bluuebunny/crossref_metadata_2025_split huggingface dataset:
Male care and life history traits in mammals
Authors: West Hannah E. R. , Capellini Isabella 
Published: June 2016

AbstractMale care has energetic and opportunity costs, and is more likely to evolve when males gain greater certainty of paternity or when future mating opportunities are scarce. However, little is known about the substantial benefits that males may provide to females and offspring. Using phylogenetic comparative methods and a sample of over 500 mammalian species, we show that mammals in which males carry the offspring have shorter lactation periods, which leads to more frequent breeding events. Provisioning the female is associated with larger litters and shorter lactation. Offspring of species with male care have similar weaning mass to those without despite being supported by a shorter lactation period, implying that they grow faster. We propose that males provide an energetic contribution during the most expensive time of female reproduction, lactation, and that different male care behaviours increase female fecundity, which in turn helps males offset the costs of caring.
Polymorphism in magic-sized Au144(SR)60 clusters
Authors: Jensen Kirsten M.Ø. , Juhas Pavol , Tofanelli Marcus A. , Heinecke Christine L. , Vaughan Gavin , Ackerson Christopher J. , Billinge Simon J. L. 
Published: June 2016

AbstractUltra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. The study reveals structural polymorphism in these archetypal nanoclusters. In addition to confirming the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. The discovery of polymorphism may open up a new dimension in nanoscale engineering.
Neonatal face-to-face interactions promote later social behaviour in infant rhesus monkeys
Authors: Dettmer Amanda M. , Kaburu Stefano S. K. , Simpson Elizabeth A. , Paukner Annika , Sclafani Valentina , Byers Kristen L. , Murphy Ashley M. , Miller Michelle , Marquez Neal , Miller Grace M. , Suomi Stephen J. , Ferrari Pier F. 
Published: June 2016

AbstractIn primates, including humans, mothers engage in face-to-face interactions with their infants, with frequencies varying both within and across species. However, the impact of this variation in face-to-face interactions on infant social development is unclear. Here we report that infant monkeys (Macaca mulatta) who engaged in more neonatal face-to-face interactions with mothers have increased social interactions at 2 and 5 months. In a controlled experiment, we show that this effect is not due to physical contact alone: monkeys randomly assigned to receive additional neonatal face-to-face interactions (mutual gaze and intermittent lip-smacking) with human caregivers display increased social interest at 2 months, compared with monkeys who received only additional handling. These studies suggest that face-to-face interactions from birth promote young primate social interest and competency.
A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions
Authors: Koorehdavoudi Hana , Bogdan Paul 
Published: June 2016

AbstractBiological systems are frequently categorized as complex systems due to their capabilities of generating spatio-temporal structures from apparent random decisions. In spite of research on analyzing biological systems, we lack a quantifiable framework for measuring their complexity. To fill this gap, in this paper, we develop a new paradigm to study a collective group ofNagents moving and interacting in a three-dimensional space. Our paradigm helps to identify the spatio-temporal states of the motion of the group and their associated transition probabilities. This framework enables the estimation of the free energy landscape corresponding to the identified states. Based on the energy landscape, we quantify missing information, emergence, self-organization and complexity for a collective motion. We show that the collective motion of the group of agents evolves to reach the most probable state with relatively lowest energy level and lowest missing information compared to other possible states. Our analysis demonstrates that the natural group of animals exhibit a higher degree of emergence, self-organization and complexity over time. Consequently, this algorithm can be integrated into new frameworks to engineer collective motions to achieve certain degrees of emergence, self-organization and complexity.
Multiscale approach predictions for biological outcomes in ion-beam cancer therapy
Authors: Verkhovtsev Alexey , Surdutovich Eugene , Solov’yov Andrey V. 
Published: June 2016

