bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is crossbreeding of cattle beneficial for mixed farming systems in Central Java?
Authors: Widi T.S.M. , Udo H.M.J. , Oldenbroek K. , Budisatria I.G.S. , Baliarti E. , van der Zijpp A.J. 
Published: July 2015

SummaryFrom 1980s onwards, Indonesia's government has been implementing crossbreeding with European beef breeds through artificial insemination to improve the beef performance of local cattle, in response to the increasing demand for meat. Crossbreeding is promoted and implemented throughout the country, regardless of the various agro-ecological zones, each endowed with different feed resources in the smallholder farming systems. This study analyses the impact at farm level of crossbreeding in the different mixed farming conditions in Central Java. Quantitative and qualitative information was collected through participatory approaches involving famers (n= 252) in four study areas representing three agro-ecological zones: Wet lowlands (subdivided in two areas based on the history of breeding local cattle and crossbreeding), Wet uplands and Dry uplands. Phenotypic characteristics, reproductive performances, and carcass characteristics of Ongole and crossbred cattle were assessed, together with farmers’ reasons for keeping Ongole or crossbred breeding stock, the functions of cattle on the farms and the Gross Margins (GM) of the cattle component on Ongole and crossbred farms. Across different agro-ecological zones, crossbreeding is not changing the farming systems: herd sizes, farm types, experience in cattle keeping and functions of cattle were about the same for Ongole and crossbred farms. The agro-ecological zones differed in the cropping pattern and feed resources; however, they did not differ in amounts of dry matter and crude protein fed to individual animals. Crossbreeding is changing the individual characteristics of cattle and consequently the market prices of animals. In general, mature female crossbred cattle were approximately 25 percent heavier than mature female local cattle. Male crossbred progeny was 16 percent heavier their local counterparts, whereas female crossbred progeny was 24 percent heavier than female local cattle. In terms of reproduction performances, both local and crossbred cows performed well with calf crops ranging between 73 and 86 percent per year. Most farmers preferred crossbred over Ongole cattle. Simmental cross is the most preferred. GM for crossbred and Ongole farms were comparable within the different study areas; selling prices of crossbreds are higher, but feed costs too. Crossbreeding will continue. It is promoted by government policies and farmers are motivated to keep crossbred cattle as body weights and market prices are higher than for Ongole cattle; however, farmers said that they do not prefer upgrading to very high levels of Simmental. A viable Ongole population is needed to reduce the risk of upgrading to too high levels of Simmental.
Temporal Stability of Implicit Sequence Knowledge
Authors: Tamayo Ricardo , Frensch Peter A. 
Published: July 2015

Abstract. Previous research has shown that explicit and implicit knowledge of artificial grammars may decay at different rates (e.g., Tamayo & Frensch, 2007 ; Tunney, 2003 ). We extend these findings to sequential regularities embedded in serial reaction time (SRT) tasks. We compared the forgetting patterns of implicit and explicit knowledge after a retention interval of 7 days without rehearsal. Explicit knowledge decayed after 7 days, whereas implicit knowledge was retained. These data were modeled according to the assumptions involved in the single-system model suggested by Shanks, Wilkinson, and Channon (2003) . The best fit for the model was obtained by modifying the parameters related to (a) the common knowledge-strength variable for implicit and explicit knowledge, and (b) reliability of the explicit test. We interpret these dissociations as a boundary condition for single-system models that assume constant random noise to explain dissociations in the forgetting patterns of implicit and explicit sequential knowledge.
Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota
Authors: Oton Eduard Vico , Quince Christopher , Nicol Graeme W , Prosser James I , Gubry-Rangin Cécile 
Published: July 2015

Abstract
Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.
Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea
Authors: Rascovan Nicolás , Maldonado Javier , Vazquez Martín P , Eugenia Farías María 
Published: July 2015

Abstract
Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the archaea, bioenergetic arsenic metabolism has only been found in the Crenarchaeota phylum. Here we report the discovery of haloarchaea (Euryarchaeota phylum) biofilms forming under the extreme environmental conditions such as high salinity, pH and arsenic concentration at 4589 m above sea level inside a volcano crater in Diamante Lake, Argentina. Metagenomic analyses revealed a surprisingly high abundance of genes used for arsenite oxidation (aioBA) and respiratory arsenate reduction (arrCBA) suggesting that these haloarchaea use arsenic compounds as bioenergetics substrates. We showed that several haloarchaea species, not only from this study, have all genes required for these bioenergetic processes. The phylogenetic analysis of aioA showed that haloarchaea sequences cluster in a novel and monophyletic group, suggesting that the origin of arsenic metabolism in haloarchaea is ancient. Our results also suggest that arsenite chemolithotrophy likely emerged within the archaeal lineage. Our results give a broad new perspective on the haloarchaea metabolism and shed light on the evolutionary history of arsenic bioenergetics.
Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities
Authors: Fiorini Francesca , Bagchi Debjani , Le Hir Hervé , Croquette Vincent 
Published: July 2015

