Environmental Effects over the First 2½ Rotation Periods of a Fertilised Poplar Short Rotation Coppice

A short rotation coppice (SRC) with poplar was established in a randomised fertilisation experiment on sandy loam soil in Potsdam (Northeast Germany). The main objective of this study was to assess if negative environmental effects as nitrogen leaching and greenhouse gas emissions are enhanced by mineral nitrogen (N) fertiliser applied to poplar at rates of 0, 50 and 75 kg N ha^?1 year^?1 and how these effects are influenced by tree age with increasing number of rotation periods and cycles of organic matter decomposition and tree growth after each harvesting event. Between 2008 and 2012, the leaching of nitrate (NO₃ ^?) was monitored with self-integrating accumulators over 6-month periods and the emissions of the greenhouse gases (GHG) nitrous oxide (N₂O) and carbon dioxide (CO₂) were determined in closed gas chambers. During the first 4 years of the poplar SRC, most nitrogen was lost through NO₃ ^? leaching from the main root zone; however, there was no significant relationship to the rate of N fertilisation. On average, 5.8 kg N ha^?1 year^?1 (13.0 kg CO_2equ) was leached from the root zone. Nitrogen leaching rates decreased in the course of the 4-year study parallel to an increase of the fine root biomass and the degree of mycorrhization. In contrast to N leaching, the loss of nitrogen by N₂O emissions from the soil was very low with an average of 0.61 kg N ha^?1 year^?1 (182 kg CO_2equ) and were also not affected by N fertilisation over the whole study period. Real CO₂ emissions from the poplar soil were two orders of magnitude higher ranging between 15,122 and 19,091 kg CO₂ ha^?1 year^?1 and followed the rotation period with enhanced emission rates in the years of harvest. As key-factors for NO₃ ^? leaching and N₂O emissions, the time after planting and after harvest and the rotation period have been identified by a mixed effects model.     

The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment

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Transmission dynamics of the great influenza pandemic of 1918 in Geneva, Switzerland: Assessing the effects of hypothetical interventions

Recurrent outbreaks of the avian H5N1 influenza virus in Asia represent a constant global pandemic threat. We characterize and evaluate hypothetical public health measures during the 1918 influenza pandemic in the Canton of Geneva, Switzerland. The transmission rate, the recovery rate, the diagnostic rate, the relative infectiousness of asymptomatic cases, and the proportion of clinical cases are estimated through least-squares fitting of the model to epidemic curve data of the cumulative number of hospital notifications. The latent period and the case fatality proportion are taken from published literature. We determine the variance and identifiability of model parameters via a simulation study. Our epidemic model agrees well with the observed epidemic data. We estimate the basic reproductive number for the spring wave R1;=1.49 (95% CI: 1.45-1.53) and the reproductive number for the fall wave R2;=3.75 (95% CI: 3.57-3.93). In addition, we estimate the clinical reporting for these two waves to be 59.7% (95% CI: 55.7-63.7) and 83% (95% CI: 79-87). We surmise that the lower reporting in the first wave can be explained by a lack of initial awareness of the epidemic and the relative higher severity of the symptoms experienced during the fall wave. We found that effective isolation measures in hospital clinics at best would only ensure control with probability 0.87 while reducing the transmission rate by >76.5% guarantees stopping an epidemic.     

A decoy set for the thermostable subdomain from chicken villin headpiece,comparison of different free energy estimators

Background  

Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures.     

crabs—A software program to generate curated reference databases for metabarcoding sequencing data

The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data have been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present crabs (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. crabs includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness and taxonomic resolution. crabs is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. crabs can be installed via docker and is available for download as a conda package and via GitHub ( https://github.com/gjeunen/reference_database_creator ).     

