nils-herrmann/clean_scirepeval huggingface dataset:
A survey of best practices for RNA seq data analysis
Venue: Genome Biology

RNA sequencing (RNA seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
Barriers to Access: Report on the Barriers Faced by Young Disabled and D/deaf People in Accessing Youth Arts Provision in Scotland

This report outlines research that investigated the barriers faced by young disabled and D/deaf people in accessing youth arts provision in Scotland. Funded by the Time to Shine National Youth Arts Strategy for Scotland, the research was conducted by Dr. Matson Lawrence in conjunction with Birds of Paradise Theatre Company. The research relates to young people aged 0 25, with specific empirical focus on young people aged 16 25. Through in depth interviews and online surveys, the research engaged with 20 disabled and D/deaf young people across Scotland, alongside a number of individuals working within the Scottish youth arts sector and in disability and D/deaf arts. The research found that young disabled and D/deaf people face multiple and intersecting barriers to accessing arts provision. Five main barriers were identified: 1. Finding suitable arts provision; 2. Availability of access information; 3. Lack of provision for access and support; 4. Travel, transport and location; and 5. Attitudes and awareness of arts providers. The research identified five key strategies to address these barriers: 1. Provision specifically for young disabled and D/deaf people; 2. Centralised information about arts opportunities; 3. Front Door to Stage Door Access provision; 4. Connections built with disabled and D/deaf communities across Scotland; and 5. Education and awareness for arts providers. These strategies offer arts providers concrete recommendations for improving disabled and D/deaf access. It is anticipated that, in light of this report, organisations and agencies providing arts opportunities to young people will be better informed of the barriers faced by young disabled and D/deaf people, and better equipped to address these barriers and improve access to their provision.
Elements pour servir a l'histoire et a la geographie industrielles du Languedoc Roussillon du debut du XIX e siecle a nos jours

Etude methodologique basee sur l'analyse des inventaires et bordereaux de versements des Archives Departementales de l'Aude, du Gard, de l'Herault, de la Lozere et des Pyrenees Orientales ainsi que sur une selection de publications (articles et livres) referencees dans differentes bibliotheques languedociennes ou roussillonnaises qui a pour but de selectionner les documents publics les plus utiles aux chercheurs sur l'histoire et la geographie industrielles de cette region entre le debut du XIXe siecle et le debut du XXIe siecle. En introduction sont rappelees les origines de cette etude (pre inventaire puis inventaire des sites potentiellement pollues) et le cadre juridique permettant la consultation des sources d'informations signalees (demande de derogation, recours a la CADA, etc. qui peuvent etre aussi tres utiles pour les sociologues, les historiens de l'art, les historiens du droit, etc.
A nightmare on the brain of the living? The endurance and limits of the collective bargaining regime

Despite pressures to liberalise its economy and strong resistance to union bargaining rights from domestic constituencies, South Africa has maintained, for more than two decades, a labour relations regime which offers trade unions and workers generous rights. The article seeks to explain the bargaining system's survival in seemingly unlikely circumstances. It argues that racial politics combined with the emergence of a trade union movement relatively independent of its nationalist ally have made the political costs of denying or retreating from a generous set of union rights prohibitive. But, while the implicit bargain may enable unions to negotiate wages and working conditions, this does not automatically mean gains for workers or the poor, for the bargaining system has proved incapable of fully resolving the conflict caused by a path dependence which ensures the persistence of racial domination in the economy.
Neutron and weak charge distributions of the 48Ca nucleus

What is the size of the atomic nucleus? This deceivably simple question is difficult to answer. Although the electric charge distributions in atomic nuclei were measured accurately already half a century ago, our knowledge of the distribution of neutrons is still deficient. In addition to constraining the size of atomic nuclei, the neutron distribution also impacts the number of nuclei that can exist and the size of neutron stars. We present an ab initio calculation of the neutron distribution of the neutron rich nucleus Ca 48. We show that the neutron skin (difference between the radii of the neutron and proton distributions) is significantly smaller than previously thought. We also make predictions for the electric dipole polarizability and the weak form factor; both quantities that are at present targeted by precision measurements. Based on ab initio results for Ca 48, we provide a constraint on the size of a neutron star.
Wide area measurement system development at the distribution level: An FNET/GridEye example
Venue: 2016 IEEE Power and Energy Society General Meeting (PESGM)

