bluuebunny/crossref_metadata_2025_split huggingface dataset:
De-hulling facilitates seed germination and ethylene production in dormant and non-dormant rice genotypes
Authors: BARIK J. K. , MOHAPATRA P. K. , PRADHAN S. K. , KARIALI E. 
Published: November 2017

SUMMARYThe hull or husk of rice, comprising the lemma and palea, provides a fitting enclosure for the caryopsis. The physiological significance of the hull in seed dormancy has been examined by comparing the effects of its removal on germination, seed vigour, assimilate mobilization and ethylene production in germinating seeds of six rice genotypes; two each belonging to dormant, semi-dormant and non-dormant groups. Hull removal promoted the above parameters in all three categories of seeds, but the effect was relatively higher in dormant seeds compared with less dormant categories. Ethylene production in non-dormant seeds was initiated after imbibition of water, normally before visible emergence of the radicle. It peaked when the radicle began to protrude and declined thereafter. In comparison, dormant seeds produced very low levels of ethylene during germination; however, hull removal resulted in a dramatic rise in its production. Overall, ethylene evolution at the radicle protrusion stage correlated negatively with germination time. It was concluded that ethylene production starts with breaking of the caryopsis coat and peaks when the radicle ruptures it completely, at the stage of radicle visible emergence. Removal of the hull facilitates germination and ethylene production can be a good indicator for the progress of germination.
Determinants of yield and quality in winter rapeseed (Brassica napus L.) under Mediterranean conditions
Authors: TSIALTAS J. T. , PAPANTONIOU A. N. , BAXEVANOS D. , PAPADOPOULOS I. I. , KARAIVAZOGLOU N. , MASLARIS N. , PAPAKOSTA D. K. 
Published: November 2017

SUMMARYWinter rapeseed was introduced into Greece a decade ago to provide oil for biodiesel. To identify agronomic traits affecting yield and quality, three hybrids and an inbred line were tested over two seasons (2005–2006 and 2006–2007) and four locations, in central and northern Greece, varying in pedo-climatic conditions. The large variations in seed yield, quality and agronomic traits were largely ascribed to location; in contrast, cultivar accounted for ⩽0·010 of the variation for many traits. Below 40°N, rapeseed is a risky crop; short season, high temperatures and low rainfall during reproductive growth diminished seed yield and oil content, increased oleic and erucic acid and minimized linolenic acid. A hybrid, Exact, with tall stature and large seeds was adaptive to such conditions. The most productive location had dense stands with tall plants bearing numerous pods on the main raceme. At the site with the coldest winter, plant density (PD) was lowest (ca. 30 plants/m2) but rapeseed compensated by producing large seeds, with high oil content and harvest index (HI). A biplot revealed that the hybrid Excalibur, outperforming the other cultivars for oil content in six out of eight trials, produced the highest and most stable oil yield. Combined data showed that seed yield and oil yield were positively correlated with PD, seed size and HI and negatively to the number of pods on branches and per plant. Large seeds had high seed oil content. Oleic acid was negatively correlated to linolenic acid concentration. High temperatures and low rainfall favoured oleic acid, which was positively associated with seed number per pod.
Genetic diversity and evolution ofPneumocystisfungi infecting wild Southeast Asian murid rodents
Authors: Latinne Alice , Bezé François , Delhaes Laurence , Pottier Muriel , Gantois Nausicaa , Nguyen Julien , Blasdell Kim , Dei-Cas Eduardo , Morand Serge , Chabé Magali 
Published: November 2017

AbstractPneumocystisorganisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity ofPneumocystisorganisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts.PneumocystisDNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of thePneumocystislineages retrieved in our phylogenetic trees correspond to knownPneumocystisspecies, but some of the remaining lineages may correspond to new undescribed species. Most of thesePneumocystisspecies infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity ofPneumocystisspecies infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history amongPneumocystisand their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation ofPneumocystisand their hosts.
Agency rulemaking in a separation of powers system
Authors: Potter Rachel Augustine , Shipan Charles R. 
Published: November 2017

AbstractRulemaking gives agencies significant power to change public policy, but agencies do not exercise this power in a vacuum. The separation of powers system practically guarantees that, at times, agencies will be pushed and pulled in different directions by Congress and the president. We argue that these forces critically affect the volume of rules produced by an agency. We develop an account of agency rulemaking in light of these factors and test our hypotheses on a data set of agency rules from 1995 to 2007. Our results show that even after accounting for factors specific to each agency, agencies do, in fact, adjust the quantity of rules they produce in response to separation of powers oversight. Further analysis shows that the president’s influence is limited to those agencies that he has made a priority.
Product options for enhanced retirement income
Authors: Donnelly C. , Young J. 
Published: November 2017

