bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine-learning Algorithm to Predict Hypotension Based on High-fidelity Arterial Pressure Waveform Analysis
Authors: Hatib Feras , Jian Zhongping , Buddi Sai , Lee Christine , Settels Jos , Sibert Karen , Rinehart Joseph , Cannesson Maxime
Published: June 2018

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background

With appropriate algorithms, computers can learn to detect patterns and associations in large data sets. The authors’ goal was to apply machine learning to arterial pressure waveforms and create an algorithm to predict hypotension. The algorithm detects early alteration in waveforms that can herald the weakening of cardiovascular compensatory mechanisms affecting preload, afterload, and contractility.

Methods

The algorithm was developed with two different data sources: (1) a retrospective cohort, used for training, consisting of 1,334 patients’ records with 545,959 min of arterial waveform recording and 25,461 episodes of hypotension; and (2) a prospective, local hospital cohort used for external validation, consisting of 204 patients’ records with 33,236 min of arterial waveform recording and 1,923 episodes of hypotension. The algorithm relates a large set of features calculated from the high-fidelity arterial pressure waveform to the prediction of an upcoming hypotensive event (mean arterial pressure < 65 mmHg). Receiver-operating characteristic curve analysis evaluated the algorithm’s success in predicting hypotension, defined as mean arterial pressure less than 65 mmHg.

Results

Using 3,022 individual features per cardiac cycle, the algorithm predicted arterial hypotension with a sensitivity and specificity of 88% (85 to 90%) and 87% (85 to 90%) 15 min before a hypotensive event (area under the curve, 0.95 [0.94 to 0.95]); 89% (87 to 91%) and 90% (87 to 92%) 10 min before (area under the curve, 0.95 [0.95 to 0.96]); 92% (90 to 94%) and 92% (90 to 94%) 5 min before (area under the curve, 0.97 [0.97 to 0.98]).

Conclusions

The results demonstrate that a machine-learning algorithm can be trained, with large data sets of high-fidelity arterial waveforms, to predict hypotension in surgical patients’ records.
Vomer Flap: A Golden Tool for the Treatment of Cleft Palate
Authors: Díaz Rafael Gómez , Díaz Oswaldo Javir Gómez , Gallardo Luz Elena Rueda
Published: June 2018

Despite the lack of consensus regarding the treatment of labio-palatal clefts, each treatment protocol is the expression of an individual perspective that accumulates the experience of each multidisciplinary group, which all pursue the same goal: to achieve adequate language development with the lowest possible impact on facial growth. To achieve this, a management scheme has been developed, this exploits vomer flaps for the closure of palatal clefts and limits dissections in the palatine segments. Modifications are presented in the design and dissection of vomer flaps, so as to use the largest amount of mucosal tissue available, thus facilitating closure of the different clefts, particularly in Veau Group III clefts.
Objective Assessment of Lingual Nerve Microsurgical Reconstruction
Authors: Biglioli Federico , Lozza Alessandro , Colletti Giacomo , Allevi Fabiana
Published: June 2018

Lingual nerve (LN) injury is one of the most serious consequences of oral surgery. Prompt microsurgical reconstruction of the nerve can alleviate most of those symptoms leading to satisfactory functional recovery.

Thirty-five patients with partial to complete LN injury underwent surgery in the period between January 2006 and May 2015. All patients underwent a preoperative clinical and neurological evaluation with the assessment of lingual tactile and pain sensory thresholds and masseteric inhibitory reflex.

All patients underwent explorative surgery and direct microneurorrhaphy of distal and proximal stumps in case of complete lesion, while the removal of traumatic neuroma and the following microneurorrhaphy of distal and proximal stumps of the injured nerve was performed in case of incomplete lesion. Nerve grafting has always been avoided because of distal stump mobilization obtained by severing the submandibular branch of the LN.

All patients but 1 exhibited good recovery of tongue sensation, never complete, both clinically and electrophysiologically: recovery of the excitability of masseteric inhibitory reflex suppression components SP1 and SP2 was observed, often with increased latencies but consistent with a functional recovery.

All patients feeling pain preoperatively experienced complete relief of algic symptoms.

The early microsurgical approach is the most suitable choice for the treatment of LN injuries.
Supraclavicular Dermo-Muscular Agenesis in an Infant With Gorlin-Goltz Syndrome
Authors: Demir Canser Yilmaz , Kocak Omer Faruk
Published: June 2018

Gorlin–Goltz syndrome (GGS) is generally characterized by the dysplasia of the skin, skeletal system, and connective tissue. In this paper, a 40-day-old baby presented with dermal and muscular agenesis on the right supraclavicular region and clinically diagnosed with GGS will be reported. To the best of the authors’ knowledge, this is the first report of GGS in the literature accompanied by muscular agenesis and also this is the youngest patient diagnosed with GGS.
Light bullets in a time-delay model of a wide-aperture mode-locked semiconductor laser
Authors: Pimenov A. , Javaloyes J. , Gurevich S. V. , Vladimirov A. G.
Published: June 2018