Electric power grid wide area monitoring system (WAMS) have been extended from the transmission to distribution level. As the first WAMS deployed at the distribution level, the frequency monitoring network FNET/GridEye uses GPS time synchronized monitors called frequency disturbance recorders (FDRs) to capture dynamic grid behaviors. In this paper, the latest developments of monitor design and the state of the art data analytics applications of FNET/GridEye are introduced. Its innovations and uniqueness are also discussed. Thanks to its low cost, easy installation and multi functionalities, FNET/GridEye works as a cost effective situational awareness tool for power grid operators and pioneers the development of WAMS in electric power grids.
UCO: A Unified Cybersecurity Ontology
Venue: AAAI Workshop: Artificial Intelligence for Cyber Security

In this paper we describe the Unified Cybersecurity Ontology (UCO) that is intended to support information integration and cyber situational awareness in cybersecurity systems. The ontology incorporates and integrates heterogeneous data and knowledge schemas from different cybersecurity systems and most commonly used cybersecurity standards for information sharing and exchange. The UCO ontology has also been mapped to a number of existing cybersecurity ontologies as well as concepts in the Linked Open Data cloud. Similar to DBpedia which serves as the core for general knowledge in Linked Open Data cloud, we envision UCO to serve as the core for cybersecurity domain, which would evolve and grow with the passage of time with additional cybersecurity data sets as they become available. We also present a prototype system and concrete use cases supported by the UCO ontology. To the best of our knowledge, this is the first cybersecurity ontology that has been mapped to general world ontologies to support broader and diverse security use cases. We compare the resulting ontology with previous efforts, discuss its strengths and limitations, and describe potential future work directions.
Feature Extraction Based Hellinger Distance Algorithm for Nonintrusive Aging Load Identification in Residential Buildings
Venue: IEEE Transactions on Industry Applications

Though steady state power features such as real power (P) reactive power (Q) and total voltage/current harmonic distortions (VTHD/ITHD) may contain sufficient information, adopting them directly for nonintrusive aging load monitoring (NIALM) identification process requires higher computational burden and larger memory. To effectively reduce the number of needed steady state power features without degrading the performance of NIALM, a Hellinger distance (HD) algorithm is proposed and presented in this paper. To minimize the training time and improve recognition accuracy, a particle swarm optimization (PSO) is adopted in this paper to optimize parameters of training algorithm in artificial neural networks (ANNs) The proposed methods are used to analyze and identify the load characteristics of aging loads in residential buildings. The results show that the accuracy can be improved by using the proposed method.
Military Justice: A Very Short Introduction

To be effective, and something more than a collection of individuals with weapons, a military unit must be commanded. Commanders are responsible for achieving the unit's objective, a function that requires them to ensure that subordinates will do as they are told. With this power comes responsibility. In some circumstances commanders can be penalized for the misconduct of subordinates. In the classical model of military justice, commanders played (and in some countries, such as the United States, still play) a powerful role. 'Military command and military discipline' considers the powers exercised by commanders in these commander centric systems in particular the disposition, or charging, power and looks at efforts to reform these systems.
Multiple scattering mechanisms causing interference effects in the differential cross sections of H D2 HD(v' 4, j' D at 3.26 eV collision energy.
Venue: The Journal of chemical physics

Differential cross sections (DCSs) for the H D2 HD(v' 4, j' D reaction at 3.26 eV collision energy have been measured using the photoloc technique, and the results have been compared with those from quantum and quasiclassical scattering calculations. The quantum mechanical DCSs are in good overall agreement with the experimental measurements. In common with previous results at 1.97 eV, clear interference patterns which appear as fingerlike structures have been found at 3.26 eV but in this case for vibrational states as high as v' 4. The oscillatory structure is prominent for low rotational states and progressively disappears as j' increases. A detailed analysis, similar to that carried out at 1.97 eV, shows that the origin of these structures could be traced to interferences between well defined classical mechanisms. In addition, at this energy, we do not observe the anomalous positive j' th trend found for the v' 4 manifold at lower collision energies, thus reinforcing our explanation that the anomalous distribution for HD(v' 4, j' at 1.97 eV only takes place for those states associated with low product recoil energies.
The Vernacular Revolution: Reclaiming Early Modern Grammatical Traditions in the Ottoman Empire
Venue: History of Humanities

This article explores the remarkable shift toward new literate uses of vernacular languages in the early modern Ottoman empire. It argues that this vernacularization occurred independently of Western European (and, more specifically, German romantic) influences. It explores, first, how vernacular languages like modern Greek, Armenian, Serbian, Bulgarian, Turkish, Kurdish, and Albanian acquired a new status as a medium of high literature and learning; second, it argues that this process was accompanied by the equally novel phenomenon of writing vernacular grammars, which promoted vernaculars as both an object of knowledge and an object of governmental concern. Thus, the early modern Ottoman empire sees both a vernacularization and the governmentalization of language. Similar patterns, it will be argued, can be found in early modern German, Russian, and Urdu, without any one language or region clearly being the sole origin or cause of this process. Hence, this wave of virtually simultaneous vernacularizations poses new questions for theories of modern nationalism and of the role of the modern humanities in them.
THE PROTECTION QUESTION: CENTRAL ASIANS AND EXTRATERRITORIALITY IN THE LATE OTTOMAN EMPIRE
Venue: International Journal of Middle East Studies

