bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation-dependent binding of a Tetrastatin peptide to αvβ3 integrin decreases melanoma progression through FAK/PI3K/Akt pathway inhibition
Authors: Lambert Eléonore , Fuselier Eloïse , Ramont Laurent , Brassart Bertrand , Dukic Sylvain , Oudart Jean-Baptiste , Dupont-Deshorgue Aurélie , Sellier Christèle , Machado Carine , Dauchez Manuel , Monboisse Jean-Claude , Maquart François-Xavier , Baud Stéphanie , Brassart-Pasco Sylvie 
Published: June 2018

AbstractTetrastatin, a 230 amino acid sequence from collagen IV, was previously demonstrated to inhibit melanoma progression. In the present paper, we identified the minimal active sequence (QKISRCQVCVKYS: QS-13) that reproduced the anti-tumor effects of whole Tetrastatin in vivo and in vitro on melanoma cell proliferation, migration and invasion. We demonstrated that QS-13 binds to SK-MEL-28 melanoma cells through the αvβ3 integrin using blocking antibody and β3 integrin subunit siRNAs strategies. Relevant QS-13 conformations were extracted from molecular dynamics simulations and their interactions with αVβ3 integrin were analyzed by docking experiments to determine the binding areas and the QS-13 amino acids crucial for the binding. The in silico results were confirmed by in vitro experiments. Indeed, QS-13 binding to SK-MEL-28 was dependent on the presence of a disulfide-bound as shown by mass spectroscopy and the binding site on αVβ3 was located in close vicinity to the RGD binding site. QS-13 binding inhibits the FAK/PI3K/Akt pathway, a transduction pathway that is largely involved in tumor cell proliferation and migration. Taken together, our results demonstrate that the QS-13 peptide binds αvβ3 integrin in a conformation-dependent manner and is a potent antitumor agent that could target cancer cells through αVβ3.
Reciprocal cross-species induction of outer membrane vesicle biogenesis via secreted factors
Authors: Horspool Alexander M. , Schertzer Jeffrey W. 
Published: June 2018

AbstractDelivery of cargo to target cells is fundamental to bacterial competitiveness. One important but poorly understood system, ubiquitous among Gram-negative organisms, involves packaging cargo into outer membrane vesicles (OMVs). These biological nanoparticles are involved in processes ranging from toxin delivery to cell-cell communication. Despite this, we know comparatively little about how OMVs are formed. Building upon the discovery that the Pseudomonas Quinolone Signal (PQS) stimulates OMV biogenesis in Pseudomonas aeruginosa, we proposed a model where PQS interacts with the outer membrane to induce curvature and ultimately OMV formation. Though this model is well supported in P. aeruginosa, it remained unclear whether other organisms produce similar compounds. Here we describe the development of a tightly controlled experimental system to test the interaction of bacterially-produced factors with target cells. Using this system, we show that multiple species respond to PQS by increasing OMV formation, that PQS accumulates in the induced vesicles, and that other bacteria secrete OMV-promoting factors. Analysis of induced vesicles indicates that recipient-mediated mechanisms exist to control vesicle size and that relatedness to the producer organism can dictate susceptibility to OMV-inducing compounds. This work provides evidence that small molecule induced OMV biogenesis is a widely conserved process and that cross-talk between systems may influence OMV production in neighboring bacteria.
Optimization-based design of an elastostatic cloaking device
Authors: Fachinotti Víctor D. , Peralta Ignacio , Albanesi Alejandro E. 
Published: June 2018

AbstractWe present a new method for the design of devices to manipulate the displacement field in Elastic materials. It consists of solving a nonlinear optimization problem where the objective function defines the error in matching a desired displacement field, and the design variables determine the required material distribution within the device. In order to facilitate fabrication, the material at a given point of the device is chosen from a set of predefined materials, giving raise to a discrete optimization problem that is converted into a continuous one using the Discrete Material Optimization technique. The candidate materials maybe simple, isotropic materials, but the device made of them behaves as a whole as a metamaterial, enabling the manipulation of the displacement field in ways that are inconceivable in nature. As an example of application, a device for elastostatic cloaking or unfeelability is designed.
Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
Authors: Mann Allison E. , Sabin Susanna , Ziesemer Kirsten , Vågene Åshild J. , Schroeder Hannes , Ozga Andrew T. , Sankaranarayanan Krithivasan , Hofman Courtney A. , Fellows Yates James A. , Salazar-García Domingo C. , Frohlich Bruno , Aldenderfer Mark , Hoogland Menno , Read Christopher , Milner George R. , Stone Anne C. , Lewis Cecil M. , Krause Johannes , Hofman Corinne , Bos Kirsten I. , Warinner Christina 
Published: June 2018

