bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cycle surface plasmon polaritons on a bare metal wire excited by relativistic electrons
Authors: op ‘t Root W.P.E.M. , Brussaard G.J.H. , Smorenburg P.W. , Luiten O.J. 
Published: December 2016

AbstractTerahertz (THz) pulses are applied in areas as diverse as materials science, communication and biosensing. Techniques for subwavelength concentration of THz pulses give access to a rapidly growing range of spatial scales and field intensities. Here we experimentally demonstrate a method to generate intense THz pulses on a metal wire, thereby introducing the possibility of wave-guiding and focussing of the full THz pulse energy to subwavelength spotsizes. This enables endoscopic sensing, single-shot subwavelength THz imaging and study of strongly nonlinear THz phenomena. We generate THz surface plasmon polaritons (SPPs) by launching electron bunches onto the tip of a bare metal wire. Bunches with 160 pC charge and ≈6 ps duration yield SPPs with 6–10 ps duration and 0.4±0.1 MV m−1 electric field strength on a 1.5 mm diameter aluminium wire. These are the most intense SPPs reported on a wire. The SPPs are shown to propagate around a 90° bend.
Catalytic enantioselective addition of Grignard reagents to aromatic silyl ketimines
Authors: Rong Jiawei , Collados Juan F. , Ortiz Pablo , Jumde Ravindra P. , Otten Edwin , Harutyunyan Syuzanna R. 
Published: December 2016

Abstractα-Chiral amines are of significant importance in medicinal chemistry, asymmetric synthesis and material science, but methods for their efficient synthesis are scarce. In particular, the synthesis of α-chiral amines with the challenging tetrasubstituted carbon stereocentre is a long-standing problem and catalytic asymmetric additions of organometallic reagents to ketimines that would give direct access to these molecules are underdeveloped. Here we report a highly enantioselective catalytic synthesis of N-sulfonyl protected α-chiral silyl amines via the addition of inexpensive, easy to handle and readily available Grignard reagents to silyl ketimines. The key to this success was our ability to suppress any unselective background addition reactions and side reduction pathway, through the identification of an inexpensive, chiral Cu-complex as the catalytically active structure.
Observation of the topological soliton state in the Su–Schrieffer–Heeger model
Authors: Meier Eric J. , An Fangzhao Alex , Gadway Bryce 
Published: December 2016

AbstractThe Su–Schrieffer–Heeger (SSH) model, which captures the most striking transport properties of the conductive organic polymer trans-polyacetylene, provides perhaps the most basic model system supporting topological excitations. The alternating bond pattern of polyacetylene chains is captured by the bipartite sublattice structure of the SSH model, emblematic of one-dimensional chiral symmetric topological insulators. This structure supports two distinct nontrivial topological phases, which, when interfaced with one another or with a topologically trivial phase, give rise to topologically protected, dispersionless boundary states. Here, using 87Rb atoms in a momentum-space lattice, we realize fully tunable condensed matter Hamiltonians, allowing us to probe the dynamics and equilibrium properties of the SSH model. We report on the experimental quantum simulation of this model and observation of the localized topological soliton state through quench dynamics, phase-sensitive injection, and adiabatic preparation.
ATP hydrolysis by UPF1 is required for efficient translation termination at premature stop codons
Authors: Serdar Lucas D. , Whiteside DaJuan L. , Baker Kristian E. 
Published: December 2016

AbstractNonsense-mediated mRNA decay (NMD) represents a eukaryotic quality control pathway that recognizes and rapidly degrades transcripts harbouring nonsense mutations to limit accumulation of non-functional and potentially toxic truncated polypeptides. A critical component of the NMD machinery is UPF1, an RNA helicase whose ATPase activity is essential for NMD, but for which the precise function and site of action remain unclear. We provide evidence that ATP hydrolysis by UPF1 is required for efficient translation termination and ribosome release at a premature termination codon. UPF1 ATPase mutants accumulate 3′ RNA decay fragments harbouring a ribosome stalled during premature termination that impedes complete degradation of the mRNA. The ability of UPF1 to impinge on premature termination, moreover, requires ATP-binding, RNA-binding and NMD cofactors UPF2 and UPF3. Our results reveal that ATP hydrolysis by UPF1 modulates a functional interaction between the NMD machinery and terminating ribosomes necessary for targeting substrates to accelerated degradation.
Validation of a genome-wide association study implied that SHTIN1 may involve in the pathogenesis of NSCL/P in Chinese population
Authors: Wang Yirui , Sun Yimin , Huang Yongqing , Pan Yongchu , Yin Aihua , Shi Bing , Du Xuefei , Ma Lan , Lan Feifei , Jiang Min , Shi Jiayu , Zhang Lei , Xiao Xue , Zhou Zhongwei , Jiang Hongbing , Wang Lin , Yang Yinxue , Cheng Jing 
Published: December 2016

