bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential mortality, aging and social security: delaying the retirement age when educational spillovers matter
Authors: LE GARREC GILLES , LHUISSIER STÉPHANE 
Published: January 2016

AbstractTo lower the forecasted increase in the social security burden linked to population aging, delaying the legal age of retirement has been privileged throughout industrialized countries. Compared with a uniform delay, some argue that those who have entered precociously the labor market should be allowed to retire earlier. They assert that such a ‘long career’ exception is all the more justified that those unskilled workers live also less long due to heavier and potentially health-damaging jobs. In this paper, we then study macroeconomic and distributional consequences of global gain in life expectancy, with or without the postponement of the legal age of retirement and with or without a ‘long career’ exception. By considering a framework where individuals decide to acquire skills depending on economic incentives and differential mortality, we focus particularly on spillover effects possibly generated by education. We show in particular that introducing a ‘long career’ exception cannot be to the advantage of future unskilled workers unless education yields no spillover effects.
Seasonal variation in major depressive episode prevalence in Canada
Authors: Patten S. B. , Williams J. V. A. , Lavorato D. H. , Bulloch A. G. M. , Fiest K. M. , Wang J. L. , Sajobi T. T. 
Published: January 2016

Background.The purpose of this paper is to describe variation, over the months of the year, in major depressive episode (MDE) prevalence. This is an important aspect of the epidemiological description of MDE, and one that has received surprisingly little attention in the literature. Evidence of seasonal variation in MDE prevalence has been weak and contradictory. Most studies have sought to estimate the prevalence of seasonal affective disorder using cut-points applied to scales assessing mood seasonality rather than MDE. This approach does not align with modern classification in which seasonal depression is a diagnostic subtype of major depression rather than a distinct category. Also, some studies may have lacked power to detect seasonal differences. We addressed these limitations by examining the month-specific occurrence of conventionally defined MDE and by pooling data from large epidemiological surveys to enhance precision in the analysis.Method.Data from two national survey programmes (the National Population Health Survey and the Canadian Community Health Survey) were used, providing ten datasets collected between 1996 and 2013, together including over 500,000. These studies assessed MDE using a short form version of the Composite International Diagnostic Interview (CIDI) for major depression, with one exception being a 2012 survey that used a non-abbreviated version of the CIDI. The proportion of episodes occurring in each month was evaluated using items from the diagnostic modules and statistical methods addressing complex design features of these trials. Overall month-specific pooled estimates and associated confidence intervals were estimated using random effects meta-analysis and a gradient was assessed using a meta-regression model that included a quadratic term.Results.There was considerable sampling variability when the month-specific proportions were estimated from individual survey datasets. However, across the various datasets, there was sufficient homogeneity to justify the pooling of these estimated proportions, producing large gains in precision. Seasonal variation was clearly evident in the pooled data. The highest proportion of episodes occurred in December, January and February and the lowest proportions occurred in June, July and August. The proportion of respondents reporting MDE in January was 70% higher than August, suggesting an association with implications for health policy. The pattern persisted with stratification for age group, sex and latitude.Conclusions.Seasonal effects in MDE may have been obscured by small sample sizes in prior studies. In Canada, MDE has clear seasonal variation, yet this is not addressed in the planning of services. These results suggest that availability of depression treatment should be higher in the winter than the summer months.
Low adherent cancer cell subpopulations are enriched in tumorigenic and metastatic epithelial-to-mesenchymal transition-induced cancer stem-like cells
Authors: Morata-Tarifa Cynthia , Jiménez Gema , García María A. , Entrena José M. , Griñán-Lisón Carmen , Aguilera Margarita , Picon-Ruiz Manuel , Marchal Juan A. 
Published: January 2016

