bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revealing patterns of cultural transmission from frequency data: equilibrium and non-equilibrium assumptions
Authors: Crema Enrico R. , Kandler Anne , Shennan Stephen 
Published: December 2016

AbstractA long tradition of cultural evolutionary studies has developed a rich repertoire of mathematical models of social learning. Early studies have laid the foundation of more recent endeavours to infer patterns of cultural transmission from observed frequencies of a variety of cultural data, from decorative motifs on potsherds to baby names and musical preferences. While this wide range of applications provides an opportunity for the development of generalisable analytical workflows, archaeological data present new questions and challenges that require further methodological and theoretical discussion. Here we examine the decorative motifs of Neolithic pottery from an archaeological assemblage in Western Germany, and argue that the widely used (and relatively undiscussed) assumption that observed frequencies are the result of a system in equilibrium conditions is unwarranted, and can lead to incorrect conclusions. We analyse our data with a simulation-based inferential framework that can overcome some of the intrinsic limitations in archaeological data, as well as handle both equilibrium conditions and instances where the mode of cultural transmission is time-variant. Results suggest that none of the models examined can produce the observed pattern under equilibrium conditions, and suggest. instead temporal shifts in the patterns of cultural transmission.
Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation
Authors: Gokey Trevor , Hang Bo , Guliaev Anton B. 
Published: December 2016

AbstractToxic metals are known to inhibit DNA repair but the underlying mechanisms of inhibition are still not fully understood. DNA repair enzymes such as human uracil-DNA glycosylase (hUNG) perform the initial step in the base excision repair (BER) pathway. In this work, we showed that cadmium [Cd(II)], a known human carcinogen, inhibited all activity of hUNG at 100 μM. Computational analyses based on 2 μs equilibrium, 1.6 μs steered molecular dynamics (SMD), and QM/MM MD determined that Cd(II) ions entered the enzyme active site and formed close contacts with both D145 and H148, effectively replacing the catalytic water normally found in this position. Geometry refinement by density functional theory (DFT) calculations showed that Cd(II) formed a tetrahedral structure with D145, P146, H148, and one water molecule. This work for the first time reports Cd(II) inhibition of hUNG which was due to replacement of the catalytic water by binding the active site D145 and H148 residues. Comparison of the proposed metal binding site to existing structural data showed that D145:H148 followed a general metal binding motif favored by Cd(II). The identified motif offered structural insights into metal inhibition of other DNA repair enzymes and glycosylases.
Mid-infrared, super-flat, supercontinuum generation covering the 2–5 μm spectral band using a fluoroindate fibre pumped with picosecond pulses
Authors: Michalska Maria , Mikolajczyk Janusz , Wojtas Jacek , Swiderski Jacek 
Published: December 2016

AbstractBroadband, mid-infrared supercontinuum generation in a step-index fluoroindate fibre is reported. By using ~70-picosecond laser pulses at 2.02 μm, provided by an optical parametric generator, a wide spectrum with a cut-off wavelength at 5.25 μm and a 5-dB bandwidth covering the entire 2–5 μm spectral interval has been demonstrated for the first time. The behaviour of the supercontinuum was investigated by changing the peak power and the wavelength of the pump pulses. This allowed the optimal pumping conditions to be determined for the nonlinear medium that was used. The optical damage threshold for the fluoroindate fibre was experimentally found to be ~200 GW/cm2.
Characterization of the Complete Mitochondrial Genome of Leucoma salicis (Lepidoptera: Lymantriidae) and Comparison with Other Lepidopteran Insects
Authors: Sun Yu-Xuan , Wang Lei , Wei Guo-Qing , Qian Cen , Dai Li-Shang , Sun Yu , Abbas Muhammad Nadeem , Zhu Bao-Jian , Liu Chao-Liang 
Published: December 2016

