bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solar-metallicity gas in the extended halo of a galaxy at z ∼ 0.12
Authors: Pradeep Jayadev , Sankar Sriram , Umasree T M , Narayanan Anand , Khaire Vikram , Gebhardt Matthew , Sameer  , Charlton Jane C 
Published: January 2020

ABSTRACT
We present the detection and analysis of a weak low-ionization absorber at z = 0.121 22 along the sightline of the blazar PG 1424+240, using spectroscopic data from both HST/COS and STIS. The absorber is a weak Mg ii analogue, with an incidence of weak C ii and Si ii, along with multicomponent C iv and O vi. The low ions are tracing a dense (nH ∼ 10−3 cm−3) parsec-scale cloud of solar or higher metallicity. The kinematically coincident higher ions are either from a more diffuse (nH ∼ 10−5–10−4 cm−3) photoionized phase of kiloparsec-scale dimensions or are tracing a warm (T ∼ 2 × 105 K) collisionally ionized transition temperature plasma layer. The absorber resides in a galaxy overdense region, with 18 luminous (&gt;L*) galaxies within a projected radius of 5 Mpc and velocity of 750 km s−1. The multiphase properties, high metallicity, and proximity to a 1.4L* galaxy, at ρ ∼ 200 kpc and separation |Δv| = 11 km s−1, favour the possibility of the absorption tracing circumgalactic gas. The absorber serves as an example of weak Mg ii–O vi systems as a means to study multiphase high-velocity clouds in external galaxies.
Fragmentation favoured in discs around higher mass stars
Authors: Cadman James , Rice Ken , Hall Cassandra , Haworth Thomas J , Biller Beth 
Published: January 2020

ABSTRACT
We investigate how a protoplanetary disc’s susceptibility to gravitational instabilities and fragmentation depends on the mass of its host star. We use 1D disc models in conjunction with 3D smoothed particle hydrodynamics simulations to determine the critical disc-to-star mass ratios at which discs become unstable against fragmentation, finding that discs become increasingly prone to the effects of self-gravity as we increase the host star mass. The actual limit for stability is sensitive to the disc temperature, so if the disc is optically thin stellar irradiation can dramatically stabilize discs against gravitational instability. However, even when this is the case we find that discs around 2 M⊙ stars are prone to fragmentation, which will act to produce wide-orbit giant planets and brown dwarfs. The consequences of this work are twofold: that low-mass stars could in principle support high disc-to-star mass ratios, and that higher mass stars have discs that are more prone to fragmentation, which is qualitatively consistent with observations that favour high-mass wide-orbit planets around higher mass stars. We also find that the initial masses of these planets depends on the temperature in the disc at large radii, which itself depends on the level of stellar irradiation.
GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly
Authors: Pavc Daša , Wang Baifan , Spindler Lea , Drevenšek-Olenik Irena , Plavec Janez , Šket Primož 
Published: January 2020

AbstractGCn and GCnCG, where n = (G2AG4AG2), fold into well-defined, dimeric G-quadruplexes with unprecedented folding topologies in the presence of Na+ ions as revealed by nuclear magnetic resonance spectroscopy. Both G-quadruplexes exhibit unique combination of structural elements among which are two G-quartets, A(GGGG)A hexad and GCGC-quartet. Detailed structural characterization uncovered the crucial role of 5′-GC ends in formation of GCn and GCnCG G-quadruplexes. Folding in the presence of 15NH4+ and K+ ions leads to 3′–3′ stacking of terminal G-quartets of GCn G-quadruplexes, while 3′-GC overhangs in GCnCG prevent dimerization. Results of the present study expand repertoire of possible G-quadruplex structures. This knowledge will be useful in DNA sequence design for nanotechnological applications that may require specific folding topology and multimerization properties.
Transport of Asian surface pollutants to the global stratosphere from the Tibetan Plateau region during the Asian summer monsoon
Authors: Bian Jianchun , Li Dan , Bai Zhixuan , Li Qian , Lyu Daren , Zhou Xiuji 
Published: January 2020