AbstractCancer stem cells are responsible for tumor progression, metastasis, therapy resistance and cancer recurrence, doing their identification and isolation of special relevance. Here we show that low adherent breast and colon cancer cells subpopulations have stem-like properties. Our results demonstrate that trypsin-sensitive (TS) breast and colon cancer cells subpopulations show increased ALDH activity, higher ability to exclude Hoechst 33342, enlarged proportion of cells with a cancer stem-like cell phenotype and are enriched in sphere- and colony-forming cells in vitro. Further studies in MDA-MB-231 breast cancer cells reveal that TS subpopulation expresses higher levels of SLUG, SNAIL, VIMENTIN and N-CADHERIN while show a lack of expression of E-CADHERIN and CLAUDIN, being this profile characteristic of the epithelial-to-mesenchymal transition (EMT). The TS subpopulation shows CXCL10, BMI-1 and OCT4 upregulation, differing also in the expression of several miRNAs involved in EMT and/or cell self-renewal such as miR-34a-5p, miR-34c-5p, miR-21-5p, miR-93-5p and miR-100-5p. Furthermore, in vivo studies in immunocompromised mice demonstrate that MDA-MB-231 TS cells form more and bigger xenograft tumors with shorter latency and have higher metastatic potential. In conclusion, this work presents a new, non-aggressive, easy, inexpensive and reproducible methodology to isolate prospectively cancer stem-like cells for subsequent biological and preclinical studies.
LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Authors: Dong Xinran , Hao Yun , Wang Xiao , Tian Weidong 
Published: January 2016

AbstractPathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher’s exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO’s usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes and identify relevant gene sets to autism that could not be found by Fisher.
Design of chimeric antigen receptors with integrated controllable transient functions
Authors: Juillerat Alexandre , Marechal Alan , Filhol Jean-Marie , Valton Julien , Duclert Aymeric , Poirot Laurent , Duchateau Philippe 
Published: January 2016

AbstractThe ability to control T cells engineered to permanently express chimeric antigen receptors (CARs) is a key feature to improve safety. Here, we describe the development of a new CAR architecture with an integrated switch-on system that permits to control the CAR T-cell function. This system offers the advantage of a transient CAR T-cell for safety while letting open the possibility of multiple cytotoxicity cycles using a small molecule drug.
Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
Authors: Wang Sheng , Peng Jian , Ma Jianzhu , Xu Jinbo 
Published: January 2016

AbstractProtein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions and solvent accessibility.
Tunable atomic spin-orbit coupling synthesized with a modulating gradient magnetic field
Authors: Luo Xinyu , Wu Lingna , Chen Jiyao , Guan Qing , Gao Kuiyi , Xu Zhi-Fang , You L. , Wang Ruquan 
Published: January 2016

AbstractWe report the observation of synthesized spin-orbit coupling (SOC) for ultracold spin-1 87Rb atoms. Different from earlier experiments where a one dimensional (1D) atomic SOC of pseudo-spin-1/2 is synthesized with Raman laser fields, the scheme we demonstrate employs a gradient magnetic field (GMF) and ground-state atoms, thus is immune to atomic spontaneous emission. The strength of SOC we realize can be tuned by changing the modulation amplitude of the GMF and the effect of the SOC is confirmed through the studies of: 1) the collective dipole oscillation of an atomic condensate in a harmonic trap after the synthesized SOC is abruptly turned on; and 2) the minimum energy state at a finite adiabatically adjusted momentum when SOC strength is slowly ramped up. The condensate coherence is found to remain very good after driven by modulating GMFs. Our scheme presents an alternative means for studying interacting many-body systems with synthesized SOC.
An integrated chinmedomics strategy for discovery of effective constituents from traditional herbal medicine
Authors: Wang Xijun , Zhang Aihua , Zhou Xiaohang , Liu Qi , Nan Yang , Guan Yu , Kong Ling , Han Ying , Sun Hui , Yan Guangli 
Published: January 2016