Recently, a mechanism of formation of light bullets (LBs) in wide-aperture passively mode-locked lasers was proposed. The conditions for existence and stability of these bullets, found in the long cavity limit, were studied theoretically under the mean field (MF) approximation using a Haus-type model equation. In this paper, we relax the MF approximation and study LB formation in a model of a wide-aperture three section laser with a long diffractive section and short absorber and gain sections. To this end, we derive a non-local delay-differential equation (NDDE) model and demonstrate by means of numerical simulations that this model supports stable LBs. We observe that the predictions about the regions of existence and stability of the LBs made previously using MF laser models agree well with the results obtained using the NDDE model. Moreover, we demonstrate that the general conclusions based upon the Haus model that regard the robustness of the LBs remain true in the NDDE model valid beyond the MF approximation, when the gain, losses and diffraction per cavity round trip are not small perturbations anymore.

This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.
Dissipative solitons with extreme spikes in the normal and anomalous dispersion regimes
Authors: Akhmediev N. , Soto-Crespo J. M. , Vouzas Peter , Devine N. , Chang Wonkeun
Published: June 2018

Prigogine’s ideas of systems far from equilibrium and self-organization (Prigogine & Lefever. 1968
J. Chem. Phys.
48
, 1695–1700 (
doi:10.1063/1.1668896
); Glansdorff & Prigogine. 1971
Thermodynamic theory of structures, stability and fluctuations
. New York, NY/London, UK: Wiley) deeply influenced physics, and soliton science in particular. These ideas allowed the notion of solitons to be extended from purely integrable cases to the concept of dissipative solitons. The latter are qualitatively different from the solitons in integrable and Hamiltonian systems. The variety in their forms is huge. In this paper, one recent example is considered—dissipative solitons with extreme spikes (DSESs). It was found that DSESs exist in large regions of the parameter space of the complex cubic–quintic Ginzburg–Landau equation. A continuous variation in any of its parameters results in a rich structure of bifurcations.

This article is part of the theme issue ‘Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)’.
The macaque anterior cingulate cortex translates counterfactual choice value into actual behavioral change
Authors: Fouragnan E , Chau BKH , Folloni D , Kolling N , Verhagen L , Klein-Flügge Miriam , Tankelevitch L , Papageorgiou GK , Aubry JF , Sallet J , Rushworth MFS
Published: June 2018

The neural mechanisms mediating sensory-guided decision making have received considerable attention but animals often pursue behaviors for which there is currently no sensory evidence. Such behaviors are guided by internal representations of choice values that have to be maintained even when these choices are unavailable. We investigated how four macaque monkeys maintained representations of the value of counterfactual choices – choices that could not be taken at the current moment but which could be taken in the future. Using functional magnetic resonance imaging, we found two different patterns of activity co-varying with values of counterfactual choices in a circuit spanning hippocampus, anterior lateral prefrontal cortex, and anterior cingulate cortex (ACC). ACC activity also reflected whether the internal value representations would be translated into actual behavioral change. To establish the causal importance of ACC for this translation process, we used a novel technique, Transcranial Focused Ultrasound Stimulation, to reversibly disrupt ACC activity.
Fast fronto-parietal cortical dynamics of conflict detection and context updating in a flanker task
Authors: Brydges Christopher R. , Barceló Francisco , Nguyen An T. , Fox Allison M.
Published: June 2018

The traditional N2 and P3 components of the human event-related potential (ERP) have been associated with cognitive control. However, recent research has found that the traditional target P3 consists of a mixture of stimulus-locked, response-locked, and latency variable P3-like positivities that can be functionally and topographically dissociated from one another. The current study aimed to extend previous results by examining target N2 and P3-like subcomponents indexing conflict detection and context updating at both low- and high-order levels in the neural hierarchy during control of target detection in a flanker task. Electroencephalographic (EEG) signals were recorded from 45 young adults while they completed a hybrid go/nogo flanker task, and Residue Iteration Decomposition (RIDE) was applied to functionally dissociate these peaks and establish their roles in conflict detection and context updating. Frequentist and Bayesian analyses showed a stimulus-locked frontal N2 revealing early conflict detection and fast categorization of nogo, congruous and incongruous trials, resulting in subsequent frontal P3-like activity (high-order context updating) elicited by infrequent nogo trials in the latency-variable RIDE cluster, and by the perceptually difficult incongruous trials in the response-locked cluster. In turn, the perceptually easier and more frequent congruous trials did not elicit frontal P3-like activity, although all trial types did elicit parietally distributed P3-like activity (low-order context updating), mostly within the latency-variable cluster. These novel findings support the presence of up to three distinct high-order task-set units regulating performance in our flanker task, as indexed by split-second, dynamic information transmission across frontal and parietal scalp regions.
A hybrid mortality prediction model of patients with cavitary pulmonary carcinomas
Authors: Saad Maliazurina
Published: June 2018