AbstractThe complete mitochondrial genome (mitogenome) ofLeucoma salicis(Lepidoptera: Lymantriidae) was sequenced and annotated. It is a circular molecule of 15,334 bp, containing the 37 genes usually present in insect mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, other thancox1, which is initiated by CGA. Three of the 13 PCGs had an incomplete termination codon, T or TA, while the others terminated with TAA. The relative synonymous codon usage of the 13 protein-coding genes (PCGs) was consistent with those of published lepidopteran sequences. All tRNA genes had typical clover-leaf secondary structures, except for thetRNASer(AGN), in which the dihydrouridine (DHU) arm could not form a stable stem-loop structure. The A + T-rich region of 325 bp had several distinctive features, including the motif ‘ATAGA’ followed by an 18 bp poly-T stretch, a microsatellite-like (AT)7element, and an 11-bp poly-A present immediately upstream oftRNAMet. Relationships among 32 insect species were determined using Maximum Likelihood (ML), Neighbor Joining (NJ) and Bayesian Inference (BI) phylogenetic methods. These analyses confirm thatL. salicisbelongs to the Lymantriidae; and that Lymantriidae is a member of Noctuoidea, and is a sister taxon to Erebidae, Nolidae and Noctuidae, most closely related to Erebidae.
A simple and low-cost combustion method to prepare monoclinic VO2 with superior thermochromic properties
Authors: Cao Ziyi , Xiao Xiudi , Lu Xuanming , Zhan Yongjun , Cheng Haoliang , Xu Gang 
Published: December 2016

AbstractIn this approach, the VO2 nanoparticles have been successfully fabricated via combusting the low-cost precursor solution consisted of NH4VO3, C2H6O2 and C2H5OH. By the XRD, TEM and XPS analysis, it can be found that the synthetic monoclinic VO2 is single crystal and no impurity is defined. After dispersing the VO2 nanoparticles into the polymer, the solar modulation of VO2-based composite film is up to 12.5% with luminous transmission and haze around 62.2% and 0.5%, respectively. In other words, the composite films show high performance of thermochromic properties. This could open an efficient way to fabricate low-cost and large-scale VO2 (M) nanoparticles and thermochromic films.
Manufacture of patient-specific vascular replicas for endovascular simulation using fast, low-cost method
Authors: Kaneko Naoki , Mashiko Toshihiro , Ohnishi Taihei , Ohta Makoto , Namba Katsunari , Watanabe Eiju , Kawai Kensuke 
Published: December 2016

AbstractPatient-specific vascular replicas are essential to the simulation of endovascular treatment or for vascular research. The inside of silicone replica is required to be smooth for manipulating interventional devices without resistance. In this report, we demonstrate the fabrication of patient-specific silicone vessels with a low-cost desktop 3D printer. We show that the surface of an acrylonitrile butadiene styrene (ABS) model printed by the 3D printer can be smoothed by a single dipping in ABS solvent in a time-dependent manner, where a short dip has less effect on the shape of the model. The vascular mold is coated with transparent silicone and then the ABS mold is dissolved after the silicone is cured. Interventional devices can pass through the inside of the smoothed silicone vessel with lower pushing force compared to the vessel without smoothing. The material cost and time required to fabricate the silicone vessel is about USD $2 and 24 h, which is much lower than the current fabrication methods. This fast and low-cost method offers the possibility of testing strategies before attempting particularly difficult cases, while improving the training of endovascular therapy, enabling the trialing of new devices, and broadening the scope of vascular research.
Relationship between handedness and joint involvement in rheumatoid arthritis
Authors: Yaku Ai , Hashimoto Motomu , Furu Moritoshi , Ito Hiromu , Yamakawa Noriyuki , Yamamoto Wataru , Fujii Takao , Matsuda Fumihiko , Mimori Tsuneyo , Terao Chikashi 
Published: December 2016

AbstractRheumatoid arthritis (RA) is characterized by autoimmune chronic joint inflammation, which is worsened by mechanical stress. It is still inconclusive whether joints on the right side or the dominant side get more damaged in RA since the limited number of patients analyzed in the previous study had made it difficult to separately analyze right-handed and left-handed patients. Here, we enrolled 334 RA patients, the biggest number of patients in studies to address this issue and separately analyzed right-handed and left-handed patients. As a result, we observed that joints on the dominant side got clinically and radiologically more involved in the right-handed patients (p ≤ 0.0030). Importantly, this tendency was also seen in the left-handed patients, while it was not statistically significant due to the small sample size. This tendency was observed in each component of clinical or radiological involvement. Thus, handedness influences the laterality of clinical and radiological joint involvement in RA.
Condensed-matter equation of states covering a wide region of pressure studied experimentally
Authors: Gordon Elijah E. , Köhler Jürgen , Whangbo Myung-Hwan 
Published: December 2016