AbstractOrofacial clefts are among the most common birth defects in humans worldwide. A large-scale, genome-wide association study (GWAS) in the Chinese population recently identified several genetic risk variants for nonsyndromic cleft lip with or without cleft palate (NSCL/P). We selected 16 significant SNPs from the GWAS I stage (P < 1.00E-5) that had not been replicated to validate their association with NSCL/P in 1931 NSCL/P cases and 2258 controls. Ultimately, we identified a NSCL/P susceptibility loci (rs17095681 at 10q25.3, intron of SHTN1 and 27.2 kb downstream of VAX1, Pmeta = 3.80E-9, OR = 0.64) in Chinese Han and Hui populations. This locus was not high LD with the reported loci in 10q25.3. It was a newly identified independent locus in 10q25.3 associated with NSCL/P. These results imply that SHTIN1 may involve in the pathogenesis of NSCL/P advance our understanding of the genetic susceptibility to NSCL/P.
Auditory biological marker of concussion in children
Authors: Kraus Nina , Thompson Elaine C. , Krizman Jennifer , Cook Katherine , White-Schwoch Travis , LaBella Cynthia R. 
Published: December 2016

AbstractConcussions carry devastating potential for cognitive, neurologic, and socio-emotional disease, but no objective test reliably identifies a concussion and its severity. A variety of neurological insults compromise sound processing, particularly in complex listening environments that place high demands on brain processing. The frequency-following response captures the high computational demands of sound processing with extreme granularity and reliably reveals individual differences. We hypothesize that concussions disrupt these auditory processes, and that the frequency-following response indicates concussion occurrence and severity. Specifically, we hypothesize that concussions disrupt the processing of the fundamental frequency, a key acoustic cue for identifying and tracking sounds and talkers, and, consequently, understanding speech in noise. Here we show that children who sustained a concussion exhibit a signature neural profile. They have worse representation of the fundamental frequency, and smaller and more sluggish neural responses. Neurophysiological responses to the fundamental frequency partially recover to control levels as concussion symptoms abate, suggesting a gain in biological processing following partial recovery. Neural processing of sound correctly identifies 90% of concussion cases and clears 95% of control cases, suggesting this approach has practical potential as a scalable biological marker for sports-related concussion and other types of mild traumatic brain injuries.
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation
Authors: Nardini Christine , Devescovi Valentina , Liu Yuanhua , Zhou Xiaoyuan , Lu Youtao , Dent Jennifer E. 
Published: December 2016

AbstractDegeneration is a hallmark of autoimmune diseases, whose incidence grows worldwide. Current therapies attempt to control the immune response to limit degeneration, commonly promoting immunodepression. Differently, mechanical stimulation is known to trigger healing (regeneration) and it has recently been proposed locally for its therapeutic potential on severely injured areas. As the early stages of healing consist of altered intra- and inter-cellular fluxes of soluble molecules, we explored the potential of this early signal to spread, over time, beyond the stimulation district and become systemic, to impact on distributed or otherwise unreachable injured areas. We report in a model of arthritis in rats how stimulations delivered in the subcutaneous dorsal tissue result, over time, in the control and healing of the degeneration of the paws’ joints, concomitantly with the systemic activation of wound healing phenomena in blood and in correlation with a more eubiotic microbiome in the gut intestinal district.
An Exceptionally Facile Two-Step Structural Isomerization and Detoxication via a Water-Assisted Double Lossen Rearrangement
Authors: Li Feng , Huang Chun-Hua , Xie Lin-Na , Qu Na , Shao Jie , Shao Bo , Zhu Ben-Zhan 
Published: December 2016