AbstractDental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
Multi-centennial fluctuations of radionuclide production rates are modulated by the Earth’s magnetic field
Authors: Pavón-Carrasco F. J. , Gómez-Paccard M. , Campuzano S. A. , González-Rouco J. F. , Osete M. L. 
Published: June 2018

AbstractThe production of cosmogenic isotopes offers a unique way to reconstruct solar activity during the Holocene. It is influenced by both the solar and Earth magnetic fields and thus their combined effect needs to be disentangled to infer past solar irradiance. Nowadays, it is assumed that the long-term variations of cosmogenic production are modulated by the geomagnetic field and that the solar field dominates over shorter wavelengths. In this process, the effects of the non-dipolar terms of the geomagnetic field are considered negligible. Here we analyse these assumptions and demonstrate that, for a constant solar modulation potential, the geomagnetic field exerts a strong modulation of multi-centennial to millennial wavelengths (periods of 800 and 2200 yr). Moreover, we demonstrate that the non-dipole terms derived from the harmonic degree 3 and above produce maximum differences of 7% in the global average radiocarbon production rate. The results are supported by the identification, for the first time, of a robust coherence between the production rates independently estimated from geomagnetic reconstructions and that inferred from natural archives. This implies the need to review past solar forcing reconstructions, with important implications both for the assessment of solar-climate relationships as well as for the present and future generation of paleoclimate models.
Correction of center of rotation and projection angle in synchrotron X-ray computed tomography
Authors: Cheng Chang-Chieh , Ching Yu-Tai , Ko Pai-Hung , Hwu Yeukuang 
Published: June 2018

AbstractAn error in tomographic reconstruction parameters can result considerable artifacts in the reconstructed image, particularly in micro-computed tomography and nano-computed tomography. This study involved designing an automatic method for efficiently correcting errors resulting from incorrectly determined rotational axes and projection angles. In this method, errors are corrected by minimizing the “total variation” of a reconstructed image, and minimization is accomplished by using the gradient descent method. Compared with two previous methods, the proposed method achieved the best reconstruction results.
High pressure minerals in the Château-Renard (L6) ordinary chondrite: implications for collisions on its parent body
Authors: Baziotis Ioannis , Asimow Paul D. , Hu Jinping , Ferrière Ludovic , Ma Chi , Cernok Ana , Anand Mahesh , Topa Dan 
Published: June 2018

AbstractWe report the first discoveries of high-pressure minerals in the historical L6 chondrite fall Château-Renard, based on co-located Raman spectroscopy, scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy and electron backscatter diffraction, electron microprobe analysis, and transmission electron microscopy (TEM) with selected-area electron diffraction. A single polished section contains a network of melt veins from ~40 to ~200 μm wide, with no cross-cutting features requiring multiple vein generations. We find high-pressure minerals in veins greater than ~50 μm wide, including assemblages of ringwoodite + wadsleyite, ringwoodite + wadsleyite + majorite-pyropess, and ahrensite + wadsleyite. In association with ahrensite + wadsleyite at both SEM and TEM scale, we find a sodic pyroxene whose Raman spectrum is indistinguishable from that of jadeite but whose composition and structure are those of omphacite. We discuss constraints on the impact record of this meteorite and the L-chondrites in general.
The extent of extra-axonal tissue damage determines the levels of CSPG upregulation and the success of experimental axon regeneration in the CNS
Authors: Kim Juhwan , Sajid Muhammad S. , Trakhtenberg Ephraim F. 
Published: June 2018