AbstractDue to its surrounding strong and deep Asian summer monsoon (ASM) circulation and active surface pollutant emissions, surface pollutants are transported to the stratosphere from the Tibetan Plateau region, which may have critical impacts on global climate through chemical, microphysical and radiative processes. This article reviews major recent advances in research regarding troposphere–stratosphere transport from the region of the Tibetan Plateau. Since the discovery of the total ozone valley over the Tibetan Plateau in summer from satellite observations in the early 1990s, new satellite-borne instruments have become operational and have provided significant new information on atmospheric composition. In addition, in situ measurements and model simulations are used to investigate deep convection and the ASM anticyclone, surface sources and pathways, atmospheric chemical transformations and the impact on global climate. Also challenges are discussed for further understanding critical questions on microphysics and microchemistry in clouds during the pathway to the global stratosphere over the Tibetan Plateau.
Mini Fronto-Orbital Approach: “Window Opening” Towards the Superomedial Orbit – A Virtual Reality-Planned Anatomic Study
Authors: Donofrio Carmine Antonio , Capitanio Jody Filippo , Riccio Lucia , Herur-Raman Aalap , Caputy Anthony J , Mortini Pietro 
Published: January 2020

Abstract

BACKGROUND
Surgical approaches to the orbit are challenging and require combined multispecialist skills. Considering its increasing relevance in neurosurgical practice, keyhole surgery could be also applied to this field. However, mastering a minimally invasive approach necessitates an extended learning curve. For this reason, virtual reality (VR) can be effectively used for planning and training in this demanding surgical technique.

OBJECTIVE
To validate the mini fronto-orbital (mFO) approach to the superomedial orbit, using VR planning and specimen dissections, conjugating the principles of skull base and keyhole neurosurgery.

METHODS
Three-dimensional measurements were performed thanks to Surgical Theater (Surgical Theater© LLC), and then, simulated craniotomies were implemented on cadaver specimens.

RESULTS
The mFO approach affords optimal exposure and operability in the target area and reduced risks of surrounding normal tissue injuries. The eyebrow skin incision, the minimal soft-tissue retraction, the limited temporalis muscle dissection and the single-piece craniotomy, as planned with VR, are the key elements of this minimally invasive approach. Furthermore, the “window-opening” cotton-tip intraorbital dissection technique, based on widening surgical corridors between neuromuscular bundles, provides a safe orientation and a deep access inside the orbit, thereby significantly limiting the risk of jeopardizing neurovascular structures.

CONCLUSION
The mFO approach associated to the window-opening dissection technique can be considered safe, effective, suitable, and convenient for treating lesions located in the superomedial orbital aspect, up to the orbital apex.
Study of the Anatomical Features of the Offending Arteries Involved in Glossopharyngeal Neuralgia
Authors: Inoue Kohei , Matsushima Toshio , Ohara Shinji , Masuoka Jun , Abe Tatsuya 
Published: January 2020

Abstract

BACKGROUND
The anatomic features of the posterior inferior cerebellar arteries (PICAs) and the anterior inferior cerebellar arteries (AICAs) as offending arteries involved in glossopharyngeal neuralgia (GPN) are important to dictate the best surgical approach.

OBJECTIVE
To study and classify the anatomic features of the offending arteries.

METHODS
All clinical data and surgical videos from 18 GPN cases that were surgically treated during the past 10 yr were retrospectively reviewed.

RESULTS
Among these 18 patients, the offending arteries involved were the PICA in 12 (66.7%), AICA in 4 (22.2%), and both PICA and AICA in 2 (11.1%). The PICA were then classified into the following groups based on their anatomic features: type I: the PICA formed an upward loop at the level of the glossopharyngeal nerve and passed between the glossopharyngeal and vestibulocochlear nerves; type II: the PICA formed an upward loop at the level of the glossopharyngeal nerve and passed between the glossopharyngeal and vagus nerves or between the rootlets of the vagus nerve; and type III: the PICA passed between the glossopharyngeal and vestibulocochlear nerves without forming a loop. The AICA had only one running pattern.