To date, developing a reliable mortality prediction model remains challenging. Although clinical predictors like age, gender and laboratory results are of considerable predictive value, the accuracy often ranges only between 60-80%. In this study, we proposed prediction models built on the basis of clinical covariates with adjustment for additional variables that was radiographically induced. The proposed method exhibited a high degree of prediction accuracy of between 83-92%, as well as overall improvement of between 6-20% in all other metrics, such as ROC Area, False Positive Rates, Recall and Root Mean Square Error. We provide a proof of concept that there is an added value for incorporating the additional variables while predicting 24-month mortality in pulmonary carcinomas patients with cavitary lesions. It is hoped that the findings will be clinically useful to the medical community.
Thought experiment: Decoding cognitive processes from the fMRI data of one individual
Authors: Wegrzyn Martin , Aust Joana , Barnstorf Larissa , Gippert Magdalena , Harms Mareike , Hautum Antonia , Heidel Shanna , Herold Friederike , Hommel Sarah M. , Knigge Anna-Katharina , Neu Dominik , Peters Diana , Schaefer Marius , Schneider Julia , Vormbrock Ria , Zimmer Sabrina M. , Woermann Friedrich G. , Labudda Kirsten
Published: June 2018

Cognitive processes, such as the generation of language, can be mapped onto the brain using fMRI. These maps can in turn be used for decoding the respective processes from the brain activation patterns. Given individual variations in brain anatomy and organization, analyzes on the level of the single person are important to improve our understanding of how cognitive processes correspond to patterns of brain activity. They also allow to advance clinical applications of fMRI, because in the clinical setting making diagnoses for single cases is imperative. In the present study, we used mental imagery tasks to investigate language production, motor functions, visuo-spatial memory, face processing, and resting-state activity in a single person. Analysis methods were based on similarity metrics, including correlations between training and test data, as well as correlations with maps from the NeuroSynth meta-analysis. The goal was to make accurate predictions regarding the cognitive domain (e.g. language) and the specific content (e.g. animal names) of single 30-second blocks. Four teams used the dataset, each blinded regarding the true labels of the test data. Results showed that the similarity metrics allowed to reach the highest degrees of accuracy when predicting the cognitive domain of a block. Overall, 23 of the 25 test blocks could be correctly predicted by three of the four teams. Excluding the unspecific rest condition, up to 10 out of 20 blocks could be successfully decoded regarding their specific content. The study shows how the information contained in a single fMRI session and in each of its single blocks can allow to draw inferences about the cognitive processes an individual engaged in. Simple methods like correlations between blocks of fMRI data can serve as highly reliable approaches for cognitive decoding. We discuss the implications of our results in the context of clinical fMRI applications, with a focus on how decoding can support functional localization.
Estimating the overlap between two malaria parasites’ var repertoires
Authors: Larremore Daniel B.
Published: June 2018

Measuring the overlap between the var gene repertoires of two P. falciparum parasites is, in principle, easy. Each parasite genome contains a repertoire of approximately 60 var genes, so upon fully sequencing both parasites’ genomes, the number of shared var sequences can be directly counted. In practice, however, only a fraction of each parasite’s var repertoire is likely to be sampled due to the difficulties of whole-genome sequencing for var genes and the stochastic sample provided by PCR techniques. Although a method exists for quantifying repertoire overlap under these subsampled conditions, its bias is well documented and the uncertainty of its estimates cannot be quantified. Here we derive and validate a method to rigorously estimate the repertoire overlap between two parasites from the overlap of their subsampled repertoires. By solving a Bayesian inference problem, this method takes into account the rates of subsampling and produces unbiased and Bayes-optimal estimates of overlap. In addition, it provides a natural framework for computing the uncertainty of its estimates, and can be used in laboratory planning by quantifying the tradeoff between sequencing effort and uncertainty.
Direct immunosensing of avian influenza A virus in whole blood using hybrid nanocomposites
Authors: Buozis John , Ahmed Syed Rahin , Chand Rohit , Nagy Éva , Neethirajan Suresh
Published: June 2018

A sandwich-based electrochemical immunosensor was designed for detection of avian influenza virus (AIV) strains H5N1 and H4N6. This sensor was developed using gold-graphene nanocomposites, immobilized viral antibodies, and CdTe quantum dot electrochemical tagging. The nanocomposites were formed by the simultaneous reduction of a gold salt and graphene using hydroquinone as the reducing agent, thus producing non-spherical gold nanoparticles on graphene sheets. Viral antibodies were immobilized on nanocomposites and CdTe quantum dots through N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide and N-hydroxysuccinimide chemistry. Cyclic voltammetry studies were used to validate the detection of H5N1 surface protein and H4N6 inactivated virus. The immunosensor detected H5 protein in phosphate buffer solution (pH 7.4) with a limit of detection (LOD) of 10 fg/mL and a linear detection range was established for 10 ng/mL to 10 pg/mL. The biosensor detected H4N6 in three parts diluted whole chicken blood with a LOD of 1.28×10−7hemagglutinating units (HAU). Commercial ELISA testing for H5N1 and H4N6 showed limits of detection of 10 ng/mL and 0.128 HAU, respectively. The sensor showed 106-fold increased detection of H4N6 virus in blood in comparison to its commercial ELISA kit counterpart. The developed immunosensor effectively change the way avian influenza is detected, monitored, and controlled; transforming time-consuming reactive methods, into rapid predictive technology.
Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California
Authors: Hanna Zachary R. , Dumbacher John P. , Bowie Rauri C.K. , Wall Jeffrey D.
Published: June 2018