AbstractN-hydroxyphthalimide (NHPI), which is best known as an organocatalyst for efficient C-H activation, has been found to be oxidized by quinoid compounds to its corresponding catalytically active nitroxide-radical. Here, we found that NHPI can be isomerized into isatoic anhydride by an unusually facile two-step method using tetrachloro-1,4-benzoquinone (TCBQ, p-chloranil), accompanied by a two-step hydrolytic dechlorination of highly toxic TCBQ into the much less toxic dihydroxylation product, 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone (chloranilic acid). Interestingly, through the complementary application of oxygen-18 isotope-labeling, HPLC combined with electrospray ionization quadrupole time-of-flight and high resolution Fourier transform ion cyclotron resonance mass spectrometric studies, we determined that water was the source and origin of oxygen for isatoic anhydride. Based on these data, we proposed that nucleophilic attack with a subsequent water-assisted Lossen rearrangement coupled with rapid intramolecular addition and cyclization in two consecutive steps was responsible for this unusual structural isomerization of NHPI and concurrent hydroxylation/detoxication of TCBQ. This is the first report of an exceptionally facile double-isomerization of NHPI via an unprecedented water-assisted double-Lossen rearrangement under normal physiological conditions. Our findings may have broad implications for future research on hydroxamic acids and polyhalogenated quinoid carcinogens, two important classes of compounds of major chemical and biological interest.
Timing and quality of sleep in a rural Brazilian family-based cohort, the Baependi Heart Study
Authors: Beijamini F. , Knutson K. L. , Lorenzi-Filho G. , Egan K. J. , Taporoski T. P. , De Paula L. K. G. , Negrão A. B. , Horimoto A. R. V. R. , Duarte N. E. , Vallada H. , Krieger J. E. , Pedrazzoli M. , Pereira A. C. , von Schantz M. 
Published: December 2016

AbstractSleep is modulated by several factors, including sex, age, and chronotype. It has been hypothesised that contemporary urban populations are under pressure towards shorter sleep duration and poorer sleep quality. Baependi is a small town in Brazil that provides a window of opportunity to study the influence of sleep patterns in a highly admixed rural population with a conservative lifestyle. We evaluated sleep characteristics, excessive daytime sleepiness, and chronotype using the Pittsburgh Sleep Quality Index, Epworth Sleepiness Scale and Morningness-Eveningness Questionnaire questionnaires, respectively. The sample consisted of 1,334 subjects from the Baependi Heart study (41.5% male; age: 46.5 ± 16.2 y, range: 18–89 years). Average self-reported sleep duration was 07:07 ± 01:31 (bedtime 22:32 ± 01:27, wake up time: 06:17 ± 01:25 hh:min), sleep quality score was 4.9 + 3.2, chronotype was 63.6 ± 10.8 and daytime sleepiness was 7.4 ± 4.8. Despite a shift towards morningness in the population, chronotype remained associated with reported actual sleep timing. Age and sex modulated the ontogeny of sleep and chronotype, increasing age was associated with earlier sleep time and shorter sleep duration. Women slept longer and later, and reported poorer sleep quality than men (p < 0.0001). This study provides indirect evidence in support of the hypothesis that sleep timing was earlier prior to full urbanisation.
Amyloid precursor protein modulates Nav1.6 sodium channel currents through a Go-coupled JNK pathway
Authors: Li Shao , Wang Xi , Ma Quan-Hong , Yang Wu-lin , Zhang Xiao-Gang , Dawe Gavin S. , Xiao Zhi-Cheng 
Published: December 2016

AbstractAmyloid precursor protein (APP), commonly associated with Alzheimer’s disease, also marks axonal degeneration. In the recent studies, we demonstrated that APP aggregated at nodes of Ranvier (NORs) in myelinated central nervous system (CNS) axons and interacted with Nav1.6. However, the physiological function of APP remains unknown. In this study, we described reduced sodium current densities in APP knockout hippocampal neurons. Coexpression of APP or its intracellular domains containing a VTPEER motif with Nav1.6 sodium channels in Xenopus oocytes resulted in an increase in peak sodium currents, which was enhanced by constitutively active Go mutant and blocked by a dominant negative mutant. JNK and CDK5 inhibitor attenuated increases in Nav1.6 sodium currents induced by overexpression of APP. Nav1.6 sodium currents were increased by APPT668E (mutant Thr to Glu) and decreased by T668A (mutant Thr to ALa) mutant, respectively. The cell surface expression of Nav1.6 sodium channels in the white matter of spinal cord and the spinal conduction velocity is decreased in APP, p35 and JNK3 knockout mice. Therefore, APP modulates Nav1.6 sodium channels through a Go-coupled JNK pathway, which is dependent on phosphorylation of APP at Thr668.
The C-terminus of IGFBP-5 suppresses tumor growth by inhibiting angiogenesis
Authors: Hwang Jae Ryoung , Cho Young-Jae , Lee Yoonna , Park Youngmee , Han Hee Dong , Ahn Hyung Jun , Lee Je-Ho , Lee Jeong-Won 
Published: December 2016