AbstractRNA helicases are implicated in most cellular RNA-dependent events. In eukaryotes however, only few have been functionally characterized. Upf1 is a RNA helicase essential for nonsense-mediated mRNA decay (NMD). Here, using magnetic tweezers and bulk assays, we observe that human Upf1 is able to translocate slowly over long single-stranded nucleic acids with a processivity >10 kb. Upf1 efficiently translocates through double-stranded structures and protein-bound sequences, demonstrating that Upf1 is an efficient ribonucleoprotein complex remodeler. Our observation of processive unwinding by an eukaryotic RNA helicase reveals that Upf1, once recruited onto NMD mRNA targets, can scan the entire transcript to irreversibly remodel the mRNP, facilitating its degradation by the NMD machinery.
Obesity-induced DNA hypermethylation of the adiponectin gene mediates insulin resistance
Authors: Kim A. Young , Park Yoon Jeong , Pan Xuebo , Shin Kyung Cheul , Kwak Soo-Heon , Bassas Abdulelah F. , Sallam Reem M. , Park Kyong Soo , Alfadda Assim A. , Xu Aimin , Kim Jae Bum 
Published: July 2015

AbstractAdiponectin plays a key role in the regulation of the whole-body energy homeostasis by modulating glucose and lipid metabolism. Although obesity-induced reduction of adiponectin expression is primarily ascribed to a transcriptional regulation failure, the underlying mechanisms are largely undefined. Here we show that DNA hypermethylation of a particular region of the adiponectin promoter suppresses adiponectin expression through epigenetic control and, in turn, exacerbates metabolic diseases in obesity. Obesity-induced, pro-inflammatory cytokines promote DNMT1 expression and its enzymatic activity. Activated DNMT1 selectively methylates and stimulates compact chromatin structure in the adiponectin promoter, impeding adiponectin expression. Suppressing DNMT1 activity with a DNMT inhibitor resulted in the amelioration of obesity-induced glucose intolerance and insulin resistance in an adiponectin-dependent manner. These findings suggest a critical role of adiponectin gene epigenetic control by DNMT1 in governing energy homeostasis, implying that modulating DNMT1 activity represents a new strategy for the treatment of obesity-related diseases.
Asymmetric synthesis of N-allylic indoles via regio- and enantioselective allylation of aryl hydrazines
Authors: Xu Kun , Gilles Thomas , Breit Bernhard 
Published: July 2015

AbstractThe asymmetric synthesis of N-allylic indoles is important for natural product synthesis and pharmaceutical research. The regio- and enantioselective N-allylation of indoles is a true challenge due to the favourable C3-allylation. We develop here a new strategy to the asymmetric synthesis of N-allylic indoles via rhodium-catalysed N-selective coupling of aryl hydrazines with allenes followed by Fischer indolization. The exclusive N-selectivities and good to excellent enantioselectivities are achieved applying a rhodium(I)/DTBM-Segphos or rhodium(I)/DTBM-Binap catalyst. This method permits the practical synthesis of valuable chiral N-allylated indoles, and avoids the N- or C-selectivity issue.
Extensive volatile loss during formation and differentiation of the Moon
Authors: Kato Chizu , Moynier Frederic , Valdes Maria C. , Dhaliwal Jasmeet K. , Day James M.D. 
Published: July 2015

AbstractLow estimated lunar volatile contents, compared with Earth, are a fundamental observation for Earth–Moon system formation and lunar evolution. Here we present zinc isotope and abundance data for lunar crustal rocks to constrain the abundance of volatiles during the final stages of lunar differentiation. We find that ferroan anorthosites are isotopically heterogeneous, with some samples exhibiting high δ66Zn, along with alkali and magnesian suite samples. Since the plutonic samples were formed in the lunar crust, they were not subjected to degassing into vacuum. Instead, their compositions are consistent with enrichment of the silicate portions of the Moon in the heavier Zn isotopes. Because of the difference in δ66Zn between bulk silicate Earth and lunar basalts and crustal rocks, the volatile loss likely occurred in two stages: during the proto-lunar disk stage, where a fraction of lunar volatiles accreted onto Earth, and from degassing of a differentiating lunar magma ocean, implying the possibility of isolated, volatile-rich regions in the Moon’s interior.
Structural basis for catalytically restrictive dynamics of a high-energy enzyme state
Authors: Kovermann Michael , Ådén Jörgen , Grundström Christin , Elisabeth Sauer-Eriksson A. , Sauer Uwe H. , Wolf-Watz Magnus 
Published: July 2015

