bluuebunny/crossref_metadata_2025_split huggingface dataset:
CATEGORICAL HARMONY AND PATH INDUCTION
Authors: WALSH PATRICK 
Published: March 2017

AbstractThis paper responds to recent work in the philosophy of Homotopy Type Theory by James Ladyman and Stuart Presnell. They consider one of the rules for identity, path induction, and justify it along ‘pre-mathematical’ lines. I give an alternate justification based on the philosophical framework of inferentialism. Accordingly, I construct a notion of harmony that allows the inferentialist to say when a connective or concept is meaning-bearing and this conception unifies most of the prominent conceptions of harmony through category theory. This categorical harmony is stated in terms of adjoints and says that any concept definable by iterated adjoints from general categorical operations is harmonious. Moreover, it has been shown that identity in a categorical setting is determined by an adjoint in the relevant way. Furthermore, path induction as a rule comes from this definition. Thus we arrive at an account of how path induction, as a rule of inference governing identity, can be justified on mathematically motivated grounds.
Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9
Authors: Qin Peiwu , Parlak Mahmut , Kuscu Cem , Bandaria Jigar , Mir Mustafa , Szlachta Karol , Singh Ritambhara , Darzacq Xavier , Yildiz Ahmet , Adli Mazhar 
Published: March 2017

AbstractImaging chromatin dynamics is crucial to understand genome organization and its role in transcriptional regulation. Recently, the RNA-guidable feature of CRISPR-Cas9 has been utilized for imaging of chromatin within live cells. However, these methods are mostly applicable to highly repetitive regions, whereas imaging regions with low or no repeats remains as a challenge. To address this challenge, we design single-guide RNAs (sgRNAs) integrated with up to 16 MS2 binding motifs to enable robust fluorescent signal amplification. These engineered sgRNAs enable multicolour labelling of low-repeat-containing regions using a single sgRNA and of non-repetitive regions with as few as four unique sgRNAs. We achieve tracking of native chromatin loci throughout the cell cycle and determine differential positioning of transcriptionally active and inactive regions in the nucleus. These results demonstrate the feasibility of our approach to monitor the position and dynamics of both repetitive and non-repetitive genomic regions in live cells.
Vulnerability of Louisiana’s coastal wetlands to present-day rates of relative sea-level rise
Authors: Jankowski Krista L. , Törnqvist Torbjörn E , Fernandes Anjali M 
Published: March 2017

AbstractCoastal Louisiana has lost about 5,000 km2 of wetlands over the past century and concern exists whether remaining wetlands will persist while facing some of the world’s highest rates of relative sea-level rise (RSLR). Here we analyse an unprecedented data set derived from 274 rod surface-elevation table-marker horizon stations, to determine present-day surface-elevation change, vertical accretion and shallow subsidence rates. Comparison of vertical accretion rates with RSLR rates at the land surface (present-day RSLR rates are 12±8 mm per year) shows that 65% of wetlands in the Mississippi Delta (SE Louisiana) may keep pace with RSLR, whereas 58% of the sites in the Chenier Plain (SW Louisiana) do not, rendering much of this area highly vulnerable to RLSR. At least 60% of the total subsidence rate occurs within the uppermost 5–10 m, which may account for the higher vulnerability of coastal Louisiana wetlands compared to their counterparts elsewhere.
TLR-exosomes exhibit distinct kinetics and effector function
Authors: Srinivasan Swetha , Su Michelle , Ravishankar Shashidhar , Moore James , Head PamelaSara , Dixon J. Brandon , Vannberg Fredrik 
Published: March 2017

AbstractThe innate immune system is vital to rapidly responding to pathogens and Toll-like receptors (TLRs) are a critical component of this response. Nanovesicular exosomes play a role in immunity, but to date their exact contribution to the dissemination of the TLR response is unknown. Here we show that exosomes from TLR stimulated cells can largely recapitulate TLR activation in distal cells in vitro. We can abrogate the action-at-a-distance signaling of exosomes by UV irradiation, demonstrating that RNA is crucial for their effector function. We are the first to show that exosomes derived from poly(I:C) stimulated cells induce in vivo macrophage M1-like polarization within murine lymph nodes. These poly(I:C) exosomes demonstrate enhanced trafficking to the node and preferentially recruit neutrophils as compared to control exosomes. This work definitively establishes the differential effector function for exosomes in communicating the TLR activation state of the cell of origin.
Differential Variance Analysis: a direct method to quantify and visualize dynamic heterogeneities
Authors: Pastore Raffaele , Pesce Giuseppe , Caggioni Marco 
Published: March 2017

