bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural retina identity is specified by lens-derived BMP signals
Authors: Pandit Tanushree , Jidigam Vijay K. , Patthey Cedric , Gunhaga Lena
Published: May 2015

The eye has served as a classical model to study cell specification and tissue induction for over a century. Nevertheless, the molecular mechanisms that regulate the induction and maintenance of eye-field cells, and the specification of neural retina cells are poorly understood. Moreover, within the developing anterior forebrain, how prospective eye and telencephalic cells are differentially specified is not well defined. In the present study, we have analyzed these issues by manipulating signaling pathways in intact chick embryo and explant assays. Our results provide evidence that at blastula stages, BMP signals inhibit the acquisition of eye-field character, but from neural tube/optic vesicle stages, BMP signals from the lens are crucial for the maintenance of eye-field character, inhibition of dorsal telencephalic cell identity and specification of neural retina cells. Subsequently, our results provide evidence that a Rax2-positive eye-field state is not sufficient for the progress to a neural retina identity, but requires BMP signals. In addition, our results argue against any essential role of Wnt or FGF signals during the specification of neural retina cells, but provide evidence that Wnt signals together with BMP activity are sufficient to induce cells of retinal pigment epithelial character. We conclude that BMP activity emanating from the lens ectoderm maintains eye-field identity, inhibits telencephalic character and induces neural retina cells. Our findings link the requirement of the lens ectoderm for neural retina specification with the molecular mechanism by which cells in the forebrain become specified as neural retina by BMP activity.
Muscle force, work and cost: a novel technique to revisit the Fenn Effect
Authors: Ortega Justus O. , Lindstedt Stan L. , Nelson Frank E. , Jubrias Sharon A. , Kushmerick Martin J. , Conley Kevin E.
Published: May 2015

Muscle produces force by forming cross bridges, using energy released from ATP. While the magnitude and duration of force production primarily determine the energy requirement, nearly a century ago Fenn observed that muscle shortening or lengthening influenced energetic cost of contraction. When work is done by the muscle, the energy cost is increased and when work is done on the muscle the energy cost is reduced. However the magnitude of the “Fenn Effect” and its mirror (Negative Fenn Effect) have not been quantitatively resolved. We describe a new technique coupling Magnetic Resonance Spectroscopy with an in vivo force clamp that can directly quantify the Fenn Effect (E=I+W, Energy liberated equals the energy cost of Isometric force production plus the Work done) and the Negative Fenn Effect (E=I–W) for one muscle, the first dorsal interosseous (FDI). ATP cost was measured during a series of contractions, each of which occurred at a constant force and for a constant duration, thus constant Force-Time Integral (FTI). In all subjects, as the FTI increased with load, there was a proportional linear increase in energy cost. In addition, the cost of producing force greatly increased when the muscle shortened, and was slightly reduced during lengthening contraction. These results, though limited to a single muscle, contraction velocity and muscle length change, do quantitatively support the Fenn Effect. We speculate that they also suggest that an elastic element within the FDI muscle functions to preserve the force generated within the cross bridges.
Syntheses and Catalytic Ability of Sugar-Incorporated N-Heterocyclic Carbene Pincer Pd Complexes Possessing Various N-Substituents
Authors: Imanaka Yosuke , Hashimoto Hideki , Nishioka Takanori
Published: May 2015

Exploration of catalysts for organic reactions in water, which is a nontoxic and nonexplosive liquid, has been studied to achieve environmentally friendly chemical processes. For such a purpose, we utilized click chemistry to incorporate sugar units into transition-metal complexes affording water-soluble complexes. In this study, a series of palladium complexes with C–C–N pincer ligands, each of which consisted of two N-heterocyclic carbenes (NHCs) and a triazole moiety with a d-glucopyranosyl unit were synthesized. These complexes possess various N-substituents, namely, methyl, isopropyl, benzyl, or d-glucopyranosyl units on the terminal NHC moieties. The diastereoselectivity in the formation of the complexes and their catalytic ability toward the Suzuki–Miyaura cross-coupling reactions in water exhibited clear N-substituent effects. The tridentate ligand with an acetylated d-glucopyranosyl unit on the terminal NHC moiety led to high diastereoselectivity in the formation of its complex, while each of the other ligands with achiral substituents on the terminal NHC units afforded both of the diastereomers with low selectivity. Catalytic reactions using the complexes were examined for the Suzuki–Miyaura cross-coupling reactions of phenylboronic acid and 4′-bromoacetophenone in water. The complex possessing an isopropyl group on the terminal NHC moiety exhibited excellent catalytic activity with TON (800000), which is comparable to the best value reported for a similar reaction.
Oxygen Consumption of Contractile C2C12 Myotubes Investigated by Scanning Electrochemical Microscopy
Authors: Igaki Yuki , Mizutani Fumio , Yasukawa Tomoyuki
Published: May 2015

