bluuebunny/crossref_metadata_2025_split huggingface dataset:
One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities
Authors: Subissi Lorenzo , Posthuma Clara C. , Collet Axelle , Zevenhoven-Dobbe Jessika C. , Gorbalenya Alexander E. , Decroly Etienne , Snijder Eric J. , Canard Bruno , Imbert Isabelle 
Published: September 2014

Significance
The 2003 severe acute respiratory syndrome (SARS) epidemic and recent emergence of Middle East respiratory syndrome highlight the potential lethality of zoonotic coronavirus infections in humans. No specific antiviral treatment options are available. Coronaviruses possess the largest known RNA virus genomes and encode a complex replication machinery consisting of 16 viral nonstructural proteins (nsps). Our study reveals that the SARS-coronavirus RNA polymerase (nsp12) needs to associate with nsp7 and nsp8 to activate its capability to replicate long RNA. Moreover, this complex associates with nsp14, the proofreading subunit required to safeguard coronavirus replication fidelity. Our study thus defines the core of an RNA-synthesizing machinery that is unique in the RNA virus world and includes several key targets for antiviral drug development.
Children’s strategic theory of mind
Authors: Sher Itai , Koenig Melissa , Rustichini Aldo 
Published: September 2014

Significance
Human interaction requires reasoning not only about other people’s observed behavior and mental states but also about their incentives and goals. The development of children’s strategic thinking is not well understood, leaving open critical questions about early human capacity for strategic interaction. We investigated strategic reasoning in 3- to 9-y-old children and adults in two strategic games that represent prevalent aspects of social interaction: incentives to mislead and competition. We find that despite strategic differences in the two games, by the age of 7 y, children’s behavior is similar to that of adults. Our findings also show an early sophisticated ability to think strategically about others in both static and repeated interactions.
Quantifying the benefits of vehicle pooling with shareability networks
Authors: Santi Paolo , Resta Giovanni , Szell Michael , Sobolevsky Stanislav , Strogatz Steven H. , Ratti Carlo 
Published: September 2014

Significance
Recent advances in information technologies have increased our participation in “sharing economies,” where applications that allow networked, real-time data exchange facilitate the sharing of living spaces, equipment, or vehicles with others. However, the impact of large-scale sharing on sustainability is not clear, and a framework to assess its benefits quantitatively is missing. For this purpose, we propose the method of shareability networks, which translates spatio-temporal sharing problems into a graph-theoretic framework that provides efficient solutions. Applying this method to a dataset of 150 million taxi trips in New York City, our simulations reveal the vast potential of a new taxi system in which trips are routinely shareable while keeping passenger discomfort low in terms of prolonged travel time.
Oxygenic photosynthesis without galactolipids
Authors: Awai Koichiro , Ohta Hiroyuki , Sato Naoki 
Published: September 2014

Significance
Cyanobacteria, as well as chloroplasts of plants and algae, are the sites of photosynthesis that produces oxygen. Photosynthetic membranes, also known as thylakoid membranes, in these organisms contain galactolipids, without exception, as the major components. Galactolipids are thus believed to be important for photosynthesis or at least for the formation of the flattened shape of thylakoid membranes. The biosynthetic pathway of galactolipids is definitely different in plants and cyanobacteria. Here we identified the final piece of the long-sought gene for the galactolipid synthesis in cyanobacteria, namely monoglucosyldiacylglycerol epimerase, which converts glucolipid to galactolipid. Cyanobacterial mutants in which this gene is disrupted still formed authentic thylakoid membranes without galactolipids and kept the ability to grow photosynthetically, indicating that galactolipids are not essential for either oxygenic photosynthesis or the development of the thylakoid membrane structure.
Transcription factor EKLF (KLF1) recruitment of the histone chaperone HIRA is essential for β-globin gene expression
Authors: Soni Shefali , Pchelintsev Nikolay , Adams Peter D. , Bieker James J. 
Published: September 2014

