bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of two mutations that cause defects in the ligninolytic system through an efficient forward genetics in the white‐rot agaricomycete Pleurotus ostreatus
Authors: Nakazawa Takehito , Izuno Ayako , Kodera Rina , Miyazaki Yasumasa , Sakamoto Masahiro , Isagi Yuji , Honda Yoichi 
Published: November 2016

SummaryWhite‐rot fungi play an important role in the global carbon cycle because they are the species that almost exclusively biodegrade wood lignin in nature. Lignin peroxidases (LiPs), manganese peroxidases (MnPs) and versatile peroxidases (VPs) are considered key players in the ligninolytic system. Apart from LiPs, MnPs and VPs, however, only few other factors involved in the ligninolytic system have been investigated using molecular genetics, implying the existence of unidentified elements. By combining classical genetic techniques with next‐generation sequencing technology, they successfully showed an efficient forward genetics approach to identify mutations causing defects in the ligninolytic system of the white‐rot fungus Pleurotus ostreatus. In this study, they identified two genes – chd1 and wtr1 – mutations in which cause an almost complete loss of Mn2+‐dependent peroxidase activity. The chd1 gene encodes a putative chromatin modifier, and wtr1 encodes an agaricomycete‐specific protein with a putative DNA‐binding domain. The chd1‐1 mutation and targeted disruption of wtr1 hamper the ability of P. ostreatus to biodegrade wood lignin. Examination of the effects of the aforementioned mutation and disruption on the expression of certain MnP/VP genes suggests that a complex mechanism underlies the ligninolytic system in P. ostreatus.
Bringing microbial diversity into focus: high‐resolution analysis of iron mats from the Lō‘ihi Seamount
Authors: Scott Jarrod J. , Glazer Brian T. , Emerson David 
Published: November 2016

SummaryThirty kilometers south of the island of Hawai‘i lies the Lō‘ihi Seamount, an active submarine volcano that hosts a network of low‐temperature hydrothermal vents enriched in ferrous iron that supports extensive microbial mats. These mats, which can be a half a meter deep, are composed of ferric iron bound to organic polymers – the metabolic byproduct of iron‐oxidizing Zetaproteobacteria. Though the role of Zetaproteobacteria in mat formation is well established, we have a limited understanding of how differences in diversity are related to mat morphology. We used Minimum Entropy Decomposition and ZetaOtu classification to demonstrate cryptic diversity between closely related Zetaproteobacteria while showing habitat and geographic specificity. Veiled mats, common structures at Lō‘ihi, exhibit distinct community composition and contain diversity not detected in other mat types, including specific Zetaproteobacteria and an unclassified Gammaproteobacteria. Our analyses also indicate that diversity can change dramatically across small spatial transects from points of active venting, yet we found comparatively few differences between major sampling sites. This study provides a better picture of the microbiome responsible for iron mat production at Lō‘ihi and has broad implications for our understanding of these globally distributed communities.
High genetic diversity of Vibrio cholerae in the European lake Neusiedler See is associated with intensive recombination in the reed habitat and the long‐distance transfer of strains
Authors: Pretzer Carina , Druzhinina Irina S. , Amaro Carmen , Benediktsdóttir Eva , Hedenström Ingela , Hervio‐Heath Dominique , Huhulescu Steliana , Schets Franciska M. , Farnleitner Andreas H. , Kirschner Alexander K. T. 
Published: November 2016