AbstractTraditional natural product discovery affords no information about compound structure or pharmacological activities until late in the discovery process and leads to low probabilities of finding compounds with unique biological properties. By integrating serum pharmacochemistry-based screening with high-resolution metabolomics analysis, we have developed a new platform, termed chinmedomics which is capable of directly discovering the bioactive constituents. In this work, the focus is on ShenQiWan (SQW) treatment of ShenYangXu (SYX, kidney-yang deficiency syndrome) as a case study, as determined by chinmedomics. With serum pharmacochemistry, a total of 34 peaks were tentatively characterised in vivo, 24 of which were parent components and 10 metabolites were detected. The metabolic profiling and potential biomarkers of SYX were also investigated and 23 differential metabolites were found. 20 highly correlated components were screened by the plotting of correlation between marker metabolites and serum constituents and considered as the main active components of SQW. These compounds are imported into a database to predict the action targets: 14 importantly potential targets were found and related to aldosterone-regulated sodium reabsorption and adrenergic signaling pathways. Our study showed that integrated chinmedomics is a powerful strategy for discovery and screening of effective constituents from herbal medicines.
Low-photon-number optical switch and AND/OR logic gates based on quantum dot-bimodal cavity coupling system
Authors: Ma Shen , Ye Han , Yu Zhong-Yuan , Zhang Wen , Peng Yi-Wei , Cheng Xiang , Liu Yu-Min 
Published: January 2016

AbstractWe propose a new scheme based on quantum dot-bimodal cavity coupling system to realize all-optical switch and logic gates in low-photon-number regime. Suppression of mode transmission due to the destructive interference effect is theoretically demonstrated by driving the cavity with two orthogonally polarized pulsed lasers at certain pulse delay. The transmitted mode can be selected by designing laser pulse sequence. The optical switch with high on-off ratio emerges when considering one driving laser as the control. Moreover, the AND/OR logic gates based on photon polarization are achieved by cascading the coupling system. Both proposed optical switch and logic gates work well in ultra-low energy magnitude. Our work may enable various applications of all-optical computing and quantum information processing.
Spatial potential ripples of azimuthal surface modes in topological insulator Bi2Te3 nanowires
Authors: Muñoz Rojo Miguel , Zhang Yingjie , Manzano Cristina V. , Alvaro Raquel , Gooth Johannes , Salmeron Miquel , Martin-Gonzalez Marisol 
Published: January 2016

AbstractTopological insulators (TI) nanowires (NW) are an emerging class of structures, promising both novel quantum effects and potential applications in low-power electronics, thermoelectrics and spintronics. However, investigating the electronic states of TI NWs is complicated, due to their small lateral size, especially at room temperature. Here, we perform scanning probe based nanoscale imaging to resolve the local surface potential landscapes of Bi2Te3 nanowires (NWs) at 300 K. We found equipotential rings around the NWs perimeter that we attribute to azimuthal 1D modes. Along the NW axis, these modes are altered, forming potential ripples in the local density of states, due to intrinsic disturbances. Potential mapping of electrically biased NWs enabled us to accurately determine their conductivity which was found to increase with the decrease of NW diameter, consistent with surface dominated transport. Our results demonstrate that TI NWs can pave the way to both exotic quantum states and novel electronic devices.
A human monoclonal antibody against HPV16 recognizes an immunodominant and neutralizing epitope partially overlapping with that of H16.V5
Authors: Xia Lin , Xian Yangfei , Wang Daning , Chen Yuanzhi , Huang Xiaofen , Bi Xingjian , Yu Hai , Fu Zheng , Liu Xinlin , Li Shaowei , An Zhiqiang , Luo Wenxin , Zhao Qinjian , Xia Ningshao 
Published: January 2016