We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity acrossS. occidentalispopulations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all CaliforniaS. occidentalispopulations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations ofS. o. occidentalisandS. o. caurinain northern California. The San Diego CountyS. o. occidentalispopulation was substantially diverged from the other threeS. occidentalispopulations. These whole-genome data support a pattern of isolation-by-distance across spotted owl populations in California, rather than elevated differentiation between currently recognized subspecies.
Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria
Authors: Cekanaviciute Egle , Pröbstel Anne-Katrin , Thomann Anna , Runia Tessel F. , Casaccia Patrizia , Sand Ilana Katz , Crabtree Elizabeth , Singh Sneha , Morrissey John , Barba Patrick , Gomez Refujia , Knight Rob , Mazmanian Sarkis K. , Graves Jennifer , Cree Bruce A.C. , Zamvil Scott S. , Baranzini Sergio E.
Published: June 2018

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by adaptive and innate immune system dysregulation. Recent work has revealed moderate alteration of gut microbial communities in subjects with MS and in experimental, induced models. However, a mechanistic understanding linking the observed changes in the microbiota and the presence of the disease is still missing. Chloroform-resistant, spore-forming bacteria have been shown to exhibit immunomodulatory properties in vitro and in vivo, but they have not yet been characterized in the context of human disease. This study addresses the community composition and immune function of this bacterial fraction in MS. We identify MS-associated spore-forming taxa and show that their presence correlates with impaired differentiation of IL-10 secreting, regulatory T lymphocytes in-vitro. Colonization of antibiotic-treated mice with spore-forming bacteria allowed us to identify some bacterial taxa favoring IL-10+ lymphocyte differentiation and others inducing differentiation of pro-inflammatory, IFNγ+ T lymphocytes. However, when fed into antibiotic-treated mice, both MS and control derived spore-forming bacteria were able to induce immunoregulatory responses.

Our analysis also identified Akkermansia muciniphila as a key organism that may interact either directly or indirectly with spore-forming bacteria to exacerbate the inflammatory effects of MS-associated gut microbiota. Thus, changes in the spore-forming fraction may influence T lymphocyte-mediated inflammation in MS. This experimental approach of isolating a subset of microbiota based on its functional characteristics may be useful to investigate other microbial fractions at greater depth.

Importance

Despite the rapid emergence of microbiome related studies in human diseases, few go beyond a simple description of relative taxa levels in a select group of patients. Our study integrates computational analysis with in vitro and in vivo exploration of inflammatory properties of both complete microbial communities and individual taxa, revealing novel functional associations. We specifically show that while small differences exist between the microbiomes of MS patients and healthy subjects, these differences are exacerbated in the chloroform resistant fraction. We further demonstrate that, when purified from MS patients, this fraction is associated with impaired immunomodulatory responses in vitro.
New Evidence of the Earliest Domestic Dogs in the Americas
Authors: Perri Angela , Widga Chris , Lawler Dennis , Martin Terrance , Loebel Thomas , Farnsworth Kenneth , kohn Luci , Buenger Brent
Published: June 2018

The domestication of dogs probably occurred in Eurasia by 16,000 years ago, with the initial peopling of the Americas potentially happening around the same time. Dogs were long thought to have accompanied the first migrations into the Americas, but conclusive evidence for Paleoindian dogs is lacking. The direct dating of two dogs from the Koster site (Greene Co., Illinois) and a newly-described dog from the Stilwell II site (Pike Co., Illinois) to between 10,190-9,630 cal BP represents the earliest evidence of domestic dogs in the Americas and individual dog burials in worldwide archaeological record. The over 4,500 year discrepancy between the timing of initial human migration into the Americas and the earliest evidence for domesticated dogs suggests either earlier dogs are going unseen or unidentified or dogs arrived later with a subsequent human migration.
Cofactors revisited – predicting the impact of flavoprotein-related diseases on a genome scale
Authors: Wegrzyn Agnieszka B. , Stolle Sarah , Rienksma Rienk A. , Martins dos Santos Vítor A. P. , Bakker Barbara M. , Suarez-Diez Maria
Published: June 2018

