bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partial preferential chromosome pairing is genotype dependent in tetraploid rose
Authors: Bourke Peter M. , Arens Paul , Voorrips Roeland E. , Esselink G. Danny , Koning‐Boucoiran Carole F. S. , van't Westende Wendy P. C. , Santos Leonardo Tiago , Wissink Patrick , Zheng Chaozhi , van Geest Geert , Visser Richard G. F. , Krens Frans. A. , Smulders Marinus J. M. , Maliepaard Chris 
Published: January 2017

SummaryIt has long been recognised that polyploid species do not always neatly fall into the categories of auto‐ or allopolyploid, leading to the term ‘segmental allopolyploid’ to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra‐high‐density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re‐mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion‐phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra‐dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co‐linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.
Inhibition of Pseudomonas aeruginosa by Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers
Authors: Howard James J. , Sturge Carolyn R. , Moustafa Dina A. , Daly Seth M. , Marshall-Batty Kimberly R. , Felder Christina F. , Zamora Danniel , Yabe-Gill Marium , Labandeira-Rey Maria , Bailey Stacey M. , Wong Michael , Goldberg Joanna B. , Geller Bruce L. , Greenberg David E. 
Published: January 2017

ABSTRACT

Pseudomonas aeruginosa
is a highly virulent, multidrug-resistant pathogen that causes significant morbidity and mortality in hospitalized patients and is particularly devastating in patients with cystic fibrosis. Increasing antibiotic resistance coupled with decreasing numbers of antibiotics in the developmental pipeline demands novel antibacterial approaches. Here, we tested peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs), which inhibit translation of complementary mRNA from specific, essential genes in
P. aeruginosa
. PPMOs targeted to
acpP
,
lpxC
, and
rpsJ
, inhibited
P. aeruginosa
growth in many clinical strains and activity of PPMOs could be enhanced 2- to 8-fold by the addition of polymyxin B nonapeptide at subinhibitory concentrations. The PPMO targeting
acpP
was also effective at preventing
P. aeruginosa
PAO1 biofilm formation and at reducing existing biofilms. Importantly, treatment with various combinations of a PPMO and a traditional antibiotic demonstrated synergistic growth inhibition, the most effective of which was the PPMO targeting
rpsJ
with tobramycin. Furthermore, treatment of
P. aeruginosa
PA103-infected mice with PPMOs targeting
acpP
,
lpxC
, or
rpsJ
significantly reduced the bacterial burden in the lungs at 24 h by almost 3 logs. Altogether, this study demonstrates that PPMOs targeting the essential genes
acpP
,
lpxC
, or
rpsJ
in
P. aeruginosa
are highly effective at inhibiting growth
in vitro
and
in vivo
. These data suggest that PPMOs alone or in combination with antibiotics represent a novel approach to addressing the problems associated with rapidly increasing antibiotic resistance in
P. aeruginosa
.
A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements
Authors: Ramírez-Vargas Gabriel , Quesada-Gómez Carlos , Acuña-Amador Luis , López-Ureña Diana , Murillo Tatiana , del Mar Gamboa-Coronado María , Chaves-Olarte Esteban , Thomson Nicholas , Rodríguez-Cavallini Evelyn , Rodríguez César 
Published: January 2017

ABSTRACT

The antimicrobial resistance (AMR) rates and levels recorded for
Clostridium difficile
are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human
C. difficile
isolates of the NAP
CR1
/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAP
CR1
isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAP
CR1
whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAP
CR1
isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in
gyrA
and
rpoB
and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAP
CR1
lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more
C. difficile
MDR strains.
Acute toxicity (LC50) of a pesticide (Carbendazim) on two native crustacean zooplankton species: Daphnia pulex Leydig, 1860 and Tumeodiaptomus diabolicus (Brehm, 1935) from northern Patagonian lakes (Chile)
Authors: Encina Francisco , De Los Ríos Escalante Patricio , Salazar Katherine 
Published: January 2017

In Chile there is an increased use of fungicides, especially in the central and southern parts of the country. The aim of this study was to test the sensitivity of two common zooplankton species, Daphnia pulex Leydig, 1860 and Tumeodiaptomus diabolicus (Brehm, 1935) to the fungicide carbendazim. The specimens came from Lake Calafquén (southern Chile), and were subjected to bioassay experiments under laboratory conditions over 48 h to seven carbendazim concentrations (0-77.70 μg/l); these bioassays were performed using adult specimens. In parallel, also literature information on the commonly used D. magna Straus, 1820, was used. It was found that T. diabolicus had a 48-h LC50 of 28.1 μg/l, while D. pulex had a 48-h LC50 of 26.1 μg/l, and finally D. magna has a 48-h LC50 of 136.1 μg/l. These results indicate that the two native zooplankton species of Chilean Patagonian lakes are considerably more sensitive to the pesticide carbendazim, than the species D. magna that is used as a standard.
Broad-Spectrum Mountain Waves
Authors: Smith Ronald B. , Kruse Christopher G. 
Published: January 2017

Abstract
Recent airborne mountain-wave measurements over New Zealand in the lower stratosphere during the Deep Propagating Gravity Wave Experiment (DEEPWAVE) campaign allow for improved spectral analysis of velocities u, υ, and w, pressure p, and temperature T fluctuations. Striking characteristics of these data are the spectral breadth and the different spectral shapes of the different physical quantities. Using idealized complex terrain as a guide, the spectra are divided into the long-wave “volume mode” arising from airflow over the whole massif and the short-wave “roughness mode” arising from flow into and out of valleys. The roughness mode is evident in the aircraft data as an intense band of w power from horizontal wavelength λ = 8–40 km. The shorter part of this band (i.e., λ = 8–15 km) falls near the nonhydrostatic buoyancy cutoff (λ = 2πU/N). It penetrates easily into the lower stratosphere but carries little u power or momentum flux. The longer part of this roughness mode (i.e., λ = 15–40 km) carries most of the wave momentum flux. The volume mode for New Zealand, in the range λ = 200–400 km, is detected using the u-power, p-power, and T-power spectra. Typically, the volume mode carries a third or less of the total wave momentum flux, but it dominates the u power and thus may control the wave breakdown aloft. Spectra from numerical simulations agree with theory and aircraft data. Problems with the monochromatic assumption for wave observation and momentum flux parameterization are discussed.
Intranasal administration of dopamine attenuates unconditioned fear in that it reduces restraint-induced ultrasound vocalizations and escape from bright light
Authors: Talbot Teddy , Mattern Claudia , de Souza Silva Maria Angelica , Brandão Marcus Lira 
Published: January 2017

Background: Although substantial evidence suggests that dopamine (DA) enhances conditioned fear responses, few studies have examined the role of DA in unconditioned fear states. Whereas DA does not cross the blood–brain barrier, intranasally-applied dopamine reaches the brain directly via the nose–brain pathways in rodents, providing an alternative means of targeting DA receptors. Intranasal dopamine (IN-DA) has been demonstrated to bind to DA transporters and to increase extracellular DA in the striatum as well as having memory-promoting effects in rats. The purpose of this study was to examine the influence of IN-DA in three tests of fear/anxiety. Methods: The three doses of DA hydrochloride (0.03, 0.3, or 1 mg/kg) were applied in a viscous castor oil gel in a volume of 5 µl to each of both nostrils of adult Wistar rats prior to testing of (a) escape from a bright light, using a two-chamber procedure, (b) restraint-induced 22 kHz ultrasound vocalizations (USVs), and (c) exploratory behavior in the elevated plus-maze (EPM). Results: IN-DA dose-dependently reduced escape from bright light and the number of USV responses to restraint. It had no influence on the exploratory behavior in the EPM. Conclusions: IN-DA application reduced escape behavior in two tests of unconditioned fear (escape from bright light and USV response to immobilization). These findings may be interpreted in light of the known antidepressant action of IN-DA and DA reuptake blockers. The results also confirm the promise of the nasal route as an alternative means for targeting the brain’s dopaminergic receptors with DA.
S100A9 induces differentiation of acute myeloid leukemia cells through TLR4
Authors: Laouedj Malika , Tardif Mélanie R. , Gil Laurine , Raquil Marie-Astrid , Lachhab Asmaa , Pelletier Martin , Tessier Philippe A. , Barabé Frédéric 
Published: January 2017

Key PointsS100A9 induces differentiation and growth arrest of AML cells via TLR4. S100A8 regulates S100A9 activity and sustains AML immature phenotype.
Cellular and molecular mechanisms of tooth root development
Authors: Li Jingyuan , Parada Carolina , Chai Yang 
Published: January 2017

ABSTRACT
The tooth root is an integral, functionally important part of our dentition. The formation of a functional root depends on epithelial-mesenchymal interactions and integration of the root with the jaw bone, blood supply and nerve innervations. The root development process therefore offers an attractive model for investigating organogenesis. Understanding how roots develop and how they can be bioengineered is also of great interest in the field of regenerative medicine. Here, we discuss recent advances in understanding the cellular and molecular mechanisms underlying tooth root formation. We review the function of cellular structure and components such as Hertwig's epithelial root sheath, cranial neural crest cells and stem cells residing in developing and adult teeth. We also highlight how complex signaling networks together with multiple transcription factors mediate tissue-tissue interactions that guide root development. Finally, we discuss the possible role of stem cells in establishing the crown-to-root transition, and provide an overview of root malformations and diseases in humans.
Neomorphic effects of the neonatal anemia (Nan-Eklf) mutation contribute to deficits throughout development
Authors: Planutis Antanas , Xue Li , Trainor Cecelia D. , Dangeti Mohan , Gillinder Kevin , Siatecka Miroslawa , Nebor Danitza , Peters Luanne L. , Perkins Andrew C. , Bieker James J. 
Published: January 2017

ABSTRACT
Transcription factor control of cell-specific downstream targets can be significantly altered when the controlling factor is mutated. We show that the semi-dominant neonatal anemia (Nan) mutation in the EKLF/KLF1 transcription factor leads to ectopic expression of proteins that are not normally expressed in the red blood cell, leading to systemic effects that exacerbate the intrinsic anemia in the adult and alter correct development in the early embryo. Even when expressed as a heterozygote, the Nan-EKLF protein accomplishes this by direct binding and aberrant activation of genes encoding secreted factors that exert a negative effect on erythropoiesis and iron use. Our data form the basis for a novel mechanism of physiological deficiency that is relevant to human dyserythropoietic anemia and likely other disease states.
Earthquake relocation for North-Western Greece using 3D crustal model; method comparison and seismotectonic interpretation.
Authors: Stavroulopoulou O. , Sokos E. , Martakis N. , Tselentis G. A. 
Published: January 2017

A dense microseismic network was installed in Northwestern Greece for a period of eleven months. A total of 1368 events were recorded and located using a 1D model. These events were also used to derive a 3D velocity model for the area. This work presents results from further processing of the data using (a) simple location method of events in a 1D medium through Hypo71 standard procedure; (b) location via the probabilistic, non-linear earthquake location method in 3D medium; (c) relocation of the events using the Double - Difference method in 1D medium; and (d) the same relocation procedure invoking 3D medium. The application of different location methodologies results in slightly different locations, which are evaluated using as criterion the compactness of hypocenter distribution. The three point method was used in order to derive linear characteristics from the hypocenter distribution and the final results were compared against the focal mechanisms of the events as computed using the polarity method and the 3D velocity model. The combination of accurately computed hypocenters and focal mechanisms provides important information for the seismotectonics of Epirus
Near-real-time evaluation of the evolution of a seismic excitation: Application to the January 8, 2013 Lemnos seismic sequence.
Authors: Teza E. , Scordilis E. M. , Papazachos C. B. , Karakaisis G. F. 
Published: January 2017

Monitoring the evolution of a seismic excitation in near-real-time sense is of high practical importance, as the quantitative results of this procedure may provide useful information to be used for the efficient planning of seismic protection measures. Furthermore, it may provide indications on the future evolution of this sequence, which is extremely important for both the public and authorities. A software package consisting of a number of sub-programs has been developed for this task. The main goal of this software is to obtain a semi -automatic evaluation of the possible evolution of a seismic excitation (sequence) already in progress. To achieve this target, successive determinations of basic parameters that characterize the sequence are performed and respective graphs are produced. In particular, the software automatically provides periodical snap-shots (within time periods defined by the user) describing how the shocks-members of the sequence are distributed in space, time, space-time and magnitude, allowing, this way, to detect possible variations in these parameters that could be connected to normal or non-normal evolution of the sequence. Application of this package has been performed during the recent seismic sequence which occurred SE of Lemnos island with a mainshock of M=5.9 (8/1/2013, 14:16 GMT). The snap-shots that described the evolution of the sequence and were produced by the application of the developed software package suggested a "normal" aftershock evolution during the first seven days of the main phase of this excitation.
Two Independent Frontal Midline Theta Oscillations during Conflict Detection and Adaptation in a Simon-Type Manual Reaching Task
Authors: Töllner Thomas , Wang Yijun , Makeig Scott , Müller Hermann J. , Jung Tzyy-Ping , Gramann Klaus 
Published: January 2017