CONCLUSION
The offending arteries involved in GPN, mainly the PICA and/or AICA, were classified into 4 different types based on their anatomic features.
Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference
Authors: Zhang Chi , Huelsenbeck John P , Ronquist Fredrik 
Published: January 2020

AbstractSampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as “convergence”) and in estimating the correct proportions of the different types of them (known as “mixing”). Here, we introduce a new class of moves, which propose trees based on their parsimony scores. The proposal distribution derived from the parsimony scores is a quickly computable albeit rough approximation of the conditional posterior distribution over candidate trees. We demonstrate with simulations that parsimony-guided moves correctly sample the uniform distribution of topologies from the prior. We then evaluate their performance against standard moves using six challenging empirical data sets, for which we were able to obtain accurate reference estimates of the posterior using long MCMC runs, a mix of topology proposals, and Metropolis coupling. On these data sets, ranging in size from 357 to 934 taxa and from 1740 to 5681 sites, we find that single chains using parsimony-guided moves usually converge an order of magnitude faster than chains using standard moves. They also exhibit better mixing, that is, they cover the most probable trees more quickly. Our results show that tree moves based on quick and dirty estimates of the posterior probability can significantly outperform standard moves. Future research will have to show to what extent the performance of such moves can be improved further by finding better ways of approximating the posterior probability, taking the trade-off between accuracy and speed into account. [Bayesian phylogenetic inference; MCMC; parsimony; tree proposal.]
Haitian-like genetic traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India
Authors: Mohanraj Regina Sumitha , Samanta Prosenjit , Mukhopadhyay Asish K. , Mandal Jharna 
Published: January 2020

Introduction.The emergence of novel strains ofVibrio choleraeO1 El Tor biotype has gained attention due to causing several epidemics around the world. Variant strains have evolved as a result of the acquisition of genes that confer extended virulence and pathogenicity.Aim.This study aimed to determine the presence of the most recently emerging Haitian-like genetic traits among the isolates from Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, Southern India. We also wanted to detect the prevalence of the sulfamethoxazole and trimethoprim (SXT) element, which is an integrating conjugative element (ICE) and the antimicrobial resistance genes present in our isolates.Methodology.Identification of Haitian-specific alleles was done by mismatched amplification mutation assay PCR (MAMA-PCR). The presence of SXT elements was carried out by PCR by detectingint, eex, att-prfCandsetRgenes. Detection of antibiotic resistance determinant,sul(1,2,3); dfr(A1,18,5) for trimethoprim resistance,tet(A,B,C,D,E,Y,G,M), tet34for tetracycline resistance anderm(A,B,C), mph(A,B), ere(A,B), msr(A,D) for azithromycin resistance were targeted by PCR. The MIC of tetracycline, ciprofloxacin and azithromycin was determined by the E-test method.Results.Of the 95 isolates, 60 % of the isolates were found to carry Haitian-specific alleles ofctxB,tcpAandrtxAgene,100 % of the isolates were found to carry SXT elements. All the isolates harboured the four conserved genes of the SXT element, except one which had onlyeex,att-prfC,setRgenes. About 99 % harbouredsul2anddfrA1genes. Notetand macrolide genes were detected. We observed a progressive increase in the MIC of azithromycin ranging from 0.75 µg ml−1to 2 µg ml−1.Conclusion.None of the isolates were the prototype El Tor biotype. All the isolates were a Haitian variant. The presence of SXT elements across all our isolates and their creeping MIC of azithromycin is a matter of concern. Further testing for other genetic determinants of resistance will be carried out in our future studies.
Building thelacoperon: A guided-inquiry activity using 3D-printed models
Authors: Gordy Claire L. , Sandefur Conner I. , Lacara Tessa , Harris Felix R. , Ramirez Melissa V. 
Published: January 2020

