bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the best distribution and effective interval using statistical characterization of uncertain variables
Authors: Joo Minho , Doh Jaehyeok , Lee Jongsoo
Published: November 2017

In this paper, an algorithm for estimating the best distribution about data containing uncertainties is proposed. The proposed algorithm combines sequence statistical modeling (SSM) and a method for determining the minimum experimental data. SSM is a method for selecting the best distribution about data using a goodness of fit (GoF) test and a comparison of the likelihood. The method used to determine the minimum experimental data determines the minimum data needed to an estimate the best distribution. The SSM presented herein is a method for selecting a suitable data distribution when considering only a parametric distribution. Thus, in this paper, the SSM was improved in order to select the correct distribution of both parametric and non-parametric distributions simultaneously. In addition, with the existing method for determining the minimum data, the data should be added based on actual experiments when the results data show an insufficient number, and there is a limitation in that the designers cannot broadly identify the data required. To overcome this limitation, SSM and random sampling are applied to the method to determine the minimum data, and thereby, ensure that the designer knows the approximate minimum data needed. To verify the validity of the proposed algorithm, it was applied to a real world case study on determining multiple statistical parameters in the bolt fastening problem. The sequence of verification methods used is as follows: First, the best distribution of the bearing surface and thread friction coefficient estimated by the proposed algorithm and based on a normal distribution are selected as comparison targets. Second, the bearing surface and thread friction coefficient data are sampled within the 95% confidence interval of the two distributions. Third, the reliability of the sampled friction coefficient data are compared using a Monte-Carlo simulation and an equation to calculate the bolt fastening force. In this study, the effectiveness of the proposed algorithm is validated.

Highlights The algorithm to determine appropriate probability distribution of data is proposed. The sequential statistical modeling is improved to consider both parametric and non-parametric distribution. The method to determine minimum data is improved to verify sufficiency of data without actual experiments. The effectiveness and validation of the proposed algorithm is verified using the bolt-fastening data.
Comparison of miniaturized percutaneous nephrolithotomy and flexible ureterorenoscopy for moderate size renal stones in elderly patients
Authors: Ozgor Faruk , Yanaral Fatih , Savun Metin , Ozdemir Harun , Caglar Ufuk , Sarilar Omer
Published: November 2017

Life expectancy has become longer, thus the number of elderly people who require treatment for nephrolithiasis has increased. We aimed to analyze the efficacy of flexible ureterorenoscopy (f‐URS) and miniaturized percutaneous nephrolithotomy (mPNL) in the management of 10 and 30 mm renal stones in patients aged >60 years. In prospective non‐randomized series, the data of patients who underwent f‐URS or mPNL for kidney stones between July 2013 and July 2016 were analyzed. The procedure was accepted as successful if the patient was achieved complete stone clearance according to CT imaging between 1–3 months postoperatively. In total 60 patients and 58 patients were underwent f‐URS and mPNL, respectively. The mean operation time, fluoroscopy time and hospitalization time were significantly shorter for the f‐URS (p < 0.001, p < 0.001, p < 0.001, respectively). According to Clavien classification system, complication rates were not significantly different between the groups (p = 0.673). The stone‐free rate was 81.7% for the f‐URS group and 77.6% for the mPNL group after a single‐session procedure (p = 0.747). Calcium oxalate monohydrate stones were the most common stone type in both groups. In multivariate analysis, multiple stones localization was only independent factor to predict complications. Our study had showed that both f‐URS and mPNL are effective treatment modalities for 10–30‐mm renal stones in elderly patients. Additionally, presence of stones in multiple location was the only predictive factor for complication development.
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

The 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

Winter 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

Pneumocystisorganisms 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.
A healthy, premoult adult king penguin (Aptenodytes patagonicus) with a markedly twisted beak
Authors: Corbeau Alexandre , Bost Charles-André
Published: November 2017

In seabirds, diet and feeding methods are related to the species morphology (Croxall, Evans, & Schreiber, 1984). Species that feed on living, mobile resources rely on a fully operational beak to efficiently seize, kill and swallow their prey. This is particularly important to diving species, such as penguins, that are highly time constrained when searching for prey at depth—as air-breathing predators, penguins must maximise their feeding efficiency during their deep foraging dives (Wilson & Wilson, 1990). This is why the observation of free-ranging penguins with physical abnormalities in good body condition is so rare. Here we report a highly unusual observation of a premoult adult king penguin (Aptenodytes patagonicusMiller) in good body condition with a highly anomalous beak.
Agency rulemaking in a separation of powers system
Authors: Potter Rachel Augustine , Shipan Charles R.
Published: November 2017

Rulemaking 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

A 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

Aim

To 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.

Methods

In 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.

Results

It 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%.

Conclusion

The 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

Introduction and purpose

Accurate 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 methods

This 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.