Significance
The β-like globin locus has provided a long-standing model for the study of cell-specific and developmental control of transcription and chromatin structure. We have previously shown that the replication-independent histone H3.3 variant is enriched at the active adult β-globin promoter. Although the erythroid Krüppel-like factor (EKLF), which is also known as Krüppel-like factor 1 (KLF1), transcription factor interacts with histone H3, it does not distinguish between the H3.1 or H3.3 variants. We now show that EKLF interacts with the H3.3 chaperone named histone cell cycle regulation defective homolog A (HIRA) and that this enables its selective recruitment of HIRA to the promoter. To our knowledge, our studies implicate HIRA for the first time in establishment of erythropoiesis and explain how critical protein interactions can lead to directed changes in histone variants at restricted sites.
Mu transpososome and RecBCD nuclease collaborate in the repair of simple Mu insertions
Authors: Choi Wonyoung , Jang Sooin , Harshey Rasika M. 
Published: September 2014

SignificanceTransposition is not finished until the gaps left in the target in the wake of transposition are repaired, yet this is the least understood aspect of transposition. This study describes to our knowledge the first in vitro assay for repair of Mu insertions, which shows that repair is controlled by both transpososome and host factors. The long flanking DNA (FD) attached to Mu is shortened in two stages, requiring collaboration between the transpososome and RecBCD at both stages. The transpososome initially regulates the timing of RecBCD entry into the FD, and then exploits RecBCD action on this DNA to promote endonucleolytic cleavage within the transpososome. The final product has short flanks, and is likely the substrate for gap repair by a host polymerase.
Ultrafast phase-change logic device driven by melting processes
Authors: Loke Desmond , Skelton Jonathan M. , Wang Wei-Jie , Lee Tae-Hoon , Zhao Rong , Chong Tow-Chong , Elliott Stephen R. 
Published: September 2014

Significance
The ever-increasing demand for faster computers is tackled by reducing the size of devices, but this is becoming almost impossible to continue. To improve the speed of computers, a solution is to increase the number of operations performed per device. Numerous operations in phase-change–based “in-memory” logic devices have previously been achieved using crystallization, but they show slow speeds, mostly due to a trade-off between the crystallization speed and stability of the initialized-glassy states. Here, we instead control melting processes to perform logic operations. Ultrafast melting speeds and diverse operations were achieved. Computer simulations and electrical measurements show the origin and kinetics of melting. These advances open the doorway for developing computers that can perform calculations at well beyond current processing rates.
Clearance of pathological antibodies using biomimetic nanoparticles
Authors: Copp Jonathan A. , Fang Ronnie H. , Luk Brian T. , Hu Che-Ming J. , Gao Weiwei , Zhang Kang , Zhang Liangfang 
Published: September 2014

Significance
The selective depletion of disease-causing antibodies using nanoparticles offers a new model in the management of type II immune hypersensitivity reactions. The demonstration of pathophysiologically inspired nanoengineering serves as a valuable prototype for additional therapeutic improvements with the goal of minimizing therapy-related adverse effects. Through the use of cell membrane-cloaked nanoparticles, nanoscale decoys with strong affinity to pathological antibodies can be administered to disrupt disease processes in a minimally toxic manner. These biomimetic nanoparticles enable indiscriminate absorption of pathological antibodies regardless of their epitope specificities. This particular approach offers much promise in treating antibody-mediated autoimmune diseases, in which target antigens on susceptible cells can vary from patient to patient.
Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley
Authors: Dai Fei , Chen Zhong-Hua , Wang Xiaolei , Li Zefeng , Jin Gulei , Wu Dezhi , Cai Shengguan , Wang Ning , Wu Feibo , Nevo Eviatar , Zhang Guoping 
Published: September 2014

Significance
Archaeological, historic, and molecular studies have indicated that the Fertile Crescent in the Near East is a major center of origin and domestication of cultivated barley. However, growing evidence in recent years supports the theory of a polyphyletic origin of barley. To our knowledge, this is the first attempt using RNA sequencing techniques and genomic similarity analysis to study the domestication of barley. We confirmed the polyphyletic origin of cultivated barley and our results revealed the genomic origin of modern cultivated barley is from both the Near East and Tibet, with different contributions on each chromosome. These findings advance our understanding of the early spread of agrarian culture, and are expected to be of wide interest to evolutionary geneticists and plant breeders.
Crystal structure of the γ-secretase component nicastrin
Authors: Xie Tian , Yan Chuangye , Zhou Rui , Zhao Yanyu , Sun Linfeng , Yang Guanghui , Lu Peilong , Ma Dan , Shi Yigong 
Published: September 2014