AbstractMany amorphous materials show spatially heterogenous dynamics, as different regions of the same system relax at different rates. Such a signature, known as Dynamic Heterogeneity, has been crucial to understand the nature of the jamming transition in simple model systems and is currently considered very promising to characterize more complex fluids of industrial and biological relevance. Unfortunately, measurements of dynamic heterogeneities typically require sophisticated experimental set-ups and are performed by few specialized groups. It is now possible to quantitatively characterize the relaxation process and the emergence of dynamic heterogeneities using a straightforward method, here validated on video microscopy data of hard-sphere colloidal glasses. We call this method Differential Variance Analysis (DVA), since it focuses on the variance of the differential frames, obtained subtracting images at different time-lags. Moreover, direct visualization of dynamic heterogeneities naturally appears in the differential frames, when the time-lag is set to the one corresponding to the maximum dynamic susceptibility. This approach opens the way to effectively characterize and tailor a wide variety of soft materials, from complex formulated products to biological tissues.
Continuous-flow DNP polarizer for MRI applications at 1.5 T
Authors: Denysenkov V. , Terekhov M. , Maeder R. , Fischer S. , Zangos S. , Vogl T. , Prisner T. F. 
Published: March 2017

AbstractHere we describe a new hyperpolarization approach for magnetic resonance imaging applications at 1.5 T. Proton signal enhancements of more than 20 were achieved with a newly designed multimode microwave resonator situated inside the bore of the imager and used for Overhauser dynamic nuclear polarization of the water proton signal. Different from other approaches in our setup the hyperpolarization is achieved continuously by liquid water flowing through the polarizer under continuous microwave excitation. With an available flow rate of up to 1.5 ml/min, which should be high enough for DNP MR angiography applications in small animals like mice and rats. The hyperpolarized liquid cooled to physiological temperature can be routed by a mechanical switch to a quartz capillary for injection into the blood vessels of the target object. This new approach allows hyperpolarization of protons without the need of an additional magnet and avoids the losses arising from the transfer of the hyperpolarized solution between magnets. The signal-to-noise improvement of this method is demonstrated on two- and three-dimensional phantoms of blood vessels.
Positive Association between Urinary Concentration of Phthalate Metabolites and Oxidation of DNA and Lipid in Adolescents and Young Adults
Authors: Lin Chien-Yu , Chen Pau-Chung , Hsieh Chia-Jung , Chen Chao-Yu , Hu Anren , Sung Fung-Chang , Lee Hui-Ling , Su Ta-Chen 
Published: March 2017

AbstractPhthalate has been used worldwide in various products for years. Little is known about the association between phthalate exposure and biomarkers of oxidative stress in adolescents and young adults. Among 886 subjects recruited from a population-based cohort during 2006 to 2008, 751 subjects (12–30 years) with complete phthalate metabolites and oxidation stress measurement were enrolled in this study. Nine urine phthalate metabolites, 8-hydroxydeoxyguanosine (8-OHdG), and 8-iso prostaglandin F2α (8-isoPGF2α) were measured in urine to assess exposure and oxidative stress to DNA and lipid, respectively. Multiple linear regression analysis revealed that an ln-unit increase in mono-methyl phthalate (MMP) concentration in urine was positively associated with an increase in urine biomarkers of oxidative stress (in μg/g; creatinine of 0.098 ± 0.028 in 8-OHdG; and 0.253 ± 0.051 in 8-isoPGF2α). There was no association between other eight phthalate metabolite concentrations and oxidative stress. In conclusion, a higher MMP concentration in urine was associated with an increase in markers of oxidative stress to DNA and lipid in this cohort of adolescents and young adults. Further studies are warranted to clarify the causal relationship between exposure to phthalate and oxidative stress.
Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy
Authors: Zhang Libing , Fu Li , Wang Hong-fei , Yang Bin 
Published: March 2017