AbstractThe presence of neutralizing epitopes in human papillomavirus (HPV) L1 virus-like particles (VLPs) is the structural basis of prophylactic vaccines. An anti-HPV16 neutralizing monoclonal antibody (N-mAb) 26D1 was isolated from a memory B cell of a human vaccinee. The pre-binding of heparan sulfate to VLPs inhibited the binding of both N-mAbs to the antigen, indicating that the epitopes are critical for viral cell attachment/entry. Hybrid VLP binding with surface loop swapping between types indicated the essential roles of the DE and FG loops for both 26D1 (DEa in particular) and H16.V5 binding. Specifically, Tyr135 and Val141 on the DEa loop were shown to be critical residues for 26D1 binding via site-directed mutagenesis. Partially overlap between the epitopes between 26D1 and H16.V5 was shown using pairwise epitope mapping and their binding difference is demonstrated to be predominantly in DE loop region. In addition, 26D1 epitope is immunodominant epitope recognized by both antibodies elicited by the authentic virus from infected individuals and polyclonal antibodies from vaccinees. Overall, a partially overlapping but distinct neutralizing epitope from that of H16.V5 was identified using a human N-mAb, shedding lights to the antibody arrays as part of human immune response to vaccination and infection.
Co-utilization of glycerol and lignocellulosic hydrolysates enhances anaerobic 1,3-propanediol production by Clostridium diolis
Authors: Xin Bo , Wang Yu , Tao Fei , Li Lixiang , Ma Cuiqing , Xu Ping 
Published: January 2016

AbstractAnaerobic fermentation using lignocellulosic hydrolysates as co-substrates is an economically attractive method to enhance 1,3-propanediol (1,3-PD) production by increasing the conversion yield from glycerol. Lignocellulosic hydrolysates contain the mixed sugars that are primarily glucose, xylose and arabinose. Therefore, these three individual sugars were used, separately, as co-substrates with glycerol, in 1,3-PD production by a Clostridium diolis strain DSM 15410, resulting in an 18%–28% increase in the 1,3-PD yield. Co-fermentation of the mixed sugars and glycerol obtained a higher intracellular NADH/NAD+ ratio and increased the 1,3-PD yield by 22% relative to fermentation of glycerol alone. Thereafter, two kinds of lignocellulosic hydrolysates, corn stover hydrolysate and corncob molasses, were individually co-fermented with glycerol. The maximum 1,3-PD yield from glycerol reached 0.85 mol/mol. Fed-batch co-fermentation was also performed, improving the 1,3-PD yield (from 0.62 mol/mol to 0.82 mol/mol). These results demonstrate that the co-fermentation strategy is an efficient and economical way to produce 1,3-PD from glycerol.
Low diversity of planktonic bacteria in the tropical ocean
Authors: Milici Mathias , Tomasch Jürgen , Wos-Oxley Melissa L. , Wang Hui , Jáuregui Ruy , Camarinha-Silva Amelia , Deng Zhi-Luo , Plumeier Iris , Giebel Helge-Ansgar , Wurst Mascha , Pieper Dietmar H. , Simon Meinhard , Wagner-Döbler Irene 
Published: January 2016

AbstractThe diversity of macro-organisms increases towards the equator, with almost no exceptions. It is the most conserved biogeographical pattern on earth and is thought to be related to the increase of temperature and productivity in the tropics. The extent and orientation of a latitudinal gradient of marine bacterioplankton diversity is controversial. Here we studied the euphotic zone of the Atlantic Ocean based on a transect covering ~12.000 km from 51°S to 47 °N. Water samples were collected at 26 stations at five depths between 20 and 200 m and sequentially filtered through 8 μm, 3 μm and 0,22 μm filters, resulting in a total of 359 samples. Illumina sequencing of the V5–V6 region of the 16S rRNA gene revealed a clear biogeographic pattern with a double inverted latitudinal gradient. Diversity was higher in mid-latitudinal regions of the Atlantic Ocean and decreased towards the equator. This pattern was conserved for bacteria from all three planktonic size fractions. Diversity showed a non-linear relationship with temperature and was negatively correlated with bacterial cell numbers in the upper depth layers (<100 m). The latitudinal gradients of marine bacterial diversity and the mechanisms that govern them are distinct from those found in macro-organisms.
Long-term fertilization alters chemically-separated soil organic carbon pools: Based on stable C isotope analyses
Authors: Dou Xiaolin , He Ping , Cheng Xiaoli , Zhou Wei 
Published: January 2016