AbstractIon-beam therapy provides advances in cancer treatment, offering the possibility of excellent dose localization and thus maximising cell-killing within the tumour. The full potential of such therapy can only be realised if the fundamental mechanisms leading to lethal cell damage under ion irradiation are well understood. The key question is whether it is possible to quantitatively predict macroscopic biological effects caused by ion radiation on the basis of physical and chemical effects related to the ion-medium interactions on a nanometre scale. We demonstrate that the phenomenon-based MultiScale Approach to the assessment of radiation damage with ions gives a positive answer to this question. We apply this approach to numerous experiments where survival curves were obtained for different cell lines and conditions. Contrary to other, in essence empirical methods for evaluation of macroscopic effects of ionising radiation, the MultiScale Approach predicts the biodamage based on the physical effects related to ionisation of the medium, transport of secondary particles, chemical interactions, thermo-mechanical pathways of biodamage and heuristic biological criteria for cell survival. We anticipate this method to give great impetus to the practical improvement of ion-beam cancer therapy and the development of more efficient treatment protocols.
GCN2 contributes to mTORC1 inhibition by leucine deprivation through an ATF4 independent mechanism
Authors: Averous Julien , Lambert-Langlais Sarah , Mesclon Florent , Carraro Valérie , Parry Laurent , Jousse Céline , Bruhat Alain , Maurin Anne-Catherine , Pierre Philippe , Proud Christopher G. , Fafournoux Pierre 
Published: June 2016

AbstractIt is well known that the GCN2 and mTORC1 signaling pathways are regulated by amino acids and share common functions, in particular the control of translation. The regulation of GCN2 activity by amino acid availability relies on the capacity of GCN2 to sense the increased levels of uncharged tRNAs upon amino acid scarcity. In contrast, despite recent progress in the understanding of the regulation of mTORC1 by amino acids, key aspects of this process remain unsolved. In particular, while leucine is well known to be a potent regulator of mTORC1, the mechanisms by which this amino acid is sensed and control mTORC1 activity are not well defined. Our data establish that GCN2 is involved in the inhibition of mTORC1 upon leucine or arginine deprivation. However, the activation of GCN2 alone is not sufficient to inhibit mTORC1 activity, indicating that leucine and arginine exert regulation via additional mechanisms. While the mechanism by which GCN2 contributes to the initial step of mTORC1 inhibition involves the phosphorylation of eIF2α, we show that it is independent of the downstream transcription factor ATF4. These data point to a novel role for GCN2 and phosphorylation of eIF2α in the control of mTORC1 by certain amino acids.
Calcitonin gene-related peptide is a key factor in the homing of transplanted human MSCs to sites of spinal cord injury
Authors: Zhang Yu , Yang Jinhua , Zhang Peng , Liu Tao , Xu Jianwei , Fan Zhihai , Shen Yixin , Li Wenjie , Zhang Huanxiang 
Published: June 2016

AbstractMesenchymal stem cells (MSCs) can be used to treat many diseases, including spinal cord injury (SCI). Treatment relies mostly on the precise navigation of cells to the injury site for rebuilding the damaged spinal cord. However, the key factors guiding MSCs to the epicenter of SCI remain unknown. Here, we demonstrated that calcitonin gene-related peptide (CGRP), a neural peptide synthesized in spinal cord, can dramatically aid the homing of human umbilical cord mesenchymal stem cells (HUMSCs) in spinal cord-transected SCI rats. First, HUMSCs exhibited chemotactic responses in vitro to CGRP. By time-lapse video analysis, increased chemotactic index (CMI), forward migration index (FMI) and speed contributed to this observed migration. Then, through enzyme immunoassay, higher CGRP concentrations at the lesion site were observed after injury. The release of CGRP directed HUMSCs to the injury site, which was suppressed by CGRP 8–37, a CGRP antagonist. We also verified that the PI3K/Akt and p38MAPK signaling pathways played a critical role in the CGRP-induced chemotactic migration of HUMSCs. Collectively, our data reveal that CGRP is a key chemokine that helps HUMSCs migrate to the lesion site and thereby can be used as a model molecule to study MSCs homing after SCI.
Temperature-dependent photoluminescence of surface-engineered silicon nanocrystals
Authors: Mitra Somak , Švrček Vladimir , Macias-Montero Manual , Velusamy Tamilselvan , Mariotti Davide 
Published: June 2016

AbstractIn this work we report on temperature-dependent photoluminescence measurements (15–300 K), which have allowed probing radiative transitions and understanding of the appearance of various transitions. We further demonstrate that transitions associated with oxide in SiNCs show characteristic vibronic peaks that vary with surface characteristics. In particular we study differences and similarities between silicon nanocrystals (SiNCs) derived from porous silicon and SiNCs that were surface-treated using a radio-frequency (RF) microplasma system.
Direct interaction of beta-amyloid with Na,K-ATPase as a putative regulator of the enzyme function
Authors: Petrushanko Irina Yu. , Mitkevich Vladimir A. , Anashkina Anastasia A. , Adzhubei Alexei A. , Burnysheva Ksenia M. , Lakunina Valentina A. , Kamanina Yulia V. , Dergousova Elena A. , Lopina Olga D. , Ogunshola Omolara O. , Bogdanova Anna Yu. , Makarov Alexander A. 
Published: June 2016

