusterProfiler package. Moreover, the protein-protein interaction (PPI) network for the hub genes was constructed using Cytoscape software. In addition, more important hub genes were analysed with function mining using the GenCLiP2 online tool. The qPCR analysis was used to verify the mRNA expression of more important hub genes in THCA tissues. Results There were 500 DEGs (167 upregulated and 333 downregulated) between the two groups. WGCNA analysis showed that the green module (428 nodes) exhibited the most significant correlation with I131 radiotherapy. A PPI network was built after the identification of 53 hub genes. In the PPI network, CDH5, KDR, CD34, FLT4, EMCN, FLT1, ROBO4, PTPRB, and CD93 exhibited higher degrees, which were mainly implicated in the vascular function. The relative expression of nine mRNAs in the THCA tissues treated with I131 was lower. Conclusion I131 radiotherapy might exert therapeutic effects by targeting CDH5, KDR, CD34, FLT4, EMCN, FLT1, ROBO4, PTPRB, and CD93 in THCA patients.
MAPE-R: An Empirical Comparison with MAPE

evaluations were very predictable: large percent errors in small pieces of census geography led to very high, biased and unreasonable error measures. This paper utilizes the MAPE-R as an error measure of block group level population estimates from a private Application Service Provider (ASP) with demographic expertise in the United States. The test involves comparing the private vendor’s 2000 block group population estimates with a large sample of the 208,668 Census 2000 block groups in the United States. The exercise will demonstrate the utility of the MAPE_R as a high-quality summary measure of error in small-area population estimates
PATHOGENICITY OF ENTOMOPATHOGENIC FUNGI AGAINST Sitophilus granarius (L.) (COLEOPTERA: CURCULIONIDAE) UNDER ABIOTIC FACTORS

Infestation to stored commodities by insect pests is an important concern, as it resulted in dire hazards to the quality and quantity of food products during storage (Phillips and Throne, 2010; Mason and McDonough, 2012). The granary weevil, Sitophilus granarius (L.) (Coleoptera: Curculionidae), is one of the destructive insect pests of stored grains (Plarre, 2010). Protection of stored grains from insect pests is currently based on the use of fumigants (phosphine etc.) and residual insecticides that cause serious harms, such as toxicity to no target organisms (Pisa et al., 2017), resistant development in insect population (Opit et al., 2012; Afful et al.,2017), residues of pesticides in treated products (Norman, 2000; Lozowicka et al., 2014) and environmental pollution (Van der Sluijs et al., 2015). Therefore, time is needed to evaluate new ways that are more sustainable and eco-friendly for stored grain insects’ management especially when consumer demands for organic food and products used for sensitive groups such as infants. The application of entomopathogenic fungi is a promising alternative to conventional chemicals for stored grains protection (Batta and Kavallieratos, 2018; George et al., 2018). EPF are naturally available enemies of insects with limited impact on environment and have low toxicity toward mammals (Zimmermann, 2007). EPF have been widely evaluated against stored products insect pests (Rumbos and Athanassiou, 2017). In this regard, most broadly tested EPF include Metarhizium anisopliae (Metschnikoff) (Batta, 2005; Michalaki et al., 2006) and Beauveria bassiana (Balsamo) (Padın et al., 2002; Kaur et al., 2014; Dal Bello et al., 2017; Rehman et al., 2019). The processes of EPF infection starts with the attachment of asexual spores to the insect cuticle then form germ tube and penetrate to the insect body, followed by multiplication of spores and produce toxins that ultimately kills the host (Pedrini et al., 2007). After that mycelium grows out from the cadaver, go through sporulation and repeat the inoculums in fungus-insect environment (Ortiz-Urquiza and Keyhani, 2013; Gabarty et al., 2014). The pathogenicity of EPF is seriously affected by the certain abiotic features of the environment; among these temperature and humidity are the most important (Sarwar, 2015). For temperature, it is assumed that high levels have negative Pak. J. Agri. Sci., Vol. 57(1), 79-86 ;2020 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/20.8661 http://www.pakjas. com.pk
The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