The oxygen consumption of single contractile myotubes was investigated by amperometric monitoring of the reduction current for oxygen using scanning electrochemical microscope (SECM) equipped with Pt microelectrode. The contraction of myotubes was induced by the application of electric pulse stimulation. The reduction current for oxygen immediately decreased after application of the electric pluses with 1.0 Hz and almost reached steady state because the activity of the oxygen consumption by respiration increased due to the contraction of myotubes accompanied with a consumption of energy.
The Real Effects of Relational Contracts
Authors: Blader Steven , Gartenberg Claudine , Henderson Rebecca , Prat Andrea
Published: May 2015

Does the “soft side” of management matter? Many managers assert that “firm culture” is strongly correlated with productivity, but there are few robust tests of this assertion. In a set of field experiments, we study driver productivity within a large US logistics company that is arguably transitioning from one relational contract to another, while leaving formal practices and incentives unchanged. We find that sites under the new contract are associated with 1/8 percent higher productivity. Our findings suggest that relational contracts have a first-order effect on productivity and that they can be altered over time.
Are the Non-Monetary Costs of Energy Efficiency Investments Large? Understanding Low Take-up of a Free Energy Efficiency Program
Authors: Fowlie Meredith , Greenstone Michael , Wolfram Catherine
Published: May 2015

We document very low take-up of an energy efficiency program that is widely believed to be privately beneficial. Program participants receive a substantial home “weatherization” retrofit; all installation and equipment costs are covered by the program. Less than 1 percent of presumptively eligible households take up the program in the control group. This rate increased only modestly after we took extraordinary efforts to inform households—via multiple channels–about the sizable benefits and zero monetary costs. These findings are consistent with high non-monetary costs associated with program participation and/or energy efficiency investments.
Learning from Experiments when Context Matters
Authors: Pritchett Lant , Sandefur Justin
Published: May 2015

Suppose a policymaker is interested in the impact of an existing social program. Impact estimates using observational data suffer potential bias, while unbiased experimental estimates are often limited to other contexts. This creates a practical trade-off between internal and external validity for evidence-based policymaking. We explore this trade-off empirically for several common policies analyzed in development economics, including microcredit, migration, and education interventions. Based on mean-squared error, non-experimental evidence within context outperforms experimental evidence from another context. This advantage declines, but may not reverse, with experimental replication. We offer four reasons these findings are of general relevance to policy evaluation.
Cooperation in a Dynamic Fishing Game: A Framed Field Experiment
Authors: Noussair Charles N. , van Soest Daan , Stoop Jan
Published: May 2015

We derive a dynamic theoretical model of renewable resource extraction. In the social optimum, maximum extraction occurs in the last period only, while in the unique subgame perfect Nash equilibrium, the resource is depleted immediately. The predictions are tested in a field experiment conducted at a recreational fishing pond. The subjects, experienced recreational fishermen, face a dynamic social dilemma, in which they risk depletion of the resource by overfishing. We find strong support for the Nash equilibrium. Fishermen exert as much effort in the last period as in preceding periods, and effort is independent of the stock of fish.
Connecting Student Loans to Labor Market Outcomes: Policy Lessons from Chile
Authors: Beyer Harald , Hastings Justine , Neilson Christopher , Zimmerman Seth
Published: May 2015

Rising student loan default rates and protests over debt suggest that many students make college enrollment and financing choices they regret. Policymakers have considered tying the availability of federally subsidized loans at degree programs to financial outcomes for past students. This paper considers the implementation of such a policy in Chile. We describe how loan repayment varied by degree type at baseline, the design of the loan reform, and how earnings-based loan caps change availability of loans and incentives for students and higher education institutions. We discuss the challenges facing policymakers seeking to link loan availability to earnings outcomes.
Testing for the Disposition Effect on Optimal Stopping Decisions
Authors: Magnani Jacopo
Published: May 2015

This paper develops a new laboratory test of the hypothesis that individual investors sell winners too early and ride losers too long. In the experiment, subjects invest in a risky asset, whose price evolves in near-continuous time, and they are provided with the option to liquidate it at a fixed salvage value. Optimal behavior is characterized by an upper and a lower stopping thresholds in the asset price space, thus producing a clear rational benchmark and eliminating known confounds. This design allows me to detect and quantify the disposition effect in a sample of 108 subjects.
Immigration Enforcement and Crime
Authors: Pinotti Paolo
Published: May 2015