AbstractBy maintaining the Na+and K+transmembrane gradient mammalian Na,K-ATPase acts as a key regulator of neuronal electrotonic properties. Na,K-ATPase has an important role in synaptic transmission and memory formation. Accumulation of beta-amyloid (Aβ) at the early stages of Alzheimer’s disease is accompanied by reduction of Na,K-ATPase functional activity. The molecular mechanism behind this phenomenon is not known. Here we show that the monomeric Aβ(1-42) forms a tight (Kdof 3 μM), enthalpy-driven equimolar complex with α1β1 Na,K-ATPase. The complex formation results in dose-dependent inhibition of the enzyme hydrolytic activity. The binding site of Aβ(1-42) is localized in the “gap” between the alpha- and beta-subunits of Na,K-ATPase, disrupting the enzyme functionality by preventing the subunits from shifting towards each other. Interaction of Na,K-ATPase with exogenous Aβ(1-42) leads to a pronounced decrease of the enzyme transport and hydrolytic activity and Src-kinase activation in neuroblastoma cells SH-SY5Y. This interaction allows regulation of Na,K-ATPase activity by short-term increase of the Aβ(1-42) level. However prolonged increase of Aβ(1-42) level under pathological conditions could lead to chronical inhibition of Na,K-ATPase and disruption of neuronal function. Taken together, our data suggest the role of beta-amyloid as a novel physiological regulator of Na,K-ATPase.
Rising levels of atmospheric oxygen and evolution of Nrf2
Authors: Gacesa Ranko , Dunlap Walter C. , Barlow David J. , Laskowski Roman A. , Long Paul F. 
Published: June 2016

AbstractIn mammals, the master transcription regulator of antioxidant defences is provided by the Nrf2 protein. Phylogenetic analyses of Nrf2 sequences are used here to derive a molecular clock that manifests persuasive evidence that Nrf2 orthologues emerged and then diverged, at two time points that correlate with well-established geochemical and palaeobiological chronologies during progression of the ‘Great Oxygenation Event’. We demonstrate that orthologues of Nrf2 first appeared in fungi around 1.5 Ga during the Paleoproterozoic when photosynthetic oxygen was being absorbed into the oceans. A subsequent significant divergence in Nrf2 is seen during the split between fungi and the Metazoa approximately 1.0–1.2 Ga, at a time when oceanic ventilation released free oxygen to the atmosphere, but with most being absorbed by methane oxidation and oxidative weathering of land surfaces until approximately 800 Ma. Atmospheric oxygen levels thereafter accumulated giving rise to metazoan success known as the Cambrian explosion commencing at ~541 Ma. Atmospheric O2 levels then rose in the mid Paleozoic (359–252 Ma) and Nrf2 diverged once again at the division between mammals and non-mammalian vertebrates during the Permian-Triassic boundary (~252 Ma). Understanding Nrf2 evolution as an effective antioxidant response may have repercussions for improved human health.
Bax Inhibitor-1 regulates hepatic lipid accumulation via ApoB secretion
Authors: Lee Hwa Young , Lee Geum-Hwa , Bhattarai Kashi Raj , Park Byung-Hyun , Koo Seung-Hoi , Kim Hyung-Ryong , Chae Han Jung 
Published: June 2016

