nils-herrmann/clean_scirepeval huggingface dataset:
Global population genetic dynamics of a highly migratory, apex predator shark
Venue: Molecular ecology

Knowledge of genetic connectivity dynamics in the world's large bodied, highly migratory, apex predator sharks across their global ranges is limited. One such species, the tiger shark (Galeocerdo cuvier) occurs worldwide in warm temperate and tropical waters, uses remarkably diverse habitats (nearshore to pelagic) and possesses a generalist diet that can structure marine ecosystems through top down processes. We investigated the phylogeography and the global population structure of this exploited, phylogenetically enigmatic shark by using 10 nuclear microsatellites (n 380) and sequences from the mitochondrial control region (CR, n 340) and cytochrome oxidase I gene (n 100) All three marker classes showed the genetic differentiation between tiger sharks from the western Atlantic and Indo Pacific ocean basins (microsatellite FST 0.129; CR PhST 0.497) the presence of North vs. southwestern Atlantic differentiation and the isolation of tiger sharks sampled from Hawaii from other surveyed locations. Furthermore, mitochondrial DNA revealed high levels of intraocean basin matrilineal population structure, suggesting female philopatry and sex biased gene flow. Coalescent and genetic distance based estimates of divergence from CR sequences were largely congruent (dcorr 0.0015 0.0050) indicating a separation of Indo Pacific and western Atlantic tiger sharks <1 million years ago. Mitochondrial haplotype relationships suggested that the western South Atlantic Ocean was likely a historical connection for interocean basin linkages via the dispersal around South Africa. Together, the results reveal unexpectedly high levels of population structure in a highly migratory, behaviourally generalist, cosmopolitan ocean predator, calling for management and conservation on smaller than anticipated spatial scales.
Aircraft engines: a proud heritage and an exciting future
Venue: The Aeronautical Journal

The 150th anniversary of the Royal Aeronautical Society has seen Rolls Royce become a global player in aerospace and a champion of British industry. Its products vary from the nimble RR300, powering two seater helicopters, all the way to the 97,000 pound thrust Trent XWB, powering future variants of the Airbus A350, and the MT30, which provides the propulsion for the Royal Navy's new Queen Elizabeth class aircraft carriers. It has built this range of products derived from the vision and innovation of its talented engineers, spurred on by the guiding principles provided by Henry Royce. This has seen it through times of war, hardship, bankruptcy and fierce competition to emerge as the leading manufacturer of aircraft engines and a provider of power across land and sea. Alongside its products, it has developed pioneering services to support its customers, analysing real time data to improve the reliability and efficiency of its engines. In keeping with its tradition of innovation, the company is continuing to develop new products and services for the next generation of power systems for land, sea and air.
Net effects of multiple stressors in freshwater ecosystems: a meta analysis.
Venue: Global change biology

The accelerating rate of global change has focused attention on the cumulative impacts of novel and extreme environmental changes (i.e. stressors) especially in marine ecosystems. As integrators of local catchment and regional processes, freshwater ecosystems are also ranked highly sensitive to the net effects of multiple stressors, yet there has not been a large scale quantitative synthesis. We analysed data from 88 papers including 286 responses of freshwater ecosystems to paired stressors and discovered that overall, their cumulative mean effect size was less than the sum of their single effects (i.e. an antagonistic interaction) Net effects of dual stressors on diversity and functional performance response metrics were additive and antagonistic, respectively. Across individual studies, a simple vote counting method revealed that the net effects of stressor pairs were frequently more antagonistic (41% than synergistic (28% additive (16% or reversed (15% Here, we define a reversal as occurring when the net impact of two stressors is in the opposite direction (negative or positive) from that of the sum of their single effects. While warming paired with nutrification resulted in additive net effects, the overall mean net effect of warming combined with a second stressor was antagonistic. Most importantly, the mean net effects across all stressor pairs and response metrics were consistently antagonistic or additive, contrasting the greater prevalence of reported synergies in marine systems. Here, a possible explanation for more antagonistic responses by freshwater biota to stressors is that the inherent greater environmental variability of smaller aquatic ecosystems fosters greater potential for acclimation and co adaptation to multiple stressors.
Graphical models for de novo and pathway based network prediction over multi modal high throughput biological data