Immigration enforcement has ambiguous implications for the crime rate of undocumented immigrants. On the one hand, expulsions reduce the pool of immigrants at risk of committing crimes, on the other they lower the opportunity cost of crime for those who are not expelled. We estimate the effect of expulsions on the crime rate of undocumented immigrants in Italy exploiting variation in enforcement toward immigrants of different nationality, due to the existence of bilateral agreements for the control of illegal migration. We find that stricter enforcement of migration policy reduces the crime rate of undocumented immigrants.
The Criminal Justice Response to Policy Interventions: Evidence from Immigration Reform
Authors: Bohn Sarah , Freedman Matthew , Owens Emily
Published: May 2015

Changes in the treatment of individuals by the criminal justice system following a policy intervention may bias estimates of the effects of the intervention on underlying criminal activity. We explore the importance of such changes in the context of the Immigration Reform and Control Act of 1986 (IRCA). Using administrative data from San Antonio, Texas, we examine variation across neighborhoods and ethnicities in police arrests and in the rate at which those arrests are prosecuted. We find that changes in police behavior around IRCA confound estimates of the effects of the policy and its restrictions on employment on criminal activity.
The Long-Run Effect of Mexican Immigration on Crime in US Cities: Evidence from Variation in Mexican Fertility Rates
Authors: Chalfin Aaron
Published: May 2015

Using historical data on the size of state-specific Mexican birth cohorts and geographic migration networks between Mexican states and US metropolitan areas, I construct an instrumental variable that predicts decadal migration from Mexico to the United States. The intuition behind this identification strategy is that larger historical birth cohorts in Mexico yield more potential migrants once each birth cohort reaches prime migration age. I report evidence that Mexican immigration is associated with a decline in property crimes and an increase in aggravated assaults. The available evidence suggests that this is not an artifact of reduced crime reporting among immigrants.
Factoryless Goods Producing Firms
Authors: Bernard Andrew B. , Fort Teresa C.
Published: May 2015

This paper documents the existence and characteristics of US firms that do not manufacture themselves, but nonetheless are heavily involved in the production of goods. These factoryless goods producing firms (FGPFs) are formally in the wholesale sector but, unlike traditional wholesale firms, FGPFs design the goods they sell and coordinate production activities. FGPFs in the wholesale sector are larger and younger, pay higher wages, span more sectors and had more manufacturing employment in previous years compared to traditional wholesalers. FGPFs are more likely to import than typical wholesalers, though their imports constitute a smaller share of their total domestic activity.
Multinational Production: Data and Stylized Facts
Authors: Ramondo Natalia , Rodríguez-Clare Andrés , Tintelnot Felix
Published: May 2015

We present a comprehensive data set on the bilateral activity of multinational firms, with focus on two variables: affiliate revenues and the number of affiliates across country pairs. Our basic data are from UNCTAD and include 59 countries, an average over 1996-2001. We implement an extrapolation procedure that fills in missing values using, alternately, FDI stocks and the bilateral number of M&A transactions. Our dataset allows for the analysis of new patterns of multinational production activities across countries, by taking into account firm rather than balance of payment variables, and both the intensive and extensive margins of multinational activities.
Principles of (Behavioral) Economics
Authors: Laibson David , List John A.
Published: May 2015

Behavioral economics has become an important and integrated component of modern economics. Behavioral economists embrace the core principles of economics—optimization and equilibrium—and seek to develop and extend those ideas to make them more empirically accurate. Behavioral models assume that economic actors try to pick the best feasible option and those actors sometimes make mistakes. Behavioral ideas should be incorporated throughout the first-year undergraduate course. Instructors should also considering allocating a lecture (or more) to a focused discussion of behavioral concepts. We describe our approach to such a lecture, highlighting six modular principles and empirical examples that support them.
Teaching a Behavioral Economics Elective: Highlighting the Science of Economics
Authors: O'Donoghue Ted
Published: May 2015

In this paper, I provide an overview of how one might teach an advanced undergraduate elective on Behavioral Economics. While I focus on the structure and themes from my own course, I also attempt to highlight ways in which instructors might choose an alternative structure. Throughout, I emphasize how a Behavioral Economics elective is a great vehicle in which to highlight to undergraduates the science of Economics.
Informal Employment in a Growing and Globalizing Low-Income Country
Authors: McCaig Brian , Pavcnik Nina
Published: May 2015

We document several facts about workforce transitions from the informal to the formal sector in Vietnam, a fast growing, industrializing, and low-income country. First, younger workers, particularly migrants, are more likely to work in the formal sector and stay there permanently. Second, the decline in the aggregate share of informal employment occurs through changes between and within birth cohorts. Third, younger, educated, male, and urban workers are more likely to switch to the formal sector than other workers initially in the informal sector. Poorly educated, older, female, rural workers face little prospect of formalization. Fourth, formalization coincides with occupational upgrading.
The Great Recession and Credit Trends across Income Groups
Authors: Amromin Gene , McGranahan Leslie
Published: May 2015