AbstractIn this study, we explored the effects of Bax Inhibitor-1 (BI-1) on ApoB aggregation in high-fat diet (HFD)-induced hepatic lipid accumulation. After 1 week on a HFD, triglycerides and cholesterol accumulated more in the liver and were not effectively secreted into the plasma, whereas after 8 weeks, lipids were highly accumulated in both the liver and plasma, with a greater effect in BI-1 KO mice compared with BI-1 WT mice. ApoB, a lipid transfer protein, was accumulated to a greater extent in the livers of HFD-BI-1 KO mice compared with HFD-BI-1 WT mice. Excessive post-translational oxidation of protein disulfide isomerase (PDI), intra-ER ROS accumulation and folding capacitance alteration were also observed in HFD-BI-1 KO mice. Higher levels of endoplasmic reticulum (ER) stress were consistently observed in KO mice compared with the WT mice. Adenovirus-mediated hepatic expression of BI-1 in the BI-1 KO mice rescued the above phenotypes. Our results suggest that BI-1-mediated enhancement of ApoB secretion regulates hepatic lipid accumulation, likely through regulation of ER stress and ROS accumulation.
Pancreatic SEC23B deficiency is sufficient to explain the perinatal lethality of germline SEC23B deficiency in mice
Authors: Khoriaty Rami , Everett Lesley , Chase Jennifer , Zhu Guojing , Hoenerhoff Mark , McKnight Brooke , Vasievich Matthew P. , Zhang Bin , Tomberg Kärt , Williams John , Maillard Ivan , Ginsburg David 
Published: June 2016

AbstractIn humans, loss of function mutations in SEC23B result in Congenital Dyserythropoietic Anemia type II (CDAII), a disease limited to defective erythroid development. Patients with two nonsense SEC23B mutations have not been reported, suggesting that complete SEC23B deficiency might be lethal. We previously reported that SEC23B-deficient mice die perinatally, exhibiting massive pancreatic degeneration and that mice with hematopoietic SEC23B deficiency do not exhibit CDAII. We now show that SEC23B deficiency restricted to the pancreas is sufficient to explain the lethality observed in mice with global SEC23B-deficiency. Immunohistochemical stains demonstrate an acinar cell defect but normal islet cells. Mammalian genomes contain two Sec23 paralogs, Sec23A and Sec23B. The encoded proteins share ~85% amino acid sequence identity. We generate mice with pancreatic SEC23A deficiency and demonstrate that these mice survive normally, exhibiting normal pancreatic weights and histology. Taken together, these data demonstrate that SEC23B but not SEC23A is essential for murine pancreatic development. We also demonstrate that two BAC transgenes spanning Sec23b rescue the lethality of mice homozygous for a Sec23b gene trap allele, excluding a passenger gene mutation as the cause of the pancreatic lethality, and indicating that the regulatory elements critical for Sec23b pancreatic function reside within the BAC transgenes.
Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes
Authors: Chu Wen-Ting , Wang Jin 
Published: June 2016

AbstractEnzyme activity (often quantified by kcat /Km ) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat /Km . This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.
3D conductive coupling for efficient generation of prominent Fano resonances in metamaterials
Authors: Liu Zhiguang , Liu Zhe , Li Jiafang , Li Wuxia , Li Junjie , Gu Changzhi , Li Zhi-Yuan 
Published: June 2016

AbstractWe demonstrate a 3D conductive coupling mechanism for the efficient generation of prominent and robust Fano resonances in 3D metamaterials (MMs) formed by integrating vertical U-shape split-ring resonators (SRRs) or vertical rectangular plates along a planar metallic hole array with extraordinary optical transmission (EOT). In such a configuration, intensified vertical E-field is induced along the metallic holes and naturally excites the electric resonances of the vertical structures, which form non-radiative “dark” modes. These 3D conductive “dark” modes strongly interfere with the “bright” resonance mode of the EOT structure, generating significant Fano resonances with both prominent destructive and constructive interferences. The demonstrated 3D conductive coupling mechanism is highly universal in that both 3D MMs with vertical SRRs and vertical plates exhibit the same prominent Fano resonances despite their dramatic structural difference, which is conceptually different from conventional capacitive and inductive coupling mechanisms that degraded drastically upon small structural deviations.
Identifying a set of influential spreaders in complex networks
Authors: Zhang Jian-Xiong , Chen Duan-Bing , Dong Qiang , Zhao Zhi-Dan 
Published: June 2016