AbstractThe relationships among the pressureP, volumeV, and temperatureTof solid-state materials are described by their equations of state (EOSs), which are often derived from the consideration of the finite-strain energy or the interatomic potential. These EOSs consist of typically three parameters to determine from experimentalP-V-Tdata by fitting analyses. In the empirical approach to EOSs, one either refines such fitting parameters or improves the mathematical functions to better simulate the experimental data. Despite over seven decades of studies on EOSs, none has been found to be accurate for all types of solids over the whole temperature and pressure ranges studied experimentally. Here we show that the simple empirical EOS,P = α1(PV) + α2(PV)2 + α3(PV)3, in which the pressurePis indirectly related to the volumeVthrough a cubic polynomial of the energy termPVwith three fitting parametersα1–α3, provides accurate descriptions for theP-vs-Vdata of condensed matter in a wide region of pressure studied experimentally even in the presence of phase transitions.
A hamster model for Marburg virus infection accurately recapitulates Marburg hemorrhagic fever
Authors: Marzi Andrea , Banadyga Logan , Haddock Elaine , Thomas Tina , Shen Kui , Horne Eva J. , Scott Dana P. , Feldmann Heinz , Ebihara Hideki 
Published: December 2016

AbstractMarburg virus (MARV), a close relative of Ebola virus, is the causative agent of a severe human disease known as Marburg hemorrhagic fever (MHF). No licensed vaccine or therapeutic exists to treat MHF, and MARV is therefore classified as a Tier 1 select agent and a category A bioterrorism agent. In order to develop countermeasures against this severe disease, animal models that accurately recapitulate human disease are required. Here we describe the development of a novel, uniformly lethal Syrian golden hamster model of MHF using a hamster-adapted MARV variant Angola. Remarkably, this model displayed almost all of the clinical features of MHF seen in humans and non-human primates, including coagulation abnormalities, hemorrhagic manifestations, petechial rash, and a severely dysregulated immune response. This MHF hamster model represents a powerful tool for further dissecting MARV pathogenesis and accelerating the development of effective medical countermeasures against human MHF.
Patient-specific structural effects on hemodynamics in the ischemic lower limb artery
Authors: Xu Pengcheng , Liu Xin , Song Qi , Chen Guishan , Wang Defeng , Zhang Heye , Yan Li , liu Dan , Huang Wenhua 
Published: December 2016

AbstractLower limb peripheral artery disease is a prevalent chronic non-communicable disease without obvious symptoms. However, the effect of ischemic lower limb peripheral arteries on hemodynamics remains unclear. In this study, we investigated the variation of the hemodynamics caused by patient-specific structural artery characteristics. Computational fluid dynamic simulations were performed on seven lower limb (including superficial femoral, deep femoral and popliteal) artery models that were reconstructed from magnetic resonance imaging. We found that increased wall shear stress (WSS) was mainly caused by the increasing severity of stenosis, bending, and branching. Our results showed that the increase in the WSS value at a stenosis at the bifurcation was 2.7 Pa. In contrast, the isolated stenosis and branch caused a WSS increase of 0.7 Pa and 0.5 Pa, respectively. The WSS in the narrow popliteal artery was more sensitive to a reduction in radius. Our results also demonstrate that the distribution of the velocity and pressure gradient are highly structurally related. At last, Ultrasound Doppler velocimeter measured result was presented as a validation. In conclusion, the distribution of hemodynamics may serve as a supplement for clinical decision-making to prevent the occurrence of a morbid or mortal ischemic event.
Interstitial Cystitis-Associated Urinary Metabolites Identified by Mass-Spectrometry Based Metabolomics Analysis
Authors: Kind Tobias , Cho Eunho , Park Taeeun D. , Deng Nan , Liu Zhenqiu , Lee Tack , Fiehn Oliver , Kim Jayoung 
Published: December 2016

