bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genes Encoding Cucumber Full-Size ABCG Proteins Show Different Responses to Plant Growth Regulators and Sclareolide
Authors: Rajsz Adam , Warzybok Anna , Migocka Magdalena 
Published: November 2015

AbstractFull-size members of the ABCG (ATP-binding cassette, subfamily G) subfamily of ABC transporters have been found only in plants and fungi. The plant genes encoding full-size ABCGs identified so far appeared to be differentially regulated under various environmental constraints, plant growth regulators, and microbial elicitors, indicating a broad functional role of these proteins in plant responses to abiotic and biotic stress. Nevertheless, the structure and physiological function of full-size ABCGs in many plant species are still unknown. We have recently identified 16 genes encoding full-size ABCG proteins in cucumber and found that the transcripts of two of them, CsABCG36 (CsPDR8) and CsABCG40 (CsPDR12), are most abundant in roots and are significantly affected by phytohormones and auxin herbicide. In this study, we analyzed the structure and phylogeny of all the full-size cucumber ABCG transporters and studied the organ expression profiles of the remaining 14 CsABCG genes. In addition, we investigated the effect of different plant growth regulators and the diterpene sclareolide on CsABCG expression in cucumber roots. Until now, the full-size plant ABCG transporters have been grouped into five different clusters. The new phylogenetic analysis of full-size ABCGs from model plants and cucumber clustered these proteins into six different subgroups. Interestingly, the expression profiles of cucumber ABCG genes assigned to the same clusters were not correlated, suggesting functional diversification or different regulatory mechanisms of the full-size cucumber ABCG proteins.
Nitrogen application increases phytolith carbon sequestration in degraded grasslands of North China
Authors: Zhao Yuying , Song Zhaoliang , Xu Xiaotian , Liu Hongyan , Wu Xiuchen , Li Zimin , Guo Fengshan , Pan Wenjie 
Published: November 2015

AbstractPhytolith‐occluded carbon (PhytOC) has significant potential for long‐term biogeochemical carbon (C) sequestration because of its high resistance against decomposition. It may also play a crucial role in slowing the increase in global CO2 concentrations and mitigating climate warming. As phytolith C sequestration flux is usually correlated with phytolith content, C content of phytoliths and above‐ground net primary productivity in plants, we hypothesize that application of fertilizers may increase phytolith C sequestration in some degraded grasslands. In this study, we conducted a field experiment to investigate the effects of external application of nitrogen (N) at six levels (0, 10, 20, 30, 40, and 50 g N m−2 year−1) from 2011 to 2013 on the potential for phytolith C sequestration in degraded grasslands. Analysis showed that N application increased the PhytOC production flux in the extremely degraded grassland from 0.003 to 0.021 t CO2 ha−1 year−1 and the flux increased with the level of N fertilization peaking in the 20 g N m−2 year−1 treatment at 700 % of the control flux, but decreased at higher N doses. Assuming half of China's grasslands are fertilized with N to recover from degradation and the phytolith C sequestration flux of degraded grasslands amended with N is half of the 700 % increase, the potential of phytolith C sequestration in China's grasslands could be increased at least 60 %. This study demonstrates that optimization of nutritional supply is a promising approach to increase long‐term phytolith C sequestration in degraded grasslands.
Preimplantation genetic diagnosis: an update on current technologies and ethical considerations
Authors: Sueoka Kou 
Published: November 2015

AbstractThe aim of reproductive medicine is to support the birth of healthy children. Advances in assisted reproductive technologies and genetic analysis have led to the introduction of preimplantation genetic diagnosis (PGD) for embryos. Indications for PGD have been a major topic in the fields of ethics and law. Concerns vary by nation, religion, population, and segment, and the continued rapid development of new technologies. In contrast to the ethical augment, technology has been developing at an excessively rapid speed. The most significant recent technological development provides the ability to perform whole genome amplification and sequencing of single embryonic cells by microarray or next‐generation sequencing methods. As new affordable technologies are introduced, patients are presented with a growing variety of PGD options. Simultaneously, the ethical guidelines for the indications for testing and handling of genetic information must also rapidly correspond to the changes.
Life on hold: Staying in identity diffusion in the late twenties
Authors: Carlsson Johanna , Wängqvist Maria , Frisén Ann 
Published: November 2015