SummaryCoastal marine Vibrio cholerae populations usually exhibit high genetic diversity. To assess the genetic diversity of abundant V. cholerae non‐O1/non‐O139 populations in the Central European lake Neusiedler See, we performed a phylogenetic analysis based on recA, toxR, gyrB and pyrH loci sequenced for 472 strains. The strains were isolated from three ecologically different habitats in a lake that is a hot‐spot of migrating birds and an important bathing water. We also analyzed 76 environmental and human V. cholerae non‐O1/non‐O139 isolates from Austria and other European countries and added sequences of seven genome‐sequenced strains. Phylogenetic analysis showed that the lake supports a unique endemic diversity of V. cholerae that is particularly rich in the reed stand. Phylogenetic trees revealed that many V. cholerae isolates from European countries were genetically related to the strains present in the lake belonging to statistically supported monophyletic clades. We hypothesize that the observed phenomena can be explained by the high degree of genetic recombination that is particularly intensive in the reed stand, acting along with the long distance transfer of strains most probably via birds and/or humans. Thus, the Neusiedler See may serve as a bioreactor for the appearance of new strains with new (pathogenic) properties.
A Focus on Quality and Safety Traits of Saccharomyces cerevisiae Isolated from Uva di Troia Grape Variety
Authors: Petruzzi Leonardo , Bevilacqua Antonio , Corbo Maria Rosaria , Speranza Barbara , Capozzi Vittorio , Sinigaglia Milena 
Published: November 2016

AbstractThe aim of this work was to study Saccharomyces cerevisiae strains isolated from vineyards of the autochthonous grape variety “Uva di Troia” located in different geographical areas of Apulian region (Southern Italy). Four hundred isolates were studied in relation to H2S production, β‐glucosidase activity, and pigments adsorption from grape skin. Thus, 81 isolates were selected, identified through the amplification of the interdelta region, and grouped in 19 biotypes (from I to XIX). The enological performances were assessed to determine the content of residual sugars, ethanol, glycerol, and volatile acidity, after a microfermentation in Uva di Troia must for each isolate. The ability to remove ochratoxin A (OTA) was studied as an additional tool to select promising strains. A geographical‐dependent technological variability was found for glycerol and volatile acidity, suggesting that the different indigenous yeasts can have a peculiar impact on the final characteristics of the corresponding wine (“Nero di Troia”). Only 2 biotypes (VI and XVII) were able to remove OTA throughout fermentation, with the highest reduction achieved by the biotype XVII (ca. 30%).
Hypoglycemic Activity of Polysaccharides from Sweet Corncob on Streptozotocin‐Induced Diabetic Rats
Authors: Ma Yong Qiang , Wang Xin , Gao Shuang 
Published: November 2016

AbstractA water‐soluble polysaccharide (SCP‐80‐I) was isolated from sweet corncob using microwave‐assisted compound‐enzyme extraction and column chromatography. SCP‐80‐I is composed mainly of arabinose, mannose, glucose, and galactose in a molar ratio of 0.369:0.824:10.759:0.333, and has a molecular mass of 18350 Da and β‐glycosides linkages in its molecular structure. The preliminary hypoglycemic and hypolipidemic activity in streptozotocin‐induced diabetic rats was investigated. Rats were administered daily with 100, 200, and 400 mg/kg SCP‐80‐I for 21 d. The SCP‐80‐I increased the rat body mass significantly and reduced the blood glucose level in a dose‐dependent manner. The SCP‐80‐I reduced liver swelling; kidney and pancreas hypertrophy; and total cholesterol, triglyceride, and low‐density lipoprotein‐C levels significantly; and increased the level of high‐density lipoproteins in streptozotocin‐induced diabetic rats. These results indicate that SCP‐80‐I exerts a potential hypoglycemic effect in streptozotocin‐induced diabetic rats.
Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data
Authors: Richardson Rodney T. , Bengtsson‐Palme Johan , Johnson Reed M. 
Published: November 2016

AbstractThe taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the trade‐offs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the rdp Naïve Bayesian Classifier, rtax and utax. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade‐off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.
The Diffusion of Values among Democracies and Autocracies
Authors: Deutsch Franziska , Welzel Christian 
Published: November 2016