It is now a standard practice in the study of complex disease to perform many high throughput omic experiments (genome wide SNP, copy number, mRNA and miRNA expression) on the same set of patient samples. These multi modal data should allow researchers to form a more complete, systems level picture of a sample, but this is only possible if they have a suitable model for integrating the data. Due to the variety of data modalities and possible combinations of data, general, flexible integration methods that will be widely applicable in many settings are desirable. In this dissertation I will present my work using graphical models for de novo structure learning of both undirected and directed sparse graphs over a mixture of Gaussian and categorical variables. Using synthetic and biological data I will show that these models are useful for both variable selection and inference. Selecting the regularization parameters is an important challenge for these models so I will also cover stability based methods for efficiently setting these parameters, and for controlling the false discovery rate of edge predictions. I will also show results from a biological application to data from metastatic melanoma patients where our methods identified a PARP1 slice site variant that is predictive of response to chemotherapy. Finally, I present work incorporating miRNA into a pathway based graphical model called PARADIGM. This extension of the model allows us to study patient specific changes in miRNA induced silencing in cancer.
Rethinking the Financialisation of Non Financial Corporations: A Reappraisal of US Empirical Data

This article assesses the claims of the shareholder value literature of the effects of financialisation on non financial corporations and, particularly, the claim that fixed capital accumulation in the United States has been impeded by the increasing financial payments of non financial corporations, and also by these firms transforming themselves into rentiers. The financialisation explanation of macro patterns assumes that trends in the 1970s and early 1980s are representative of the pre financialisation era but that is not so. Another complication is the global sphere. The vast expansion of majority owned foreign affiliates from the mid 1990s suggests that the managers of US non financial corporations did not abandon growth objectives. Claims about rentieralisation also require further investigation. On the one hand, it is misleading to treat all external investment as a financial asset and to assume that corporate dividends provide a robust proxy for financialisation. On the other hand, the shift to external accumulation by US non financial corporations is obscured due in part to the conceptual limitations of direct investment data, and the widespread strategy of forming non bank holding companies to funnel cross border activities.
What to Verify for Optimal Truthful Mechanisms without Money
Venue: AAMAS

We aim at identifying a minimal set of conditions under which algorithms with good approximation guarantees are truthful without money. In line with recent literature, we wish to express such a set via verification assumptions, i.e. kind of agents' misbehavior that can be made impossible by the designer. We initiate this research endeavour for the paradigmatic problem in approximate mechanism design without money, facility location. It is known how truthfulness imposes (even severe) losses and how certain notions of verification are unhelpful in this setting; one is thus left powerless to solve this problem satisfactorily in presence of selfish agents. We here address this issue and characterize the minimal set of verification assumptions needed for the truthfulness of optimal algorithms, for both social cost and max cost objective functions. En route, we give a host of novel conceptual and technical contributions ranging from topological notions of verification to a lower bounding technique for truthful mechanisms that connects methods to test truthfulness (i.e. cycle monotonicity) with approximation guarantee.
Mechanism Design with Selective Verification
Venue: EC

We introduce a general approach based on selective verification and obtain approximate mechanisms without money for maximizing the social welfare in the general domain of Utilitarian Voting. Having a good allocation in mind, a mechanism with verification selects few critical agents and detects, using a verification oracle, whether they have reported truthfully. If yes, the mechanism produces the desired allocation. Otherwise, the mechanism ignores any misreports and proceeds recursively with the remaining agents. We obtain randomized truthful (or almost truthful) mechanisms without money that verify only O(ln m/eps) agents, where m is the number of outcomes, independently of the total number of agents, and are (1 eps) approximate for the social welfare. We also show that any truthful mechanism with a constant approximation ratio needs to verify Omega(log m) agents. A remarkable property of our mechanisms is immunity (to agent misreports) namely that their outcome depends only on the reports of the truthful agents.
Conceptual Model to Identify Technological Synergic Relationships of Strategic Level in a Medium sized Chilean Port

The present study focuses on a medium sized Chilean port to analyze a mixed network composed of private/public actors, permanently linked to an uncertain strategic ambience. Their linkage to an uncertain macro ambience is complex which may present degrees of synergy with those strategies dealing with political, economic, social, technological and environmental aspects (PESTE) Later, this research identifies the strategic ambience of the Port Community and its synergic links with the other actors who compose the mixed network. Taking into account each actor's strategic statements, it is possible to infer that each public organization and private enterprise elaborates its strategies individually, dismissing joint collaboration as a factor to improve efficiency and effectiveness in their port activities. In the proposed conceptual model design, each actor's innovation strategies are linked to the corresponding technological synergic effect (TSE) With the diagnosis of the strategic ambience of the Community, it is possible to transform the strategies used by the mixed network into technological strategic descriptors. Finally, the technological strategic statements expressed by the Community are conceptually evaluated and compared to existing strategic and innovation actions followed by the members of the Port Community.
Delamination Characterization and Comparative Assessment of Delamination Control Techniques in Abrasive Water Jet Drilling of CFRP