AbstractAn emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or ‘invisible’ states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme’s catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes’ conformational dynamics and hence their catalytic power—a key aspect in rational design of enzymes catalysing novel reactions.
Low-temperature thermodynamics with quantum coherence
Authors: Narasimhachar Varun , Gour Gilad 
Published: July 2015

AbstractThermal operations are an operational model of non-equilibrium quantum thermodynamics. In the absence of coherence between energy levels, exact state transition conditions under thermal operations are known in terms of a mathematical relation called thermo-majorization. But incorporating coherence has turned out to be challenging, even under the relatively tractable model wherein all Gibbs state-preserving quantum channels are included. Here we find a mathematical generalization of thermal operations at low temperatures, ‘cooling maps’, for which we derive the necessary and sufficient state transition condition. Cooling maps that saturate recently discovered bounds on coherence transfer are realizable as thermal operations, motivating us to conjecture that all cooling maps are thermal operations. Cooling maps, though a less-conservative generalization to thermal operations, are more tractable than Gibbs-preserving operations, suggesting that cooling map-like models at general temperatures could be of use in gaining insight about thermal operations.
Genome-wide microRNA screening reveals that the evolutionary conserved miR-9a regulates body growth by targeting sNPFR1/NPYR
Authors: Suh Yoon Seok , Bhat Shreelatha , Hong Seung-Hyun , Shin Minjung , Bahk Suhyoung , Cho Kyung Sang , Kim Seung-Whan , Lee Kyu-Sun , Kim Young-Joon , Jones Walton D. , Yu Kweon 
Published: July 2015

AbstractMicroRNAs (miRNAs) regulate many physiological processes including body growth. Insulin/IGF signalling is the primary regulator of animal body growth, but the extent to which miRNAs act in insulin-producing cells (IPCs) is unclear. Here we generate a UAS-miRNA library of Drosophila stocks and perform a genetic screen to identify miRNAs whose overexpression in the IPCs inhibits body growth in Drosophila. Through this screen, we identify miR-9a as an evolutionarily conserved regulator of insulin signalling and body growth. IPC-specific miR-9a overexpression reduces insulin signalling and body size. Of the predicted targets of miR-9a, we find that loss of miR-9a enhances the level of sNPFR1. We show via an in vitro binding assay that miR-9a binds to sNPFR1 mRNA in insect cells and to the mammalian orthologue NPY2R in rat insulinoma cells. These findings indicate that the conserved miR-9a regulates body growth by controlling sNPFR1/NPYR-mediated modulation of insulin signalling.
Intra-unit-cell magnetic correlations near optimal doping in YBa2Cu3O6.85
Authors: Mangin-Thro L. , Sidis Y. , Wildes A. , Bourges P. 
Published: July 2015

AbstractThe pseudo-gap phenomenon in copper oxide superconductors is central to any description of these materials as it prefigures the superconducting state itself. A magnetic intra-unit-cell order was found to occur just at the pseudo-gap temperature in four cuprate high-Tc superconducting families. Here we present polarized neutron-scattering measurements of nearly optimally doped YBa2Cu3O6.85, carried out on two different spectrometers, that reveal several features. The intra-unit-cell order consists of finite-sized planar domains that are very weakly correlated along the c axis. At high temperature, only the out-of-plane magnetic components correlate, indicating a strong Ising anisotropy. An aditional in-plane response develops at low temperature, giving rise to an apparent tilt of the magnetic moment. The discovery of these two regimes puts stringent constraints, which are tightly bound to the pseudo-gap physics, on the intrinsic nature of intra-unit-cell order.
Revisiting the intraperoxisomal pathway of mammalian PEX7
Authors: Rodrigues Tony A. , Grou Cláudia P. , Azevedo Jorge E. 
Published: July 2015

