bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing
Authors: Goldstein Sarah , Beka Lidia , Graf Joerg , Klassen Jonathan L. 
Published: July 2018

AbstractBackgroundShort-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have extreme %GC content remains challenging. Long-read, single-molecule sequencing technologies such as the Oxford Nanopore MinION have the potential to overcome these difficulties, although the best approach for harnessing their potential remains poorly evaluated.ResultsWe sequenced nine bacterial genomes spanning a wide range of GC contents using Illumina MiSeq and Oxford Nanopore MinION sequencing technologies to determine the advantages of each approach, both individually and combined. Assemblies using only MiSeq reads were highly accurate but lacked contiguity, a deficiency that was partially overcome by adding MinION reads to these assemblies. Even more contiguous genome assemblies were generated by using MinION reads for initial assembly, but these were more error-prone and required further polishing. This was especially pronounced when Illumina libraries were biased, as was the case for our strains with both high and low GC content. Increased genome contiguity dramatically improved the annotation of insertion sequences and secondary metabolite biosynthetic gene clusters, likely because long-reads can disambiguate these highly repetitive but biologically important genomic regions.ConclusionsGenome assembly using short-reads is challenged by repetitive sequences and extreme GC contents. Our results indicate that these difficulties can be largely overcome by using single-molecule, long-read sequencing technologies such as the Oxford Nanopore MinION. Using MinION reads for assembly followed by polishing with Illumina reads generated the most contiguous genomes and enabled the accurate annotation of important but difficult to sequence genomic features such as insertion sequences and secondary metabolite biosynthetic gene clusters. The combination of Oxford Nanopore and Illumina sequencing is cost effective and dramatically advances studies of microbial evolution and genome-driven drug discovery.
Searching for structure in collective systems
Authors: Twomey Colin R. , Hartnett Andrew T. , Grobis Matthew M. , Romanczuk Pawel 
Published: July 2018

AbstractCollective systems such as fish schools, bird flocks, and neural networks are comprised of many mutually-influencing individuals, often without long-term leaders, well-defined hierarchies, or persistent relationships. The remarkably organized group-level behaviors readily observable in these systems contrast with the ad hoc, often difficult to observe, and complex interactions among their constituents. While these complex individual-level dynamics are ultimately the drivers of group-level coordination, they do not necessarily offer the most parsimonious description of a group’s macroscopic properties. Rather, the factors underlying group organization may be better described at some intermediate, mesoscopic scale. We introduce a novel method from information-theoretic first principles to find a compressed description of a system based on the actions and mutual dependencies of its constituents, thus revealing the natural structure of the collective. We emphasize that this method is computationally tractable and requires neither pairwise nor Gaussian assumptions about individual interactions.
An EDS1 EP-domain surface mediating timely transcriptional reprogramming of immunity genes
Authors: Bhandari Deepak D. , Lapin Dmitry , Kracher Barbara , von Born Patrick , Bautor Jaqueline , Niefind Karsten , Parker Jane E. 
Published: July 2018

AbstractPlant intracellular NLR receptors recognize pathogen interference to trigger immunity. NLR signalling mechanisms have not been resolved. Enhanced disease susceptibility 1 (EDS1) heterodimers are recruited by Toll-interleukin1-receptor domain NLRs (TNLs) to transcriptionally mobilize resistance pathways. Using an Arabidopsis EDS1 heterodimer crystal structure we interrogate the conserved but functionally uncharacterized EDS1 α-helical EP-domain. We identify EP-domain positively charged residues lining a cavity that are essential for TNL immunity signalling, beyond heterodimer formation. Mutating arginine (R493) to alanine creates a weak EDS1 allele which disables TNL immunity against bacteria producing a virulence factor, coronatine (COR). Arabidopsis plants expressing EDS1R493A are slow to mobilize defence gene expression changes, independently of COR. The transcriptional delay has severe consequences for pathogen resistance and for countering bacterial COR. We uncover a set of host immunity genes whose repression by COR is blocked by wild-type EDS1 but not by EDS1R493A in the TNL response. These data uncover an EDS1 signalling surface lining the heterodimer EP-domain cavity which confers timely transcriptional reprogramming of host defence pathways and blocks bacterial virulence in NLR receptor immunity.
Sensing Plant Physiology and Environmental Stress by Automatically Tracking Fj and Fi Features in PSII Chlorophyll Fluorescence Induction
Authors: Xia Qian , Tan Jinglu , Cheng Shengyang , Jiang Yongnian , Guo Ya 
Published: July 2018