AbstractSignificant questions remain in respect to cellulose’s structure and polymorphs, particularly the cellulose surface layers and the bulk crystalline core as well as the conformational differences. Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with conventional SFG-VS (non-TIR) enables selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose, revealing their differences for the first time. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous while the surface layers of Iβ cellulose are crystalline but with different structural and spectroscopic signatures compared with its crystalline core. The differences between hydrogen bonding networks of cellulose surface and crystalline core were also shown by the SFG signal. The discovery here represents yet another instance of the importance of spectroscopic observations in transformative advances to understand the structure of the cellulosic biomass.
Rare-metal-free high-performance Ga-Sn-O thin film transistor
Authors: Matsuda Tokiyoshi , Umeda Kenta , Kato Yuta , Nishimoto Daiki , Furuta Mamoru , Kimura Mutsumi 
Published: March 2017

AbstractOxide semiconductors have been investigated as channel layers for thin film transistors (TFTs) which enable next-generation devices such as high-resolution liquid crystal displays (LCDs), organic light emitting diode (OLED) displays, flexible electronics, and innovative devices. Here, high-performance and stable Ga-Sn-O (GTO) TFTs were demonstrated for the first time without the use of rare metals such as In. The GTO thin films were deposited using radiofrequency (RF) magnetron sputtering. A high field effect mobility of 25.6 cm2/Vs was achieved, because the orbital structure of Sn was similar to that of In. The stability of the GTO TFTs was examined under bias, temperature, and light illumination conditions. The electrical behaviour of the GTO TFTs was more stable than that of In-Ga-Zn-O (IGZO) TFTs, which was attributed to the elimination of weak Zn-O bonds.
Atrial structure, function and arrhythmogenesis in aged and frail mice
Authors: Jansen Hailey J. , Moghtadaei Motahareh , Mackasey Martin , Rafferty Sara A. , Bogachev Oleg , Sapp John L. , Howlett Susan E. , Rose Robert A. 
Published: March 2017

AbstractAtrial fibrillation (AF) is prevalent in aging populations; however not all individuals age at the same rate. Instead, individuals of the same chronological age can vary in health status from fit to frail. Our objective was to determine the impacts of age and frailty on atrial function and arrhythmogenesis in mice using a frailty index (FI). Aged mice were more frail and demonstrated longer lasting AF compared to young mice. Consistent with this, aged mice showed longer P wave duration and PR intervals; however, both parameters showed substantial variability suggesting differences in health status among mice of similar chronological age. In agreement with this, P wave duration and PR interval were highly correlated with FI score. High resolution optical mapping of the atria demonstrated reduced conduction velocity and action potential duration in aged hearts that were also graded by FI score. Furthermore, aged mice had increased interstitial fibrosis along with changes in regulators of extracellular matrix remodelling, which also correlated with frailty. These experiments demonstrate that aging results in changes in atrial structure and function that create a substrate for atrial arrhythmias. Importantly, these changes were heterogeneous due to differences in health status, which could be identified using an FI.
Suggestive evidence of a multi-cytokine resistin pathway in humans and its role on cardiovascular events in high-risk individuals
Authors: Menzaghi Claudia , Marucci Antonella , Antonucci Alessandra , De Bonis Concetta , Ortega Moreno Lorena , Salvemini Lucia , Copetti Massimiliano , Trischitta Vincenzo , Di Paola Rosa 
Published: March 2017