In this paper, we document trends in credit use across income groups in the period surrounding the Great Recession. We investigate trends in access to different credit markets, including mortgages, home equity, automobiles, and student loans. We disentangle growth rates of new market entrants from the aggregates and analyze overall as well as within-county growth rate differentials across income strata. Our findings may provide insight into the financial well-being of different income groups in the context of the Great Recession.
Capital and Wealth in the Twenty-First Century
Authors: Weil David N.
Published: May 2015

In Capital in the Twenty-First Century, Thomas Piketty uses the market value of tradable assets to measure both productive capital and wealth. As a measure of wealth this is problematic because it ignores the value of human capital and transfer wealth, which have grown enormously over the last 300 years. Thus the constancy of the wealth/income ratio as portrayed in his data is an illusion. Further, the types of wealth that he does not measure are more equally distributed than tradable assets. The approach also incorrectly identifies capital gains due to reduced discount rates as increases in the capital stock.
Yes, r > g. So What?
Authors: Mankiw N. Gregory
Published: May 2015

Piketty argues that r > g is the “the central contradiction of capitalism” and that it will lead to an “endless inegalitarian spiral.” As a result, he argues for a new global tax on capital. In this brief essay, I explain why I am not persuaded by either his prediction or his prescription.
The Effect of Unemployment Benefits on the Duration of Unemployment Insurance Receipt: New Evidence from a Regression Kink Design in Missouri, 2003–2013
Authors: Card David , Johnston Andrew , Leung Pauline , Mas Alexandre , Pei Zhuan
Published: May 2015

We provide new evidence on the effect of the unemployment insurance (UI) weekly benefit amount on unemployment insurance spells based on administrative data from the state of Missouri covering the period 2003-2013. Identification comes from a regression kink design that exploits the quasi-experimental variation around the kink in the UI benefit schedule. We find that UI durations are more responsive to benefit levels during the recession and its aftermath, with an elasticity between 0.65 and 0.9 as compared to about 0.35 pre-recession.
Veterans' Labor Force Participation: What Role Does the VA's Disability Compensation Program Play?
Authors: Coile Courtney , Duggan Mark , Guo Audrey
Published: May 2015

We explore time trends in the labor force participation of veterans and non-veterans and investigate whether they are consistent with a rising role for the Department of Veterans Affairs' Disability Compensation (DC) program, which pays benefits to veterans with service-connected disabilities and has grown rapidly since 2000. Using 35 years of March CPS data, we find that veterans' labor force participation declined over time in a way that coincides closely with DC growth and that veterans have become more sensitive to economic shocks. Our findings suggest that DC program growth has contributed to recent declines in veterans' labor force participation.
Human Capital and Growth
Authors: Lucas Robert E.
Published: May 2015

This paper describes a growth model with the property that human capital accumulation can account for all observed growth. The model is shown to be consistent with evidence on individual productivities as measured by census earnings data. The central hypothesis is that we learn more when we interact with more productive people.
Killer Cities: Past and Present
Authors: Hanlon W. Walker , Tian Yuan
Published: May 2015

The industrial cities of the 19th century were incredibly unhealthy places to live. How much progress has been made in reducing these negative health effects over the past 150 years? To help answer this question, we compare mortality patterns in 19th century England to those in Chinese urban areas in 2000. We document that substantial improvements have been made in improving health in cities over this period. Unlike historical English cities, large cities in China have lower mortality than less populated areas. However, we also provide evidence that in China a substantial relationship between industrial pollution and mortality remains.
Corporate Culture, Societal Culture, and Institutions
Authors: Guiso Luigi , Sapienza Paola , Zingales Luigi
Published: May 2015

While both cultural and legal norms (institutions) help foster cooperation, culture is the more primitive of the two and itself sustains formal institutions. Cultural changes are rarer and slower than changes in legal institutions, which makes it difficult to identify the role played by culture. Cultural changes and their effects are easier to identify in simpler, more controlled, environments, such as corporations. Corporate culture, thus, is not only interesting per se, but also as a laboratory to study the role of societal culture and the way it can be changed.
The Market for Training Services: A Demand Experiment with Bangladeshi Garment Factories
Authors: Macchiavello Rocco , Rabbani Atonu , Woodruff Christopher
Published: May 2015

We marketed a training program for lower level managers (line supervisors) to large factories in the Bangladeshi ready-made garment industry. Take-up of the program (even for a free slot) was low, due to intense production pressures, fire-fighting and concerns over retention of trained workers. Take-up is quite insensitive to pricing. There was higher interest and demand in training modules aimed at improving production processes and quality, rather than human resources and social compliance. Since the program was priced close to a commercially viable rate, it might be possible to develop a market provided they could be proved to be effective.
The Effect of Extended Unemployment Insurance Benefits: Evidence from the 2012–2013 Phase-Out
Authors: Farber Henry S. , Rothstein Jesse , Valletta Robert G.
Published: May 2015