HistoChoice® as an alternative to formalin fixation of undecalcified bone specimens

We compared histochemical and immunohistochemical staining as well as fluorochrome labeling in murine bone specimens that were fixed with 10% neutral buffered formalin to those fixed with HistoChoice®. We showed that sections from undecalcified tibiae fixed for 4 h in HistoChoice® resulted in enhanced toluidine blue and Von Kossa histochemical staining compared to formalin fixation. HistoChoice® produced comparable or improved staining for alkaline phosphatase. Acid phosphatase localization was better in formalin fixed specimens, but osteoclasts were visuralized more easily in HistoChoice® fixed specimens. As expected, immunohistochemical labeling was antibody dependent; some antibodies labeled better in HistoChoice® fixed specimens while others were better in formalin fixed specimens. Toluidine blue, Von Kossa, and alkaline phosphatase staining of sections fixed for 12 h produced sections that were similar to 4 h fixed sections. Fixation for 12 h preserved acid phosphatase activity better. Increasing fixation to 12 h affected immunolocalization differentially. Bone sialoprotein labeling in HistoChoice® fixed specimens was comparable to formalin fixed samples. On the other hand, after 12 h formalin fixation, osteocalcin labeling was comparable to HistoChoice®. For most histochemical applications, fixing murine bone specimens for 4 h with HistoChoice® yielded superior staining compared to formalin fixation. If immunohistochemical localization is desired, however, individual antibodies must be tested to determine which fixation process retains antigenicity better. In addition, there was no detectable difference in the intensity of fluorochrome labeling using either fixative. Finally, fixation duration did not alter the intensity of labeling.     

A systematic review to calculate background miscarriage rates using life table analysis

The objectives of the current study were to calculate: (1) the expected rates of miscarriage by gestational week; (2) the cumulative risk of miscarriage; and (3) the remaining risk of miscarriage for gestational weeks five through 20, through a systematic review of the literature. We searched MEDLINE for articles published in English through the end of 2009. References of articles were also searched. Four studies were identified to have the three necessary pieces of information for the proposed calculations: (1) gestational age at study entry, (2) pregnancy outcome; and (3) the gestational age at which the pregnancy outcome occurred. Data were extracted from each study and Life Table Analysis Methods were conducted. Weekly miscarriage rates varied in the early gestational weeks with the highest rate documented at >20 miscarriages per 1000 women-weeks at each week of gestation prior to week 13. By week 14, the rate for all studies became relatively comparable and fell below 10 miscarriages per 1000 woman-weeks at risk and fell even lower through week 20. The cumulative risk of miscarriage for weeks 5 through 20 of gestation ranged from 11 miscarriages per 100 women to 22 miscarriages per 100 women (11-22%). Based on data from comparable study populations, a range of background miscarriage rates by week of gestation for weeks 5 through 20, the cumulative risk of miscarriage, and the remaining risk of miscarriage are presented. Wider variation of miscarriage rates and risks occurred early in gestation (<14 weeks).     

Development of Sjogren's syndrome in nonobese diabetic-derived autoimmune-prone C57BL/6.NOD-Aec1Aec2 mice is dependent on complement component-3

The role of complement in the etiology of Sj?gren's syndrome (SjS), a human autoimmune disease manifested primarily by salivary and lacrimal gland dysfunction resulting in dry mouth/dry eye syndrome, remains ill-defined. In the present study, we examined the role of complement component-3 (C3) using a newly constructed C3-gene knockout mouse, C57BL/6.NOD-Aec1Aec2.C3(-/-). Inactivation of C3 in the parental C57BL/6.NOD-Aec1Aec2 strain, a model of primary SjS, resulted in a diminished or total absence of both preclinical and clinical manifestations during development and onset of disease, including reduced acinar cell apoptosis, reduced levels of caspase-3, lack of leukocyte infiltration of submandibular glands, reduced synthesis of disease-associated autoantibodies, maintenance of normal glandular architecture, and retention of normal saliva secretion. In addition, C57BL/6-NOD.Aec1Aec2.C3(-/-) mice did not exhibit increased numbers of marginal zone B cells, a feature of SjS-prone C57BL/6-NOD.Aec1Aec2 mice. Interestingly, C57BL/6-NOD.Aec1Aec2.C3(-/-) mice retained some early pathological manifestations, including activation of serine kinases with proteolytic activity for parotid secretory protein. This improvement in the clinical manifestations of SjS-like disease in C57BL/6.NOD-Aec1Aec2.C3(-/-) mice, apparently a direct consequence of C3 deficiency, supports a much more important role for complement in the adaptive autoimmune response than previously recognized, possibly implicating an essential role for innate immunity.