AbstractOver the past couple of years, our knowledge about diffusion processes has increased greatly. So far, the focus has been on public policies, political institutions, and civil society repertories. Our paper breaks new ground by exploring value diffusion at the societal level. Using the World Values Survey data, we are interested in the diffusion of emancipative values in different regime types, building a bridge between research on the micro foundations and macro political expressions of democratization and political regimes. In particular, we wish to understand whether the psychological bedrock of a pro‐democratic mass culture – emancipative values – is diffusing between countries and, if yes, to what extent this diffusion is limited to democracies or also makes inroads into autocratically governed societies.
Interspecific interactions between feral pigs and native birds reveal both positive and negative effects
Authors: Natusch Daniel J. D. , Mayer Martin , Lyons Jessica A. , Shine Richard 
Published: November 2016

AbstractIn tropical Australian rainforests, predators and scavengers aggregate beneath emergent trees that house large colonies of metallic starlings (Aplonis metallica), feeding in the nutrient‐rich open areas below. Analysis of camera‐trap records shows that the presence of feral pigs (Sus scrofa) is associated with an absence of birds (cockatoos and brush turkeys), presumably reflecting behavioural avoidance (pigs pose a direct danger to birds). However, bird numbers increase as soon as pigs depart, then fall if pigs are absent for long periods. Feral pigs thus displace native birds from these resource hotspots; but by turning over the soil and enhancing the birds' access to food, the pigs also have a positive impact on food availability for the avifauna. Thus, although invasive species have caused irreparable environmental damages worldwide, they may also provide positive benefits for certain species. The net benefit of such interspecific interactions will depend on the outcome of both positive and negative effects.
An evaluation of inpatient morbidity and critical care provision in Zambia
Authors: Dart P. J. , Kinnear J. , Bould M. D. , Mwansa S. L. , Rakhda Z. , Snell D. 
Published: November 2016

SummaryThe aim of this study was to objectively measure demand for critical care services in a southern African tertiary referral centre. We carried out a point prevalence study of medical and surgical admissions over a 48‐h period at the University Teaching Hospital, Lusaka, recording the following: age; sex; diagnosis; Human Immunodeficiency Virus (HIV) status and National Early Warning Score. One‐hundred and twenty medical and surgical admissions were studied. Fifty‐four patients (45%) had objective evidence of a requirement for critical care review and potential or probable admission to an intensive care unit, according to the Royal College of Physicians (UK) guidelines. A greater than expected HIV rate was also noted; 53 of 75 tested patients (71%). When applied to the estimated 17,496 annual acute admissions, this would equate to 7873 patients requiring critical care input annually at this hospital alone. In contrast to this demand, we identified 109 critical care beds nationally, and only eight at this institution.
Intensive care medicine in rural sub‐Saharan Africa
Authors: Dünser M. W. , Towey R. M. , Amito J. , Mer M. 
Published: November 2016

SummaryWe undertook an audit in a rural Ugandan hospital that describes the epidemiology and mortality of 5147 patients admitted to the intensive care unit. The most frequent admission diagnoses were postoperative state (including following trauma) (2014/5147; 39.1%), medical conditions (709; 13.8%) and traumatic brain injury (629; 12.2%). Intensive care unit mortality was 27.8%, differing between age groups (p < 0.001). Intensive care unit mortality was highest for neonatal tetanus (29/37; 78.4%) and lowest for foreign body aspiration (4/204; 2.0%). Intensive care unit admission following surgery (333/1431; 23.3%), medical conditions (327/1431; 22.9%) and traumatic brain injury (233/1431; 16.3%) caused the highest number of deaths. Of all deaths in the hospital, (1431/11,357; 12.6%) occurred in the intensive care unit. Although the proportion of hospitalised patients admitted to the intensive care unit increased over time, from 0.7% in 2005/6 to 2.8% in 2013/4 (p < 0.001), overall hospital mortality decreased (2005/6, 4.8%; 2013/14, 4.0%; p < 0.001). The proportion of intensive care patients whose lungs were mechanically ventilated was 18.7% (961/5147). This subgroup of patients did not change over time (2006, 16%; 2015, 18.4%; p = 0.12), but their mortality decreased (2006, 59.5%; 2015, 44.3%; p < 0.001).
Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis
Authors: Acharya C. , Betrapally N. S. , Gillevet P. M. , Sterling R. K. , Akbarali H. , White M. B. , Ganapathy D. , Fagan A. , Sikaroodi M. , Bajaj J. S. 
Published: November 2016