Significance
γ-Secretase is a four-component intramembrane protease associated with the onset of Alzheimer's disease. Nicastrin is the putative substrate-recruiting component of the γ-secretase complex, but no atomic-resolution structure had been identified on γ-secretase or any of its four components. Here we report the first atomic-resolution crystal structure of a eukaryotic nicastrin which shares significant sequence homology with human nicastrin. This structure reveals the fine details of nicastrin and allows structure modeling of human nicastrin. Analysis of the structural details yields a working model showing how nicastrin might function to recruit substrate protein. The nicastrin structure also allows reevaluation of the previously proposed transmembrane helix assignment in the γ-secretase complex. Our structural analysis provides insights into the assembly and function of γ-secretase.
Distinctive signature of indium gallium nitride quantum dot lasing in microdisk cavities
Authors: Woolf Alexander , Puchtler Tim , Aharonovich Igor , Zhu Tongtong , Niu Nan , Wang Danqing , Oliver Rachel , Hu Evelyn L. 
Published: September 2014

Significance
The III-nitride family of materials has already demonstrated tremendous optical efficiency and versatility for devices across a broad range of wavelengths. Quantum dots formed in these materials, with advantages such as improved carrier confinement, should offer even greater device efficiency. They are also important constituents for fundamental studies of light−matter interaction. However, that promise has been far from realized, and this is a complex problem to address. This work, through a comparative study of quantum dot, quantum well, and fragmented quantum well gain media in compact microdisk cavities, allows better understanding of the limitations to lasing for the quantum dot samples. These results allow both improved device efficiency and fundamental insights into quantum dot−cavity interactions in these materials.
Synthesis of (±)-terpendole E
Authors: Teranishi Takaaki , Murokawa Tetsuro , Enomoto Masaru , Kuwahara Shigefumi 
Published: September 2014

Abstract
The first synthesis of the racemate of terpendole E, a specific inhibitor of the mitotic kinesin Eg5, has been achieved from a known tricyclic dihydroxy ketone by a 13-step sequence that involves diastereoselective installation of its C3 quaternary stereocenter via a cyclopropyl ketone intermediate and Pd-mediated two-step construction of the indole ring moiety as the key transformations.
National Wage Trends and Migration in a Chinese Village Economy: A Micro Level Modeling Approach Based on a Composite Utility Function
Authors: Kleinwechter Ulrich , Grethe Harald 
Published: September 2014

AbstractChina's economy is experiencing a regime shift away from a fully elastic supply of labor from a large pool of rural surplus labor and toward a situation of increasing labor scarcity and rising wage rates. Moreover, faster wage increases in the regions of origin of many rural–urban migrants are likely to affect the dynamics of inter‐regional migration. These wage trends have implications at the local level, in particular in a setting in which migration connects rural communities to the national labor market and in which migration is of high importance for the livelihoods of rural households. Taking a village perspective, this article develops a village computable general equilibrium model to study local impacts of current wage trends in China. As a central piece of the model, the role of access to migration for household livelihoods is recognized. Access to migration is linked to household demographics and included in the model through a composite utility function that captures household preferences and disutilities associated with alternative off‐farm activities. Simulation results illustrate how households’ utility considerations affect migration responses to national wage changes. Statements about possible impacts on village level labor supply, land use, and agricultural production are made. When migration wages and local off‐farm wages are simulated to increase, an overall increase in household and village migration and a higher supply of labor to local off‐farm labor markets is accompanied by a contraction of farm production. Although land is reallocated between households with different migration responses, total agricultural output declines.
Transaction Costs in Payment for Environmental Service Contracts
Authors: Peterson Jeffrey M. , Smith Craig M. , Leatherman John C. , Hendricks Nathan P. , Fox John A. 
Published: September 2014