Composite laminates are used in many applications in industries like aerospace and aircraft due to their extremely high strength to weight ratio and corrosion resistance properties. The composite laminates are difficult to machine materials, which results into low drilling efficiency and drilling induced delamination, thus it is important to develop an innovative advanced drilling process to overcome the difficulties related in the machining of composite materials. This work is focused on comprehensive experimental characterization to understand the effect of cutting parameters on the delamination extent during abrasive water jet drilling of carbon fiber reinforced polymer. Processing parameters, such as standoff distance and water pressure plays dominant role in delamination than abrasive flow rate. It also describes the development of different techniques for controlling the delamination in abrasive water jet drilling process, such as backup plate, pre drilled hole and water immersion (under water) The analysis shows that abrasive water jet drilling with backup plate yields lower delamination, hole size variation and hole surface roughness.
Limited Rate Feedback in a MIMO Wiretap Channel With a Cooperative Jammer
Venue: IEEE Transactions on Signal Processing

We study strategies for enhanced secrecy using cooperative jamming in secure communication systems with limited rate feedback. A Gaussian multiple input multiple output (MIMO) wiretap channel with a jamming helper is considered. The transmitter and helper both require channel state information (CSI) which is quantized at the receiver and fed back through two sum rate limited feedback channels. The quantization errors result in reduced beamforming gain from the transmitter, as well as interference leakage from the helper. First, under the assumption that the eavesdropper's CSI is completely unknown, we derive a lower bound on the average main channel rate and find the feedback bit allocation that maximizes the jamming power under a constraint on the bound. For the case where statistical CSI for the eavesdropper's channel is available, we derive a lower bound on the average secrecy rate, and we optimize the bound to find a suitable bit allocation and the transmit powers allocated to the transmitter and helper. For the case where the transmitter and helper have the same number of antennas, we obtain a closed form solution for the optimal bit allocation. Simulations verify the theoretical analysis and demonstrate the significant performance gain that results with intelligent feedback bit allocation and power control.
MIMO Wiretap Channel Under Receiver Side Power Constraints With Applications to Wireless Power Transfer and Cognitive Radio
Venue: IEEE Transactions on Communications

We consider the multiple input multiple output (MIMO) wiretap channel under a minimum receiver side power constraint in addition to the usual maximum transmitter side power constraint. This problem is motivated by energy harvesting communications with wireless energy transfer, where an added goal is to deliver a minimum amount of energy to a receiver in addition to delivering secure data to another receiver. In this paper, we characterize the exact secrecy capacity of the MIMO wiretap channel under transmitter and receiver side power constraints. We first show that solving this problem is equivalent to solving the secrecy capacity of the wiretap channel under a double sided correlation matrix constraint on the channel input. We show the converse by extending the channel enhancement technique to our case. We present two achievable schemes that achieve the secrecy capacity: the first achievable scheme uses a Gaussian codebook with a fixed mean, and the second achievable scheme uses artificial noise (or cooperative jamming) together with a Gaussian codebook. The role of the mean or the artificial noise is to enable energy transfer without sacrificing from the secure rate. This is the first instance of a channel model where either the use of a mean signal or the use of channel prefixing via artificial noise is strictly necessary for the MIMO wiretap channel. We then extend our work to consider a maximum receiver side power constraint instead of a minimum receiver side power constraint. This problem is motivated by cognitive radio applications, where an added goal is to decrease the received signal energy (interference temperature) at a receiver. We further extend our results to: requiring receiver side power constraints at both receivers; considering secrecy constraints at both receivers to study broadcast channels with confidential messages; and removing the secrecy constraints to study the classical broadcast channel.
Nuevas perspectivas en la investigacion docente de la historia economica

One of the most significant changes in the university legislation approved in Bologna was the impulse of the practical classes at degree studies. The combination of theoretical and practical elements would reinforce the range of knowledge that the university students would obtain in the context of a common European education. Though in some matters the practical education was coming being a habitual matter, in others could have supposed a challenge for the teachers. In the present communication we present some examples of practices and fieldwork realized in the subjects of Economic History, but also with multidisciplinary character, which reinforces the common bows with other related matters. The idea was born in a Project of Educational Innovation of the University of Valladolid.
Ocular Findings in Infants With Microcephaly Associated With Presumed Zika Virus Congenital Infection in Salvador, Brazil.
Venue: JAMA ophthalmology