AbstractThis study on interstitial cystitis (IC) aims to identify a unique urine metabolomic profile associated with IC, which can be defined as an unpleasant sensation including pain and discomfort related to the urinary bladder, without infection or other identifiable causes. Although the burden of IC on the American public is immense in both human and financial terms, there is no clear diagnostic test for IC, but rather it is a disease of exclusion. Very little is known about the clinically useful urinary biomarkers of IC, which are desperately needed. Untargeted comprehensive metabolomic profiling was performed using gas-chromatography/mass-spectrometry to compare urine specimens of IC patients or health donors. The study profiled 200 known and 290 unknown metabolites. The majority of the thirty significantly changed metabolites before false discovery rate correction were unknown compounds. Partial least square discriminant analysis clearly separated IC patients from controls. The high number of unknown compounds hinders useful biological interpretation of such predictive models. Given that urine analyses have great potential to be adapted in clinical practice, research has to be focused on the identification of unknown compounds to uncover important clues about underlying disease mechanisms.
Genetically manipulated phages with improved pH resistance for oral administration in veterinary medicine
Authors: Nobrega Franklin L. , Costa Ana Rita , Santos José F. , Siliakus Melvin F. , van Lent Jan W. M. , Kengen Servé W. M. , Azeredo Joana , Kluskens Leon D. 
Published: December 2016

AbstractOrally administered phages to control zoonotic pathogens face important challenges, mainly related to the hostile conditions found in the gastrointestinal tract (GIT). These include temperature, salinity and primarily pH, which is exceptionally low in certain compartments. Phage survival under these conditions can be jeopardized and undermine treatment. Strategies like encapsulation have been attempted with relative success, but are typically complex and require several optimization steps. Here we report a simple and efficient alternative, consisting in the genetic engineering of phages to display lipids on their surfaces. Escherichia coli phage T7 was used as a model and the E. coli PhoE signal peptide was genetically fused to its major capsid protein (10 A), enabling phospholipid attachment to the phage capsid. The presence of phospholipids on the mutant phages was confirmed by High Performance Thin Layer Chromatography, Dynamic Light Scattering and phospholipase assays. The stability of phages was analysed in simulated GIT conditions, demonstrating improved stability of the mutant phages with survival rates 102–107 pfu.mL−1 higher than wild-type phages. Our work demonstrates that phage engineering can be a good strategy to improve phage tolerance to GIT conditions, having promising application for oral administration in veterinary medicine.
Biological characteristics comparison of HBV rtA181T mutants with truncated or substituted HBsAg expression in vitro and in vivo model systems
Authors: Zhou Ling-Yun , Chen En-Qiang , Wang Meng-Lan , Chen Lan-Lan , Liu Cui-Ping , Zeng Fan , Tang Hong 
Published: December 2016

AbstractThe hepatitis B virus(HBV) polymerase rtA181T mutation is selected during long-term antiviral therapy. As the polymerase gene completely overlaps with the envelope (S) gene, HBV rtA181T mutation also carries sW172 mutations. In this study, we investigated whether there were biological differences between rtA181T/sW172* (coding truncated HBsAg) and rtA181T/sW172L (coding substituted HBsAg) mutants. In cell experiments, a slight decline of viral replication was observed in both two mutants as compared to wild-type strains, but the levels of supernatant HBsAg and HBV DNA in rtA181T/sW172* were significantly lower than those in rtA181T/sW172L transfected cells. In animal experiments, we were amazed to find that viral replication in rtA181T/sW172* mutant increased and maintained significantly longer than that in rtA181T/sW172L mutant, while no significant difference was observed between rtA181T/sW172L and wild-type strains. Compared with wild-type strains, there were intracellular accumulations of HBsAg and HBcAg in rtA181/sW172* but none in rtA181/sW172L mutant strains. Importantly, we also found that truncated HBsAg could increase the activity of HBV core promoter, but substituted HBsAg could not. In summary, the characteristics of above two rtA181T mutants mentioned above were significantly different, and it is necessary and important for us to distinguish sW172* truncated mutation from sW172L substituted mutation.
Altered systemic bile acid homeostasis contributes to liver disease in pediatric patients with intestinal failure
Authors: Xiao Yong-Tao , Cao Yi , Zhou Ke-Jun , Lu Li-Na , Cai Wei 
Published: December 2016