AbstractPayment for environmental service contracts commonly require actions beyond adoption of a practice, such as undergoing specified enrollment procedures, granting consent to being monitored, and paying penalties for violations. These provisions are a bundle of attributes a landholder must accept with contract enrollment, leading to transaction costs in the contracting process. This article develops a principal–agent framework to study the links between these transaction costs and the well‐known information asymmetries between the landholders and the government agency offering contracts. Using stated choice data collected from a sample of farmers, we estimate a mixed logit model to quantify the contribution of different contract attributes on contract willingness‐to‐accept (WTA). More stringent provisions in contracts were found to raise individual WTA by widely differing amounts across farmers, but the average effects imply that overall contract supply is sensitive to stringency. From a series of microsimulations based on the estimated model, we find that transaction costs create a significant drain on the cost‐effectiveness of contracting from the agency's point of view, similar in magnitude to the inefficiency created by hidden information. Although stringent contractual terms raise program expenditures, they may be justified if they raise compliance rates enough to offset the added cost. We also simulate an implicit frontier to trace out the change in compliance needed to justify a given increase in stringency. For environmental benefits in the range of previous estimates, this analysis suggests that stringent terms would need to substantially raise compliance rates to be cost effective.
Nutritional Efficiency Wages and Unemployment: Where's the Beef?
Authors: Powell Benjamin , Murphy Ryan 
Published: September 2014

AbstractWe modify the standard nutritional efficiency wage model to allow for the fact that employers can directly provide calories to their workers rather than paying a higher wage to induce employees to spend more on their own caloric consumption. We derive the various theoretical outcomes that are possible depending on the assumptions about the transaction costs of directly providing calories. We argue that in most real‐world situations the ability of employers to directly provide calories undermines the traditional efficiency wage theory as a cause of equilibrium unemployment.
ballaxy: web services for structural bioinformatics
Authors: Hildebrandt Anna Katharina , Stöckel Daniel , Fischer Nina M. , de la Garza Luis , Krüger Jens , Nickels Stefan , Röttig Marc , Schärfe Charlotta , Schumann Marcel , Thiel Philipp , Lenhof Hans-Peter , Kohlbacher Oliver , Hildebrandt Andreas 
Published: September 2014

Abstract
Motivation: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together.
Results: In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.
Availability and implementation:  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy . Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/ . ballaxy is licensed under the terms of the GPL.
Supplementary information : Supplementary data are available at Bioinformatics online.
Contact: anna.hildebrandt@bioinf.uni-sb.de or andreas.hildebrandt@uni-mainz.de
String graph construction using incremental hashing
Authors: Ben-Bassat Ilan , Chor Benny 
Published: September 2014

Abstract
Motivation : New sequencing technologies generate larger amount of short reads data at decreasing cost. De novo sequence assembly is the problem of combining these reads back to the original genome sequence, without relying on a reference genome. This presents algorithmic and computational challenges, especially for long and repetitive genome sequences. Most existing approaches to the assembly problem operate in the framework of de Bruijn graphs. Yet, a number of recent works use the paradigm of string graph , using a variety of methods for storing and processing suffixes and prefixes, like suffix arrays, the Burrows–Wheeler transform or the FM index. Our work is motivated by a search for new approaches to constructing the string graph, using alternative yet simple data structures and algorithmic concepts.
Results : We introduce a novel hash-based method for constructing the string graph. We use incremental hashing, and specifically a modification of the Karp–Rabin fingerprint, and Bloom filters. Using these probabilistic methods might create false-positive and false-negative edges during the algorithm’s execution, but these are all detected and corrected. The advantages of the proposed approach over existing methods are its simplicity and the incorporation of established probabilistic techniques in the context of de novo genome sequencing. Our preliminary implementation is favorably comparable with the first string graph construction of Simpson and Durbin (2010) (but not with subsequent improvements). Further research and optimizations will hopefully enable the algorithm to be incorporated, with noticeable performance improvement, in state-of-the-art string graph-based assemblers.
Availability and implementation : A beta version of all source code used in this work can be downloaded from http://www.cs.tau.ac.il/~bchor/StringGraph/
Contact: ilanbb@gmail.com or benny@cs.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.