bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association of hormone signalling genes, transcription and changes in shoot anatomy during moso bamboo growth
Authors: Li Long , Cheng Zhanchao , Ma Yanjun , Bai Qingsong , Li Xiangyu , Cao Zhihua , Wu Zhongneng , Gao Jian 
Published: May 2017

SummaryMoso bamboo is a large, woody bamboo with the highest ecological, economic and cultural value of all the bamboo types and accounts for up to 70% of the total area of bamboo grown. However, the spatiotemporal variation role of moso bamboo shoot during growth period is still unclear. We found that the bamboo shoot growth can be divided into three distinct periods, including winter growth, early growth and late growth based on gene expression and anatomy. In the early growth period, lateral buds germinated from the top of the bamboo joint in the shoot tip. Intercalary meristems grew vigorously during the winter growth period and early growth period, but in the late growth period, mitosis in the intercalary meristems decreased. The expression of cell cycle‐associated genes and the quantity of differentially expressed genes were higher in early growth than those in late growth, appearing to be influenced by hormonal concentrations. Gene expression analysis indicates that hormone signalling genes play key roles in shoot growth, while auxin signalling genes play a central role. In situ hybridization analyses illustrate how auxin signalling genes regulate apical dominance, meristem maintenance and lateral bud development. Our study provides a vivid picture of the dynamic changes in anatomy and gene expression during shoot growth in moso bamboo, and how hormone signalling‐associated genes participate in moso bamboo shoot growth.
Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice
Authors: Wambugu Peterson , Ndjiondjop Marie‐Noelle , Furtado Agnelo , Henry Robert 
Published: May 2017

SummaryAmylose content (AC) is a key quality trait in rice. A cross between Oryza glaberrima (African rice) and Oryza sativa (Asian rice) segregating for AC was analysed by sequencing bulks of individuals with high and low AC. SNP associated with the granule bound starch synthase (GBSS1) locus on chromosome 6 were polymorphic between the bulks. In particular, a G/A SNP that would result in an Asp to Asn mutation was identified. This amino acid substitution may be responsible for differences in GBSS activity as it is adjacent to a disulphide linkage conserved in all grass GBSS proteins. Other polymorphisms in genomic regions closely surrounding this variation may be the result of linkage drag. In addition to the variant in the starch biosynthesis gene, SNP on chromosomes 1 and 11 linked to AC was also identified. SNP was found in the genes encoding the NAC and CCAAT‐HAP5 transcription factors that have previously been linked to starch biosynthesis. This study has demonstrated that the approach of sequencing bulks was able to identify genes on different chromosomes associated with this complex trait.
Characterization of field‐scale dryland salinity with depth by quasi‐3d inversion of DUALEM‐1 data
Authors: Huang J. , Kilminster T. , Barrett‐Lennard E. G. , Triantafilis J. 
Published: May 2017

AbstractTo understand the limitations of saline soil and determine best management practices, simple methods need to be developed to determine the salinity distribution in a soil profile and map this variation across the landscape. Using a field study in southwestern Australia, we describe a method to map this distribution in three dimensions using a DUALEM‐1 instrument and the EM4Soil inversion software. We identified suitable parameters to invert the apparent electrical conductivity (ECa – mS/m) data acquired with a DUALEM‐1, by comparing the estimates of true electrical conductivity (σ – mS/m) derived from electromagnetic conductivity images (EMCI) to values of soil electrical conductivity of a soil‐paste extract (ECe) which exhibited large ranges at 0–0.25 (32.4 dS/m), 0.25–0.50 (18.6 dS/m) and 0.50–0.75 m (17.6 dS/m). We developed EMCI using EM4Soil and the quasi‐3d (q‐3d), cumulative function (CF) forward modelling and S2 inversion algorithm with a damping factor (λ) of 0.07. Using a cross‐validation approach, where we removed one in 15 of the calibration locations and predicted ECe, the prediction was shown to have high accuracy (RMSE = 2.24 dS/m), small bias (ME = −0.03 dS/m) and large Lin's concordance (0.94). The results were similar to those from linear regression models between ECa and ECe for each depth of interest but were slightly less accurate (2.26 dS/m). We conclude that the q‐3d inversion was more efficient and allowed for estimates of ECe to be made at any depth. The method can be applied elsewhere to map soil salinity in three dimensions.
Complete Genome Sequence of a Novel Multidrug-Resistant Klebsiella pneumoniae Phage, vB_Kpn_IME260
Authors: Xing Shaozhen , Pan Xiangchun , Sun Qiang , Pei Guangqian , An Xiaoping , Mi Zhiqiang , Huang Yong , Zhao Baohua , Tong Yigang 
Published: May 2017