AbstractInsulin-like growth factor-binding protein 5 (IGFBP-5) plays a role in cell growth, differentiation, and apoptosis. In this study, we found that IGFBP5 was markedly downregulated in ovarian cancer tissue. We investigated the functional significance of IGFBP-5 as a tumor suppressor. To determine functional regions of IGFBP-5, truncation mutants were prepared and were studied the effect on tumor growth. Expression of C-terminal region of IGFBP-5 significantly decreased tumor growth in an ovarian cancer xenograft. A peptide derived from the C-terminus of IGFBP-5 (BP5-C) was synthesized to evaluate the minimal amino acid motif that retained anti-tumorigenic activity and its effect on angiogenesis was studied. BP5-C peptide decreased the expression of VEGF-A and MMP-9, phosphorylation of Akt and ERK, and NF-kB activity, and inhibited angiogenesis in in vitro and ex vivo systems. Furthermore, BP5-C peptide significantly decreased tumor weight and angiogenesis in both ovarian cancer orthotopic xenograft and patient-derived xenograft mice. These results suggest that the C-terminus of IGFBP-5 exerts anti-cancer activity by inhibiting angiogenesis via regulation of the Akt/ERK and NF-kB–VEGF/MMP-9 signaling pathway, and might be considered as a novel angiogenesis inhibitor for the treatment of ovarian cancer.
Glycosuria and Renal Outcomes in Patients with Nondiabetic Advanced Chronic Kidney Disease
Authors: Hung Chi-Chih , Lin Hugo You-Hsien , Lee Jia-Jung , Lim Lee Moay , Chiu Yi-Wen , Chiang Heng-Pin , Hwang Shang-Jyh , Chen Hung-Chun 
Published: December 2016

AbstractSodium glucose cotransporter 2 inhibitors have shown a potential for renoprotection beyond blood glucose lowering. Glycosuria in nondiabetic patients with chronic kidney disease (CKD) is sometimes noted. Whether glycosuria in CKD implies a channelopathy or proximal tubulopathy is not known. The consequence of glycosuria in CKD is also not studied. We performed a cross-sectional study for the association between glycosuria and urine electrolyte excretion in 208 nondiabetic patients. Fractional excretion (FE) of glucose >4% was 3.4%, 6.3% and 62.5% in CKD stage 3, 4 and 5, respectively. These patients with glycosuria had higher FE sodium, FE potassium, FE uric acid, UPCR, and urine NGAL-creatinine ratio. We conducted a longitudinal study for the consequence of glycosuria, defined by dipstick, in 769 nondiabetic patients with stage 4–5 CKD. Glycosuria was associated with a decreased risk for end-stage renal disease (adjusted hazard ratio: 0.77; CI = 0.62–0.97; p = 0.024) and for rapid renal function decline (adjusted odds ratio: 0.63; CI = 0.43–0.95; p = 0.032); but glycosuria was not associated with all-cause mortality or cardiovascular events. The results were consistent in the propensity-score matched cohort. Glycosuria is associated with increased fractional excretion of electrolytes and is related to favorable renal outcomes in nondiabetic patients with stage 5 CKD.
Down-regulation of common NFκB-iNOS pathway by chronic Thalidomide treatment improves Hepatopulmonary Syndrome and Muscle Wasting in rats with Biliary Cirrhosis
Authors: Li Tzu-Hao , Lee Pei-Chang , Lee Kuei-Chuan , Hsieh Yun-Cheng , Tsai Chang-Youh , Yang Ying-Ying , Huang Shiang-Fen , Tsai Tung-Hu , Hsieh Shie-Liang , Hou Ming-Chih , Lin Han-Chieh , Lee Shou-Dong 
Published: December 2016