AbstractA new stream of research proposes how people can increase their income in retirement by pooling their mortality risk. How one of these mortality risk-sharing rules could be implemented in practice, as part of a retirement income scheme, is considered. A potential advantage of the scheme is that a retiree’s housing wealth can be monetised to provide an income stream. This would mean that retirees can continue living in their home, without needing to downsize. It may be most attractive to the millions of single pensioners, particularly those who are “asset-rich and cash-poor”. Other types of assets that could be included and how to mitigate selection risks are assessed. A way of smoothing the raw mortality credits in order to make the scheme more appealing to potential members is proposed. An illustrative premium calculation suggests that the cost of the smoothing is very small compared to the potential attractiveness of an enhanced, smoothed income.
Effect of translational couch shifts in volumetric modulated arc therapy (VMAT) plans and predicting its impact on daily dose delivery
Authors: Padannayil Noufal M. , Abdullah Kallikuzhiyil K. , Subha Pallimanhayil A. R. , Sadanadan Sanudev 
Published: November 2017

AbstractAimTo evaluate the impact of couch translational shifts on dose–volume histogram (DVH) and radiobiological parameters [tumour control probability (TCP), equivalent uniform dose (EUD) and normal tissue complication probability (NTCP)] of volumetric modulated arc therapy (VMAT) plans and to develop a simple and swift method to predict the same online, on a daily basis.MethodsIn total, ten prostate patients treated with VMAT technology were selected for this study. The plans were generated using Eclipse TPS and delivered using Clinac ix LINAC equipped with a Millennium 120 multileaf collimator. In order to find the effect of systematic translational couch shifts on the DVH and radiobiological parameters, errors were introduced in the clinically accepted base plan with an increment of 1 mm and up to 5 mm from the iso-centre in both positive and negative directions of each of the three axis, x [right–left (R-L)], y [superior–inferior (S-I)] and z [anterior–posterior (A-P)]. The percentages of difference in these parameters (∆D, ∆TCP, ∆EUD and ∆NTCP) were analyzed between the base plan and the error introduced plans. DVHs of the base plan and the error plans were imported into the MATLAB software (R2013a) and an in-house MATLAB code was generated to find the best curve fitted polynomial functions for each point on the DVH, there by generating predicted DVH for planning target volume (PTV), clinical target volume (CTV) and organs at risks (OARs). Functions f(x, vj), f(y, vj) and f(z, vj) were found to represent the variation in the dose when there are couch translation shifts in R-L, S-I and A-P directions, respectively. The validation of this method was done by introducing daily couch shifts and comparing the treatment planning system (TPS) generated DVHs and radiobiological parameters with MATLAB code predicted parameters.ResultsIt was noted that the variations in the dose to the CTV, due to both systematic and random shifts, were very small. For CTV and PTV, the maximum variations in both DVH and radiobiological parameters were observed in the S-I direction than in the A-P or R-L directions. ∆V70 Gy and ∆V60 Gy of the bladder varied more due to S-I shift whereas, ∆V40 Gy, ∆EUD and ∆NTCP varied due to A-P shifts. All the parameters in rectum were most affected by the A-P shifts than the shifts in other two directions. The maximum percentage of deviation between the TPS calculated and MATLAB predicted DVHs of plans were calculated for targets and OARs and were found to be less than 0·5%.ConclusionThe variations in the parameters depend upon the direction and magnitude of the shift. The DVH curves generated by the TPS and predicted by the MATLAB showed good correlation.
Semi-permanent tattoos in breast radiotherapy (STaBRad) study: a randomised-controlled clinical trial comparing the ‘Precision Plus Micropigmentation System’ to permanent skin tattoos in radical breast radiotherapy patients
Authors: O’Neill A. , McAleer S. , McCarty H. , Clarke J. , Drake A. , Hurwitz J. , Clayton A. , Shaw E. , Vennard H. , Gray S. , Robinson J. , Simpson B. , Stevenson M. , Hanna G. G. , O’Sullivan J. M. 
Published: November 2017

AbstractIntroduction and purposeAccurate and reproducible patient positioning is a critical step in radiotherapy for breast cancer. This has seen the use of permanent skin markings becoming standard practice in many centres. Permanent skin markings may have a negative impact on long-term cosmetic outcome, which may in turn, have psychological implications in terms of body image. The aim of this study was to investigate the feasibility of using a semi-permanent tattooing device for the administration of skin marks for breast radiotherapy set-up.Materials and methodsThis was designed as a phase II double-blinded randomised-controlled study comparing our standard permanent tattoos with the Precision Plus Micropigmentation (PPMS) device method. Patients referred for radical breast radiotherapy were eligible for the study. Each study participant had three marks applied using a randomised combination of the standard permanent and PPMS methods and was blinded to the type of each mark. Follow up was at routine appointments until 24 months post radiotherapy. Participants and a blind assessor were invited to score the visibility of each tattoo at each follow-up using a Visual Analogue Scale. Tattoo scores at each time point and change in tattoo scores at 24 months were analysed by a general linear model using the patient as a fixed effect and the type of tattoo (standard or research) as covariate. A simple questionnaire was used to assess radiographer feedback on using the PPMS.ResultsIn total, 60 patients were recruited to the study, of which 55 were available for follow-up at 24 months. Semi-permanent tattoos were more visible at 24 months than the permanent tattoos. Semi-permanent tattoos demonstrated a greater degree of fade than the permanent tattoos at 24 months (final time point) post completion of radiotherapy. This was not statistically significant, although it was more apparent for the patient scores (p=0·071) than the blind assessor scores (p=0·27). No semi-permanent tattoos required re-marking before the end of radiotherapy and no adverse skin reactions were observed.ConclusionThe PPMS presents a safe and feasible alternative to our permanent tattooing method. An extended period of follow-up is required to fully assess the extent of semi-permanent tattoo fade.
Looking Within or Reaching Out?: The Effects of Religion on Private School Enrollments in an Era of School Choice
Authors: Pelz Mikael L. , den Dulk Kevin R. 
Published: November 2017

AbstractThe proliferation of school choice policies has expanded schooling options for parents. While this trend coincides with a decline in private school enrollment, it is unclear how these policies affect enrollment among various religious traditions and religiosity. We study the impact of religion and school choice initiatives on the decision to enroll in different types of private schools in this new era. We evaluate two concurrent theories on the role of religion in the enrollment trends of private schools. Religious school enrollment may be motivated by (1) the desire to transmit a religious social identity, or (2) the secular goods associated with religious-based education. Using state-level data, we test these two explanations by estimating fixed effects regression models predicting private school market shares between 1993–2011 among different religious groups. We find support for both theories, particularly for a robust private school market aided by school choice policies.
LRPPRC-mediated folding of the mitochondrial transcriptome
Authors: Siira Stefan J. , Spåhr Henrik , Shearwood Anne-Marie J. , Ruzzenente Benedetta , Larsson Nils-Göran , Rackham Oliver , Filipovska Aleksandra 
Published: November 2017

AbstractThe expression of the compact mammalian mitochondrial genome requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, and here we use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA–protein interactions in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome. We demonstrate that the LRPPRC–SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization, and polyadenylation. Our findings reveal a general mechanism where extensive RNA–protein interactions ensure that RNA is accessible for its biological functions.
Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients
Authors: Hawley Alyse K. , Nobu Masaru K. , Wright Jody J. , Durno W. Evan , Morgan-Lang Connor , Sage Brent , Schwientek Patrick , Swan Brandon K. , Rinke Christian , Torres-Beltrán Monica , Mewis Keith , Liu Wen-Tso , Stepanauskas Ramunas , Woyke Tanja , Hallam Steven J. 
Published: November 2017

AbstractMicrobial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant “microbial dark matter” phylum Marinimicrobia along defined energy gradients. We show that evolutionary diversification of major Marinimicrobia clades appears to be closely related to energy yields, with increased co-metabolic interactions in more deeply branching clades. Several of these clades appear to participate in the biogeochemical cycling of sulfur and nitrogen, filling previously unassigned niches in the ocean. Notably, two Marinimicrobia clades, occupying different energetic niches, express nitrous oxide reductase, potentially acting as a global sink for the greenhouse gas nitrous oxide.
To infinity and some glimpses of beyond
Authors: Kevrekidis Panayotis G. , Siettos Constantinos I. , Kevrekidis Yannis G. 
Published: November 2017

AbstractWhen mathematical and computational dynamic models reach infinity in finite time, extending analysis and numerics beyond it becomes a notorious challenge. We suggest how, upon suitable transformations, it may become possible to go beyond infinity with the solution becoming again well behaved and the computations continuing normally. In our Ordinary Differential Equation examples the crossing of infinity occurs instantaneously. For Partial Differential Equations, the crossing of infinity may persist for finite time, necessitating the introduction of buffer zones, within which an appropriate transformation is adaptively identified. Along the path of our analysis, we present a regularization process via complexification and explore its impact on the dynamics; we also discuss a set of compactification transformations and their intuitive implications. This methodology could be useful toward a systematic approach to bypassing infinity and thus going beyond it in a broader range of evolution equation models.
Structural insights into Legionella RidL-Vps29 retromer subunit interaction reveal displacement of the regulator TBC1D5
Authors: Bärlocher Kevin , Hutter Cedric A. J. , Swart A. Leoni , Steiner Bernhard , Welin Amanda , Hohl Michael , Letourneur François , Seeger Markus A. , Hilbi Hubert 
Published: November 2017

AbstractLegionella pneumophilacan cause Legionnaires’ disease and replicates intracellularly in a distinctLegionella-containing vacuole (LCV). LCV formation is a complex process that involves a plethora of type IV-secreted effector proteins. The effector RidL binds the Vps29 retromer subunit, blocks retrograde vesicle trafficking, and promotes intracellular bacterial replication. Here, we reveal that the 29-kDa N-terminal domain of RidL (RidL2–281) adopts a “foot-like” fold comprising a protruding β-hairpin at its “heel”. The deletion of the β-hairpin, the exchange to Glu of Ile170in the β-hairpin, or Leu152in Vps29 abolishes the interaction in eukaryotic cells and in vitro. RidL2–281or RidL displace the Rab7 GTPase-activating protein (GAP) TBC1D5 from the retromer and LCVs, respectively, and TBC1D5 promotes the intracellular growth ofL. pneumophila. Thus, the hydrophobic β-hairpin of RidL is critical for binding of theL. pneumophilaeffector to the Vps29 retromer subunit and displacement of the regulator TBC1D5.
Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors
Authors: Dahlin Jayme L. , Nelson Kathryn M. , Strasser Jessica M. , Barsyte-Lovejoy Dalia , Szewczyk Magdalena M. , Organ Shawna , Cuellar Matthew , Singh Gurpreet , Shrimp Jonathan H. , Nguyen Nghi , Meier Jordan L. , Arrowsmith Cheryl H. , Brown Peter J. , Baell Jonathan B. , Walters Michael A. 
Published: November 2017

AbstractMany compounds with potentially reactive chemical motifs and poor physicochemical properties are published as selective modulators of biomolecules without sufficient validation and then propagated in the scientific literature as useful chemical probes. Several histone acetyltransferase (HAT) inhibitors with these liabilities are now routinely used to probe epigenetic pathways. We profile the most commonly used HAT inhibitors and confirm that the majority of them are nonselective interference compounds. Most (15 out of 23, 65%) of the inhibitors are flagged by ALARM NMR, an industry-developed counter-screen for promiscuous compounds. Biochemical counter-screens confirm that most of these compounds are either thiol-reactive or aggregators. Selectivity panels show many of these compounds modulate unrelated targets in vitro, while several also demonstrate nonspecific effects in cell assays. These data demonstrate the usefulness of performing counter-screens for bioassay promiscuity and assay interference, and raise caution about the utility of many widely used, but insufficiently validated, compounds employed in chemical biology.
Shaping bacterial population behavior through computer-interfaced control of individual cells
Authors: Chait Remy , Ruess Jakob , Bergmiller Tobias , Tkačik Gašper , Guet Călin C. 
Published: November 2017

AbstractBacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell–cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.
Structure and immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein
Authors: Battles Michael B. , Más Vicente , Olmedillas Eduardo , Cano Olga , Vázquez Mónica , Rodríguez Laura , Melero José A. , McLellan Jason S. 
Published: November 2017

AbstractHuman metapneumovirus (hMPV) is a frequent cause of bronchiolitis in young children. Its F glycoprotein mediates virus–cell membrane fusion and is the primary target of neutralizing antibodies. The inability to produce recombinant hMPV F glycoprotein in the metastable pre-fusion conformation has hindered structural and immunological studies. Here, we engineer a pre-fusion-stabilized hMPV F ectodomain and determine its crystal structure to 2.6 Å resolution. This structure reveals molecular determinants of strain-dependent acid-induced fusion, as well as insights into refolding from pre- to post-fusion conformations. A dense glycan shield at the apex of pre-fusion hMPV F suggests that antibodies against this site may not be elicited by host immune responses, which is confirmed by depletion studies of human immunoglobulins and by mouse immunizations. This is a major difference with pre-fusion F from human respiratory syncytial virus (hRSV), and collectively our results should facilitate development of effective hMPV vaccine candidates.