AbstractNewly synthesized peroxisomal proteins containing a cleavable type 2 targeting signal (PTS2) are transported to the peroxisome by a cytosolic PEX5-PEX7 complex. There, the trimeric complex becomes inserted into the peroxisomal membrane docking/translocation machinery (DTM), a step that leads to the translocation of the cargo into the organelle matrix. Previous work suggests that PEX5 is retained at the DTM during all the steps occurring at the peroxisome but whether the same applies to PEX7 was unknown. By subjecting different pre-assembled trimeric PEX5-PEX7-PTS2 complexes to in vitro co-import/export assays we found that the export competence of peroxisomal PEX7 is largely determined by the PEX5 molecule that transported it to the peroxisome. This finding suggests that PEX7 is also retained at the DTM during the peroxisomal steps and implies that cargo proteins are released into the organelle matrix by DTM-embedded PEX7. The release step does not depend on PTS2 cleavage. Rather, our data suggest that insertion of the trimeric PEX5-PEX7-PTS2 protein complex into the DTM is probably accompanied by conformational alterations in PEX5 to allow release of the PTS2 protein into the organelle matrix.
Machine learning plus optical flow: a simple and sensitive method to detect cardioactive drugs
Authors: Lee Eugene K. , Kurokawa Yosuke K. , Tu Robin , George Steven C. , Khine Michelle 
Published: July 2015

AbstractCurrent preclinical screening methods do not adequately detect cardiotoxicity. Using human induced pluripotent stem cell-derived cardiomyocytes (iPS-CMs), more physiologically relevant preclinical or patient-specific screening to detect potential cardiotoxic effects of drug candidates may be possible. However, one of the persistent challenges for developing a high-throughput drug screening platform using iPS-CMs is the need to develop a simple and reliable method to measure key electrophysiological and contractile parameters. To address this need, we have developed a platform that combines machine learning paired with brightfield optical flow as a simple and robust tool that can automate the detection of cardiomyocyte drug effects. Using three cardioactive drugs of different mechanisms, including those with primarily electrophysiological effects, we demonstrate the general applicability of this screening method to detect subtle changes in cardiomyocyte contraction. Requiring only brightfield images of cardiomyocyte contractions, we detect changes in cardiomyocyte contraction comparable to – and even superior to – fluorescence readouts. This automated method serves as a widely applicable screening tool to characterize the effects of drugs on cardiomyocyte function.
Comparative assessment of vaccine vectors encoding ten malaria antigens identifies two protective liver-stage candidates
Authors: Longley Rhea J. , Salman Ahmed M. , Cottingham Matthew G. , Ewer Katie , Janse Chris J. , Khan Shahid M. , Spencer Alexandra J. , Hill Adrian V. S. 
Published: July 2015

AbstractThe development of an efficacious Plasmodium falciparum malaria vaccine remains a top priority for global health. Vaccination with irradiated sporozoites is able to provide complete sterile protection through the action of CD8+ T cells at the liver-stage of infection. However, this method is currently unsuitable for large-scale deployment and focus has instead turned to the development of sub-unit vaccines. Sub-unit vaccine efforts have traditionally focused on two well-known pre-erythrocytic antigens, CSP and TRAP, yet thousands of genes are expressed in the liver-stage. We sought to assess the ability of eight alternative P. falciparum pre-erythrocytic antigens to induce a high proportion of CD8+ T cells. We show that all antigens, when expressed individually in the non-replicating viral vectors ChAd63 and MVA, are capable of inducing an immune response in mice. Furthermore, we also developed chimeric P. berghei parasites expressing the cognate P. falciparum antigen to enable assessment of efficacy in mice. Our preliminary results indicate that vectors encoding either PfLSA1 or PfLSAP2 are capable of inducing sterile protection dependent on the presence of CD8+ T cells. This work has identified two promising P. falciparum liver-stage candidate antigens that will now undergo further testing in humans.
Growth, Quantitative Growth Analysis and Applications of Graphene on γ-Al2O3 catalysts
Authors: Park Jaehyun , Lee Joohwi , Choi Jung-Hae , Hwang Do Kyung , Song Yong-Won 
Published: July 2015

AbstractThe possibilities offered by catalytic γ-Al2O3 substrates are explored and the mechanism governing graphene formation thereon is elucidated using both numerical simulations and experiments. The growth scheme offers metal-free synthesis at low temperature, grain-size customization, large-area uniformity of electrical properties, single-step preparation of graphene/dielectric structures and readily detachable graphene. We quantify based on thermodynamic principles the activation energies associated with graphene nucleation/growth on γ-Al2O3, verifying the low physical and chemical barriers. Importantly, we derive a universal equation governing the adsorption-based synthesis of graphene over a wide range of temperatures in both catalytic and spontaneous growth regimes. Experimental results support the equation, highlighting the catalytic function of γ-Al2O3 at low temperatures. The synthesized graphene is manually incorporated as a ‘graphene sticker’ into an ultrafast mode-locked laser.