Unemployment Insurance benefit durations were extended during the Great Recession, reaching 99 weeks for most recipients. The extensions were rolled back and eventually terminated by the end of 2013. Using matched CPS data from 2008-2014, we estimate the effect of extended benefits on unemployment exits separately during the earlier period of benefit expansion and the later period of rollback. In both periods, we find little or no effect on job-finding but a reduction in labor force exits due to benefit availability. We estimate that the rollbacks reduced the labor force participation rate by about 0.1 percentage point in early 2014.
Disability Insurance and the Great Recession
Authors: Maestas Nicole , Mullen Kathleen J. , Strand Alexander
Published: May 2015

The US Social Security Disability Insurance (SSDI) program is designed to provide income support to workers who become unable to work because of a severe, long-lasting disability. In this study, we use administrative data to estimate the effect of labor market conditions, as measured by the unemployment rate, on the number of SSDI applications, the number and composition of initial allowances and denials, and the timing of applications relative to disability onset. We analyze the period of the Great Recession, and compare this period with business cycle effects over the past two decades, from 1992 through 2012.
Do Strict Capital Requirements Raise the Cost of Capital? Bank Regulation, Capital Structure, and the Low-Risk Anomaly
Authors: Baker Malcolm , Wurgler Jeffrey
Published: May 2015

Traditional capital structure theory predicts that reducing banks' leverage reduces the risk and cost of equity but does not change the weighted average cost of capital, and thus the rates for borrowers. We confirm that the equity of better-capitalized banks has lower beta and idiosyncratic risk. However, over the last 40 years, lower risk banks have not had lower costs of equity (lower stock returns), consistent with a stock market anomaly previously documented in other samples. A calibration suggests that a binding ten percentage point increase in Tier 1 capital to risk-weighted assets could double banks' risk premia over Treasury bills.
Satellites, Self-reports, and Submersion: Exposure to Floods in Bangladesh
Authors: Guiteras Raymond , Jina Amir , Mobarak A. Mushfiq
Published: May 2015

A burgeoning “Climate-Economy” literature has uncovered many effects of changes in temperature and precipitation on economic activity, but has made considerably less progress in modeling the effects of other associated phenomena, like natural disasters. We develop new, objective data on floods, focusing on Bangladesh. We show that rainfall and self-reported exposure are weak proxies for true flood exposure. These data allow us to study adaptation, giving accurate measures of both long-term averages and short term variation in exposure. This is important in studying climate change impacts, as people will not only experience new exposures, but also experience them differently.
Moving up the Energy Ladder: The Effect of an Increase in Economic Well-Being on the Fuel Consumption Choices of the Poor in India
Authors: Hanna Rema , Oliva Paulina
Published: May 2015

Rising household wealth may potentially impact both total fuel consumption and fuel-type composition, resulting in significant health and environmental implications. Using data from a field experiment in India, we explore the effects of a transfer program that provided poor, rural households with greater levels of assets and cash. Total fuel consumption rose as a result of the transfers. Households shifted from using electricity rather than kerosene as their primary form of light, but total kerosene consumption also rose. In contrast, we did not observe a shift to cleaner cooking fuels.
Secular Stagnation: A Supply-Side View
Authors: Gordon Robert J.
Published: May 2015

Secular stagnation on the supply side takes the form of a slow 1.6 percent annual growth rate of US potential real GDP, roughly half the 3.1 percent annual growth rate of actual real GDP realized from 1972 to 2004. This slowdown stems from a sharp decline in the growth rate of aggregate hours of work and of output per hour. This paper attributes the productivity growth decline to diminishing returns in the digital revolution that had its peak effect business hardware, software, and best practices in the late 1990s but has resulted in little change in those methods over the past decade.
The Labor Market Impacts of Forced Migration
Authors: Ruiz Isabel , Vargas-Silva Carlos
Published: May 2015

During the 1990s the Kagera region of Tanzania experienced a forced migration shock. A series of geographical barriers led to a higher concentration of forced migrants in some parts of the region relative to others, resulting in a natural experiment. Using panel data (pre and post forced migration shock), we find that greater exposure to the refugee shock resulted in Tanzanians having a lower likelihood of working outside the household as employees. However, employees more affected by the shock had a higher probability of being in professional occupations and being part of a pensions program.
Falling Through the Cracks? Grade Retention and School Dropout among Children of Likely Unauthorized Immigrants
Authors: Amuedo-Dorantes Catalina , Lopez Mary J.
Published: May 2015