SummaryBackgroundOpioid use is epidemic in cirrhosis, which could precipitate hepatic encephalopathy (HE) potentially through gut dysbiosis and inflammation.AimTo define the effect of opioids on readmissions and on gut microbiota composition and functionality.MethodsCohort 1 had 200 cirrhotic in‐patients (with/without opioid use) followed prospectively through the index hospitalisation and 6 months post discharge. Readmissions (HE‐related/unrelated) were compared between patients discharged on opioids compared to the rest, including using a multi‐variable analysis. Cohort 2 consisted of 72 cirrhotics on chronic opioids who were age/model for end‐stage liver disease (MELD) and prior HE‐balanced with 72 cirrhotics not on opioids. Stool microbiota composition (multi‐tagged sequencing), predicted functionality (PiCRUST), endotoxemia and systemic inflammation (IL‐6, IL‐17) were compared.ResultsCohort 1: Chronic opioid use was statistically similar between those admitted with/without HE, and was judged to be an HE precipitant in <5% of cases during the index hospitalisation. Of the 144 patients alive at 6 months, 82 were readmitted. The opioid users had a significantly higher all cause (69% vs. 48%, P = 0.008), but not HE‐related readmissions (30% vs. 41%, P = 0.30). On regression, opioid therapy and female gender were predictive of readmission independent of MELD score and previous HE. Cohort 2: Significant dysbiosis was noted in the opioid cohort, especially in HE+opioid patients with lower autochthonous taxa and Bacteroidaceae relative abundance. PiCRUST showed highest aromatic amino acid and endotoxin production in opioid users. Opioid users also had higher endotoxemia and IL‐6 but not IL‐17.ConclusionChronic opioid use in cirrhosis is associated with increased endotoxemia, dysbiosis and all‐cause readmissions.
The contribution of clinical and psychosocial factors to fatigue in 182 patients with inflammatory bowel disease: a cross‐sectional study
Authors: Artom M. , Czuber‐Dochan W. , Sturt J. , Murrells T. , Norton C. 
Published: November 2016

SummaryBackgroundFatigue is a frequently reported and predominant symptom experienced by patients with inflammatory bowel disease (IBD) and its impact has been associated with poorer quality of life (QoL). The complex interplay between disease‐related variables and potentially modifiable psychosocial factors in IBD‐fatigue has yet to be unravelled.AimTo evaluate the contribution of clinical, sociodemographic and psychosocial factors to the severity and impact of IBD‐fatigue and QoL.MethodIn a cross‐sectional study, 182 patients with IBD were recruited from three tertiary referral hospitals’ out‐patient clinics in London. Fatigue was assessed utilising the Inflammatory Bowel Disease‐Fatigue Scale (IBD‐F), the Multidimensional Fatigue Inventory (MFI); and QoL by the Inflammatory Bowel Disease Questionnaire (IBDQ). Patients completed self‐report questionnaires evaluating emotional, cognitive and behavioural factors potentially correlated with fatigue. Sociodemographic data were collected. Disease‐related and laboratory data were retrieved from patients’ hospital electronic medical records.ResultIn hierarchical regression models, disease activity was the only clinical factor consistently associated with severity and impact of fatigue and QoL (P = 0.01). More negative fatigue perceptions were significantly associated with greater IBD‐F1 scores (P = 0.01). When controlling for clinical factors (disease activity and anti‐TNF therapy), negative perceptions of fatigue, and all‐or‐nothing and avoidance behaviours explained an additional 41% of the variance in fatigue impact (IBD‐F2).ConclusionsApart from disease activity, emotional and behavioural factors and patients’ negative fatigue perceptions may be key factors to be addressed. Further exploration of these factors in longitudinal and intervention studies may help to develop effective models of fatigue management.
Pharmacokinetic interaction between taxanes and amiodarone leading to severe toxicity
Authors: Hammann Felix , Gotta Verena , Conen Katrin , Medinger Michael , Cesana Philipp , Rochlitz Christoph , Taegtmeyer Anne B. 
Published: November 2016