AbstractQuantification of dynamics of soil organic carbon (SOC) pools under the influence of long-term fertilization is essential for predicting carbon (C) sequestration. We combined soil chemical fractionation with stable C isotope analyses to investigate the C dynamics of the various SOC pools after 25 years of fertilization. Five types of soil samples (0–20, 20–40 cm) including the initial level (CK) and four fertilization treatments (inorganic nitrogen fertilizer, IN; balanced inorganic fertilizer, NPK; inorganic fertilizer plus farmyard manure, MNPK; inorganic fertilizer plus corn straw residue, SNPK) were separated into recalcitrant and labile fractions and the fractions were analysed for C content, C:N ratios, δ13C values, soil C and N recalcitrance indexes (RIC and RIN). Chemical fractionation showed long-term MNPK fertilization strongly increased the SOC storage in both soil layers (0–20 cm = 1492.4 gC m2 and 20–40 cm = 1770.6 gC m2) because of enhanced recalcitrant C (RC) and labile C (LC). The 25 years of inorganic fertilizer treatment did not increase the SOC storage mainly because of the offsetting effects of enhanced RC and decreased LC, whereas no clear SOC increases under the SNPK fertilization resulted from the fast decay rates of soil C.
Metacommunity analysis of amoeboid protists in grassland soils
Authors: Fiore-Donno Anna Maria , Weinert Jan , Wubet Tesfaye , Bonkowski Michael 
Published: January 2016

AbstractThis study reveals the diversity and distribution of two major ubiquitous groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes (plasmodial slime-moulds) that are rarely, if ever, recovered in environmental sampling studies. We analyzed 150 grassland soil samples from three Biodiversity Exploratories study regions in Germany. We developed specific primers targeting the V2 variable region in the first part of the small subunit of the ribosomal RNA gene for high-throughput pyrotag sequencing. From ca. 1 million reads, applying very stringent filtering and clustering parameters to avoid overestimation of the diversity, we obtained 273 acanthamoebal and 338 myxomycete operational taxonomic units (OTUs, 96% similarity threshold). This number is consistent with the genetic diversity known in the two investigated lineages, but unequalled to date by any environmental sampling study. Only very few OTUs were identical to already known sequences. Strikingly different OTUs assemblages were found between the three German regions (PerMANOVA p.value = 0.001) and even between sites of the same region (multiple-site Simpson-based similarity indices <0.4), showing steep biogeographical gradients.
Synthesis, characterization and application of reversible PDLLA-PEG-PDLLA copolymer thermogels in vitro and in vivo
Authors: Shi Kun , Wang Ya-Li , Qu Ying , Liao Jin-Feng , Chu Bing-Yang , Zhang Hua-Ping , Luo Feng , Qian Zhi-Yong 
Published: January 2016

AbstractIn this study, a series of injectable thermoreversible and thermogelling PDLLA-PEG-PDLLA copolymers were developed and a systematic evaluation of the thermogelling system both in vitro and in vivo was performed. The aqueous PDLLA-PEG-PDLLA solutions above a critical gel concentration could transform into hydrogel spontaneously within 2 minutes around the body temperature in vitro or in vivo. Modulating the molecular weight, block length and polymer concentration could adjust the sol-gel transition behavior and the mechanical properties of the hydrogels. The gelation was thermally reversible due to the physical interaction of copolymer micelles and no crystallization formed during the gelation. Little cytotoxicity and hemolysis of this polymer was found and the inflammatory response after injecting the hydrogel to small-animal was acceptable. In vitro and in vivo degradation experiments illustrated that the physical hydrogel could retain its integrity as long as several weeks and eventually be degraded by hydrolysis. A rat model of sidewall defect-bowel abrasion was employed and a significant reduction of post-operative adhesion has been found in the group of PDLLA-PEG-PDLLA hydrogel-treated, compared with untreated control group and commercial hyaluronic acid (HA) anti-adhesion hydrogel group. As such, this PDLLA-PEG-PDLLA hydrogel might be a promising candidate of injectable biomaterial for medical applications.