Results

In 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.

Conclusion

The 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

The 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.
Does the Motor System Facilitate Spatial Imagery?
Authors: Krüger Markus , Krist Horst
Published: November 2017

Abstract. Recent studies have ascertained a link between the motor system and imagery in children. A motor effect on imagery is demonstrated by the influence of stimuli-related movement constraints (i. e., constraints defined by the musculoskeletal system) on mental rotation, or by interference effects due to participants’ own body movements or body postures. This link is usually seen as qualitatively different or stronger in children as opposed to adults. In the present research, we put this interpretation to further scrutiny using a new paradigm: In a motor condition we asked our participants (kindergartners and third-graders) to manually rotate a circular board with a covered picture on it. This condition was compared with a perceptual condition where the board was rotated by an experimenter. Additionally, in a pure imagery condition, children were instructed to merely imagine the rotation of the board. The children’s task was to mark the presumed end position of a salient detail of the respective picture. The children’s performance was clearly the worst in the pure imagery condition. However, contrary to what embodiment theories would suggest, there was no difference in participants’ performance between the active rotation (i. e., motor) and the passive rotation (i. e., perception) condition. Control experiments revealed that this was also the case when, in the perception condition, gaze shifting was controlled for and when the board was rotated mechanically rather than by the experimenter. Our findings indicate that young children depend heavily on external support when imagining physical events. Furthermore, they indicate that motor-assisted imagery is not generally superior to perceptually driven dynamic imagery.
Age Differences in the Desirability of Narcissism
Authors: Berenson Kathy R. , Ellison William D. , Clasing Rachel
Published: November 2017

Abstract. Young adult narcissism has been the focus of much discussion in the personality literature and popular press. Yet no previous studies have addressed whether there are age differences in the relative desirability of narcissistic and non-narcissistic self-descriptions, such as those presented as answer choices on the Narcissistic Personality Inventory (NPI; Raskin & Hall, 1979 ). In Study 1, younger age was associated with less negative evaluations of narcissistic (vs. non-narcissistic) statements in general, and more positive evaluations of narcissistic statements conveying leadership/authority. In Study 2, age was unrelated to perceiving a fictional target person as narcissistic, but younger age was associated with more positive connotations for targets described with narcissistic statements and less positive connotations for targets described with non-narcissistic statements, in terms of the inferences made about the target’s altruism, conscientiousness, social status, and self-esteem. In both studies, age differences in the relative desirability of narcissism remained statistically significant when adjusting for participants’ own narcissism, and the NPI showed measurement invariance across age. Despite perceiving narcissism similarly, adults of different ages view the desirability of NPI answer choices differently. These results are important when interpreting cross-generational differences in NPI scores, and can potentially facilitate cross-generational understanding.
Colli and Jones Receive 2017 Study of the Earth’s Deep Interior Focus Group Award for Graduate Research
Authors:   AGU
Published: November 2017

Lorenzo Colli and Tim Jones will receive the 2017 Study of the Earth’s Deep Interior Focus Group Award for Graduate Research at the 2017 American Geophysical Union Fall Meeting, to be held 11–15 December in New Orleans, La. This award is given annually “in recognition of advances that contribute to the understanding of the deep interior of the Earth or other planetary bodies using a broad range of observational, experimental, and/or theoretical approaches.”
Erratum: Organocatalyzed synthesis of fluorinated poly(aryl thioethers)
Authors: Park Nathaniel H. , Gomes Gabriel dos Passos , Fevre Mareva , Jones Gavin O. , Alabugin Igor V. , Hedrick James L.
Published: November 2017

A correction to this article has been published and is linked from the HTML version of this article.
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

The 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

Microbial 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

When 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

Legionella 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

Many 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

Bacteria 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

Human 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.
Activating cobalt(II) oxide nanorods for efficient electrocatalysis by strain engineering
Authors: Ling Tao , Yan Dong-Yang , Wang Hui , Jiao Yan , Hu Zhenpeng , Zheng Yao , Zheng Lirong , Mao Jing , Liu Hui , Du Xi-Wen , Jaroniec Mietek , Qiao Shi-Zhang
Published: November 2017

Designing high-performance and cost-effective electrocatalysts toward oxygen evolution and hydrogen evolution reactions in water–alkali electrolyzers is pivotal for large-scale and sustainable hydrogen production. Earth-abundant transition metal oxide-based catalysts are particularly active for oxygen evolution reaction; however, they are generally considered inactive toward hydrogen evolution reaction. Here, we show that strain engineering of the outermost surface of cobalt(II) oxide nanorods can turn them into efficient electrocatalysts for the hydrogen evolution reaction. They are competitive with the best electrocatalysts for this reaction in alkaline media so far. Our theoretical and experimental results demonstrate that the tensile strain strongly couples the atomic, electronic structure properties and the activity of the cobalt(II) oxide surface, which results in the creation of a large quantity of oxygen vacancies that facilitate water dissociation, and fine tunes the electronic structure to weaken hydrogen adsorption toward the optimum region.
Author Correction: Injection of embryonic stem cell-derived macrophages ameliorates fibrosis in a murine model of liver injury
Authors: Haideri Sharmin S. , McKinnon Alison C. , Taylor A. Helen , Kirkwood Phoebe , Lewis Philip J. Starkey , O’Duibhir Eoghan , Vernay Bertrand , Forbes Stuart , Forrester Lesley M.
Published: November 2017

The following ethical statement was added to the end of the Methods section in the HTML and PDF versions of this Article: The animal experiments were approved and conducted in accordance to the UK Home Office regulations (Project Licence No.70/7847). Erratum to: doi:10.1038/s41536-017-0017-0
Dynamic, continuous multitasking training leads to task-specific improvements but does not transfer across action selection tasks
Authors: Bender Angela D. , Filmer Hannah L. , Naughtin Claire K. , Dux Paul E.
Published: November 2017

The ability to perform multiple tasks concurrently is an ever-increasing requirement in our information-rich world. Despite this, multitasking typically compromises performance due to the processing limitations associated with cognitive control and decision-making. While intensive dual-task training is known to improve multitasking performance, only limited evidence suggests that training-related performance benefits can transfer to untrained tasks that share overlapping processes. In the real world, however, coordinating and selecting several responses within close temporal proximity will often occur in high-interference environments. Over the last decade, there have been notable reports that training on video action games that require dynamic multitasking in a demanding environment can lead to transfer effects on aspects of cognition such as attention and working memory. Here, we asked whether continuous and dynamic multitasking training extends benefits to tasks that are theoretically related to the trained tasks. To examine this issue, we asked a group of participants to train on a combined continuous visuomotor tracking task and a perceptual discrimination task for six sessions, while an active control group practiced the component tasks in isolation. A battery of tests measuring response selection, response inhibition, and spatial attention was administered before and immediately after training to investigate transfer. Multitasking training resulted in substantial, task-specific gains in dual-task ability, but there was no evidence that these benefits generalized to other action control tasks. The findings suggest that training on a combined visuomotor tracking and discrimination task results in task-specific benefits but provides no additional value for untrained action selection tasks.
Hydrogen Adsorption on Nearly Zigzag-Edged Nanoribbons: A Density Functional Theory Study
Authors: Mananghaya Michael Rivera , Santos Gil Nonato , Yu Dennis , Stampfl Catherine
Published: November 2017

The realistic shapes of N doped graphene nanoribbons (GNRs) can be realized by considering nearly zigzag-edged (NZE) imperfections and pyridine defects (3NV). The paper focuses on NZE-GNRs with 3NV that is populated by Scandium abbreviated as Sc/NZE-3NVGNRs. Systematic calculations have clarified roles of the nano-shapes of NZE-3NVGNRs in its formation, energetics, stability and electron states functionalized with Sc using density functional theory (DFT) formalisms. According to DFT calculations, the magnitude of the spin that is attributed to the rise of magnetic order is closely linked to the altered shape of the ribbon edges. Also, calculations show that the stability of Sc functionalization at the 3NV and NZE site is thermodynamically stable and is dictated by a strong binding energy (BE). The magnitude of the BE is enhanced when the zigzag edge is short or the ribbon width is narrow, suggesting a reduced clustering of Sc atoms over the Sc-doped NZE-3NVGNRs. Results also show that as the length of the zigzag edge in Sc/NZE-3NVGNRs increases it creates considerable distortion on the appearance of the structure. Finally, the Sc/NZE-3NVGNRs as a potential candidate for hydrogen storage was evaluated and it was found that it could adsorb multiple hydrogen molecules.
Individuals of the common Namib Day Gecko vary in how adaptive simplification alters sprint biomechanics
Authors: Collins Clint E. , Higham Timothy E.
Published: November 2017

Locomotion inextricably links biomechanics to ecology as animals maneuver through mechanically challenging environments. Faster individuals are more likely to escape predators, surviving to produce more offspring. Fast sprint speed evolved several times in lizards, including geckos. However, the underlying mechanisms determining performance await discovery in many clades. Novel morphological structures influence these mechanisms by adding complexity to the government of locomotion. Gecko adhesion coevolves with modified muscles, tendons, and reflexes. We explored how the Namib Day Gecko, Rhoptropus afer, sprints on ecologically relevant substrates. Locomotion requires that many moving parts of the animal work together; we found knee and ankle extension are the principal drivers of speed on a level surface while contributions to sprinting uphill are more evenly distributed among motions of the femur, knee, and ankle. Although geckos are thought to propel themselves with specialized, proximally located muscles that retract and rotate the femur, we show with path analysis that locomotion is altered in this secondarily terrestrial gecko. We present evidence of intraspecific variation in the use of adhesive toe pads and suggest that the subdigital adhesive toe pad may increase sprint speed in this species. We argue kinematics coevolve with the secondarily terrestrial lifestyle of this species.
Design of Cultured Neuron Networks in vitro with Predefined Connectivity Using Asymmetric Microfluidic Channels
Authors: Gladkov Arseniy , Pigareva Yana , Kutyina Daria , Kolpakov Vladimir , Bukatin Anton , Mukhina Irina , Kazantsev Victor , Pimashkin Alexey
Published: November 2017