AbstractUndergraduate biology courses rely heavily on visual representation of information. Students view images of plants, animals, and microbes, interpret data presented in graphs, and use drawings to understand how cells and molecules interact in three dimensions. Traditional teaching approaches exclude students with visual impairments and disadvantage students with disabilities that affect their interpretation and processing of visual and spatial information as well as students who simply do not identify as “visual learners”. By using new technologies to develop tactile teaching tools (TTTs) that can be employed in classrooms, we aim to create inclusive learning environments and more effectively instruct diverse learners. The advent of affordable and accessible 3D printing technology makes it possible to create tactile models that represent molecules, cells, and entire organisms more accurately than traditional visual representations. We describe the assessment of a 3D gene expression puzzle as a guided inquiry learning activity in which students must correctly assemble a series of components in order to achieve an output. Upon completion of the puzzle, the TTT provides tactile feedback through vibration to signal transcriptional activation. Analysis of pre- and post-assessment performance demonstrated statistically significant increases in individual students’ paired assessment scores in two different classroom implementations, with a greater effect size at a rural minority-serving institution than an urban R1 university. These encouraging preliminary data suggest that TTTs with guided-inquiry learning disproportionately benefit disadvantaged student populations and could serve as a tool in leveling the playing field when teaching abstract biological concepts in diverse educational settings.
Ultrasound imaging links soleus muscle neuromechanics and energetics during human walking with elastic ankle exoskeletons
Authors: Nuckols R.W. , Dick T.J.M , Beck O.N. , Sawicki G.S. 
Published: January 2020

ABSTRACTUnpowered exoskeletons with springs in parallel to human plantar flexor muscle-tendons can reduce the metabolic cost of walking. We used ultrasound imaging to look ‘under the skin’ and measure how exoskeleton stiffness alters soleus muscle contractile dynamics and shapes the user’s metabolic rate during walking. Eleven participants (4F, 7M; age: 27.7 ± 3.3 years) walked on a treadmill at 1.25 m s-1and 0% grade with elastic ankle exoskeletons (rotational stiffness: 0-250 Nm rad-1) in one training and two testing days. Metabolic savings were maximized (4.2%) at a stiffness of 50 Nm rad-1. As exoskeleton stiffness increased, the soleus muscle operated at longer lengths and improved economy (force/activation) during early stance, but this benefit was offset by faster shortening velocity and poorer economy in late stance. Changes in soleus activation rate correlated with changes in users’ metabolic rate (p= 0.038, R2= 0.44), highlighting a crucial link between muscle neuromechanics and exoskeleton performance; perhaps informing future ‘muscle-in-the loop’ exoskeleton controllers designed to steer contractile dynamics toward more economical force production.
Role of prefrontal cortex projections to the nucleus accumbens core in mediating the effects of ceftriaxone on cued cocaine relapse
Authors: Bechard Allison R. , Logan Carly N. , Mesa Javier , Hernandez Yasmin Padovan , Blount Harrison , Hodges Virginia L. , Knackstedt Lori A. 
Published: January 2020

AbstractCeftriaxone is an antibiotic that reliably attenuates the reinstatement of cocaine-seeking after extinction while preventing the nucleus accumbens (NA) core glutamate efflux that drives reinstatement. However, when rats undergo abstinence without extinction, ceftriaxone attenuates context-primed relapse but NA core glutamate efflux still increases. Here we sought to determine if the same would occur when relapse is prompted by both context and discrete cues (context+cues) after cocaine abstinence. Male rats self-administered intravenous cocaine for 2 hr/day for 2 weeks. Cocaine delivery was accompanied by drug-associated cues (light+tone). Rats were then placed into abstinence with daily handling but no extinction training for two weeks. Ceftriaxone (200 mg/kg IP) or vehicle was administered during the last 6 days of abstinence. During a context+cue relapse test, microdialysis procedures were conducted. Rats were perfused at the end of the test for later Fos analysis. A separate cohort of rats was infused with the retrograde tracer cholera toxin B in the NA core and underwent the same self-administration and relapse procedures. Ceftriaxone increased baseline glutamate and attenuated both context+cue-primed relapse and NA core glutamate efflux during this test. Ceftriaxone reduced Fos expression in regions sending projections to the NA core (prefrontal cortex, basolateral amygdala, ventral tegmental area) and specifically reduced Fos in prelimbic cortex and not infralimbic cortex neurons projecting to the NA core. Thus, when relapse is primed by drug-associated cues and context, ceftriaxone is able to attenuate relapse by preventing NA core glutamate efflux, likely through reducing activity in prelimbic NA core-projecting neurons.
A super sensitive auxin-inducible degron system with an engineered auxin-TIR1 pair
Authors: Nishimura Kohei , Yamada Ryotaro , Hagihara Shinya , Iwasaki Rie , Uchida Naoyuki , Kamura Takumi , Takahashi Koji , Torii Keiko U. , Fukagawa Tatsuo 
Published: January 2020