We evaluate how intensified interior immigration enforcement impacts the likelihood that children of unauthorized immigrants will repeat a grade or drop out of school. Using a weighted index of the intensity of interior immigration enforcement at the MSA level, we find that increased enforcement has the largest impact on younger children ages 6 to 13. The estimates, which account for the non-random residential location of children and their families, reveal that increased enforcement raises young children's probability of repeating a grade by 6 percent and their likelihood of dropping out of school by 25.2 percent.
(Indirect) Input Linkages
Authors: Eslava Marcela , Fieler Ana Cecília , Xu Daniel Yi
Published: May 2015

Relative to backward firms, technologically-advanced firms source inputs from other advanced firms. These sourcing patterns lead to a magnification effect of technology adoption. A firm that adopts higher-technology increases the relative supply and demand for higher-technology inputs. As a result, it positively influences the technology of other firms in its production chain. Using data from a Colombian manufacturing survey, we provide evidence that advanced firms disproportionately value advanced inputs. More novel, we provide suggestive evidence that technological advancements in some firms increase the technology of other firms indirectly linked to them through a common input market.
The Ll.LtrB intron from Lactococcus lactis excises as circles in vivo: insights into the group II intron circularization pathway
Authors: Monat Caroline , Quiroga Cecilia , Laroche-Johnston Felix , Cousineau Benoit
Published: May 2015

Group II introns are large ribozymes that require the assistance of intron-encoded or free-standing maturases to splice from their pre-mRNAs in vivo. They mainly splice through the classical branching pathway, being released as RNA lariats. However, group II introns can also splice through secondary pathways like hydrolysis and circularization leading to the release of linear and circular introns, respectively. Here, we assessed in vivo splicing of various constructs of the Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis. The study of excised intron junctions revealed, in addition to branched intron lariats, the presence of perfect end-to-end intron circles and alternatively circularized introns. Removal of the branch point A residue prevented Ll.LtrB excision through the branching pathway but did not hinder intron circle formation. Complete intron RNA circles were found associated with the intron-encoded protein LtrA forming nevertheless inactive RNPs. Traces of double-stranded head-to-tail intron DNA junctions were also detected in L. lactis RNA and nucleic acid extracts. Some intron circles and alternatively circularized introns harbored variable number of non-encoded nucleotides at their splice junction. The presence of mRNA fragments at the splice junction of some intron RNA circles provides insights into the group II intron circularization pathway in bacteria.
Conserved RNA secondary structures and long-range interactions in hepatitis C viruses
Authors: Fricke Markus , Dünnes Nadia , Zayas Margarita , Bartenschlager Ralf , Niepmann Michael , Marz Manja
Published: May 2015

Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5′ untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3′ UTR. We propose an alternative structure in the 5′ UTR, conserved secondary structures of 5B stem–loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3′ end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5′ and 3′ UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5′–3′ UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.
The welfare of ornamental fish in the home aquarium
Authors: Walster Chris , Rasidi Ellen , Saint-Erne Nick , Loh Richmond
Published: May 2015

The welfare of ornamental fish kept in aquariums or ponds has historically been taken for granted by fish keepers, the ornamental fish industry and animal welfare organisations. This is attributed to the low cost of many ornamental fish, lack of reliable information about their health care, or a perceived lack of veterinarians with skills in aquatic animal health. Moreover, it is not uncommon for our veterinary colleagues to refer potential fish clients to fish stores or pet stores, as had been done in the past with less commonly seen species like birds and ‘pocket pets’. Slowly, veterinary surgeons and veterinary organisations are increasingly becoming involved in aquatic veterinary medicine to help improve the welfare of pet fish. This article presents the current status of ornamental fish welfare, the issues and their causes, and provides further sources of information.
The Benefits of Good Teaching Extend Beyond Course Achievement
Authors: Loes Chad N. , Pascarella Ernest T
Published: May 2015

This paper synthesizes research from the Wabash National Study on Liberal Arts Education, the National Study on Student Learning, and the Research on Iowa Student Experiences study that estimates the influence of certain effective instructional practices on a range of student outcomes. Student perceptions of two specific teacher behaviors – instructor clarity and instructor organization – are associated with gains in a number of important student outcomes including critical thinking, propensity for lifelong learning, academic motivation, persistence to the second year of college, graduate degree plans, likelihood of obtaining a bachelor's degree, and student use of deep approaches to learning.
Keeping it real: Exploring an interdisciplinary breaking bad news role-play as an integrative learning opportunity.
Authors: Sweeney Catherine , O'Sullivan Eleanor , McCarthy Marian
Published: May 2015