ABSTRACT

Klebsiella pneumoniae
is the most common clinically important opportunistic bacterial pathogen and its infection is often iatrogenic. Its drug resistance poses a grave threat to public health. The genomic data reported here comprise an important resource for research on phage therapy in the control of drug-resistant bacteria.
Complete Genome Sequence of the Livestock-Associated Methicillin-Resistant Strain Staphylococcus aureus subsp.
aureus
08S00974 (Sequence Type 398)
Authors: Makarova Olga , Johnston Paul , Walther Birgit , Rolff Jens , Roesler Uwe 
Published: May 2017

ABSTRACT

We report here the complete genome sequence of the livestock-associated methicillin-resistant
Staphylococcus aureus
strain 08S00974 from sequence type 398 (ST398 LA-MRSA) isolated from a fatting pig at a farm in Germany.
New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing
Authors: Foo Soon Man , Eng Wilhelm Wei Han , Lee Yin Peng , Gui Kimberly , Gan Han Ming 
Published: May 2017

ABSTRACT

The acquisition of
Photorhabdus
insect-related (Pir) toxin-like genes in
Vibrio parahaemolyticus
has been linked to hepatopancreatic necrosis disease in shrimp. We report the whole-genome sequences of genetically virulent and avirulent
V. parahaemolyticus
isolated from a Malaysian aquaculture pond and show that they represent previously unreported sequence types of
V. parahaemolyticus
.
Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2
Authors: Tharek Munirah , Sim Kee-Shin , Khairuddin Dzulaikha , Amir Hamzah Ghazali , Najimudin Nazalan 
Published: May 2017

ABSTRACT

Escherichia coli
strain USML2 was originally isolated from the inner leaf tissues of surface-sterilized phytopathogenic-free oil palm (
Elaeis guineensis
Jacq.). We present here the whole-genome sequence of this plant-endophytic strain. The genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted coding sequences, and a G+C content of 50.8%.
Complete Coding Sequence of a Case of Chikungunya Virus Imported into Australia
Authors: Huang Bixing , Pyke Alyssa T. , McMahon Jamie , Warrilow David 
Published: May 2017

ABSTRACT
A case of chikungunya virus infection was imported from India into Australia in late 2016. Infection was diagnosed by real-time reverse transcription-PCR and confirmed by culture isolation and genome sequencing. Phylogenetic analysis of the genome sequence indicated that the virus grouped with the east/central/south African genotype.
A seizure-induced T8 burst fracture re-presenting as an acute abdomen
Authors: Smith Radford Arran James , Poland Nigel , Cope Simon 
Published: May 2017

A male aged 44 years presented to the emergency department with a 1-week history of intermittent right-sided abdominal pain radiating to the midline. Examination demonstrated a tender right upper quadrant with voluntary guarding and a low grade fever. One week previously, he had been admitted to hospital after an isolated, self-terminating seizure secondary to an deliberate venlafaxine overdose. His upper abdominal symptoms started immediately postseizure but at the time were attributed to musculoskeletal chest pain by the discharging team. Acute cholecystitis was suspected, but liver function tests, amylase and an erect chest radiograph were unremarkable.The abdominal pain responded well to morphine, permitting a thorough reassessment of the patient, which revealed midthoracic spine tenderness, previously undetected. Prior to this, the patient had not complained of any back pain. A CT scan confirmed a burst fracture of T8 requiring urgent transfer to the local spinal unit for posterior stabilisation.
Long-term outcomes of the Boston type I keratoprosthesis in eyes with previous herpes simplex virus keratitis
Authors: Fry Melinda , Aravena Carolina , Yu Fei , Kattan Jaffer , Aldave Anthony J 
Published: May 2017

PurposeTo report the long-term outcomes of the Boston type I keratoprosthesis (Kpro) in eyes with prior herpes simplex virus (HSV) keratitis.MethodsRetrospective review of all Kpro procedures performed by a single surgeon from 1 May 2004 to 1 January 2015.Results13 of 173 Kpro procedures were performed in 11 eyes with prior HSV keratitis. There was not a significant difference in the percentage of eyes with and without prior HSV keratitis with preoperative (9% vs 8%, p=1.00) or postoperative (57% vs 60%, p=1.00) corrected distance visual acuity (CDVA) ≥20/200 or in the percentage of contralateral eyes with preoperative CDVA ≥20/50 (55% vs 30%, p=0.18). While several postoperative complications occurred approximately twice as often in eyes with prior HSV keratitis, including persistent epithelial defect (63.6% vs 34.1%; p=0.10), corneal infiltrate (27.3% vs 12.3%; p=0.17) and sterile vitritis (18.2% vs 9.4%; p=0.31), only cystoid macular oedema (45.5% vs 12.3%; p=0.01) was significantly more common. Similarly, while the Kpro retention failure rate in eyes with prior HSV keratitis was twice than that in eyes without it (0.15 vs 0.07 per year), the difference was not statistically significant (p=0.09).ConclusionAs greater than half of patients with unilateral HSV keratitis undergoing Kpro implantation have CDVA ≥20/50 in the contralateral eye, and as the Kpro retention failure rate in eyes with prior HSV keratitis is twice than that in eyes without prior HSV keratitis, caution should be exercised when considering Kpro implantation in these patients.
Value of pulmonary artery pressure in predicting in-hospital and one-year mortality after valve replacement surgery in middle-aged and aged patients with rheumatic mitral disease: an observational study
Authors: Jiang Lei , Wei Xue-biao , He Peng-cheng , Feng Du , Liu Yuan-hui , Liu Jin , Chen Ji-yan , Yu Dan-qing , Tan Ning 
Published: May 2017

ObjectivesTo investigate the role of pulmonary artery pressure (PAP) in predicting in-hospital death after valve replacement surgery in middle-aged and aged patients with rheumatic mitral disease.DesignAn observational study.SettingGuangdong General Hospital, China.Participants1639middle-aged and aged patients (mean age 57±6 years) diagnosed with rheumatic mitral disease, undergoing valve replacement surgery and receiving coronary angiography and transthoracic echocardiography before operation, were enrolled.InterventionsAll participants underwent valve replacement surgery and received coronary angiography before operation.Primary and secondary outcome measuresIn-hospital death and 1-year mortality after operation.MethodsIncluded patients were divided into four groups based on the preoperative PAP obtained by echocardiography: group A (PAP≤30 mm Hg); group B (>30 mm Hg<PAP≤50 mm Hg), group C (>50 mm Hg<PAP≤70 mm Hg) and group D (PAP>70 mm Hg). The relationship between PAP and in-hospital death and cumulative rate of 1-year mortality was evaluated.ResultsIn-hospital mortality rate increased gradually but significantly as the PAP level increased, with 1.9% in group A (n=268), 2.3% in group B (n=771), 4.7% in group C (n=384) and 10.2% in group D (n=216) (p<0.001). Multivariate analysis showed that PAP>70 mm Hg was an independent predictor of in-hospital death (OR=2.93, 95% CI 1.61 to 5.32, p<0.001). PAP>52.5 mm Hg had a sensitivity of 60.3% and specificity of 67.7% in predicting in-hospital death (area under the curve=0.672, 95% CI 0.602 to 0.743, p<0.001). Kaplan–Meier analysis showed that patients with PAP>52.5 mm Hg had higher 1-year mortality after operation than those without (log-rank=21.51, p<0.001).ConclusionsPAP could serve as a predictor of postoperative in-hospital and 1-year mortality after valve replacement surgery in middle-aged and aged patients with rheumatic mitral disease.
Understanding the implementation and adoption of an information technology intervention to support medicine optimisation in primary care: qualitative study using strong structuration theory
Authors: Jeffries Mark , Phipps Denham , Howard Rachel L , Avery Anthony , Rodgers Sarah , Ashcroft Darren 
Published: May 2017

ObjectivesUsing strong structuration theory, we aimed to understand the adoption and implementation of an electronic clinical audit and feedback tool to support medicine optimisation for patients in primary care.DesignThis is a qualitative study informed by strong structuration theory. The analysis was thematic, using a template approach. An a priori set of thematic codes, based on strong structuration theory, was developed from the literature and applied to the transcripts. The coding template was then modified through successive readings of the data.SettingClinical commissioning group in the south of England.ParticipantsFour focus groups and five semi-structured interviews were conducted with 18 participants purposively sampled from a range of stakeholder groups (general practitioners, pharmacists, patients and commissioners).ResultsUsing the system could lead to improved medication safety, but use was determined by broad institutional contexts; by the perceptions, dispositions and skills of users; and by the structures embedded within the technology. These included perceptions of the system as new and requiring technical competence and skill; the adoption of the system for information gathering; and interactions and relationships that involved individual, shared or collective use. The dynamics between these external, internal and technological structures affected the adoption and implementation of the system.ConclusionsSuccessful implementation of information technology interventions for medicine optimisation will depend on a combination of the infrastructure within primary care, social structures embedded in the technology and the conventions, norms and dispositions of those utilising it. Future interventions, using electronic audit and feedback tools to improve medication safety, should consider the complexity of the social and organisational contexts and how internal and external structures can affect the use of the technology in order to support effective implementation.
Vanadium sesquioxide (V2O3)-based semiconducting temperature sensitive resistors for uncooled microbolometers
Authors: Abdel-Rahman Mohamed , Alduraibi Mohammad , Zia Muhammad Fakhar , Bahidra Esme , Alasaad Amr 
Published: May 2017

This paper reports on a semiconducting resistor material based on vanadium sesquioxide (V2O3) with electrical resistivity and temperature coefficient of resistance (TCR) appropriate for microbolometer applications. In this work, V2O3-based semiconducting resistor material was synthesized and electrically characterized. The developed material was prepared by annealing, in O2 and N2 atmospheres, a cascaded multilayer structure composed of V2O3 (10 nm) and V (5 nm) room temperature sputter coated thin films. The developed 55 nm thin film microbolometer resistor material possessed high temperature sensitivity from 20[Formula: see text]C to 45[Formula: see text]C with a TCR of −3.68%/[Formula: see text]C and room temperature resistivity of 0.57 [Formula: see text] for O2 annealed samples and a TCR of −3.72%/[Formula: see text]C and room temperature resistivity of 0.72 [Formula: see text] for N2 annealed samples. The surface morphologies of the synthesized thin films were studied using atomic force microscopy showing no significant post-growth annealing effect on the smoothness of the samples surfaces.
Localization in quantum field theory
Authors: Balachandran A. P. 
Published: May 2017

In non-relativistic quantum mechanics, Born’s principle of localization is as follows: For a single particle, if a wave function [Formula: see text] vanishes outside a spatial region [Formula: see text], it is said to be localized in [Formula: see text]. In particular, if a spatial region [Formula: see text] is disjoint from [Formula: see text], a wave function [Formula: see text] localized in [Formula: see text] is orthogonal to [Formula: see text]. Such a principle of localization does not exist compatibly with relativity and causality in quantum field theory (QFT) (Newton and Wigner) or interacting point particles (Currie, Jordan and Sudarshan). It is replaced by symplectic localization of observables as shown by Brunetti, Guido and Longo, Schroer and others. This localization gives a simple derivation of the spin-statistics theorem and the Unruh effect, and shows how to construct quantum fields for anyons and for massless particles with “continuous” spin. This review outlines the basic principles underlying symplectic localization and shows or mentions its deep implications. In particular, it has the potential to affect relativistic quantum information theory and black hole physics.
Yang–Mills matrix mechanics and quantum phases
Authors: Pandey Mahul , Vaidya Sachindeo 
Published: May 2017