ABSTRACTThis study adds to the understanding of the dark side of identity development by investigating what it means to experience long‐term identity diffusion during the late twenties. In a study of change and stability in identity status between ages 25 and 29 (N = 124; 63 women), seven participants were assigned to identity diffusion at both ages. Longitudinal analysis of interviews with these participants showed that long‐term experiences of identity diffusion may be described through individuals' approach to changing life conditions, the extent to which they engage in meaning making, and how they develop their personal life direction. In questionnaires, participants reported few signs of psychological distress. Even so, qualitative analyses showed a general trend among participants to keep life on hold through decreased activity or increased haphazard activity in relation to changing life conditions, to make little new meaning, and in some cases to dissolve their personal life direction.
Individual estimates of age at detectable amyloid onset for risk factor assessment
Authors: Bilgel Murat , An Yang , Zhou Yun , Wong Dean F. , Prince Jerry L. , Ferrucci Luigi , Resnick Susan M. 
Published: November 2015

AbstractIntroductionIndividualized estimates of age at detectable amyloid‐beta (Aβ) accumulation, distinct from amyloid positivity, allow for analysis of onset age of Aβ accumulation as an outcome measure to understand risk factors.MethodsUsing longitudinal Pittsburgh compound B (PiB) positron emission tomography data from Baltimore Longitudinal Study of Aging, we estimated the age at which each PiB+ individual began accumulating Aβ. We used survival analysis methods to quantify risk of accumulating Aβ and differences in onset age of Aβ accumulation in relation to APOE ε4 status and sex among 36 APOE ε4 carriers and 83 noncarriers.ResultsAge at onset of Aβ accumulation for the APOE ε4− and ε4+ groups was 73.1 and 60.7, respectively. APOE ε4 positivity conferred a threefold risk of accumulating Aβ after adjusting for sex and education.DiscussionEstimation of onset age of amyloid accumulation may help gauge treatment efficacy in interventions to delay symptom onset in Alzheimer's disease.
Minimum time path planning of robotic manipulator in drilling/spot welding tasks
Authors: Zhang Qiang , Zhao Ming-Yong 
Published: November 2015

Abstract
In this paper, a minimum time path planning strategy is proposed for multi points manufacturing problems in drilling/spot welding tasks. By optimizing the travelling schedule of the set points and the detailed transfer path between points, the minimum time manufacturing task is realized under fully utilizing the dynamic performance of robotic manipulator. According to the start-stop movement in drilling/spot welding task, the path planning problem can be converted into a traveling salesman problem (TSP) and a series of point to point minimum time transfer path planning problems. Cubic Hermite interpolation polynomial is used to parameterize the transfer path and then the path parameters are optimized to obtain minimum point to point transfer time. A new TSP with minimum time index is constructed by using point-point transfer time as the TSP parameter. The classical genetic algorithm (GA) is applied to obtain the optimal travelling schedule. Several minimum time drilling tasks of a 3-DOF robotic manipulator are used as examples to demonstrate the effectiveness of the proposed approach.
Highlights In this paper, an optimization strategy is proposed for solving minimum time manufacturing path planning in multi points manufacturing tasks. According to the start-stop movement in drilling/spot welding task, the path planning problem is converted into a traveling salesman problem (TSP) and a series of point to point minimum time transfer path planning problems. Cubic Hermite interpolation polynomial is used to parameterize the transfer path and then the path parameters are optimized to obtain minimum point to point transfer time. A new TSP with minimum time index is constructed and then solved by using a classical genetic algorithm (GA). Numerical test is executed to demonstrate the effectiveness of the proposed approach.
Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships
Authors: Sakr Rita A. , Schizas Michail , Carniello Jose V. Scarpa , Ng Charlotte K.Y. , Piscuoglio Salvatore , Giri Dilip , Andrade Victor P. , De Brot Marina , Lim Raymond S. , Towers Russell , Weigelt Britta , Reis-Filho Jorge S. , King Tari A. 
Published: November 2015

Purpose: Lobular carcinoma in situ (LCIS) has been proposed as a non‐obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing.Methods: DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair‐related genes. Single nucleotide variants and insertions and deletions were identified using state‐of‐the‐art bioinformatics approaches.Results: The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1).Conclusion: LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS–LCIS and LCIS–ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non‐obligate precursors of ILC.
Human Rights Responsibility of Multinational Corporations, Political Ecology of Injustice: Learning from Bhopal Thirty Plus?
Authors: BAXI Upendra 
Published: November 2015