AbstractFollowing a step excitation, chlorophyll fluorescence (ChlF) from photosystem II of a dark-adapted plant leaf exhibits the well-known OJIP pattern. The OJIP induction has been widely applied in plant science, agriculture engineering, and environmental engineering. While the J and I phases are related to transitions of photochemical reaction redox states, characteristic fluorescence intensities for the two phases (Fj and Fi) are often treated as fixed time points in routine measurement and thus do not account for variations in plant and experimental conditions, which (1) neglects the time differences, potentially useful information for characterizing plant status and environmental factors, and (2) leads to errors in measured Fj and Fi values. In this work, a method for consistent measurement of Fj and Fi was developed through polynomial fitting and curvature analysis. The method measures the curvatures in the OJIP curve and automatically tracks the characteristic transition points under variable sample and experimental conditions. Experiments were carried out to demonstrate the concept and classification capabilities of the developed method. This research established a new framework to analyze ChlF and enhanced the applications of ChlF.
A toolbox for nodule development studies in chickpea: a hairy-root transformation protocol and an efficient laboratory strain of Mesorhizobium sp
Authors: Mandal Drishti , Sinharoy Senjuti 
Published: July 2018

AbstractMesorhizobium sp. produces root nodules in chickpea. Chickpea and model legume Medicago truncatula are members of inverted repeat lacking clade (IRLC). The rhizobia after internalization inside plant cell called ‘bacteroid’. Nodule Specific Cysteine-rich (NCR) peptides in IRLC legumes guide bacteroids to a ‘terminally differentiated swollen (TDS)’ form. Bacteroids in chickpea are less TDS than those in Medicago. Nodule development in chickpea indicates recent evolutionary diversification and merits further study. A hairy root transformation protocol and an efficient laboratory strain are prerequisites for performing any genetic study on nodulation. We have standardized a protocol for composite plant generation in chickpea with a transformation frequency above 50%, as shown by fluorescent markers. This protocol also works well in different ecotypes of chickpea. Localization of subcellular markers in these transformed roots is similar to Medicago. When checked inside transformed nodules, peroxisomes were concentrated along the periphery of the nodules, while ER and golgi bodies surrounded the symbiosomes. Different Mesorhizobium strains were evaluated for their ability to initiate nodule development, and efficiency of nitrogen fixation. Inoculation with different strains resulted in different shapes of TDS bacteroids with variable nitrogen fixation. Our study provides a toolbox to study nodule development in the crop legume chickpea.
Notch signalling patterns retinal composition by regulatingatoh7during post-embryonic growth
Authors: Saturnino Alicia Pérez , Lust Katharina , Wittbrodt Joachim 
Published: July 2018

AbstractPatterning of a continuously growing naive field in the context of a life-long growing organ, the teleost eye is of highest functional relevance. Intrinsic and extrinsic signals were proposed to regulate lineage specification in progenitors that exit the stem cell niche in the ciliary marginal zone (CMZ). The proper cell type composition arising from those progenitors is prerequisite for retinal function. Our findings in the teleost medaka (Oryzias latipes) uncover that the Notch–Atoh7 axis continuously patterns the CMZ. The complement of cell-types originating from the two juxtaposed progenitors marked by Notch or Atoh7 activity contains all constituents of a retinal column. Modulation of Notch signalling specifically in Atoh7-expressing cells demonstrates the crucial role of this axis in generating the correct cell type proportions. After transiently blocking Notch signalling, retinal patterning and differentiation is reinitiatedde novo. Taken together we show that Notch activity in the CMZ continuously structures the growing retina by juxtaposing Notch and Atoh7 progenitors giving rise to distinct, complementary lineages, revealing a coupling ofde novopatterning and cell-type specification in the respective lineages.
Prolonged balloon tamponade in the initial management of inferior vena cava injury following complicated filter retrieval, without the need for surgery
Authors: Lee Jonathan TL , Goh Gerard S , Joseph Tim , Koukounaras Jim , Phan Tuan , Clements Warren 
Published: July 2018