AbstractIn cells and tissues resistin affects IL-1β, IL-6, IL-8, IL-12 and TNF-α expression, thus suggesting the existence of a multi-cytokine “resistin pathway”. We investigated whether such pathway does exist in humans and, if so, if it is associated with cardiovascular risk factors and with major adverse cardiovascular events (MACE). Serum cytokines were measured in 280 healthy subjects from the Gargano Study 2 (GS2) whose BMI, waist circumference, HOMAIR, triglycerides, HDL-cholesterol, systolic and diastolic blood pressure data were available and in 353 patients with type 2 diabetes and coronary artery disease from the Gargano Heart Study (GHS)-prospective design (follow-up 5.4 ± 2.5 years; 71 MACE). In GS2, cytokines mRNA levels in white blood cells were also measured. In GS2, resistin mRNA was correlated with all cytokines expression (all p < 0.001), but IL-12B. Consistently, serum resistin was correlated with all serum cytokines (all p < 0.001), but IL-12. Expression (eRPS) and serum (sRPS) resistin pathway scores (excluding IL-12) were each other correlated (p < 0.001) and both associated with cardiovascular risk factors (all p < 0.01). In GHS, sRPS was independently associated with MACE (HR = 1.44, 95% CI = 1.10–1.90). Our data indicate the existence of a resistin pathway, which is associated with cardiovascular risk factors and which strongly and independently predicts MACE.
Action observation activates neurons of the monkey ventrolateral prefrontal cortex
Authors: Simone Luciano , Bimbi Marco , Rodà Francesca , Fogassi Leonardo , Rozzi Stefano 
Published: March 2017

AbstractPrefrontal cortex is crucial for exploiting contextual information for the planning and guidance of behavioral responses. Among contextual cues, those provided by others’ behavior are particularly important, in primates, for selecting appropriate reactions and suppressing the inappropriate ones. These latter functions deeply rely on the ability to understand others’ actions. However, it is largely unknown whether prefrontal neurons are activated by action observation. To address this issue, we recorded the activity of ventrolateral prefrontal (VLPF) neurons of macaque monkeys during the observation of videos depicting biological movements performed by a monkey or a human agent, and object motion. Our results show that a population of VLPF neurons respond to the observation of biological movements, in particular those representing goal directed actions. Many of these neurons also show a preference for the agent performing the action. The neural response is present also when part of the observed movement is obscured, suggesting that these VLPF neurons code a high order representation of the observed action rather than a simple visual description of it.
High Photoresponsivity Ge-dot PhotoMOSFETs for Low-power Monolithically-Integrated Si Optical Interconnects
Authors: Kuo Ming-Hao , Lee Meng-Chun , Lin Horng-Chih , George Tom , Li Pei-Wen 
Published: March 2017

AbstractWe report the demonstration of high-photoresponsivity Ge-dot photoMOSFETs in a standard MOS configuration for the detection of 850–1550 nm illumination. Each device has a self-organized, gate-stacking heterostructure of SiO2/Ge-dot/SiO2/SiGe-channel which is simultaneously fabricated in a single oxidation step. Superior control of the geometrical size and chemical composition for our Ge nanodots/SiO2/Si1-xGex-shell MOS structure enables the practically-achievable, gate-stacking design for our Ge-dot photoMOSFETs. Both the gate oxide thickness and the diameter of the Ge dots are controllable. Large photocurrent enhancement was achieved for our Ge-dot photoMOSFETs when electrically-biased at ON- and OFF-states based on the Ge dot mediating photovoltaic and photoconductive effects, respectively. Both photoelectric conversion efficiency and response speed are significantly improved by reducing the gate-oxide thickness from 38.5 nm to 3.5 nm, and by decreasing Ge-dot size from 90 nm to 50 nm for a given areal density of Ge dots. Photoresponsivity ("Equation missing") values as high as 1.2 × 104 A/W and 300 A/W are measured for 10 nW illumination at 850 nm and 1550 nm, respectively. A response time of 0.48 ns and a 3 dB-frequency of 2 GHz were achieved for 50 nm-Ge-dot photoMOSFETs with channel lengths of 3 μm under pulsed 850 nm illumination.
Inhibitory interneuron circuits at cortical and spinal levels are associated with individual differences in corticomuscular coherence during isometric voluntary contraction
Authors: Matsuya Ryosuke , Ushiyama Junichi , Ushiba Junichi 
Published: March 2017