AbstractThis article addresses human rights responsibilities of multinational corporations (MNCs) in the light of what I describe as the four Bhopal catastrophes. More than thirty years of struggle by the valiant violated people to seek justice is situated in the contemporary efforts of the United Nations to develop a new discursivity for human rights and business—from the Global Compact to the Draft Norms on the Responsibilities of Transnational Corporations and Other Business Enterprises with Regard to Human Rights, the Guiding Principles on Business and Human Rights, and the more recent process to elaborate a legally-binding international instrument.
How Important Is Financial Risk?
Authors: Bartram Söhnke M. , Brown Gregory W. , Waller William 
Published: November 2015

AbstractWe explore the determinants of equity price risk of nonfinancial corporations. Operating and asset characteristics are by far the most important determinants of risk. For the median firm, financial risk accounts for only 15% of observed stock price volatility. Furthermore, financial risk has declined over the last 3 decades, indicating that any upward trend in equity volatility was driven entirely by economic risk factors. This explains why financial distress (as opposed to economic distress) was surprisingly uncommon in the nonfinancial sector during the 2007–2009 crisis even as measures of equity volatility reached unprecedented highs.
A Synthesis of Two Factor Estimation Methods
Authors: Connor Gregory , Korajczyk Robert A. , Uhlaner Robert T. 
Published: November 2015

AbstractTwo-pass cross-sectional regression (TPCSR) is frequently used in estimating factor risk premia. Recent papers argue that the common practice of grouping assets into portfolios to reduce the errors-in-variables (EIV) problem leads to loss of efficiency and masks potential deviations from asset pricing models. One solution that allows the use of individual assets while overcoming the EIV problem is iterated TPCSR (ITPCSR). ITPCSR converges to a fixed point regardless of the initial factors chosen. ITPCSR is intimately linked to the asymptotic principal components (APC) method of estimating factors since the ITPCSR estimates are the APC estimates, up to a rotation.
Estimating the critical immunity threshold for preventing hepatitis A outbreaks in men who have sex with men
Authors: REGAN D. G. , WOOD J. G. , BENEVENT C. , ALI H. , SMITH L. WATCHIRS , ROBERTSON P. W. , FERSON M. J. , FAIRLEY C. K. , DONOVAN B. , LAW M. G. 
Published: November 2015

SUMMARYSeveral outbreaks of hepatitis A in men who have sex with men (MSM) were reported in the 1980s and 1990s in Australia and other countries. An effective hepatitis A virus (HAV) vaccine has been available in Australia since 1994 and is recommended for high-risk groups including MSM. No outbreaks of hepatitis A in Australian MSM have been reported since 1996. In this study, we aimed to estimate HAV transmissibility in MSM populations in order to inform targets for vaccine coverage in such populations. We used mathematical models of HAV transmission in a MSM population to estimate the basic reproduction number (R0) and the probability of an HAV epidemic occurring as a function of the immune proportion. We estimated a plausible range forR0of 1·71–3·67 for HAV in MSM and that sustained epidemics cannot occur once the proportion immune to HAV is greater than ~70%. To our knowledge this is the first estimate ofR0and the critical population immunity threshold for HAV transmission in MSM. As HAV is no longer endemic in Australia or in most other developed countries, vaccination is the only means of maintaining population immunity >70%. Our findings provide impetus to promote HAV vaccination in high-risk groups such as MSM.
Loss in MCL-1 function sensitizes non-Hodgkin’s lymphoma cell lines to the BCL-2-selective inhibitor venetoclax (ABT-199)
Authors: Phillips D C , Xiao Y , Lam L T , Litvinovich E , Roberts-Rapp L , Souers A J , Leverson J D 
Published: November 2015