SummaryAdvanced techniques have been described to remove embedded inferior vena cava (IVC) filters including the loop snare and modified loop snare (Hangman) techniques. Retrieval of embedded filters have been associated with higher rates of complications including IVC injury and stenosis. We report two challenging embedded retrievals complicated by IVC injury and haemorrhage. Haemostasis was successfully achieved with prolonged balloon tamponade, suggesting that injury to the IVC during filter retrieval may not need urgent surgery. However, both patients received short‐term complications related to caval thrombosis and patients in this cohort should be closely observed after retrieval. These cases support rigorous attention to filter indication and follow‐up.
A 22‐Year Follow‐Up (Range 16 to 23) of Original Subjects with Baseline Alcohol Use Disorders from the Collaborative Study on Genetics of Alcoholism
Authors: Schuckit Marc A. , Smith Tom L. , Danko George , Kramer John , Bucholz Kathleen K. , McCutcheon Vivia , Chan Grace , Kuperman Samuel , Hesselbrock Victor , Dick Danielle M. , Hesselbrock Michie , Porjesz Bernice , Edenberg Howard J. , Nureberger John I. , Gregg Marcy , Schoen Lara , Kawamura Mari , Mendoza Lee Anne 
Published: July 2018

BackgroundRecent reports indicate higher‐than‐expected problematic drinking in older populations. However, few data describe how to predict which older individuals are most likely to demonstrate alcohol‐related problems, including those with earlier alcohol use disorders (AUDs). These analyses evaluate predictors of alcohol outcomes in individuals with earlier AUDs in the Collaborative Study on Genetics of Alcoholism (COGA).MethodsOriginal COGA participants with baseline AUDs at about age 40 were interviewed 13 to 26 years later and placed into clinically derived outcome categories. Chi‐square and analysis of variance evaluated baseline differences across 4 outcome groups, with significant items entered into binary logistic regression backwards elimination analyses predicting outcomes.ResultsLow‐Risk Drinkers (N = 100) at follow‐up were predicted by baseline higher levels of response to alcohol (high LRs), lower histories of alcohol treatment, experience with fewer types of illicit drugs, and were more likely to have been widowed. At follow‐up, Problem Drinkers (N = 192) differed from High‐Risk Drinkers (N = 93) who denied multiple alcohol problems by exhibiting baseline lower LRs, higher Sensation Seeking, and a higher proportion who were widowed. Abstinent (N = 278) outcomes were predicted by a history of higher baseline AUD treatments, higher alcohol problems, lower usual drinks, as well as older age and European American heritage. Thirty‐four subjects (4.9%) could not be classified and were not included in these analyses.ConclusionsThese results generated from AUD individuals from both treatment and nontreatment settings reinforce low probabilities of recent Low‐Risk Drinking in individuals with AUDs, but also suggest many individuals with AUDs demonstrate good outcomes 2 decades later.
The Stratification of Attendance at Cultural Activities in Canada
Authors: Vanzella‐Yang Adam 
Published: July 2018

AbstractScholars have debated the relative applicability of homology and omnivorousness, two theories of cultural stratification, for explaining links between socioeconomic position and cultural repertoires. However, the discussion has mostly focused on musical tastes rather than attendance at cultural activities. Using data from the 2010 Canadian General Social Survey on Time Use, I examine how measures of socioeconomic position predict attendance at 12 different kinds of cultural activities. I apply three analytical techniques to this data set: (1) binary logistic regressions to investigate the socioeconomic bases of attendance at each cultural activity; (2) ordered logistic regression to assess the nature of the relationship between socioeconomic position and omnivorous attendance; and (3) latent class analysis to identify clusters of attendance and the socioeconomic bases thereof. Controlling for demographic factors, I find that education and income are positively associated with attendance at each activity and with omnivorous cultural engagement. The latent class model reveals four distinct groups: highbrow omnivores, selective omnivores, univores, and inactive people. Education and income predict membership in the omnivorous groups, with stronger effects for highbrow omnivores. I confirm that omnivorousness is associated with cultural and economic elites, but also reveal different gradations of omnivorousness, thus suggesting that the two theoretical frameworks are to a degree entangled with one another.
The effects of kisspeptin on β‐cell function, serum metabolites and appetite in humans
Authors: Izzi‐Engbeaya Chioma , Comninos Alexander N. , Clarke Sophie A. , Jomard Anne , Yang Lisa , Jones Sophie , Abbara Ali , Narayanaswamy Shakunthala , Eng Pei Chia , Papadopoulou Deborah , Prague Julia K. , Bech Paul , Godsland Ian F. , Bassett Paul , Sands Caroline , Camuzeaux Stephane , Gomez‐Romero Maria , Pearce Jake T. M. , Lewis Matthew R. , Holmes Elaine , Nicholson Jeremy K. , Tan Tricia , Ratnasabapathy Risheka , Hu Ming , Carrat Gaelle , Piemonti Lorenzo , Bugliani Marco , Marchetti Piero , Johnson Paul R. , Hughes Stephen J. , James Shapiro A. M. , Rutter Guy A. , Dhillo Waljit S. 
Published: July 2018

AimsTo investigate the effect of kisspeptin on glucose‐stimulated insulin secretion and appetite in humans.Materials and methodsIn 15 healthy men (age: 25.2 ± 1.1 years; BMI: 22.3 ± 0.5 kg m−2), we compared the effects of 1 nmol kg−1 h−1 kisspeptin versus vehicle administration on glucose‐stimulated insulin secretion, metabolites, gut hormones, appetite and food intake. In addition, we assessed the effect of kisspeptin on glucose‐stimulated insulin secretion in vitro in human pancreatic islets and a human β‐cell line (EndoC‐βH1 cells).ResultsKisspeptin administration to healthy men enhanced insulin secretion following an intravenous glucose load, and modulated serum metabolites. In keeping with this, kisspeptin increased glucose‐stimulated insulin secretion from human islets and a human pancreatic cell line in vitro. In addition, kisspeptin administration did not alter gut hormones, appetite or food intake in healthy men.ConclusionsCollectively, these data demonstrate for the first time a beneficial role for kisspeptin in insulin secretion in humans in vivo. This has important implications for our understanding of the links between reproduction and metabolism in humans, as well as for the ongoing translational development of kisspeptin‐based therapies for reproductive and potentially metabolic conditions.
Assessing gastrointestinal motility in healthy horses comparing auscultation, ultrasonography and an acoustic gastrointestinal surveillance biosensor: a randomised, blinded, controlled crossover proof of principle study
Authors: VanderBroek A. R. , Reef V. B. , Aitken M. R. , Stefanovski D. , Southwood L. L. 
Published: July 2018

SummaryBackgroundAuscultation and ultrasonography are noninvasive techniques used to assess gastrointestinal motility in horses. Recently, noninvasive acoustic gastrointestinal surveillance (AGIS) biosensors evaluating intestinal motility have been validated in humans.ObjectivesTo compareAGISto auscultation and ultrasonography for detecting decreased motility after xylazine administration.Study designRandomised, blinded, controlled cross‐over proof of principle study.MethodsSix healthy horses were evaluated under fasted and nonfasted conditions and randomly assigned to receive treatment with 0.4 mg/kg xylazine or an equivalent volume of 0.9% NaCl intravenously. After a 48‐h washout period, the process was repeated with the alternate treatment. Motility was assessed pre and posttreatment. Borborygmi were assessed in each abdominal quadrant and graded on a scale of 0–3, with 3 being continuous borborygmi. Duodenal, jejunal and caecal contractions were assessed ultrasonographically in consistent locations. FourAGISbiosensors were applied in standardised locations (duodenum, caecum, ventral midline, right dorsal colon). The biosensors measure acoustic signals and data were recorded in transport metric. Data were analysed using cross‐classified multilevel random effects logistic regression including area under the receiver operator characteristic curve (AUC ROC). Sensitivity, specificity and accuracy were calculated for each modality.ResultsAll three modalities detected a reduction in gastrointestinal motility following xylazine administration withAUC ROCbeing 0.85, 0.84 and 0.86 for auscultation, ultrasonography andAGISrespectively. The sensitivity, specificity and accuracy for auscultation was 88, 71 and 75%; for ultrasonography was 67, 63 and 64%; and forAGISwas 69, 70 and 70%, respectively.Main limitationsThe study was performed in normal healthy horses and application of this device to clinical patients warrants further investigation.ConclusionsIn this proof of principle study,AGISwas able to discriminate between horses given xylazine from those given 0.9% NaCl with comparable accuracy as auscultation and ultrasonography.The Summary is available in Spanish ‐ see Supporting Information
Mining of high‐utility itemsets with negative utility
Authors: Singh Kuldeep , Shakya Harish Kumar , Singh Abhimanyu , Biswas Bhaskar 
Published: July 2018