The Zika virus (ZIKV) has rapidly reached epidemic proportions, especially in northeastern Brazil, and has rapidly spread to other parts of the Americas. A recent increase in the prevalence of microcephaly in newborn infants and vision threatening findings in these infants is likely associated with the rapid spread of ZIKV.  To evaluate the ocular findings in infants with microcephaly associated with presumed intrauterine ZIKV infection in Salvador, Bahia, Brazil.  Case series at a tertiary hospital. Twenty nine infants with microcephaly (defined by a cephalic circumference of =32 cm) with a presumed diagnosis of congenital ZIKV were recruited through an active search and referrals from other hospitals and health unities. The study was conducted between December 1 and December 21, 2015.  All infants and mothers underwent systemic and ophthalmic examinations from December 1 through December 21, 2015, in the Roberto Santos General Hospital, Salvador, Brazil. Anterior segment and retinal, choroidal, and optic nerve abnormalities were documented using a wide field digital imaging system. The differential diagnosis included toxoplasmosis, rubella, cytomegalovirus, herpes simplex virus, syphilis, and human immunodeficiency virus, which were ruled out through serologic and clinical examinations.  Ocular abnormalities associated with ZIKV.  Twenty three of 29 mothers (79.3% reported suspected ZIKV infection signs and symptoms during pregnancy, 18 in the first trimester, 4 in the second trimester, and 1 in the third trimester. Of the 29 infants (58 eyes) examined (18 [62.1% female) ocular abnormalities were present in 17 eyes (29.3% of 10 children (34.5% Bilateral findings were found in 7 of 10 patients presenting with ocular lesions, the most common of which were focal pigment mottling of the retina and chorioretinal atrophy in 11 of the 17 eyes with abnormalities (64.7% followed by optic nerve abnormalities in 8 eyes (47.1% bilateral iris coloboma in 1 patient (2 eyes [11.8% and lens subluxation in 1 eye (5.9% Conclusions and Relevance Congenital infection due to presumed ZIKV exposure is associated with vision threatening findings, which include bilateral macular and perimacular lesions as well as optic nerve abnormalities in most cases.
Residual stress in polyethylene pipes

This paper deals with residual stress in polyethylene (PE) pipes as an important factor that influences their lifetime. Residual hoop stress distribution in a PE pipe was determined using a methodology previously carried out by the authors on polypropylene pipes. Axial residual stress magnitude was determined by comparison of experimental data and finite element modelling. Based on the obtained results, a new simplified methodology for determining the residual hoop stress is proposed. The method needs only one circular specimen made of pipe, but, unlike older methods, provides a more precise estimation of residual hoop stress distribution taking into account its exponential shape. Some older results from literature are recalculated using this method and residual hoop stress of various PE pipe grades and dimensions are then compared. To provide an idea of residual hoop stress influence on lifetime of a pipe, a lifetime estimation is carried out for the examined pipe.
Learning Representations for Counterfactual Inference
Venue: ICML

Observational studies are rising in importance due to the widespread accumulation of data in fields such as healthcare, education, employment and ecology. We consider the task of answering counterfactual questions such as, "Would this patient have lower blood sugar had she received a different medication?" We propose a new algorithmic framework for counterfactual inference which brings together ideas from domain adaptation and representation learning. In addition to a theoretical justification, we perform an empirical comparison with previous approaches to causal inference from observational data. Our deep learning algorithm significantly outperforms the previous state of the art.
Bounding and Minimizing Counterfactual Error
Venue: ArXiv

There is intense interest in applying machine learning methods to problems of causal inference which arise in applications such as healthcare, economic policy, and education. In this paper we use the counterfactual inference approach to causal inference, and propose new theoretical results and new algorithms for performing counterfactual inference. Building on an idea recently proposed by Johansson et al. our results and methods rely on learning so called "balanced" representations: representations that are similar between the factual and counterfactual distributions. We give a novel, simple and intuitive bound, showing that the expected counterfactual error of a representation is bounded by a sum of the factual error of that representation and the distance between the factual and counterfactual distributions induced by the representation. We use Integral Probability Metrics to measure distances between distributions, and focus on two special cases: the Wasserstein distance and the Maximum Mean Discrepancy (MMD) distance. Our bound leads directly to new algorithms, which are simpler and easier to employ compared to those suggested in Johansson et al. Experiments on real and simulated data show the new algorithms match or outperform state of the art methods.