AbstractCorticomuscular coherence (CMC) is an oscillatory synchronization of 15–35 Hz (β-band) between electroencephalogram (EEG) of the sensorimotor cortex and electromyogram of contracting muscles. Although we reported that the magnitude of CMC varies among individuals, the physiological mechanisms underlying this variation are still unclear. Here, we aimed to investigate the associations between CMC and intracortical inhibition (ICI) in the primary motor cortex (M1)/recurrent inhibition (RI) in the spinal cord, which probably affect oscillatory neural activities. Firstly, we quantified ICI from changes in motor-evoked potentials induced by paired-pulse transcranial magnetic stimulation in M1 during tonic isometric voluntary contraction of the first dorsal interosseous. ICI showed a significant, negative correlation with the strength of EEG β-oscillation, but not with the magnitude of CMC across individuals. Next, we quantified RI from changes in H-reflexes induced by paired-pulse electrical nerve stimulation to the posterior tibial nerve during isometric contraction of the soleus muscle. We observed a significant, positive correlation between RI and peak CMC across individuals. These results suggest that the local inhibitory interneuron networks in cortical and spinal levels are associated with the oscillatory activity in corticospinal loop.
An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3
Authors: Nelson Tiffanie M. , Vuillermin Peter , Hodge Jason , Druce Julian , Williams David T. , Jasrotia Rekha , Alexandersen Soren 
Published: March 2017

AbstractHuman parechovirus types 1–16 (HPeV1–16) are positive strand RNA viruses in the family Picornaviridae. We investigated a 2015 outbreak of HPeV3 causing illness in infants in Victoria, Australia. Virus genome was extracted from clinical material and isolates and sequenced using a combination of next generation and Sanger sequencing. The HPeV3 outbreak genome was 98.7% similar to the HPeV3 Yamagata 2011 lineage for the region encoding the structural proteins up to nucleotide position 3115, but downstream of that the genome varied from known HPeV sequences with a similarity of 85% or less. Analysis indicated that recombination had occurred, may have involved multiple types of HPeV and that the recombination event/s occurred between March 2012 and November 2013. However the origin of the genome downstream of the recombination site is unknown. Overall, the capsid of this virus is highly conserved, but recombination provided a different non-structural protein coding region that may convey an evolutionary advantage. The indication that the capsid encoding region is highly conserved at the amino acid level may be helpful in directing energy towards the development of a preventive vaccine for expecting mothers or antibody treatment of young infants with severe disease.
Pramipexole restores depressed transmission in the ventral hippocampus following MPTP-lesion
Authors: Castro-Hernández Javier , Adlard Paul A. , Finkelstein David I. 
Published: March 2017

AbstractThe hippocampus has a significant association with memory, cognition and emotions. The dopaminergic projections from both the ventral tegmental area and substantia nigra are thought to be involved in hippocampal activity. To date, however, few studies have investigated dopaminergic innervation in the hippocampus or the functional consequences of reduced dopamine in disease models. Further complicating this, the hippocampus exhibits anatomical and functional differentiation along its dorso-ventral axis. In this work we investigated the role of dopamine on hippocampal long term potentiation using D-amphetamine, which stimulates dopamine release, and also examined how a dopaminergic lesion affects the synaptic transmission across the anatomic subdivisions of the hippocampus. Our findings indicate that a 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine induced dopaminergic lesion has time-dependent effects and impacts mainly on the ventral region of the hippocampus, consistent with the density of dopaminergic innervation. Treatment with a preferential D3 receptor agonist pramipexole partly restored normal synaptic transmission and Long-Term Potentiation. These data suggest a new mechanism to explain some of the actions of pramipexole in Parkinson´s disease.
Environment-induced changes in selective constraints on social learning during the peopling of the Americas
Authors: Buchanan Briggs , Chao Anne , Chiu Chun-Huo , Colwell Robert K. , O’Brien Michael J. , Werner Angelia , Eren Metin I. 
Published: March 2017

AbstractThe weaponry technology associated with Clovis and related Early Paleoindians represents the earliest well-defined evidence of humans in Pleistocene North America. We assess the technological diversity of these fluted stone points found at archaeological sites in the western and eastern halves of North America by employing statistical tools used in the quantification of ecological biodiversity. Our results demonstrate that the earliest hunters in the environmentally heterogeneous East used a more diverse set of points than those in the environmentally homogenous West. This and other evidence shows that environmental heterogeneity in the East promoted the relaxation of selective constraints on social learning and increased experimentation with point designs.