This article examines the impact of the Ottoman Empire's battle against legal imperialism on the status of Central Asians in its domains, specifically after the promulgation of a nationality law in 1869 that classified them as foreigners. It traces how the threat of Muslim colonial subjects attaining European consular protections led to the emergence of a "Central Asian protection question" whether Afghans, Bukharans, and Chinese Muslims had legitimate claims to European legal nationality and, by extension, capitulatory privileges. Through a number of case studies, the article shows how the Ottoman Foreign Ministry fused international legal norms and pan Islamic claims to arrive at the position that Central Asians from informally colonized lands were not "real" subjects of European empires, and that they were under the exclusive protection of the caliphate. This strategy, I argue, undermined the creation of an Ottoman citizenship boundary and opened up a complex field of inter and intraimperial contestation about who was a foreigner. In contrast to positive associations with legal pluralism in this period, Central Asian migrants and pilgrims who were protected by the caliph but not recognized as Ottomans or European subjects found that they could not benefit from practices such as forum shopping and affiliation switching. And while the notion of foreignness remained subject to multiple and conflicting interpretations across the empire, I argue that nationality as a legal category was incontrovertibly becoming a defining feature of these foreign Muslims' rights and status in the sultan's domains.
European Legal Doctrines on Intervention and the Status of the Ottoman Empire within the 'Family of Nations' Throughout the Nineteenth Century

This article examines the status of the Ottoman Empire in the 'Family of Nations' throughout the nineteenth century. I tackle this broad question through the prism of legal doctrines on intervention in the internal affairs of the Ottoman Empire as put forward by European scholars, for I believe that they reveal something about European conceptions of the 'Family of Nations' and of international law. Western international lawyers paid particular attention to and constructed a jurisprudence around allegedly urgent cases, during which violent counterinsurgency campaigns undertaken by Ottoman authorities led to disturbances or massacres. In turn, these led to collective and military interventions in the Ottoman Empire by European powers. The jurisprudence of legal scholars often concerned intervention on the part of European powers in Greece (1827 1833) Lebanon (1880 1861) Crete (1866 1867 and in the late 1890s) and Macedonia (1905 1908) Their doctrines also encompassed famous cases of non intervention, such as the 'Bulgarian horrors' of the mid 1870s and the massacre of the Ottoman Armenians in the 1890s and 1900s. These interventions would subsequently be labelled interventions d'humanite, or 'humanitarian interventions' In the elegant formulation of Eliana Augusti,
Bringing the Empire Back In: The Gradual Discovery of the Ottoman Empire in Turkish Foreign Policy

This article traces the emergence of references to the Ottoman Empire in the discourse and practice of Turkish foreign policy since the late 1940s. It argues that present day emphasis on the Ottoman Empire and its legacy in Turkey has not happened in a vacuum, but rather has been a gradual process that has taken place over decades, helping to justify Turkey's foreign policy. The article also shows that politicians from different sections of the political spectrum were crucial in reclaiming the Ottoman past in foreign policy. The consequences of this reclamation have been twofold. First, foreign policy, both in terms of practice and discourse, has become yet another venue, among many, for the continuous framing and reframing of Turkey's past, paving the way for further Ottomanisation of the Turkish identity. Second, this Ottomanisation, or reclaiming of aspects that characterised the Ottoman Empire, has helped Turkey's political actors justify and legitimise Turkey's policies not only externally but, at times, also internally as was the case in the 1990s, when some of these political actors tried to deal with Kurdish separatism by using the legacy of the Ottoman Empire.
Conversion and Apostasy in the Late Ottoman Empire