The architecture of neuron connectivity in brain networks is one of the basic mechanisms by which to organize and sustain a particular function of the brain circuitry. There are areas of the brain composed of well-organized layers of neurons connected by unidirectional synaptic connections (e.g., cortex, hippocampus). Re-engineering of the neural circuits with such a heterogeneous network structure in culture may uncover basic mechanisms of emergent information functions of these circuits. In this study, we present such a model designed with two subpopulations of primary hippocampal neurons (E18) with directed connectivity grown in a microfluidic device with asymmetric channels. We analysed and compared neurite growth in the microchannels with various shapes that promoted growth dominantly in one direction. We found an optimal geometric shape features of the microchannels in which the axons coupled two chambers with the neurons. The axons grew in the promoted direction and formed predefined connections during the first 6 days in vitro (DIV). The microfluidic devices were coupled with microelectrode arrays (MEAs) to confirm unidirectional spiking pattern propagation through the microchannels between two compartments. We found that, during culture development, the defined morphological and functional connectivity formed and was maintained for up to 25 DIV.
Cascading predator effects in a Fijian coral reef ecosystem
Authors: Rasher Douglas B. , Hoey Andrew S. , Hay Mark E.
Published: November 2017

Coral reefs are among Earth’s best-studied ecosystems, yet the degree to which large predators influence the ecology of coral reefs remains an open and contentious question. Recent studies indicate the consumptive effects of large reef predators are too diffuse to elicit trophic cascades. Here, we provide evidence that such predators can produce non-consumptive (fear) effects that flow through herbivores to shape the distribution of seaweed on a coral reef. This trophic cascade emerged because reef topography, tidal oscillations, and shark hunting behaviour interact to create predictable “hot spots” of fear on the reef where herbivores withhold feeding and seaweeds gain a spatial refuge. Thus, in risky habitats, sharks can exert strong ecological impacts even though they are trophic generalists that rarely feed. These findings contextualize the debate over whether predators influence coral reef structure and function and move us to ask not if, but under what specific conditions, they generate trophic cascades.
Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stage in wheat
Authors: Hussain Babar , Lucas Stuart James , Ozturk Levent , Budak Hikmet
Published: November 2017

Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder’s Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
Dye-sensitized solar cells based on a push-pull zinc phthalocyanine bearing diphenylamine donor groups: computational predictions face experimental reality
Authors: Milan Riccardo , Selopal Gurpreet Singh , Cavazzini Marco , Orlandi Simonetta , Boaretto Rita , Caramori Stefano , Concina Isabella , Pozzi Gianluca
Published: November 2017

Computational studies have suggested that the integration of secondary amine as donor groups in the structure of unsymmetrical zinc phthalocyanine (ZnPc) should have positive effects on photovoltaic performance, once the molecule is integrated as light harvester in dye sensitized solar cells (DSSCs). Aiming at obtaining experimental confirmation, we synthesized a peripherally substituted push-pull ZnPc bearing three electron donating diphenylamine substituents and a carboxylic acid anchoring group and integrated it as sensitizer in TiO2-based DSSCs. Detailed functional characterization of solar energy converting devices resulted in ruling out the original hypothesis. The causes of this discrepancy have been highlighted, leading to a better understanding of the conditions for an effective design of push-pull diarylamino substituted ZnPcs for DSSCs.
Health and disease phenotyping in old age using a cluster network analysis
Authors: Valenzuela Jesus Felix , Monterola Christopher , Tong Victor Joo Chuan , Ng Tze Pin , Larbi Anis
Published: November 2017

Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree. We show, by way of a correspondence analysis between the two sets of clusters, that they correspond to coarse-grained and fine-grained structure of the network relationships. The clusters obtained from the minimum spanning tree mapped to various conceptual domains and corresponded to physiological and syndromic states. Hierarchical ordering of these clusters identified six common themes based on interactions with physiological systems and common underlying substrates of age-associated morbidity and disease chronicity, functional disability, and quality of life. These findings provide a starting point for indepth analyses of ageing that incorporate immunologic, metabolomic and proteomic biomarkers, and ultimately offer low-level-based typologies of healthy and unhealthy ageing.