AbstractThe failure of mature central nervous system (CNS) projection neurons to regenerate axons over long distances drastically limits the recovery of functions lost after various CNS injuries and diseases. Although a number of manipulations that stimulate some degree of axon regeneration that overcomes the inhibitory environment after CNS injury have been discovered, the extent of regeneration remains very limited, emphasizing the need for improved therapies. Regenerating axons need nerve tissue environment capable of supporting their growth, and severe extra-axonal tissue damage and remodeling after injury may disrupt such environment. Here, we used traumatic injury to the mouse optic nerve as a model system to investigate how the extent of extra-axonal tissue damage affects experimental axon regeneration. Axon regeneration was stimulated by the shRNA-mediated knockdown (KD) of Pten gene expression in the retinal ganglion cells, and the extent of extra-axonal tissue damage was varied by changing the duration of optic nerve crush. Although no axons were spared using either 1 or 5 seconds crush, we found that Pten KD-stimulated axon regeneration was significantly reduced in 5 seconds compared with 1 second crush. The more severe extra-axonal tissue damage did not cause tissue atrophy, but led to significantly higher upregulation of axon growth-inhibiting chondroitin sulfate proteoglycan (CSPG) in the glial scar and also enlarged glial scar size, compared with less severely damaged tissue. Thus, the success of axon-regenerating approaches that target neuronal intrinsic mechanisms of axon growth is dependent on the preservation of appropriate extra-axonal tissue environment, which may need to be co-concurrently repaired by tissue remodeling methods.
Multiplex STR amplification sensitivity in a silicon microchip
Authors: Cornelis Senne , Fauvart Maarten , Gansemans Yannick , Vander Plaetsen Ann-Sophie , Colle Frederik , Wiederkehr Rodrigo S. , Deforce Dieter , Stakenborg Tim , Van Nieuwerburgh Filip 
Published: June 2018

AbstractThe demand for solutions to perform forensic DNA profiling outside of centralized laboratories is increasing. We here demonstrate highly sensitive STR amplification using a silicon micro-PCR (µPCR) chip. Exploiting industry-standard semiconductor manufacturing processes, a device was fabricated that features a small form factor thanks to an integrated heating element covering three parallel micro-reactors with a reaction volume of 0.5 µl each. Diluted reference DNA samples (1 ng–31 pg) were amplified on the µPCR chip using the forensically validated AmpFISTR Identifier Plus kit, followed by conventional capillary electrophoresis. Complete STR profiles were generated with input DNA quantities down to 62 pg. Occasional allelic dropouts were observed from 31 pg downward. On-chip STR profiles were compared with those of identical samples amplified using a conventional thermal cycler for direct comparison of amplification sensitivity in a forensic setting. The observed sensitivity was in line with kit specifications for both µPCR and conventional PCR. Finally, a rapid amplification protocol was developed. Complete STR profiles could be generated in less than 17 minutes from as little as 125 pg template DNA. Together, our results are an important step towards the development of commercial, mass-produced, relatively cheap, handheld devices for on-site testing in forensic DNA analysis.
Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies
Authors: Ottaviani Javier I. , Fong Redmond , Kimball Jennifer , Ensunsa Jodi L. , Britten Abigail , Lucarelli Debora , Luben Robert , Grace Philip B. , Mawson Deborah H. , Tym Amy , Wierzbicki Antonia , Khaw Kay-Tee , Schroeter Hagen , Kuhnle Gunter G. C. 
Published: June 2018