AbstractIntestinal failure (IF)-associated liver disease (IFALD), as a major complication, contributes to significant morbidity in pediatric IF patients. However, the pathogenesis of IFALD is still uncertain. We here investigate the roles of bile acid (BA) dysmetabolism in the unclear pathogenesis of IFALD. It found that the histological evidence of pediatric IF patients exhibited liver injury, which was characterized by liver bile duct proliferation, inflammatory infiltration, hepatocyte apoptosis and different stages of fibrosis. The BA compositions were altered in serum and liver of pediatric IF patients, as reflected by a primary BA dominant composition. In IF patients, the serum FGF19 levels decreased significantly, and were conversely correlated with ileal inflammation grades (r = −0.50, p < 0.05). In ileum, the inflammation grades were inversely associated with farnesoid X receptor (FXR) expression (r = −0.55, p < 0.05). In liver, the expression of induction of the rate-limiting enzyme in bile salt synthesis, cytochrome P450 7a1 (CYP7A1) increased evidently. In conclusion, ileum inflammation decreases FXR expression corresponding to reduce serum FGF19 concentration, along with increased hepatic bile acid synthesis, leading to liver damages in IF patients.
Lamins and metabolism
Authors: Charar Chayki , Gruenbaum Yosef 
Published: December 2016

Lamins are nuclear intermediate filaments (IFs) with important roles in most nuclear activities, including nuclear organization and cell-cycle progression. Mutations in human lamins cause over 17 different diseases, termed laminopathies. Most of these diseases are autosomal dominant and can be roughly divided into four major groups: muscle diseases, peripheral neuronal diseases, accelerated aging disorders and metabolic diseases including Dunnigan type familial partial lipodystrophy (FLPD), acquired partial lipodystrophy (APL) and autosomal dominant leucodystrophy. Mutations in lamins are also associated with the metabolic syndrome (MS). Cells derived from patients suffering from metabolic laminopathies, as well as cells derived from the corresponding animal models, show a disruption of the mechanistic target of rapamycin (mTOR) pathway, abnormal autophagy, altered proliferative rate and down-regulation of genes that regulate adipogenesis. In addition, treating Hutchinson–Gilford progeria syndrome (HGPS) cells with the mTOR inhibitor rapamycin improves their fate. In this review, we will discuss the ways by which lamin genes are involved in the regulation of cell metabolism.
Health-Related Behaviour Among Children of Childhood Cancer Survivors in Germany
Authors: Balcerek M. , Schuster T. , Korte E. , Seidel J. , Schilling R. , Hölling H. , Borgmann-Staudt A. 
Published: December 2016

Abstract
Purpose: Childhood cancer survivors fear that previous therapy could not only impair their own but also their children’s health. We examined whether health-related behaviour in children of childhood cancer survivors differs from the general population.
Methods: Our first nationwide survey wave (2013–2014) surveyed offspring health in 396 German childhood cancer survivors known to have a child of their own. Answers about health behaviour were analysed using descriptive statistics. Data were collected for 418 offspring and 394 could be integrated for matched-pair analyses with data from the German general population (KIGGS, n=17 641).
Results: Teeth-cleaning routine, body-mass-index or subjective body image evaluation by parents were no different from children in the general population. Parents who included a cancer survivor smoked less in the presence of their children (p=0.01). During pregnancy, mothers in cancer survivor parent pairs abstained from drinking alcohol more often (p=0.01) and smoked less (p=0.05). While the calculated effect sizes (Phi) were generally low (0.135–0.247), children from cancer survivors played less outdoors than peers did (p=0.01). Boys participated in sports outside a club more often (p=0.05) and watched less TV on weekdays (p=0.01) and girls spent more time on the computer during weekdays than peers did (p=0.01).
Conclusions: This study provides the first data for health-related behaviour in cancer survivors’ offspring and sheds light on differences to parenting in the general population. Multivariate analyses in a larger study population are needed to relate these differences to fear issues in cancer survivors.
Rapid synthesis of cyclic oligomeric depsipeptides with positional, stereochemical, and macrocycle size distribution control
Authors: Batiste Suzanne M. , Johnston Jeffrey N. 
Published: December 2016

Significance
This work resonates with the intense, rapidly broadening interest in macrocycle synthesis, enabling the preparation of collections of size-congener macrocycles in a single reaction. More specifically, we have outlined the use of the Mitsunobu reaction to forge ester linkages between hydroxy acid monomers for depsipeptides in an oligomerization/macrocyclization mode. Additionally, we disclose that salt additives, which are normally contraindicated in a Mitsunobu reaction, are able to either enhance ring-size diversity (collections) or optimize the production of one macrocycle (selection) in an ion-templated fashion. Combination of this strategy and contemporary chemical methods allows rapid access to cyclodepsipeptide natural products and their unnatural isomers.