Flavin adenine dinucleotide (FAD) and its precursor flavin mononucleotide (FMN) are redox cofactors that are required for the activity of more than hundred human enzymes. Mutations in the genes encoding these proteins cause severe phenotypes, including a lack of energy supply and accumulation of toxic intermediates. Ideally, patients should be diagnosed before they show symptoms so that treatment and/or preventive care can start immediately. This can be achieved by standardized newborn screening tests. However, many of the flavin-related diseases lack appropriate biomarker profiles. Genome-scale metabolic models can aid in biomarker research by predicting altered profiles of potential biomarkers. Unfortunately, current models, including the most recent human metabolic reconstructions Recon and HMR, typically treat enzyme-bound flavins incorrectly as free metabolites. This in turn leads to artificial degrees of freedom in pathways that are strictly coupled. Here, we present a reconstruction of human metabolism with a curated and extended flavoproteome. To illustrate the functional consequences, we show that simulations with the curated model – unlike simulations with earlier Recon versions - correctly predict the metabolic impact of multiple-acyl-CoA-dehydrogenase deficiency as well as of systemic flavin-depletion. Moreover, simulations with the new model allowed us to identify a larger number of biomarkers in flavoproteome-related diseases, without loss of accuracy. We conclude that adequate inclusion of cofactors in constraint-based modelling contributes to higher precision in computational predictions.
NaturalWolbachiainfections are common in the major malaria vectors in Central Africa
Authors: Ayala Diego , Akone-Ella Ousman , Rahola Nil , Kengne Pierre , Ngangue Marc F. , Mezeme Fabrice , Makanga Boris K. , Costantini Carlo , Simard Frédéric , Prugnolle Franck , Roche Benjamin , Duron Olivier , Paupy Christophe
Published: June 2018

During the last decade, the endosymbiont bacteriumWolbachiahas emerged as a biological tool for vector disease control. However, for long time, it was believed thatWolbachiawas absent in natural populations ofAnopheles.The recent discovery that species within theAnopheles gambiaecomplex hostsWolbachiain natural conditions has opened new opportunities for malaria control research in Africa. Here, we investigated the prevalence and diversity ofWolbachiainfection in 25 AfricanAnophelesspecies in Gabon (Central Africa). Our results revealed the presence ofWolbachiain 16 of these species, including the major malaria vectors in this area. The infection prevalence varied greatly among species, confirming that sample size is a key factor to detect the infection. Moreover, our sequencing and phylogenetic analyses showed the important diversity ofWolbachiastrains that infectAnopheles.Co-evolutionary analysis unveiled patterns ofWolbachiatransmission withinAnophelesspecies, suggesting that past independent acquisition events were followed by co-cladogenesis. The large diversity ofWolbachiastrains that infect natural populations ofAnophelesoffers a promising opportunity to select suitable phenotypes for suppressingPlasmodiumtransmission and/or manipulatingAnophelesreproduction, which in turn could be used to reduce the malaria burden in Africa.
Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK
Authors: Farrer A. G. , Bekvalac J. , Redfern R. , Gully N. , Dobney K. , Cooper A. , Weyrich L. S.
Published: June 2018

The trillions of microorganisms that live in association with the human body (microbiota) are critical for human health and disease, but there is a limited understanding of how cultural and environmental factors shaped our microbiota diversity through time. However, biomolecular remnants of the human oral microbiota - recovered from the calcified dental plaque (calculus) of our long-dead ancestors - are providing a new means of exploring this key relationship of our evolutionary history. Here, we correlate extensive experimental, archaeological, and biological metadata with 128 ancient dental calculus specimens from Medieval and Post-Medieval London, UK (1066 – 1853 CE). We identify a significant association between microbiota and oral geography (i.e. tooth type and tooth surface), which has confounded ancient microbiota studies to date. By controlling for oral geography, however, we identify the first associations between ancient microbiota and cultural and environmental signatures. We find significant links between ancient British microbiota structure and health, including skeletal markers of stress that may reflect low socioeconomic status. Furthermore, this study provides baseline data to explore factors that drive microbiota differentiation within and between ancient populations and highlights the potential of ancient microbiota to infer detailed health and sociocultural information about the past.
The evolutionary potential of diet-dependent effects on lifespan and fecundity in a multi-parental population ofDrosophila melanogaster
Authors: Ng’oma Enoch , Fidelis Wilton , Middleton Kevin M. , King Elizabeth G.
Published: June 2018

The nutritional conditions experienced by a population play a major role in shaping trait evolution in many taxa. Constraints exerted by nutrient limitation or nutrient imbalance can influence the maximal value that fitness components such as reproduction and lifespan attains, and organisms may shift how resources are allocated to different structures and functions in response to changes in nutrition. Whether the phenotypic changes associated with changes in nutrition represent an adaptive response is largely unknown. Further, it is unclear whether the response of fitness components to diet even has the potential to evolve in most systems. In this study, we use an admixed multiparental population ofDrosophila melanogasterreared in three different diet conditions to estimate quantitative genetic parameters for lifespan and fecundity. We find significant genetic variation for both traits in our population and show that lifespan has moderate to high heritabilities within diets. Genetic correlations for lifespan between diets were significantly less than one, demonstrating a strong genotype by diet interaction. These findings demonstrate substantial standing genetic variation in our population that is comparable to natural populations and highlights the potential for adaptation to changing nutritional environments.
RNA-Seq analysis of compatible and incompatible styles of Pyrus species at the beginning of pollination
Authors: Guan Yaqin , Li Kun , Wang Yongzhang , Ma Chunhui
Published: June 2018

In Rosaceae, incompatible pollen can penetrate into the style during the gametophytic self-incompatibility response. It is therefore considered a stylar event rather than a stigmatic event. In this study, we explored the differences in gene expression between compatibility and incompatibility in the early stage of pollination. The self-compatible pear variety “Jinzhuili” is a naturally occurring bud mutant from “Yali”, a leading Chinese native cultivar exhibiting typical gametophytic self-incompatibility. We collected the styles of ‘Yali’ and ‘Jinzhuili’ at 0.5 and 2 h after self-pollination and then performed high-throughput sequencing. According to the pathway enrichment analysis of the differentially expressed genes, “plant-pathogen interaction” was the most represented pathway. Quantitative PCR was used to validate these differential genes. The expression levels of genes related to pollen growth and disease inhibition, such as LRR (LEUCINE-RICH REPEAT EXTENSIN), resistance, and defensin, differed significantly between compatible and incompatible pollination. Interestingly, at 0.5 h, most of these genes were upregulated in the compatible pollination system compared with the incompatible pollination system. Calcium ion transport, which requires ATPase, also demonstrated upregulated expression. In summary, the self-incompatibility reaction was initiated when the pollen came into contact with the stigma.
Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation
Authors: Veil Marina , Yampolsky Lev , Grüning Björn , Onichtchouk Daria
Published: June 2018

The zebrafish embryo is mostly transcriptionally quiescent during the first 10 cell cycles, until the main wave of Zygotic Genome Activation (ZGA) occurs, accompanied by fast chromatin remodeling. At ZGA, homologs of mammalian stem cell transcription factors (TFs) Pou5f3, Nanog and Sox19b bind to thousands of developmental enhancers to initiate transcription. So far, how these TFs influence chromatin dynamics at ZGA has remained unresolved. To address this question, we analyzed nucleosome positions in wild-type and Maternal-Zygotic (MZ) mutants for pou5f3 and nanog by MNase-seq. We show that Nanog, Sox19b and Pou5f3 bind to the High Nucleosome Affinity Regions (HNARs). HNARs are spanning over 600 bp, featuring high in vivo and predicted in vitro nucleosome occupancy and high predicted propeller twist DNA shape value. We suggest a two-step nucleosome destabilization-depletion model, where the same intrinsic DNA properties of HNAR promote both high nucleosome occupancy and differential binding of TFs. In the first step, already prior to ZGA, Pou5f3 and Nanog destabilize nucleosomes on HNAR centers genome-wide. In the second step, post-ZGA, Nanog, Pou5f3 and SoxB1 maintain open chromatin state on the subset of HNARs, acting synergistically. Nanog binds to the HNAR center, while the Pou5f3 stabilizes the flanks. The HNAR model will provide a useful tool for genome regulatory studies in the variety of biological systems.
Dynamics of spreading microbial swarms and films
Authors: Srinivasan Siddarth , Kaplan C. Nadir , Mahadevan L.
Published: June 2018

Bacterial swarming and biofilm formation are collective multicellular phenomena through which diverse microbial species colonize and spread over water-permeable tissue. During both modes of surface translocation, fluid uptake and transport play a key role in shaping the overall morphology and spreading dynamics. Here, usingBacillus subtilisas our model experimental system, we develop a generalized two-phase thin-film model that couples hydrodynamics, mechanics, osmotic flux and nutrient transport to describe the expansion of both highly motile bacterial swarms, and sessile bacterial biofilms. We show that swarm expansion corresponds to steady-state solutions in a nutrient-rich, capillarity dominated regime. In contrast, biofilm colony growth is described by transient solutions associated with a nutrient-limited, extracellular polymer stress driven limit. We apply our unified framework to explain a range of recent experimental observations associated with the shape, form and dynamics ofEscherichia coliandBacillus subtilisswarms and biofilms. Our results demonstrate how hydrodynamics and transport serve as key physical constraints in regulating biological organization and function in microbial communities.
Targeting BMI1 and MCL1 for Lung Adenocarcinoma Treatment
Authors: Lin Erh-Hsuan , Hsu Chiung-Fang , Jan Yi-Hua , Lin Tsung-Hsien , Chang Hsiang-Yi , Cheng Chun-Ming , Hsu Hui-Jan , Chen Wei-Wei , Chen Bo-Hung , Tsai Hsing-Fang , Li Jung-Jung , Huang Chi-Ying , Chuang Shih-Hsien , Chang Jia-Ming , Hsiao Michael , Wu Cheng-Wen
Published: June 2018