AbstractIdentifying a set of influential spreaders in complex networks plays a crucial role in effective information spreading. A simple strategy is to choose top-rranked nodes as spreaders according to influence ranking method such as PageRank, ClusterRank andk-shell decomposition. Besides, some heuristic methods such as hill-climbing, SPIN, degree discount and independent set based are also proposed. However, these approaches suffer from a possibility that some spreaders are so close together that they overlap sphere of influence or time consuming. In this report, we present a simply yet effectively iterative method named VoteRank to identify a set of decentralized spreaders with the best spreading ability. In this approach, all nodes vote in a spreader in each turn, and the voting ability of neighbors of elected spreader will be decreased in subsequent turn. Experimental results on four real networks show that under Susceptible-Infected-Recovered (SIR) and Susceptible-Infected (SI) models, VoteRank outperforms the traditional benchmark methods on both spreading rate and final affected scale. What’s more, VoteRank has superior computational efficiency.
Pharmacogenetics-Guided Phase I Study of Capecitabine on an Intermittent Schedule in Patients with Advanced or Metastatic Solid Tumours
Authors: Soo Ross Andrew , Syn Nicholas , Lee Soo-Chin , Wang Lingzhi , Lim Xn-Yii , Loh Marie , Tan Sing-Huang , Zee Ying-Kiat , Wong Andrea Li-Ann , Chuah Benjamin , Chan Daniel , Lim Siew-Eng , Goh Boon-Cher , Soong Richie , Yong Wei-Peng 
Published: June 2016

AbstractThe FDA-approved starting dosage of capecitabine is 1,250 mg/m2, and market research indicates that U.S. physicians routinely prescribe 1,000 mg/m2. Retrospective analyses however report reduced toxicity and efficacy in a subset of patients with the 3R/3R genotype of the thymidylate synthase gene enhancer region (TSER). This study sought to develop TSER genotype-specific guidelines for capecitabine dosing. Capecitabine was dose-escalated in advanced and/or metastatic cancer patients with TSER 3R/3R (Group A; N = 18) or 2R/2R + 2R/3R (Group B; N = 5) from 1,250 to 1,625 mg/m2 b.i.d., every 2 weeks on/1 week off for up to 8 cycles. Parent and metabolites pharmacokinetics, adverse events, and tumour response were assessed. The maximum tolerated and recommended doses in 3R/3R patients are 1,625 mg/m2 and 1,500 mg/m2. At 1,500 mg/m2, one in nine 3R/3R patients experienced a dose-limiting toxicity. Dosing guidelines for 2R/2R + 2R/3R remain undetermined due to poor accrual. The results indicate that 3R/3R patients may be amenable to 1,500 mg/m2 b.i.d. on an intermittent schedule, and is the first to prospectively validate the utility of TSER pharmacogenetic-testing before capecitabine treatment.
Ethnic specific association of the CAV1/CAV2 locus with primary open-angle glaucoma
Authors: Rong Shi Song , Chen Li Jia , Leung Christopher K. S. , Matsushita Kenji , Jia Liyun , Miki Atsuya , Chiang Sylvia W. Y. , Tam Pancy O. S. , Hashida Noriyasu , Young Alvin L. , Tsujikawa Motokazu , Zhang Mingzhi , Wang Ningli , Nishida Kohji , Pang Chi Pui 
Published: June 2016

AbstractA single-nucleotide polymorphism (SNP) rs4236601 at the CAV1/CAV2 locus is associated with primary open-angle glaucoma (POAG). Rs4236601 is common in Caucasians but rare in East Asians. Here we conducted a haplotype-tagging SNP analysis followed by replication in a total of 848 POAG cases and 1574 controls drawn from 3 cities in China and 1 city in Japan. Two SNPs, rs4236601 (odds ratio [OR] = 6.25; P = 0.0086) and a tagging-SNP rs3801994 (OR = 1.32; P = 0.042), were associated with POAG in the Hong Kong Chinese cohort after age and gender adjustments. Rs4236601 was associated with POAG also in Shantou (OR = 6.09; P = 0.0037) and Beijing (OR = 3.92; P = 0.030) cohorts after age and gender adjustment, with a pooled-OR of 5.26 (P = 9.0 × 10−6) in Chinese; but it is non-polymorphic in the Osaka cohort. SNP rs3801994 showed a similar trend of effect in the Shantou and Beijing cohorts, with a pooled-OR of 1.23 (P = 0.022) and 1.20 (P = 0.063) in Chinese, prior to and after age and gender adjustment, respectively; but it showed a reverse effect in the Osaka cohort (OR = 0.58; P = 0.033) after the adjustments. We have thus confirmed the association of rs4236601 with POAG in different Chinese cohorts. Also, we found a common SNP rs3801994 of diverse associations with POAG between Chinese and Japanese.