AbstractAs a population, non-Hodgkin’s lymphoma (NHL) cell lines positive for the t(14;18) translocation and/or possessing elevated BCL2 copy number (CN; BCL2High) are exquisitely sensitive to navitoclax or the B-cell lymphoma protein-2 (BCL-2)-selective inhibitor venetoclax. Despite this, some BCL2High cell lines remain resistant to either agent. Here we show that the MCL-1-specific inhibitor A-1210477 sensitizes these cell lines to navitoclax. Chemical segregation of this synergy with the BCL-2-selective inhibitor venetoclax or BCL-XL-selective inhibitor A-1155463 indicated that MCL-1 and BCL-2 are the two key anti-apoptotic targets for sensitization. Similarly, the CDK inhibitor flavopiridol downregulated MCL-1 expression and synergized with venetoclax in BCL2High NHL cell lines to a similar extent as A-1210477. A-1210477 also synergized with navitoclax in the majority of BCL2Low NHL cell lines. However, chemical segregation with venetoclax or A-1155463 revealed that synergy was driven by BCL-XL inhibition in this population. Collectively these data emphasize that BCL2 status is predictive of venetoclax potency in NHL not only as a single agent, but also in the adjuvant setting with anti-tumorigenic agents that inhibit MCL-1 function. These studies also potentially identify a patient population (BCL2Low) that could benefit from BCL-XL (navitoclax)-driven combination therapy.
Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA
Authors: Lou Yuan-Chao , Weng Tsai-Hsuan , Li Yi-Chuan , Kao Yi-Fen , Lin Wei-Feng , Peng Hwei-Ling , Chou Shan-Ho , Hsiao Chwan-Deng , Chen Chinpan 
Published: November 2015

AbstractPmrA, an OmpR/PhoB family response regulator, manages genes for antibiotic resistance. Phosphorylation of OmpR/PhoB response regulator induces the formation of a symmetric dimer in the N-terminal receiver domain (REC), promoting two C-terminal DNA-binding domains (DBDs) to recognize promoter DNA to elicit adaptive responses. Recently, determination of the KdpE–DNA complex structure revealed an REC–DBD interface in the upstream protomer that may be necessary for transcription activation. Here, we report the 3.2-Å-resolution crystal structure of the PmrA–DNA complex, which reveals a similar yet different REC–DBD interface. However, NMR studies show that in the DNA-bound state, two domains tumble separately and an REC–DBD interaction is transiently populated in solution. Reporter gene analyses of PmrA variants with altered interface residues suggest that the interface is not crucial for supporting gene expression. We propose that REC–DBD interdomain dynamics and the DBD–DBD interface help PmrA interact with RNA polymerase holoenzyme to activate downstream gene transcription.
Minimal evolution time and quantum speed limit of non-Markovian open systems
Authors: Meng Xiangyi , Wu Chengjun , Guo Hong 
Published: November 2015

AbstractWe derive a sharp bound as the quantum speed limit (QSL) for the minimal evolution time of quantum open systems in the non-Markovian strong-coupling regime with initial mixed states by considering the effects of both renormalized Hamiltonian and dissipator. For a non-Markovian quantum open system, the possible evolution time between two arbitrary states is not unique, among the set of which we find that the minimal one and its QSL can decrease more steeply by adjusting the coupling strength of the dissipator, which thus provides potential improvements of efficiency in many quantum physics and quantum information areas.
Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism
Authors: Guan Hong-Hsiang , Yoshimura Masato , Chuankhayan Phimonphan , Lin Chien-Chih , Chen Nai-Chi , Yang Ming-Chi , Ismail Asma , Fun Hoong-Kun , Chen Chun-Jung 
Published: November 2015

AbstractST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOTTM). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.
Reduced cortical microvascular oxygenation in multiple sclerosis: a blinded, case-controlled study using a novel quantitative near-infrared spectroscopy method
Authors: Yang Runze , Dunn Jeff F. 
Published: November 2015

AbstractHypoxia (low oxygen) is associated with many brain disorders as well as inflammation, but the lack of widely available technology has limited our ability to study hypoxia in human brain. Multiple sclerosis (MS) is a poorly understood neurological disease with a significant inflammatory component which may cause hypoxia. We hypothesized that if hypoxia were to occur, there should be reduced microvascular hemoglobin saturation (StO2). In this study, we aimed to determine if reduced StO2 can be detected in MS using frequency domain near-infrared spectroscopy (fdNIRS). We measured fdNIRS data in cortex and assessed disability of 3 clinical isolated syndrome (CIS), 72 MS patients and 12 controls. Control StO2 was 63.5 ± 3% (mean ± SD). In MS patients, 42% of StO2 values were more than 2 × SD lower than the control mean. There was a significant relationship between StO2 and clinical disability. A reduced microvascular StO2 is supportive (although not conclusive) that there may be hypoxic regions in MS brain. This is the first study showing how quantitative NIRS can be used to detect reduced StO2 in patients with MS, opening the door to understanding how microvascular oxygenation impacts neurological conditions.
Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages
Authors: Chen Jie , Zhang Hui , Liu Wei , Lian Juyu , Ye Wanhui , Shen Weijun 
Published: November 2015

AbstractCharacterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage.