bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal in‐feed amino acid ratio for broiler breeder hens based on deletion studies
Authors: Dorigam J. C. P. , Sakomura N. K. , Sarcinelli M. F. , Gonçalves C. A. , de Lima M. B. , Peruzzi N. J. 
Published: November 2016

SummaryAn ideal amino acid ratio (IAAR) for breeder hens is needed for maximum nitrogen retention (NR) taking into account nitrogen deposition in body (NDB), feathers (NDF) and egg mass (NEM) to improve dietary protein efficiency. Thus, the aim of this study was to apply the deletion method to derive the IAAR for broiler breeder hens. The nitrogen balance trials were performed from 31 to 35 weeks and from 46 to 50 weeks. Twelve treatments with eight replicates and one hen per cage were used. A balanced diet (BD) was formulated to meet the requirement of all nutrients. The other diets were formulated diluting 55% of BD with corn starch and refilled with amino acids (AAs) and other ingredients, except the AA tested. Each trial lasted 25 days. Feather losses, egg production and egg weight were recorded daily, and the samples were stored to further determine NEM and nitrogen in feather losses (NDFL). At the start and the end of each period, a group of birds were slaughtered to further determine NDB and NDF. The NR was calculated as the sum of NDB, NDF, NDFL, NEM and the nitrogen maintenance requirement (NMR). The deletion of valine greatly depressed the NR in peak production (31 to 35 weeks) while the deletion of the isoleucine greatly depressed the NR of the hens from 46 to 50 weeks of age. The percentual reduction in NR and the per cent of the AA to delete from the BD were used to calculate the AA requirement. The average IAAR was Lys 100, Met+Cys 86, Trp 23, Thr 80, Arg 113, Val 90, Ile 91, Leu 133, Phe+Tyr 108, Gly+Ser 94 and His 35. The IAAR was in line with the recommendation from the literature, validating deletion method with the advantages from a rapid and low‐cost procedure.
How Would Rural Hospitals Be Affected by Loss of the Affordable Care Act's Medicare Low‐Volume Hospital Adjustment?
Authors: Whitaker Rebecca Garr , Holmes G. Mark , Pink George H. 
Published: November 2016

AbstractPurposeThe low‐volume hospital (LVH) payment adjustment established in the Patient Protection and Affordable Care Act (ACA) of 2010 is scheduled to sunset on October 1, 2017. The purpose of this analysis was: (1) to estimate the effect of the ACA LVH adjustment on qualifying hospitals’ profitability margins; and (2) to examine hospital and market characteristics of the hospitals that would be most adversely affected by the loss of the ACA LVH adjustment.Methods2004‐2015 data from the Hospital Cost Report Information System, Hospital Market Service Area File and Nielsen‐Claritas Pop‐Facts file were used to estimate difference‐in‐difference regression models with hospital‐level random effects in order to determine whether the ACA LVH adjustment improved qualifying rural hospitals’ profitability margins. Recycled predictions estimated the effect of losing the ACA LVH adjustment on profitability margins. Bivariate analyses explored associations between the predicted profitability margins and hospital and market characteristics.FindingsThe ACA LVH adjustment significantly improved Sole Community Hospitals’ Medicare inpatient margins in the year they received the adjustment, and it had a large but statistically insignificant effect on the profitability margins of other rural hospitals. Hospitals that would be the most adversely affected by loss of the ACA LVH adjustment were more likely to be small, located in the South, and in high‐poverty markets with higher proportions of black and uninsured individuals.ConclusionsElimination of the ACA LVH adjustment would have differential effects on subgroups of hospitals, and those located in markets serving historically underserved populations would be the most adversely affected.
Growth of Hatchery‐reared Juveniles of the Australasian Sea Cucumber, Australostichopus mollis, Fed with Artificial and Natural Diets
Authors: Zamora Leonardo N. , Maxwell Kimberley H. , Jeffs Andrew G. 
Published: November 2016

AbstractAustralostichopus mollis is the most common and valuable sea cucumber species on the coasts of New Zealand and southern Australia. However, information supporting the development of artificial diets to advance the aquaculture of this species is scarce. In this study, the nutrient absorption, growth, pigmentation, and survival of small (111 mg) and large (434 mg) early juveniles were measured. The juveniles were fed with mussel biodeposits (MB); a commercial hatchery diet‐powdered macroalgae (HD); and artificial diets with different protein levels, 5% (5P) and 10% (10P), respectively. During the experiment, survival was greater than 66% in all diet treatments, with the juveniles feeding actively and absorbing all major macronutrients. The small juveniles, which were starting pigmentation, had higher growth rates (0.8–2.5%/d) than the large juveniles (0.2–1.2%/d), which were completing pigmentation. Growth was higher with the MB and HD diets than with the 5P and 10P diets, which could be explained by differences in the food consumption and nutrient absorption among the diet treatments. This study shows the feasibility of developing artificial diets without depending on naturally available ingredients; however, palatability and consumption need to be improved in order to make artificial diets for this species more effective and commercially available.
New records of cold‐water coral sites and fish fauna characterization of a potential network existing in the Mediterranean Sea
Authors: D'Onghia Gianfranco , Calculli Crescenza , Capezzuto Francesca , Carlucci Roberto , Carluccio Angela , Maiorano Porzia , Pollice Alessio , Ricci Pasquale , Sion Letizia , Tursi Angelo 
Published: November 2016

AbstractNew cold‐water coral (CWC) sites were recorded along the Apulian margin (Central Mediterranean). The species composition and depth distribution of CWCs were updated. A distribution of the CWC sites coincident with the course of the dense‐water masses that flow between the Southern Adriatic and Northern Ionian was confirmed. The faunal assemblages of five of these CWC sites were investigated and compared using experimental longlines during the spring–summer and autumn–winter seasons, between 2010 and 2014. Differences in ecological variables amongst the sites in each season were evaluated by means of a set of univariate and multivariate methods (analysis of variance, permutational multivariate analysis of variance, non‐metric multidimensional scaling). Although some differences were detected in relation to the different depths examined during spring–summer, the CWC sites showed similar features in terms of species richness and diversity as well as in the abundance of the same fish species (Galeus melastomus, Conger conger, Helicolenus dactylopterus, Merluccius merluccius, Phycis blennoides and Pagellus bogaraveo) most probably because of the distribution of adult specimens in structurally complex and heterogeneous habitats, which act as a potential ‘refuge network’ with respect to commercial fishing. The presence of maturing and mature individuals as well as post‐reproductive females indicates that these CWC sites also act as spawning areas, representing a potential ‘renewal network’ for the fish populations. The term ‘network’ used here refers to several similar subsystems (CWC sites) that play the same ecological role in a wider system (Apulian margin). These CWC communities need coherent conservation measures and management strategies according to the Ecosystem Approach to Fisheries.
ROBUST UTILITY MAXIMIZATION WITH LÉVY PROCESSES
Authors: NEUFELD ARIEL , NUTZ MARCEL 
Published: November 2016

AbstractWe study a robust portfolio optimization problem under model uncertainty for an investor with logarithmic or power utility. The uncertainty is specified by a set of possible Lévy triplets, that is, possible instantaneous drift, volatility, and jump characteristics of the price process. We show that an optimal investment strategy exists and compute it in semi‐closed form. Moreover, we provide a saddle point analysis describing a worst‐case model.
Dietary quality and household food insecurity among Mexican children and adolescents
Authors: Rodríguez Luis A. , Mundo‐Rosas Verónica , Méndez‐Gómez‐Humarán Ignacio , Pérez‐Escamilla Rafael , Shamah‐Levy Teresa 
Published: November 2016

AbstractSeventy percent of Mexican households experience some level of food insecurity (FI). Studies have shown positive associations between FI and poor dietary quality. As far as it is known, this is the first time the Healthy Eating Index (HEI‐2010) has been used to assess dietary quality of children and adolescents in Mexico, and to examine if FI is related to it. The objective of this research is to assess dietary quality and its association with FI among Mexican children and adolescents from a nationally representative cross‐sectional sample. We analyzed data from 4635 2–19‐year‐old Mexican children and adolescents participating in the Mexican National Health and Nutrition Survey (Ensanut 2012). FI was measured using the Latin American and Caribbean Household Food Security Scale (ELCSA) and dietary quality with the HEI‐2010. We examined the association between FI and dietary quality using multivariate linear regressions. Dietary quality was worst as FI became more severe among children and adolescents compared with their counterparts living in households with food security. Specifically, FI had a negative association with fruits, vegetables, and protein foods, and a positive association with refined grains consumption. Dairy intake was negatively associated with FI among older children and adolescents. Added sugars were not associated with FI, but intake was excessive across the population at 15% of total daily energy intake. Decreasing FI may help improve dietary quality of Mexican children and adolescents.
Sequence capture and next‐generation sequencing of ultraconserved elements in a large‐genome salamander
Authors: Newman Catherine E. , Austin Christopher C. 
Published: November 2016

AbstractAmidst the rapid advancement in next‐generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes—up to 40 times the size of the human genome—and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time‐consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is detrimental to species facing decline. Here, we use a salamander endemic to the southeastern United States, Plethodon serratus, to test the utility of an established protocol for sequence capture of ultraconserved elements (UCEs) in resolving intraspecific phylogeographic relationships and delimiting cryptic species. Without modifying the standard laboratory protocol, we generated a data set consisting of over 600 million reads for 85 P. serratus samples. Species delimitation analyses support recognition of seven species within P. serratus sensu lato, and all phylogenetic relationships among the seven species are fully resolved under a coalescent model. Results also corroborate previous data suggesting nonmonophyly of the Ouachita and Louisiana regions. Our results demonstrate that established UCE protocols can successfully be used in phylogeographic studies of salamander species, providing a powerful tool for future research on evolutionary history of amphibians and other organisms with large genomes.
Buchnera has changed flatmate but the repeated replacement of co‐obligate symbionts is not associated with the ecological expansions of their aphid hosts
Authors: Meseguer A. S. , Manzano‐Marín A. , Coeur d'Acier A. , Clamens A.‐L. , Godefroid M. , Jousselin E. 
Published: November 2016

AbstractSymbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long‐term obligate interactions. Recent evidence suggests that these associations are not always evolutionarily stable and that symbiont replacement, and/or supplementation of an obligate symbiosis by an additional bacterium, has occurred during the history of many insect groups. Yet, the factors favouring one symbiont over another in this evolutionary dynamic are not well understood; progress has been hindered by our incomplete understanding of the distribution of symbionts across phylogenetic and ecological contexts. While many aphids are engaged into an obligate symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in species of the Lachninae subfamily, this relationship has evolved into a ‘ménage à trois’, in which Buchnera is complemented by a cosymbiont, usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial genes from 128 species of Cinara (the most diverse Lachninae genus), we reveal a highly dynamic dual symbiotic system in this aphid lineage. Most species host both Serratia and Buchnera but, in several clades, endosymbionts related to Sodalis, Erwinia or an unnamed member of the Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences from four aphid species confirm that these coresident symbionts fulfil essential metabolic functions not ensured by Buchnera. We further demonstrate through comparative phylogenetic analyses that cosymbiont replacement is not associated with the adaptation of aphids to new ecological conditions. We propose that symbiont succession was driven by factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome deterioration or competitive interactions between bacteria with similar metabolic capabilities.
Multilocus resistance evolution to azole fungicides in fungal plant pathogen populations
Authors: Mohd‐Assaad Norfarhan , McDonald Bruce A. , Croll Daniel 
Published: November 2016

AbstractEvolution of fungicide resistance is a major threat to food production in agricultural ecosystems. Fungal pathogens rapidly evolved resistance to all classes of fungicides applied to the field. Resistance to the commonly used azole fungicides is thought to be driven mainly by mutations in a gene (CYP51) encoding a protein of the ergosterol biosynthesis pathway. However, some fungi gained azole resistance independently of CYP51 mutations and the mechanisms leading to CYP51‐independent resistance are poorly understood. We used whole‐genome sequencing and genome‐wide association studies (GWAS) to perform an unbiased screen of azole resistance loci in Rhynchosporium commune, the causal agent of the barley scald disease. We assayed cyproconazole resistance in 120 isolates collected from nine populations worldwide. We found that mutations in highly conserved genes encoding the vacuolar cation channel YVC1, a transcription activator, and a saccharopine dehydrogenase made significant contributions to fungicide resistance. These three genes were not previously known to confer resistance in plant pathogens. However, YVC1 is involved in a conserved stress response pathway known to respond to azoles in human pathogenic fungi. We also performed GWAS to identify genetic polymorphism linked to fungal growth rates. We found that loci conferring increased fungicide resistance were negatively impacting growth rates, suggesting that fungicide resistance evolution imposed costs. Analyses of population structure showed that resistance mutations were likely introduced into local populations through gene flow. Multilocus resistance evolution to fungicides shows how pathogen populations can evolve a complex genetic architecture for an important phenotypic trait within a short time span.
PrgU: a suppressor of sex pheromone toxicity in Enterococcus faecalis
Authors: Bhatty Minny , Camacho Martha I. , Gonzalez‐Rivera Christian , Frank Kristi L. , Dale Jennifer L. , Manias Dawn A. , Dunny Gary M. , Christie Peter J. 
Published: November 2016

SummaryUpon sensing of the peptide pheromone cCF10, Enterococcus faecalis cells carrying pCF10 produce three surface adhesins (PrgA, PrgB or Aggregation Substance, PrgC) and the Prg/Pcf type IV secretion system and, in turn, conjugatively transfer the plasmid at high frequencies to recipient cells. Here, we report that cCF10 induction is highly toxic to cells sustaining a deletion of prgU, a small orf located immediately downstream of prgB on pCF10. Upon pheromone exposure, these cells overproduce the Prg adhesins and display impaired envelope integrity, as evidenced by antibiotic susceptibility, misplaced division septa and cell lysis. Compensatory mutations in regulatory loci controlling expression of pCF10‐encoded prg/pcf genes, or constitutive PrgU overproduction, block production of the Prg adhesins and render cells insensitive to pheromone. Cells engineered to overproduce PrgB, even independently of other pCF10‐encoded proteins, have severely compromised cell envelopes and strong growth defects. PrgU has an RNA‐binding fold, and prgB‐prgU gene pairs are widely distributed among E. faecalis isolates and other enterococcal and staphylococcal species. Together, our findings support a model in which PrgU proteins represent a novel class of RNA‐binding regulators that act to mitigate toxicity accompanying overproduction of PrgB‐like adhesins in E. faecalis and other clinically‐important Gram‐positive species.
Discovery of the type VII ESX‐1 secretion needle?
Authors: Ates Louis S. , Brosch Roland 
Published: November 2016

SummaryMycobacterium tuberculosis, the etiological agent of human tuberculosis, harbours five ESAT‐6/type VII secretion (ESX/T7S) systems. The first esx gene clusters were identified during the genome‐sequencing project of M. tuberculosis H37Rv. Follow‐up studies revealed additional genes playing important roles in ESX/T7S systems. Among the latter genes, one can find those that encode Pro‐Glu (PE) and Pro‐Pro‐Glu (PPE) proteins as well as a gene cluster that is encoded >260 kb upstream of the esx‐1 locus and encodes ESX‐1 secretion‐associated proteins EspA (Rv3616c), EspC (Rv3615c) and EspD (Rv3614c). The espACD cluster has been suggested to have an important function in ESX‐1 secretion since EspA‐EspC and EsxA–EsxB are mutually co‐dependent on each other for secretion. However, the molecular mechanism of this co‐dependence and interaction between the substrates remained unknown. In this issue of Molecular Microbiology, Lou and colleagues show that EspC forms high‐molecular weight polymerization complexes that resemble selected components of type II, III and/or IV secretion systems of Gram‐negative bacteria. Indeed, EspC‐multimeric complexes form filamentous structures that could well represent a secretion needle of ESX‐1 type VII secretion systems. This exciting observation opens new avenues for research to discover and characterize ESX/T7S components and elucidates the co‐dependence of EsxA/B secretion with EspA/C.
Reason After Revelation: Karl Barth on Divine Word and Human Words
Authors: Woodard‐Lehman Derek Alan 
Published: November 2016