Lung cancer is the leading cause of cancer-associated death worldwide. Early metastasis and the recurrence remain major challenges for lung cancer treatment in clinic. Targeting the cancer stemness could be a potential strategy to restrain tumor progression. In the current study, we found that in lung adenocarcinoma (LAC), BMI1 and MCL1 play crucial roles in invasion, chemo-resistance, and tumor initiation. JNK signaling is a link between oncogenic pathway or environment stress to cancer stemness. The activation of JNK, either by EGFR or chemotherapy agent, stabilized BMI1 and MCL1 proteins through suppressing the expression of E3-ubiquitin ligase HUWE1. In lung cancer patient samples, high level of BMI1 is correlated with poor survival, and the expression of BMI1 is positively correlated with MCL1. A novel small-molecule BI-44 was synthesized, which effectively suppressed BMI1/MCL1 expression and inhibited tumor formation and progression in preclinical models. Targeting BMI1/MCL1 provides the basis for a new therapeutic approach in the treatment of LAC.
A hyperactive variant of theEscherichia colianaerobic transcription factor FNR enhances ionizing radiation resistance
Authors: Bruckbauer Steven T. , Trimarco Joseph D. , Wood Elizabeth A. , Battista John R. , Cox Michael M.
Published: June 2018

We have previously generated four replicate populations of ionizing radiation (IR)- resistantEscherichia colithough directed evolution. Sequencing of isolates from these populations revealed that mutations affecting DNA repair (through DNA double-strand break repair and replication restart), ROS amelioration, and cell wall metabolism were prominent. Three mutations involved in DNA repair explained the IR resistance phenotype in one population, and similar DNA repair mutations were prominent in two others. The remaining population, IR-3-20, had no mutations in the key DNA repair proteins, suggesting that it had taken a different evolutionary path to IR resistance. Here, we present evidence that a variant of the anaerobic metabolism transcription factor FNR isolated from population IR-3-20 can play a role in IR resistance. An FNR variant is unique to IR-3-20 and suggests a role for altered global metabolism through the FNR regulon as a means for experimentally-evolved IR resistance.
A RhoA–YAP–c-Myc signaling axis promotes the development of polycystic kidney disease
Authors: Cai Jing , Song Xuewen , Wang Wei , Watnick Terry , Pei York , Qian Feng , Pan Duojia
Published: June 2018

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited disorder caused by mutations in PKD1 or PKD2 and affects one in 500–1000 humans. Limited treatment is currently available for ADPKD. Here we identify the Hippo signaling effector YAP and its transcriptional target, c-Myc, as promoters of cystic kidney pathogenesis. While transgenic overexpression of YAP promotes proliferation and tubule dilation in mouse kidneys, loss of YAP/TAZ or c-Myc suppresses cystogenesis in a mouse ADPKD model resulting from Pkd1 deficiency. Through a comprehensive kinase inhibitor screen based on a novel three-dimensional (3D) culture of Pkd1 mutant mouse kidney cells, we identified a signaling pathway involving the RhoGEF (guanine nucleotide exchange factor) LARG, the small GTPase RhoA, and the RhoA effector Rho-associated kinase (ROCK) as a critical signaling module between PKD1 and YAP. Further corroborating its physiological importance, inhibition of RhoA signaling suppresses cystogenesis in 3D culture of Pkd1 mutant kidney cells as well as Pkd1 mutant mouse kidneys in vivo. Taken together, our findings implicate the RhoA–YAP–c-Myc signaling axis as a critical mediator and potential drug target in ADPKD.
SwissFEL Aramis beamline photon diagnostics
Authors: Juranić Pavle , Rehanek Jens , Arrell Christopher A. , Pradervand Claude , Ischebeck Rasmus , Erny Christian , Heimgartner Peter , Gorgisyan Ishkhan , Thominet Vincent , Tiedtke Kai , Sorokin Andrey , Follath Rolf , Makita Mikako , Seniutinas Gediminas , David Christian , Milne Christopher J. , Lemke Henrik , Radovic Milan , Hauri Christoph P. , Patthey Luc
Published: June 2018

The SwissFEL Aramis beamline, covering the photon energies between 1.77 keV and 12.7 keV, features a suite of online photon diagnostics tools to help both users and FEL operators in analysing data and optimizing experimental and beamline performance. Scientists will be able to obtain information about the flux, spectrum, position, pulse length, and arrival time jitter versus the experimental laser for every photon pulse, with further information about beam shape and size available through the use of destructive screens. This manuscript is an overview of the diagnostics tools available at SwissFEL and presents their design, working principles and capabilities. It also features new developments like the first implementation of a THz-streaking based temporal diagnostics for a hard X-ray FEL, capable of measuring pulse lengths to 5 fs r.m.s. or better.
A comparative experimental and theoretical investigation of hydrogen-bond, halogen-bond and π–π interactions in the solid-state supramolecular assembly of 2- and 4-formylphenyl arylsulfonates
Authors: Andleeb Hina , Khan Imtiaz , Bauzá Antonio , Tahir Muhammad Nawaz , Simpson Jim , Hameed Shahid , Frontera Antonio
Published: June 2018