Adverse eventA drug interaction leading to severe skin and mucosal toxicity.Drugs implicatedPaclitaxel, docetaxel and amiodarone.The patientA 77‐year‐old woman with a history of hypertension, hyperlipidemia, and palpitations, managed with amiodarone, was treated for HER2‐positive invasive ductal breast cancer with paclitaxel and trastuzumab as an adjunct to surgery.Evidence that links the drug to the eventThere was a strong temporal relationship between the taxane therapy and the development of severe skin and mucosal toxicity due to an unexpected reduction in taxane clearance.ManagementInitially, conversion of paclitaxel to docetaxel, then cessation of docetaxel, symptomatic treatment, rehydration and placement of a nasogastric tube.MechanismIncreased exposure to paclitaxel and subsequently docetaxel due to interaction with amiodarone was suspected and confirmed on pharmacokinetic sampling. Analysis of two blood samples taken 9 and 10 days after docetaxel revealed plasma levels of 4.73 and 4.09 ng ml−1, respectively, leading to a 79% decreased individual (Bayesian maximum a posteriori) clearance estimate of 9.15 l h−1, corresponding to an estimated fivefold increase in AUC. Paclitaxel was also present in these samples (20 and 21 days after the last administration).Implications for therapyAmiodarone inhibits cytochrome P450 (CYP) isoforms 2C8 and 3A4 as well as P‐glycoprotein (P‐gp) for which taxanes are substrates. However, interactions with amiodarone are not specified in the prescribing information. Clinicians should be aware of this interaction, particularly in an ageing population, where more patients requiring taxanes may already be receiving amiodarone for a comorbid cardiac condition.
Natural forest regeneration and ecological restoration in human‐modified tropical landscapes
Authors: Martínez‐Ramos Miguel , Pingarroni Aline , Rodríguez‐Velázquez Jorge , Toledo‐Chelala Lilibeth , Zermeño‐Hernández Isela , Bongers Frans 
Published: November 2016

AbstractIn human‐modified tropical landscapes (HMLs) the conservation of biodiversity, functions and services of forest ecosystems depends on persistence of old growth forest remnants, forest regeneration in abandoned agricultural fields, and restoration of degraded lands. Understanding the impacts of agricultural land uses (ALUs) on forest regeneration is critical for biodiversity conservation in HMLs. Here, we develop a conceptual framework that considers the availability of propagules and the environment prevailing after field abandonment as two major determinants of forest regeneration in HMLs. The framework proposes that regeneration potential decreases with size, duration and severity of agricultural disturbance, reducing propagule availability and creating ill‐suited environmental conditions for regeneration. We used studies from Southern Mexico to assess this framework. First, we identify regeneration bottlenecks that trees face during transit from seed to follow‐up life stages, using demographic analysis of dominant pioneer species in recently abandoned fields. Then, we explore effects of ALUs on forest regeneration at the field and landscape scales, addressing major legacies. Finally, we integrate agricultural disturbance with landscape composition to predict attributes of successful second growth forests in HMLs, and provide indicators useful to select tree native species for active restoration. An indicator of disturbance inflicted by ALUs, based on farmers’ information, predicted better regeneration potential than measurements of soil and microclimate conditions at time of abandonment. Cover of cattle pastures in the landscape was a stronger indicator of forest regenerating attributes than cover of old growth forest remnants. To conclude, we offer recommendations to promote forest regeneration and biodiversity conservation in HMLs.