AbstractThe accurate assessment of dietary intake is crucial to investigate the effect of diet on health. Currently used methods, relying on self-reporting and food composition data, are known to have limitations and might not be suitable to estimate the intake of many bioactive food components. An alternative are nutritional biomarkers, which can allow an unbiased assessment of intake. They require a careful evaluation of their suitability, including: (a) the availability of a precise, accurate and robust analytical method, (b) their specificity (c) a consistent relationship with actual intake. We have evaluated human metabolites of a microbiome-derived flavan-3-ol catabolite, 5-(3′,4′-dihydroxyphenyl)-[gamma]-valerolactone (gVL), as biomarker of flavan-3-ol intake in large epidemiological studies. Flavan-3-ols are widely consumed plant bioactives, which have received considerable interest due to their potential ability to reduce CVD risk. The availability of authentic standards allowed the development of a validated high-throughput method suitable for large-scale studies. In dietary intervention studies, we could show that gVL metabolites are specific for flavan-3-ols present in tea, fruits, wine and cocoa-derived products, with a strong correlation between intake and biomarker (Spearman’s r = 0.90). This biomarker will allow for the first time to estimate flavan-3-ol intake and further investigation of associations between intake and disease risk.
Vesicle-associated membrane protein 7-mediated eosinophil degranulation promotes allergic airway inflammation in mice
Authors: Willetts Lian , Felix Lindsey C. , Jacobsen Elizabeth A. , Puttagunta Lakshmi , Condjella Rachel M. , Zellner Katie R. , Ochkur Sergei I. , Kim John D. , Luo Huijun , Lee Nancy A. , Lee James J. , Moqbel Redwan , Lacy Paige 
Published: June 2018

AbstractEosinophil degranulation is a determining factor in allergy-mediated airway pathology. Receptor-mediated degranulation in eosinophils requires vesicle-associated membrane protein 7 (VAMP-7), a principal component of the SNARE fusion machinery. The specific contribution of eosinophil degranulation to allergen-induced airway responses remains poorly understood. We generated mice withVAMP-7gene deficiency exclusively in eosinophils (eoCRE/V7) from a cross using eosinophil-specificCrerecombinase-expressing mice crossed withVAMP-7f/fmice. Eosinophils fromeoCRE/V7mice showed deficient degranulation responses in vitro, and responses continued to be decreased following ex vivo intratracheal adoptive transfer ofeoCRE/V7eosinophils intoIL-5/hE2/EPX−/−mice. Consistent with diminished degranulation responses, reduced airway hyperresponsiveness was observed in ovalbumin-sensitized and challengedeoCRE/V7mice following methacholine inhalation. Therefore, VAMP-7 mediates eosinophil degranulation both in vitro and ex vivo, and this event augments airway hyperresponsiveness.
Assessment of Subjective Visual Vertical (SVV) Using the “Bucket Test” and the Virtual SVV System
Authors: Michelson Patricia L. , McCaslin Devin L. , Jacobson Gary P. , Petrak Michelle , English Lauren , Hatton Kelsey 
Published: June 2018

ObjectiveThe purpose of this study was to describe the variability and test–retest reliability of a commercially available subjective visual vertical (SVV) system known as Virtual SVV (Interacoustics). In addition, the study aimed to compare the reliability of the Virtual system with a previously established bucket test of SVV.Study DesignFifteen participants with normal hearing, normal middle ear function, and normal utricular function were included in the study. Each participant underwent static SVV testing using both the Virtual system and the bucket test. Subjects completed 2 testing sessions to determine test–retest reliability. For each test, data were collected with the head at 0°, tilted 45° to the right, and tilted 45° to the left.SettingThis study was conducted in a balance function laboratory embedded in a large, tertiary care otology clinic.ResultsThe mean SVV values obtained with the Virtual system were within 1°–2° from 0 with the head positioned at 0°, which is in agreement with many other studies of SVV with the head at 0° (Akin & Murnane, 2009; Halmagyi & Curthoys, 1999; Zwergal, Rettinger, Frenzel, Dieterich, & Strupp, 2009). Using the intraclass correlation coefficient, test–retest reliability of the Virtual system was excellent in the 45° left position and fair to good in the 45° right and 0° position. Test–retest reliability of the bucket test was poor in all head positions.ConclusionsThe Virtual system is a more reliable measure of static SVV than the bucket test. Therefore, the Virtual system could be utilized as a screening device for utricular dysfunction in busy clinical settings.
Does Contralateral Inhibition of Transient Evoked Otoacoustic Emissions Suggest Sex or Ear Laterality Effects?
Authors: Stuart Andrew , Kerls Alyssa N. 
Published: June 2018

Purpose
The purpose of this study was to examine contralateral inhibition of transient evoked otoacoustic emissions (TEOAEs) in young adults with normal hearing as a function of ear and sex.