The response of the human acute myeloid leukemia cell line THP-1 to phorbol esters has been widely studied to test candidate leukemia therapies and as a model of cell cycle arrest and monocyte-macrophage differentiation. Here we have employed Cap Analysis of Gene Expression (CAGE) to analyze a dense time course of transcriptional regulation in THP-1 cells treated with phorbol myristate acetate (PMA) over 96 h. PMA treatment greatly reduced the numbers of cells entering S phase and also blocked cells exiting G2/M. The PMA-treated cells became adherent and expression of mature macrophage-specific genes increased progressively over the duration of the time course. Within 1–2 h PMA induced known targets of tumor protein p53 (TP53), notably CDKN1A, followed by gradual down-regulation of cell-cycle associated genes. Also within the first 2 h, PMA induced immediate early genes including transcription factor genes encoding proteins implicated in macrophage differentiation (EGR2, JUN, MAFB) and down-regulated genes for transcription factors involved in immature myeloid cell proliferation (MYB, IRF8, GFI1). The dense time course revealed that the response to PMA was not linear and progressive. Rather, network-based clustering of the time course data highlighted a sequential cascade of transient up- and down-regulated expression of genes encoding feedback regulators, as well as transcription factors associated with macrophage differentiation and their inferred target genes. CAGE also identified known and candidate novel enhancers expressed in THP-1 cells and many novel inducible genes that currently lack functional annotation and/or had no previously known function in macrophages. The time course is available on the ZENBU platform allowing comparison to FANTOM4 and FANTOM5 data.
Effects of Surface-Bound Collagen-Mimetic Peptides on Macrophage Uptake and Immunomodulation

The interaction between collagen/collagen-like peptides and the commonly expressed immune cell receptor LAIR-1 (leukocyte-associated immunoglobulin-like receptor-1) regulates and directs immune responses throughout the body. Understanding and designing these interactions within the context of biomaterials could advance the development of materials used in medical applications. In this study, we investigate the immunomodulatory effects of biomaterials engineered to display a human collagen III-derived ligand peptide (LAIR1-LP) that targets LAIR-1. Specifically, we examine the effects of LAIR1-LP functionalized surfaces on uptake of polymeric particles and cell debris by macrophages polarized toward inflammatory or healing phenotypes. We observed that culture of macrophages on LAIR1-LP functionalized surfaces increased their uptake of PLGA micro- and nano-particles, as well as apoptotic fibroblasts, while reducing their secretion of TNFα in response to LPS/IFNγ pro-inflammatory stimulation, when compared to cells seeded on control surfaces. To investigate the role of LAIR-1 in the observed LAIR1-LP-induced effects, we used siRNA to knock down LAIR-1 expression and found that cells lacking LAIR-1 exhibited enhanced particle uptake on LAIR1-LP and control surfaces. Furthermore, analysis of gene expression showed that LAIR-1 knockdown led to increase expression of other receptors involved in cell uptake, including CD-36, SRA-1, and beta-2 integrin. Together, our study suggests that LAIR1-LP enhances macrophage uptake potentially through interactions with collagen-domain binding surface receptors, and inhibits inflammation through interaction with LAIR-1.
The Influence of Host Dispersal on the Gene Flow and Genetic Diversity of Generalist and Specialist Ectoparasites‡