AbstractThalidomide can modulate the TNFα-NFκB and iNOS pathway, which involve in the pathogenesis of hepatopulmonary syndrome (HPS) and muscle wasting in cirrhosis. In bile duct ligated-cirrhotic rats, the increased circulating CD16+(inflammatory) monocytes and its intracellular TNFα, NFκB, monocyte chemotactic protein (MCP-1) and iNOS levels were associated with increased circulating MCP-1/soluable intercellular cell adehesion molecule-1 (sICAM-1), pulmonary TNFα/NOx, up-regulated M1 polarization, exacerbated angiogenesis and hypoxemia (increased AaPO2) in bronchoalveolar lavage (BAL) fluid and pulmonary homogenates. Meanwhile, a significant correlation was noted between circulating CD16+monocyte/M1 (%) macrophages in BAL; M1 (%) macrophages in BAL/pulmonary iNOS mRNA expression; pulmonary iNOS mRNA expression/relative pulmonary MVD; pulmonary NOx level/AaPO2; circulating CD16+monocyte/M1 (%) macrophages in muscle homogenates; 3-nitrotyrosine (representative of peroxynitrite) concentration/M1 (%) macrophages in muscle homogenates. Thein vitrodata demonstrated an iNOS-dependent inhibition of thalidomide on the TNFα-stimulated angiogenesis and myogenesis in human pulmonary artery endothelial cells (HPAECs) and C2C12 myoblasts. Significantly, the co-culture of CD16+monocyte from different rats with HPAECs, or co-culture of supernatant of above mixed cultures with HPAECs or C2C12 myoblasts stimulated angiogenesis, migration and myogenesis. Our findings demonstrate that TNFα inhibitor thalidomide markedly diminishes the severity of experimental HPS and muscle wasting by down-regulation of common peripheral and local NFκB-iNOS pathway.
Bacteriophage T5 gene D10 encodes a branch-migration protein
Authors: Wong Io Nam , Sayers Jon R. , Sanders Cyril M. 
Published: December 2016

AbstractHelicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPaseactivity did not. DNA footprinting and purine-base interference assays demonstrated that D10 engages these substrates with a defined polarity that may be established by protein-nucleobase contacts. Bioinformatic analysis of the nucleotide databases revealed genes predicted to encode proteins related to D10 in archaebacteria, bacteriophages and in viruses known to infect a range of eukaryotic organisms.
Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic
Authors: Yebra Gonzalo , Hodcroft Emma B. , Ragonnet-Cronin Manon L. , Pillay Deenan , Brown Andrew J. Leigh ,   PANGEA_HIV Consortium, Fraser Christophe , Kellam Paul , de Oliveira Tulio , Dennis Ann , Hoppe Anne , Kityo Cissy , Frampton Dan , Ssemwanga Deogratius , Tanser Frank , Keshani Jagoda , Lingappa Jairam , Herbeck Joshua , Wawer Maria , Essex Max , Cohen Myron S. , Paton Nicholas , Ratmann Oliver , Kaleebu Pontiano , Hayes Richard , Fidler Sarah , Quinn Thomas , Novitsky Vladimir ,   ICONIC Project, Haywards Andrew , Nastouli Eleni , Morris Steven , Clark Duncan , Kozlakidis Zisis 
Published: December 2016

AbstractHIV molecular epidemiology studies analyse viral pol gene sequences due to their availability, but whole genome sequencing allows to use other genes. We aimed to determine what gene(s) provide(s) the best approximation to the real phylogeny by analysing a simulated epidemic (created as part of the PANGEA_HIV project) with a known transmission tree. We sub-sampled a simulated dataset of 4662 sequences into different combinations of genes (gag-pol-env, gag-pol, gag, pol, env and partial pol) and sampling depths (100%, 60%, 20% and 5%), generating 100 replicates for each case. We built maximum-likelihood trees for each combination using RAxML (GTR + Γ), and compared their topologies to the corresponding true tree’s using CompareTree. The accuracy of the trees was significantly proportional to the length of the sequences used, with the gag-pol-env datasets showing the best performance and gag and partial pol sequences showing the worst. The lowest sampling depths (20% and 5%) greatly reduced the accuracy of tree reconstruction and showed high variability among replicates, especially when using the shortest gene datasets. In conclusion, using longer sequences derived from nearly whole genomes will improve the reliability of phylogenetic reconstruction. With low sample coverage, results can be highly variable, particularly when based on short sequences.
Evidence for a magma reservoir beneath the Taipei metropolis of Taiwan from both S-wave shadows and P-wave delays
Authors: Lin Cheng-Horng 
Published: December 2016

AbstractThere are more than 7 million people living near the Tatun volcano group in northern Taiwan. For the safety of the Taipei metropolis, in particular, it has been debated for decades whether or not these volcanoes are active. Here I show evidence of a deep magma reservoir beneath the Taipei metropolis from both S-wave shadows and P-wave delays. The reservoir is probably composed of either a thin magma layer overlay or many molten sills within thick partially molten rocks. Assuming that 40% of the reservoir is partially molten, its total volume could be approximately 350 km3. The exact location and geometry of the magma reservoir will be obtained after dense seismic arrays are deployed in 2017–2020.