One of the most firmly established factors determining the speed of human behavioral responses toward action-critical stimuli is the spatial correspondence between the stimulus and response locations. If both locations match, the time taken for response production is markedly reduced relative to when they mismatch, a phenomenon called the Simon effect. While there is a consensus that this stimulus-response (S-R) conflict is associated with brief (4–7 Hz) frontal midline theta (fmθ) complexes generated in medial frontal cortex, it remains controversial (1) whether there are multiple, simultaneously active theta generator areas in the medial frontal cortex that commonly give rise to conflict-related fmθ complexes; and if so, (2) whether they are all related to the resolution of conflicting task information. Here, we combined mental chronometry with high-density electroencephalographic measures during a Simon-type manual reaching task and used independent component analysis and time-frequency domain statistics on source-level activities to model fmθ sources. During target processing, our results revealed two independent fmθ generators simultaneously active in or near anterior cingulate cortex, only one of them reflecting the correspondence between current and previous S-R locations. However, this fmθ response is not exclusively linked to conflict but also to other, conflict-independent processes associated with response slowing. These results paint a detailed picture regarding the oscillatory correlates of conflict processing in Simon tasks, and challenge the prevalent notion that fmθ complexes induced by conflicting task information represent a unitary phenomenon related to cognitive control, which governs conflict processing across various types of response-override tasks.SIGNIFICANCE STATEMENTHumans constantly monitor their environment for and adjust their cognitive control settings in response to conflicts, an ability that arguably paves the way for survival in ever-changing situations. Anterior cingulate-generated frontal midline theta (fmθ) complexes have been hypothesized to play a role in this conflict-monitoring function. However, it remains a point of contention whether fmθ complexes govern conflict processing in a unitary, paradigm-nonspecific manner. Here, we identified two independent fmθ oscillations triggered during a Simon-type task, only one of them reflecting current and previous conflicts. Importantly, this signal differed in various respects (cortical origin, intertrial history) from fmθ phenomena in other response-override tasks, challenging the prevalent notion of conflict-induced fmθ as a unitary phenomenon associated with the resolution of conflict.
Contact system activation and high thrombin generation in hyperthyroidism
Authors: Kim Namhee , Gu Ja-Yoon , Yoo Hyun Ju , Han Se Eun , Kim Young Il , Nam-Goong Il Sung , Kim Eun Sook , Kim Hyun Kyung 
Published: January 2017

BackgroundHyperthyroidism is associated with increased thrombotic risk. As contact system activation through formation of neutrophil extracellular traps (NET) has emerged as an important trigger of thrombosis, we hypothesized that the contact system is activated along with active NET formation in hyperthyroidism and that their markers correlate with disease severity.Subjects and methodsIn 61 patients with hyperthyroidism and 40 normal controls, the levels of coagulation factors (fibrinogen, and factor VII, VIII, IX, XI and XII),D-dimer, thrombin generation assay (TGA) markers, NET formation markers (histone–DNA complex, double-stranded DNA and neutrophil elastase) and contact system markers (activated factor XII (XIIa), high-molecular-weight kininogen (HMWK), prekallikrein and bradykinin) were measured.ResultsPatients with hyperthyroidism showed higher levels of fibrinogen (median (interquartile range), 315 (280–344) vs 262 (223–300),P = 0.001),D-dimer (103.8 (64.8–151.5) vs 50.7 (37.4–76.0),P < 0.001), peak thrombin (131.9 (102.2–159.4) vs 31.6 (14.8–83.7),P < 0.001) and endogenous thrombin potential (649 (538–736) vs 367 (197–1147),P = 0.021) in TGA with 1 pM tissue factor, neutrophil elastase (1.10 (0.39–2.18) vs 0.23 (0.20–0.35),P < 0.001), factor XIIa (66.9 (52.8–87.0) vs 73.0 (57.1–86.6),P < 0.001), HMWK (6.11 (4.95–7.98) vs 3.83 (2.60–5.68),P < 0.001), prekallikrein (2.15 (1.00–6.36) vs 1.41 (0.63–2.22),P = 0.026) and bradykinin (152.4 (137.6–180.4) vs 118.3 (97.1–137.9),P < 0.001) than did normal controls. In age- and sex-adjusted logistic regression analysis, fibrinogen, factor VIII, IX and XIIa,D-dimer, peak thrombin, neutrophil elastase, HMWK and bradykinin showed significant odds ratios representing hyperthyroidism’s contribution to coagulation and contact system activation. Free T4 was significantly correlated with factors VIII and IX,D-dimer, double-stranded DNA and bradykinin.ConclusionThis study demonstrated that contact system activation and abundant NET formation occurred in the high thrombin generation state in hyperthyroidism and were correlated with free T4 level.
Additive Manufacturing, Modeling and Performance Evaluation of 3D Printed Fins for Surfboards
Authors: Gately Reece D. , Beirne Stephen , Latimer Geoff , Shirlaw Matthew , Kosasih Buyung , Warren Andrew , Steele Julie R. , in het Panhuis Marc 
Published: January 2017

AbstractWe demonstrate that Additive Manufacturing (3D printing) is a viable approach to rapidly prototype personalised fins for surfboards. Surfing is an iconic sport that is extremely popular in coastal regions around the world. We use computer aided design and 3D printing of a wide range of composite materials to print fins for surfboards, e.g. ABS, carbon fibre, fibre glass and amorphous thermoplastic poly(etherimide) resins. The mechanical characteristics of our 3D printed fins were found to be comparable to commercial fins. Computational fluid dynamics was employed to calculate longitudinal (drag) and tangential (turning) forces, which are important for surfboard maneuverability, stability and speed. A commercial tracking system was used to evaluate the performance of 3D printed fins under real-world conditions (i.e. surfing waves). These data showed that the surfing performance of surfboards with 3D printed fins is similar to that of surfboards with commercial fins.