The dispersal and subsequent gene flow within parasite species is the result of a complex interaction between parasite life history, host life history and abiotic environmental factors. To gain more insights into the drivers responsible for parasite dispersal, COI mtDNA genetic data derived from six southern African generalist parasite species, including fleas, mites and ticks were compared with four specialist species from the same geographic region. Generalist tick species represented by Amblyomma hebraeum, Hyalomma truncatum and H. rufipes all occur temporarily on highly mobile ungulate hosts and showed high levels of haplotypic genetic diversity and high levels of dispersal with an average intraspecific global Fst (population differentiation index) value of 0.27 (±0.13). Generalist parasites, such as fleas, Listropsylla agrippinae and Chiastopsylla rossi, and one mite species, Laelaps muricola, that are all semi-permanent on the host and restricted to less mobile hosts species, showed a similar high level of genetic diversity, but an intermediate average Fst value of 0.67 (±0.11). Highly specialised semi-permanent parasites, such as the mite L. giganteus and the permanent lice Polyplax praomydis, Hoplopleura patersoni and P. arvicanthis recorded the lowest level of genetic diversity and a low level of gene flow among geographic sampling localities with an average Fst value of 0.95 (±0.05). This study provides strong support for the Specialist Generalist Variation Hypothesis (SGVH) and highlights the role that host dispersal and host specialisation by parasites play in the dispersal and evolution of ectoparasites.
Identification of atypical Frankia strains by fatty acid analysis

Ineffective, non-infective actinomycetous isolates obtained from actinorhizal nodules of Coriaria nepalensis and Datisca cannabina were identified as Frankia using whole cell fatty acid analysis. The isolates exhibited fatty-acid patterns very similar to those of confirmed Frankia strains from other host plants ( Alnus, Casuarina, Colletia, Comptonia, Elaeagnus and Hippophae ). All Frankia strains, including Coriaria and Datisca isolates, showed fatty-acid profiles very distinct from those of other actinomycetes used as controls ( Actinomyces, Geodermatophilus, Nocardia, Mycobacterium and Streptomyces ). For the genus Frankia , a characteristic pattern of five fatty acids (15:0; 15:1; 16:0 iso; 17:0 and 17:1) was found. These fatty acids comprised 75% or more of the total content. All Frankia strains could be placed into three subgroups. Coriaria isolates were found in the largest subgroup which contained most Frankia strains from other hosts while ineffective strains from Alnus, Elaeagnus and Datisca were distributed in all three subgroups of Frankia .
Insights Into Potato Spindle Tuber Viroid Quasi-Species From Infection to Disease

Viroids are non-coding RNA plant pathogens that are characterized by their possession of a high mutation level. Although the sequence heterogeneity in viroid infected plants is well understood, shifts in viroid population dynamics due to mutations over the course of infection remain poorly understood. In this study, the ten most abundant sequence variants of potato spindle tuber viroid RG1 (PSTVd) expressed at different time intervals in PSTVd infected tomato plants were identified by high-throughput sequencing. The sequence variants, forming a quasi-species, were subjected to both the identification of the regions favoring mutations and the effect of the mutations on viroid secondary structure and viroid derived small RNAs (vd-sRNA). At week 1 of PSTVd infection, 25% of the sequence variants were similar to the “master” sequence (i.e., the sequence used for inoculation). The frequency of the master sequence within the population increased to 70% at week 2 after PSTVd infection, and then stabilized for the rest of the disease cycle (i.e., weeks 3 and 4). While some sequence variants were abundant at week 1 after PSTVd infection, they tended to decrease in frequency over time. For example, the variants with insertions at positions 253 or 254, positions that could affect the Loop E as well as the metastable hairpin I structure that has been shown important during replication and viroid infectivity, resulted in decreased frequency. Data obtained by in silico analysis of the viroid derived small RNAs (vd-sRNA) was also analyzed. A few mutants had the potential of positively affecting the viroid’s accumulation by inducing the RNA silencing of the host’s defense related genes. Variants with mutations that could negatively affect viroid abundance were also identified because their derived vd-sRNA were no longer capable of targeting any host mRNA or of changing its target sequence from a host defense gene to some other non-important host gene. Together, these findings open avenues into understanding the biological role of sequence variants, this viroid’s interaction with host components, stable and metastable structures generated by mutants during the course of infection, and the influence of sequence variants on stabilizing viroid population dynamics.