SELIM DERINGIL, Conversion and Apostasy in the Late Ottoman Empire (Cambridge, UK:  2012) In his most recent book, Selim Deringil cogently elucidates the tangled web of Ottoman state concerns, local tensions, diplomatic intrigue and interests, and the issues of modernization, nationalism, citizenship, and religious identity within the late Ottoman Empire's Tanzimat and Abdulhamid II periods. Specifically, conversion and apostasy among Ottoman subjects, both Muslim and Christian, act as his lens into this above mentioned tangled web particularly related to how the central Ottoman state's view of conversion and apostasy transformed in the nineteenth century. Building upon the arguments of his own Well protected Domains and Ussama Makdisi's Artillery of Heaven and The Culture of Sectarianism, Deringil argues that as nationalism spread within the Ottoman Empire, the importance of religion and religious identity within the context of conversion and apostasy did not fade over time, but became inextricably connected to national identity. This was most apparent in many of the Balkan nationalist wars for independence wherein national and religious identities were synonymous. In fact, conversion from Islam to Christianity and vice versa constituted a major catastrophe and embarrassment for the empire in terms of imperial interests and international diplomatic relations. So much so, Deringil claims that for the empire, its diverse communities, and international powers, conversion and apostasy came to represent a form of "de nationalization," which he defines as "the loss of a soul and a body from an increasingly 'nationally imagined' community. This loss was also seen as a symbolic rape of the community's honor.[3]" Deringil provides four fascinating case studies to illustrate this phenomenon.The first two cases deal with so called crypto Christians. Since, one's national identity, and consequently citizenship and potential loyalty, could not be disentangled from one's religion, with the proclamation of the Tanzimat and the promise of equal protection under the law regardless of religious affiliation, it now became imperative for the Ottoman state to define, test, and maintain its diverse population's religious identities so as not to upset the tenuous domestic and international obsessions with the empire's diverse populations and potential nationalist aspirations. Long lived crypto Christian communities, such as the Kromlides and Stavriotes, now came under intense state scrutiny. These two communities had lived openly for centuries as Christians, but claimed Muslim identity. With the declaration of the new religious freedoms, they wanted to be officially recognized as Christians once again. Yet, the central state desperately feared that to allow such "reversion" would cause an avalanche of "reconversions," thus undermining Ottoman Islamic identity and facilitating further Great Power interference with the empire's internal sovereignty.The other two cases deal with the opposite flow of conversion, i.
Modernity as a Code: The Ottoman Empire and the Global Movement of Codification

Codification was a founding feature of Ottoman legal reform from the 1840s until the demise of the empire. This article seeks to situate the Ottoman project of codification in the context of the global codification momentum, which set the ground for a transnational common imagination of the law during the "long nineteenth century" When analyzed from the perspective of glocalization Ottoman codes, much like codes elsewhere, stand out as essential signifiers of modernity in the socio legal sphere.
Characterization of PET/CT images using texture analysis: the past, the present. any future?
Venue: European Journal of Nuclear Medicine and Molecular Imaging

After seminal papers over the period 2009 2011, the use of texture analysis of PET/CT images for quantification of intratumour uptake heterogeneity has received increasing attention in the last 4 years. Results are difficult to compare due to the heterogeneity of studies and lack of standardization. There are also numerous challenges to address. In this review we provide critical insights into the recent development of texture analysis for quantifying the heterogeneity in PET/CT images, identify issues and challenges, and offer recommendations for the use of texture analysis in clinical research. Numerous potentially confounding issues have been identified, related to the complex workflow for the calculation of textural features, and the dependency of features on various factors such as acquisition, image reconstruction, preprocessing, functional volume segmentation, and methods of establishing and quantifying correspondences with genomic and clinical metrics of interest. A lack of understanding of what the features may represent in terms of the underlying pathophysiological processes and the variability of technical implementation practices makes comparing results in the literature challenging, if not impossible. Since progress as a field requires pooling results, there is an urgent need for standardization and recommendations/guidelines to enable the field to move forward. We provide a list of correct formulae for usual features and recommendations regarding implementation. Studies on larger cohorts with robust statistical analysis and machine learning approaches are promising directions to evaluate the potential of this approach.
Neural Programmer Interpreters
Venue: ICLR

We propose the neural programmer interpreter (NPI) a recurrent and compositional neural network that learns to represent and execute programs. NPI has three learnable components: a task agnostic recurrent core, a persistent key value program memory, and domain specific encoders that enable a single NPI to operate in multiple perceptually diverse environments with distinct affordances. By learning to compose lower level programs to express higher level programs, NPI reduces sample complexity and increases generalization ability compared to sequence to sequence LSTMs. The program memory allows efficient learning of additional tasks by building on existing programs. NPI can also harness the environment (e.g. a scratch pad with read write pointers) to cache intermediate results of computation, lessening the long term memory burden on recurrent hidden units. In this work we train the NPI with fully supervised execution traces; each program has example sequences of calls to the immediate subprograms conditioned on the input. Rather than training on a huge number of relatively weak labels, NPI learns from a small number of rich examples. We demonstrate the capability of our model to learn several types of compositional programs: addition, sorting, and canonicalizing 3D models. Furthermore, a single NPI learns to execute these programs and all 21 associated subprograms.