AbstractAuxin-InducibleDegron (AID) technology enables conditional depletion of targeted proteins. However, the applicability of the AID in vertebrate cells has been limited due to cytotoxicity caused by high auxin concentrations. Here, we establish an improved AID system using an engineered orthogonal auxin-TIR1 pair, which exhibits over 1,000 times stronger binding. With ~1,000-fold less auxin concentration, we achieved to generate the AID-based knockout cells in various human and mouse cell lines in a single transfection.
Vacuolar sucrose homeostasis is critical for development, seed properties and survival of dark phases of Arabidopsis
Authors: Vu Duc Phuong , Rodrigues Cristina Martins , Jung Benjamin , Meissner Garvin , Klemens Patrick A.W. , Holtgräwe Daniela , Fürtauer Lisa , Nägele Thomas , Nieberl Petra , Pommerrenig Benjamin , Neuhaus H. Ekkehard 
Published: January 2020

AbstractAlthough we know that most of the cellular sucrose is present in the cytosol and vacuole, our knowledge on the impact of this sucrose compartmentation on plant properties is still fragmentary. Here we attempted to alter the intracellular sucrose compartmentation of Arabidopsis mesophyll cells by either, overexpression of the vacuolar sucrose loaderBvTST2.1 or by generation of mutants with decreased vacuolar invertase activity (amiR vi1-2). Surprisingly,BvTST2.1overexpression led to increased monosaccharide levels in leaves, while sucrose remained constant. Latter observation allows the conclusion, that vacuolar invertase activity in mesophyll vacuoles exceeds sucrose uptake in Arabidopsis, which gained independent support by analyses on tobacco leaves transiently overexpressingBvTST2.1 and the invertase inhibitorNbVIF. However, we observed strongly increased sucrose levels in leaf extracts from independentamiR vi1-2lines and non-aqueous fractionations confirmed that sucrose accumulation in corresponding vacuoles.amiR vi1-2lines exhibited impaired early development and decreased weight of seeds. When germinated in the dark, mutant seedlings showed problems to convert sucrose into monosaccharides. Cold temperatures induced marked downregulation of the expression of bothVIgenes, while frost tolerance ofamiR vi1-2mutants was similar to WT indicating that increased vacuolar sucrose levels fully compensate for low monosaccharide concentrations.HighlightVacuolar sucrose accumulation in Arabidopsis is limited by high invertase activity and disturbed vacuolar sucrose homeostasis impairs plant germination, development, seed properties and survival under darkness.
Search for and function of different genes in phloem and xylem of poplar
Authors: Li Xiaoyan , Jiang Xiangning 
Published: January 2020

AbstractWe used the microarray data of poplar gene in the laboratory and the GPDNN model to preprocess the data and conduct the median adjustment, and then studied and analyzed the phloem and xylem genes with good clustering effect. Among them, a gene that was significantly different and related to plant hormones was selected for analysis. Firstly, the function of this gene was predicted to be auxin response factor. All genes of auxin response factor family were selected from poplar transcription factor database for evolutionary and homologous affinity analysis, and the relationship with homology was analyzed according to the expression semaphore correlation between genes. Finally, the number of up-regulated, down-regulated and fine-tuned genes in the tissues of budding, root, xylem and phloem was selected by using the median, and the relationship between the number of up-regulated genes and their semaphores and auxin content in the tissues was analyzed.