Method

Young female (
n
= 50) and male (
n
= 50) adults with normal hearing participated. TEOAEs were measured bilaterally with 80 dB peSPL nonlinear clicks and 60 dB peSPL linear clicks with and without a contralateral broadband noise elicitor at 65 dB SPL. Absolute TEOAE inhibition and normalized TEOAE inhibition (i.e., percentage of inhibition) were examined.

Results

With both 80 and 60 dB peSPL evoking stimuli, there were significant main effects of ear and sex (
p
< .05). TEOAE levels were larger in women and in the right ear. There were no statistically significant main effects of ear and sex on absolute TEOAE inhibition (
p
> .05). Significant main effects of ear and sex were, however, found with normalized TEOAE inhibition (
p
< .05; greater in men and in the left ear). Statistically significant negative correlations and significant linear predictive relations were found between TEOAE levels and normalized TEOAE inhibitions in both ears (
p
< .001). There is no evidence of the same with absolute inhibition of TEOAEs (
p
> .05).

Conclusions
If one considers that efferent inhibition of TEOAEs is an absolute quantity, the significant effect of ear and sex on normalized inhibition and the negative association and linear predictive relationship between TEOAE level and inhibition can be viewed as spurious effects. As such, contralateral inhibition of TEOAEs does not suggest sex or ear laterality effects.
The Roles of Retrieval Practice Versus Errorless Learning in Strengthening Lexical Access in Aphasia
Authors: Schuchard Julia , Middleton Erica L. 
Published: June 2018

Purpose
The purpose of this study was to determine how 2 methods known to improve naming impairment in aphasia (i.e., retrieval practice and errorless learning) affect lexical access. We hypothesized that instances of naming during retrieval practice use and strengthen item-specific connections in each of 2 stages of lexical access: Stage 1, meaning-to-word connections, and Stage 2, word-to-phonology connections. In contrast, errorless learning prioritizes opportunities for repeating words, which we expect to primarily strengthen item-specific connections in Stage 2 because repetition circumvents the need for semantically driven word retrieval.

Method
We tested the outcomes of retrieval practice versus errorless learning training for items that were selected because the naming errors they elicited suggested weakened connections at Stage 1 or at Stage 2 of lexical access for each of 10 individuals with chronic aphasia. Each participant's Stage 1 items and Stage 2 items were divided evenly between the 2 training conditions. Naming tests were administered 1 day and 1 week after training to assess retention of training gains. We also examined whether the participants' pretraining naming error profiles were associated with the relative efficacy of retrieval practice versus errorless learning.

Results
The posttraining naming tests showed an advantage of retrieval practice over errorless learning for Stage 1 items and an advantage of errorless learning over retrieval practice for Stage 2 items. In addition, greater percentages of phonological error naming responses prior to training were associated with greater posttraining accuracy in the errorless learning condition relative to the retrieval practice condition.

Conclusions
The findings suggest that the advantage of retrieval practice for naming impairment in aphasia largely results from greater strengthening of practiced semantic–lexical connections compared with errorless learning, which prioritizes repetition and, therefore, mainly confers strengthening of practiced lexical–phonological connections. Understanding how specific training conditions improve naming can help predict the relative efficacy of each method for individuals with aphasia.
Two Recent Developments in QCD Spectroscopy
Authors: Seth Kamal K. 
Published: June 2018

The presentation has two parts, the first, and main part, is devoted to the presentation of results fromthe first measurements of the production of Λ, Σ Ξ and Ω hyperons at large timelike momentutransfers of 13.6, 14.2 and 17.4 GeV/c2 made using e+e− annihilation data taken at the CESER election-positron collider at Cornell using the CLEOc detector. The measurements reveal interesting features of hyperon production systematics and timelike form factors, and provide evidence for diquark correlations in hyperon structure.
The second part of the presentation is devoted to measurements of photoproduction of J/ψ near threshold energies, EG = 8 − 12 GeV, at the new photon physics facility, GlueX, at the Jefferson Laboratory. The first preliminary results are presented. These are expected to shed light on the gluon structure of protons, gluons which mediate the production of J/ψ in the reaction,γp → J/ψ → e+e−.