Palliative care is a complex area of healthcare that is best delivered by an interdisciplinary team approach. Breaking bad news is an inherent part of caring for people with life-limiting conditions. The purpose of this study was to explore an interdisciplinary breaking bad news role-play in a palliative care module. The participants were undergraduate medical and nursing students. Qualitative data from focus groups, student and facilitator feedback and a role-play recording were thematically analysed. The findings revealed that the role-play led to increased understanding of and changes in attitudes towards key palliative care principles, interdisciplinary teamwork, and communication of bad news. There was evidence of increased self-awareness. The findings suggest that the interdisciplinary breaking bad news role-play was a rich integrative learning experience that was valued by students.
CPU sharing techniques for performance isolation in multi-tenant relational database-as-a-service
Authors: Das Sudipto , Narasayya Vivek R. , Li Feng , Syamala Manoj
Published: May 2015

Multi-tenancy and resource sharing are essential to make a Database-as-a-Service (DaaS) cost-effective. However, one major consequence of resource sharing is that the performance of one tenant's workload can be significantly affected by the resource demands of co-located tenants. The lack of performance isolation in a shared environment can make DaaS less attractive to performance-sensitive tenants. Our approach to performance isolation in a DaaS is to isolate the key resources needed by the tenants' workload. In this paper, we focus on the problem of effectively sharing and isolating CPU among co-located tenants in a multi-tenant DaaS. We show that traditional CPU sharing abstractions and algorithms are inadequate to support several key new requirements that arise in DaaS: (a) absolute and fine-grained CPU reservations without static allocation; (b) support elasticity by dynamically adapting to bursty resource demands; and (c) enable the DaaS provider to suitably tradeoff revenue with fairness. We implemented these new scheduling algorithms in a commercial DaaS prototype and extensive experiments demonstrate the effectiveness of our techniques.
Toward a distance oracle for billion-node graphs
Authors: Qi Zichao , Xiao Yanghua , Shao Bin , Wang Haixun
Published: May 2015

The emergence of real life graphs with billions of nodes poses significant challenges for managing and querying these graphs. One of the fundamental queries submitted to graphs is the
shortest distance query.
Online BFS (breadth-first search) and offline pre-computing pairwise shortest distances are prohibitive in time or space complexity for billion-node graphs. In this paper, we study the feasibility of building
distance oracles
for billion-node graphs. A distance oracle provides approximate answers to shortest distance queries by using a pre-computed data structure for the graph. Sketch-based distance oracles are good candidates because they assign each vertex a sketch of bounded size, which means they have linear space complexity. However, state-of-the-art sketch-based distance oracles lack efficiency or accuracy when dealing with big graphs. In this paper, we address the scalability and accuracy issues by focusing on optimizing the three key factors that affect the performance of distance oracles:
landmark selection, distributed BFS
, and
answer generation.
We conduct extensive experiments on both real networks and synthetic networks to show that we can build distance oracles of affordable cost and efficiently answer shortest distance queries even for billion-node graphs.
Multi-core, main-memory joins
Authors: Balkesen Cagri , Alonso Gustavo , Teubner Jens , Özsu M. Tamer
Published: May 2015

In this paper we experimentally study the performance of main-memory, parallel, multi-core join algorithms, focusing on sort-merge and (radix-)hash join. The relative performance of these two join approaches have been a topic of discussion for a long time. With the advent of modern multi-core architectures, it has been argued that sort-merge join is now a better choice than radix-hash join. This claim is justified based on the width of SIMD instructions (sort-merge outperforms radix-hash join once SIMD is sufficiently wide), and NUMA awareness (sort-merge is superior to hash join in NUMA architectures). We conduct extensive experiments on the original and optimized versions of these algorithms. The experiments show that, contrary to these claims, radix-hash join is still clearly superior, and sort-merge approaches to performance of radix only when very large amounts of data are involved. The paper also provides the fastest implementations of these algorithms, and covers many aspects of modern hardware architectures relevant not only for joins but for any parallel data processing operator.
Storage management in the NVRAM era
Authors: Pelley Steven , Wenisch Thomas F. , Gold Brian T. , Bridge Bill
Published: May 2015

Emerging nonvolatile memory technologies (NVRAM) offer an alternative to disk that is persistent, provides read latency similar to DRAM, and is byte-addressable. Such NVRAMs could revolutionize online transaction processing (OLTP), which today must employ sophisticated optimizations with substantial software overheads to overcome the long latency and poor random access performance of disk. Nevertheless, many candidate NVRAM technologies exhibit their own limitations, such as greater-than-DRAM latency, particularly for writes.