To explore the operational role of noncovalent interactions in supramolecular architectures with designed topologies, a series of solid-state structures of 2- and 4-formylphenyl 4-substituted benzenesulfonates was investigated. The compounds are 2-formylphenyl 4-methylbenzenesulfonate, C14H12O4S, 3a, 2-formylphenyl 4-chlorobenzenesulfonate, C13H9ClO4S, 3b, 2-formylphenyl 4-bromobenzenesulfonate, C13H9BrO4S, 3c, 4-formylphenyl 4-methylbenzenesulfonate, C14H12O4S, 4a, 4-formylphenyl 4-chlorobenzenesulfonate, 4b, C13H9ClO4S, and 4-formylphenyl 4-bromobenzenesulfonate, C13H9BrO4S, 4c. The title compounds were synthesized under basic conditions from salicylaldehyde/4-hydroxybenzaldehydes and various aryl sulfonyl chlorides. Remarkably, halogen-bonding interactions are found to be important to rationalize the solid-state crystal structures. In particular, the formation of O...X (X = Cl and Br) and type I X...X halogen-bonding interactions have been analyzed by means of density functional theory (DFT) calculations and characterized using Bader's theory of `atoms in molecules' and molecular electrostatic potential (MEP) surfaces, confirming the relevance and stabilizing nature of these interactions. They have been compared to antiparallel π-stacking interactions that are formed between the arylsulfonates.
A comparative study of the influence of political systems on the art markets of East Asia and China
Authors: Robertson Iain
Published: June 2018

Purpose

The purpose of this paper is to define and characterise the precise nature of these cultural systems and their resulting impact on the respective art and artists of each territory, by ascertaining the impact on those systems of their respective government and governance.

Design/methodology/approach

This paper is based on three approaches to art market modelling. All three are based on political ideologies. The first, which typifies the art markets of Western Europe and the USA, is predicated on a Pluralist and Neo-Liberal ideology. The others correspond to the systems of government in China, Taiwan, South Korea and Japan.

Findings

It has been shown in this paper that political systems and their accompanying ideology, born of cultural preferences, have impacted on the art markets of China, Taiwan, South Korea and Japan. It has been demonstrated that all four markets are employing variants of the international norm.

Research limitations/implications

The art that is exported from East Asia will only be accepted by East Asian national markets when East Asian art markets exercise a majority influence on emerging and transitional markets. It is not the intention of this paper to pursue this thought beyond the possibility that it may occur.

Practical implications

The ineluctable conclusion is, therefore, that the global art market is moving towards a bipolar affair.

Social implications

This paper also suggests the disengagement of East Asian and Chinese “culture” and art from a global (western) norm and production and consumption of national culture in East Asia by East Asians.

Originality/value

The paper looks (for the first time) at the direct (and subliminal) influence of political systems on art markets and the consequential effects of political ideology on the art markets of East Asia and China. The paper arrives at a series of precise definitions for the way that these art markets operate.
Assessment on external corrosion rates for API pipeline steels exposed to acidic sand-clay soil
Authors: Quej-Ake L.M. , Contreras A. , Liu H.B , Alamilla J.L. , Sosa E.
Published: June 2018

Purpose

The purpose of this paper is to study the susceptibility to corrosion processes of X60, X65 and X70 steels immersed in sand-clay soil with pH 3.0, using electrochemical techniques, scanning electron microscopy (SEM), energy dispersive spectroscopy and X-ray diffraction (XRD).

Design/methodology/approach

Natural acidic soil sample was collected as close as possible to buried pipes (1.2 m in depth) in a Right of Way from south of Mexico. Both steels and soil were characterized through SEM and XRD. Then, open circuit potential was recorded for all steels exposed to soil at different exposure times. Thus, the electrochemical impedance spectroscopy (EIS) was traced, and anodic polarization curves were obtained.

Findings

The steel corrosion processes started when the active sites were exposed to natural acidic soil. However, corrosion rates decreased for three steels as immersion time increased, obtaining the highest corrosion rate for X60 steel (0.46 mm/year for 5 h). This behavior could be attributed to corrosion products obtained at different exposure times. While, 5 h after removing corrosion products, X65 steel was more susceptible to corrosion (1.29 mm/year), which was corroborated with EIS analysis. Thus, corrosion products for the three steels exposed to natural acidic soil depended on different microstructures, percentage of pearlite and ferrite phases, in which different corrosion processes could occur. Therefore, the active sites for carbon steel surfaces could be passivated with corrosion products.

Practical implications

The paper identifies the any implication for the research.

Originality/value

Some anodic peaks could be caused by metallic dissolution and was recorded using high positive polarization (high field of perturbation). In addition, the inductive effects and diffusion process were interpreted at low frequency ranges using EIS. According to X-ray diffraction (XRD), acidic soil had Muscovite containing aluminum and iron phases that were able to generate hydrogen proton at the presence of water; it might be promoted at the beginning of deterioration on low carbon steels. Steel surface cleaning after removing corrosion products was considered to study the possible diffusion phenomena on damaged steel surfaces using EIS.