The [Formula: see text] Yang–Mills matrix model coupled to fundamental fermions is studied in the adiabatic limit, and quantum critical behavior is seen at special corners of the gauge field configuration space. The quantum scalar potential for the gauge field induced by the fermions diverges at the corners, and is intimately related to points of enhanced degeneracy of the fermionic Hamiltonian. This in turn leads to superselection sectors in the Hilbert space of the gauge field, the ground states in different sectors being orthogonal to each other. The [Formula: see text] Yang–Mills matrix model coupled to two Weyl fermions has three quantum phases. When coupled to a massless Dirac fermion, the number of quantum phases is four. One of these phases is the color-spin locked phase. This paper is an extended version of the lectures given by the second author (SV) at the International Workshop on Quantum Physics: Foundations and Applications, Bangalore, in February 2016, and is based on [1].
Intersection type calculi of bounded dimension
Authors: Dudenhefner Andrej , Rehof Jakob 
Published: May 2017

A notion of
dimension
in intersection typed λ-calculi is presented. The dimension of a typed λ-term is given by the minimal
norm
of an
elaboration
(a proof theoretic decoration) necessary for typing the term at its type, and, intuitively, measures intersection introduction as a resource.

Bounded-dimensional intersection type calculi are shown to enjoy subject reduction, since terms can be elaborated in non-increasing norm under β-reduction. We prove that a multiset interpretation (corresponding to a non-idempotent and non-linear interpretation of intersection) of dimensionality corresponds to the number of simultaneous constraints required during search for inhabitants. As a consequence, the inhabitation problem is decidable in bounded multiset dimension, and it is proven to be EXPSPACE-complete. This result is a substantial generalization of inhabitation for the rank 2-fragment, yielding a calculus with decidable inhabitation which is independent of rank.
Our results give rise to a new criterion (dimensional bound) for subclasses of intersection type calculi with a decidable inhabitation problem, which is orthogonal to previously known criteria, and which should have immediate applications in synthesis. Additionally, we give examples of dimensional analysis of fragments of the intersection type system, including conservativity over simple types, rank 2-types, and normal form typings, and we provide some observations towards dimensional analysis of other systems. It is suggested (for future work) that our notion of dimension may have semantic interpretations in terms of of reduction complexity.
Type directed compilation of row-typed algebraic effects
Authors: Leijen Daan 
Published: May 2017

Algebraic effect handlers, introduced by Plotkin and Power in 2002,
are recently gaining in popularity as a purely functional approach to
modeling effects. In this article, we give a full overview of
practical algebraic effects in the context of a compiled
implementation in the Koka language. In particular, we show how
algebraic effects generalize over common constructs like exception
handling, state, iterators and async-await. We give an effective type
inference algorithm based on extensible effect rows using scoped
labels, and a direct operational semantics. Finally, we show an
efficient compilation scheme to common runtime platforms (like
JavaScript) using a type directed selective CPS translation.
Towards scalable configuration testing in variable software
Authors: Rothberg Valentin , Dietrich Christian , Ziegler Andreas , Lohmann Daniel 
Published: May 2017

Testing a software product line such as Linux implies building the source with different configurations. Manual approaches to generate configurations that enable code of interest are doomed to fail due to the high amount of variation points distributed over the feature model, the build system and the source code. Research has proposed various approaches to generate covering configurations, but the algorithms show many drawbacks related to run-time, exhaustiveness and the amount of generated configurations. Hence, analyzing an entire Linux source can yield more than 30 thousand configurations and thereby exceeds the limited budget and resources for build testing.
In this paper, we present an approach to fill the gap between a systematic generation of configurations and the necessity to fully build software in order to test it. By merging previously generated configurations, we reduce the number of necessary builds and enable global variability-aware testing. We reduce the problem of merging configurations to finding maximum cliques in a graph. We evaluate the approach on the Linux kernel, compare the results to common practices in industry, and show that our implementation scales even when facing graphs with millions of edges.