AbstractHigh‐utility itemset (HUI) mining is an important tasks during data mining. Recently, many algorithms have been proposed to discover HUIs. Most of the algorithms work only for itemsets with positive utility values. However, in the real world, items are found with both positive and negative utility values. To address this issue, we propose an algorithm named Efficient High‐utility Itemsets mining with Negative utility (EHIN) to find all HUIs with negative utility. EHIN utilises 2 new upper bounds for pruning, named revised subtree and revised local utility. To reduce dataset scans, the proposed algorithm uses transaction merging and dataset projection techniques. An array‐based utility‐counting technique is also utilised to calculate upper‐bound efficiently. EHIN utilises various properties and pruning strategies to mine HUIs with negative utility. The experimental results show that the proposed algorithm is 28 times faster, and it consumes up to 10 times less memory than the state‐of‐the‐art algorithm FHN. Moreover, a key advantage is that EHIN always performs better for dense datasets.
An anisotropic damage model for tensile fatigue
Authors: Vijay Akhil , Sadeghi Farshid 
Published: July 2018

AbstractFatigue damage in materials is considered to be the effect of material degradation, and the dispersion in fatigue life is attributed to variability in microstructure. This paper presents a numerical model to simulate fatigue damage evolution using continuum damage mechanics to characterize material degradation. An explicit microstructure topology representation is achieved using Voronoi tessellations. Unlike conventional models which use a scalar approximation for damage, this model treats the damage variable as an anisotropic tensor. The model is used to simulate tensile fatigue failure in thin steel specimen. The fatigue life estimations from the model compares well with published experimental results. The results predict a high variability in fatigue life that is characteristic of metals and alloys, as compared with the existing isotropic damage models available in the literature. The model was also used to study the influence of material inhomogeneity on fatigue life dispersion.
Patients’ experiences of isolation in psychiatric inpatient care: Insights from a meta‐ethnographic study
Authors: Lindgren Britt‐Marie , Ringnér Anders , Molin Jenny , Graneheim Ulla H. 
Published: July 2018

AbstractHistorically, people with mental ill‐health have been isolated from society. Although mental health care has moved from closed to more open forms of care, in many societies care is still provided in locked wards, and people with mental ill‐health are sometimes secluded from their fellow patients, families, friends, and visitors. The aim of this study was to illuminate patients’ experiences of isolation in psychiatric inpatient care. A systematic review of qualitative research was conducted, and the key findings were subjected to meta‐ethnographic synthesis. The findings were twofold: ‘being admitted to prison’ and ‘having access to shelter’. The experience of isolated care as prison‐like symbolizes patients’ longing for freedom and feeling restricted and limited by rules, stripped of rights, abandoned, controlled, powerless, and unsupported. In contrast, the experience of isolation as shelter symbolizes safety and the opportunity to regain control over one's own situation. A stigmatizing public view holds that people with mental ill‐health are dangerous and unpredictable and, therefore, unsafe to themselves and others. Being placed in isolation because these fears contribute to self‐stigma among patients. Promoting a sheltered experience in which isolation is used with respect for patients and the reasons are made explicit may encourage recovery. A shift in emphasis in ward culture from observation to engagement is needed to reduce blame, shift patient experiences from prison to shelter, and to support autonomy as a therapeutic intervention.