In this paper, we reconsider OLTP durability management to optimize recovery performance and forward-processing throughput for emerging NVRAMs. First, we demonstrate that using NVRAM as a drop-in replacement for disk allows near-instantaneous recovery, but software complexity necessary for disk (i.e., Write Ahead Logging/ARIES) limits transaction throughput. Next, we consider the possibility of removing software-managed DRAM buffering. Finally, we measure the cost of ordering writes to NVRAM, which is vital for correct recovery. We consider three recovery mechanisms:
NVRAM Disk-Replacement, In-Place Updates
(transactions persist data in-place), and
NVRAM Group Commit
(transactions commit/persist atomically in batches). Whereas
In-Place Updates
offers the simplest design, it introduces persist synchronizations at every page update.
NVRAM Group Commit
minimizes persist synchronization, offering up to a 50% throughput improvement for large synchronous persist latencies.
Multi-query optimization in MapReduce framework
Authors: Wang Guoping , Chan Chee-Yong
Published: May 2015

MapReduce has recently emerged as a new paradigm for large-scale data analysis due to its high scalability, fine-grained fault tolerance and easy programming model. Since different jobs often share similar work (e.g., several jobs scan the same input file or produce the same map output), there are many opportunities to optimize the performance for a batch of jobs. In this paper, we propose two new techniques for multi-job optimization in the MapReduce framework. The first is a generalized grouping technique (which generalizes the recently proposed MRShare technique) that merges multiple jobs into a single job thereby enabling the merged jobs to share both the scan of the input file as well as the communication of the common map output. The second is a materialization technique that enables multiple jobs to share both the scan of the input file as well as the communication of the common map output via partial materialization of the map output of some jobs (in the map and/or reduce phase). Our second contribution is the proposal of a new optimization algorithm that given an input batch of jobs, produces an optimal plan by a judicious partitioning of the jobs into groups and an optimal assignment of the processing technique to each group. Our experimental results on Hadoop demonstrate that our new approach significantly outperforms the state-of-the-art technique, MRShare, by up to 107%.
Highly available transactions
Authors: Bailis Peter , Davidson Aaron , Fekete Alan , Ghodsi Ali , Hellerstein Joseph M. , Stoica Ion
Published: May 2015

To minimize network latency and remain online during server failures and network partitions, many modern distributed data storage systems eschew transactional functionality, which provides strong semantic guarantees for groups of multiple operations over multiple data items. In this work, we consider the problem of providing Highly Available Transactions (HATs): transactional guarantees that do not suffer unavailability during system partitions or incur high network latency. We introduce a taxonomy of highly available systems and analyze existing ACID isolation and distributed data consistency guarantees to identify which can and cannot be achieved in HAT systems. This unifies the literature on weak transactional isolation, replica consistency, and highly available systems. We analytically and experimentally quantify the availability and performance benefits of HATs---often two to three orders of magnitude over wide-area networks---and discuss their necessary semantic compromises.
From "think like a vertex" to "think like a graph"
Authors: Tian Yuanyuan , Balmin Andrey , Corsten Severin Andreas , Tatikonda Shirish , McPherson John
Published: May 2015

To meet the challenge of processing rapidly growing graph and network data created by modern applications, a number of distributed graph processing systems have emerged, such as Pregel and GraphLab. All these systems divide input graphs into partitions, and employ a "think like a vertex" programming model to support iterative graph computation. This vertex-centric model is easy to program and has been proved useful for many graph algorithms. However, this model hides the partitioning information from the users, thus prevents many algorithm-specific optimizations. This often results in longer execution time due to excessive network messages (e.g. in Pregel) or heavy scheduling overhead to ensure data consistency (e.g. in GraphLab). To address this limitation, we propose a new "think like a graph" programming paradigm. Under this graph-centric model, the partition structure is opened up to the users, and can be utilized so that communication within a partition can bypass the heavy message passing or scheduling machinery. We implemented this model in a new system, called Giraph++, based on Apache Giraph, an open source implementation of Pregel. We explore the applicability of the graph-centric model to three categories of graph algorithms, and demonstrate its flexibility and superior performance, especially on well-partitioned data. For example, on a web graph with 118 million vertices and 855 million edges, the graph-centric version of connected component detection algorithm runs 63X faster and uses 204X fewer network messages than its vertex-centric counterpart.
Gestural query specification
Authors: Nandi Arnab , Jiang Lilong , Mandel Michael
Published: May 2015

Direct, ad-hoc interaction with databases has typically been performed over console-oriented conversational interfaces using query languages such as SQL. With the rise in popularity of gestural user interfaces and computing devices that use gestures as their exclusive modes of interaction, database query interfaces require a fundamental rethinking to work without keyboards. We present a novel query specification system that allows the user to query databases using a series of gestures. We present a novel gesture recognition system that uses both the interaction and the state of the database to classify gestural input into relational database queries. We conduct exhaustive systems performance tests and user studies to demonstrate that our system is not only performant and capable of interactive latencies, but it is also more usable, faster to use and more intuitive than existing systems.