AbstractThough little understood, Karl Barth's moral theology is widely criticized. Indeed, it is so widely criticized because it is so little understood. Among ethicists, the principal objects of criticism are Barth's account of practical reason and the account of revelation on which it depends. This essay argues that such criticisms miss their mark, because they rest on an incomplete understanding of Barth's doctrine of the Word of God that results in an incorrect understanding of his doctrine of divine command. Because critics neglect his account of subjective reception of revelation through which divine command is heard, they ignore the account of disputation, deliberation, and decision present in his account of scriptural interpretation and ecclesial confession. By laying out the discursive practices of scriptural interpretation and ecclesial confession, and by drawing out the deliberative dimensions of Kantian self‐legislation and Hegelian mutual recognition at work in interpretation and confession alike, this essay argues that these practices provide a fuller account of what Barth calls “practical casuistry,” as well as his most fulsome and winsome account of practical reason.
Transcriptional response of Erwinia amylovora to copper shock: in vivo role of the copA gene
Authors: Águila‐Clares Begoña , Castiblanco Luisa F. , Quesada José Miguel , Penyalver Ramón , Carbonell Juan , López María M. , Marco‐Noales Ester , Sundin George W. 
Published: November 2016

SummaryFire blight is a devastating plant disease caused by the bacterium Erwinia amylovora, and its control is frequently based on the use of copper‐based compounds whose mechanisms of action are not well known. Consequently, in this article, we investigate the response of E. amylovora to copper shock by a whole‐genome microarray approach. Transcriptional analyses showed that, in the presence of copper, 23 genes were increased in expression; these genes were classified mainly into the transport and stress functional categories. Among them, the copA gene was strongly induced and regulated in a finely tuned manner by copper. Mutation of copA, soxS, arcB, yjcE, ygcF, yhhQ, galF and EAM_3469 genes revealed that tolerance to copper in E. amylovora can be achieved by complex physiological mechanisms, including: (i) the control of copper homeostasis through, at least, the extrusion of Cu(I) by a P‐type ATPase efflux pump CopA; and (ii) the overcoming of copper toxicity caused by oxidative stress by the expression of several reactive oxygen species (ROS)‐related genes, including the two major transcriptional factors SoxS and ArcB. Furthermore, complementation analyses demonstrated the important role of copA for copper tolerance in E. amylovora, not only in vitro, but also in inoculated pear shoots.
Comparative evaluation of pan‐fungal real‐time PCR, galactomannan and (1‐3)‐β‐D‐glucan assay for invasive fungal infection in paediatric cancer patients
Authors: Gupta Prashant , Ahmad Abrar , Khare Vineeta , Kumar Archana , Banerjee Gopa , Verma Nitya , Singh Mastan 
Published: November 2016

SummaryLimited specific data and investigations are available for the diagnosis of Invasive Fungal Infection (IFI) in paediatrics cancer patients. Three non‐invasive tests; Platelia Aspergillus EIA for galactomannan (GM), β‐D‐glucan (BDG) assay and pan‐fungal real‐time PCR for fungal DNA in blood were evaluated. One hundred twenty‐five paediatrics cancer patients at the high risk of IFI were enrolled. Single blood and serum samples were evaluated by all the three methods. Patients were classified into 10 proven, 52 probable and 63 no IFI cases in accordance with EORTC MSG 2008 revised guidelines. The sensitivity, specificity, PPV and NPV of all the three tests in proven, probable and no IFIs cases were analysed singly and in combination. The sensitivity, specificity, PPV and NPV of GM, BDG and pan‐fungal real‐time PCR were: 87%, 61%, 81%, 69.5% for GM, 88%, 59.5%, 81%, 71.4% for BDG and 89%, 69.2%, 85%, 67.5% for PCR (95% CI). Among different combinations, best combination was found to be GM and PCR with sensitivity, specificity, PPV and NPV of 98.2%, 89.3%, 97.1% and 90% respectively. Single samples must be evaluated by combination of tests.