bluuebunny/crossref_metadata_2025_split huggingface dataset:
The liquid politics of an urban age
Authors: Diep Loan 
Published: June 2018

AbstractIn fragile social and economic societies, water governance systems have rarely managed to meet everyone’s needs, but rather misrecognised the demand of those excluded from decision-making structures. Across regions, underlying socio-political issues have often remained unaddressed on the basis that water scarcity is primarily caused by geo-climatic conditions. Exclusionary governance is one central driver to migratory patterns along with instabilities in political regimes. It is reflected in poor service provision and tends to perpetuate injustices. Several commitments of the New Urban Agenda (NUA) set objectives of universal and equitable water provision through multi-stakeholder involvement in urban planning processes. It thereby demonstrates efforts deployed towards ‘good governance’ for transparent, accountable and participatory decision-making. However, several studies have pointed out the questionable role of citizens in NUA. Building on their argument, the present article reflects on exclusionary patterns that the NUA aims to tackle and the mechanisms it proposes to achieve this. This article aims to highlight how power relations in water governance produce and reproduce exclusion in access, such as through population movements. It questions how NUA envisions water governance structures based on collaboration between multiple stakeholders in different contexts, and highlights the need to scrutinise the people-centric language adopted in its commitments. With references to water politics from Latin America and the Middle East and North Africa (MENA) region, it adopts a political ecology approach looking at questions of inclusivity for marginalised groups and discusses approaches for the active involvement of these people in water governance models.
The Franciscan Usus Pauper: using poverty to put life in the perspective of plenitude
Authors: Speelman Willem Marie 
Published: June 2018

AbstractIn general, poverty is approached as a pernicious problem. But poverty has always been a spiritual way of life too. For people like Francis of Assisi poverty was not only a problem, but also a mystery of a life in the perspective of perfection. Listening to his story may enrich social, political, and economic approaches to poverty, for it reveals some tactics for turning an obvious curse into a blessing. Focusing on the poor life of Francis and the Franciscans in the thirteenth century, and its early monetary economy, this article tries to come to know, alleviate, and value poverty. Sometimes a phenomenological description is needed to gain a deeper understanding of structures of monetary deprivation, of sharing gifts and needs, and of encountering a mystery. When Francis left the world, he learned that poverty is a fall depriving him of his fundamental relations. But he chose not to approach his poverty as a problem that must be solved, because this would mean that he had to turn himself into a ‘priceable object’ and ‘sell himself’. On the contrary, Francis chose to wait and listen to the voice of God and of the people that he met on the road: poor, merchants, pilgrims, and lepers. He learned that poverty is also a call expressing a longing for presence. Filling the emptiness of this longing with food and things may not be a sufficient response to the calling. Francis’s response to the calling transformed the fall into a descent to his own self and to others, and the problem into a mystery. A mystery is not a problem to be solved, but a question calling for an encounter. A first effect of the way Francis lived his poverty was that young men came to join him. They learned that approaching people without having any possessions was a very effective way to truly meet them: poverty revealed in encounters. To live without property became the mission of the brotherhood: an economy of trust, in which the act of sharing gifts, as well as needs was the motor. This mission eventually became a pastoral mission among the people in the cities, especially merchants. Living without property became very easy, because the cities would provide the brothers with everything they needed, and more. To save the original spirit of vivere sine proprio, the Franciscans developed the usus pauper (restricted use), which was a way of living a life in conformity with the poor in their new social and economic environment. In our times, people are learning to re-value practices of ‘de-ownership’. The Franciscan practice of usus pauper may help them understand why and how especially someone who lives a life according to the standards of the poor can be there for poor people, and alleviate the poverty that they share: he or she knows his or her real needs, values matters and people realistically, understands the importance of sharing, and is capable of seeing all people and all matters in the perspective of abundance.
Regional elections in Russia: instruments of authoritarian legitimacy or instability?
Authors: Ross Cameron 
Published: June 2018

AbstractThis study examines three rounds of regional assembly and gubernatorial elections in Russia that took place in September 2015, 2016 and 2017. In particular, it examines the ways in which the regime has manipulated the elections to guarantee the victory of United Russia. The study shows that the Kremlin has adopted a new electoral strategy. Rather than engaging in the risky business of outright fraud during the vote count, which was an important factor in sparking mass protests against the regime, in the wake of the 2011 elections to the State Duma, the authorities have decided to concentrate their efforts on preventing opposition parties and candidates from registering for the elections. Whilst other forms of electoral malpractice have continued to be practiced, such as coercing or bribing voters to turn out and vote for United Russia, promoting “carousel voting” (multiple voting by groups of mobilised citizens), or ballot stuffing, much more focus has been paid in these elections on manipulating the registration process in favour of United Russia. As is clearly demonstrated, scores of opposition candidates and party lists, have been prevented from competing because of problems with their registration documents. However, whilst this strategy has helped United Russia win large majorities in all of the gubernatorial and assembly elections, it has also created lacklustre and predictable contests, and this in turn has led to a sharp decline in turnout, particularly in the gubernatorial elections. There is a real danger that these low levels of turnout may gradually erode the legitimacy of United Russia, embolden the opposition, and threaten the stability of the regime.
SpliceRover: interpretable convolutional neural networks for improved splice site prediction
Authors: Zuallaert Jasper , Godin Fréderic , Kim Mijung , Soete Arne , Saeys Yvan , De Neve Wesley 
Published: June 2018

Abstract

Motivation
During the last decade, improvements in high-throughput sequencing have generated a wealth of genomic data. Functionally interpreting these sequences and finding the biological signals that are hallmarks of gene function and regulation is currently mostly done using automated genome annotation platforms, which mainly rely on integrated machine learning frameworks to identify different functional sites of interest, including splice sites. Splicing is an essential step in the gene regulation process, and the correct identification of splice sites is a major cornerstone in a genome annotation system.

Results
In this paper, we present SpliceRover, a predictive deep learning approach that outperforms the state-of-the-art in splice site prediction. SpliceRover uses convolutional neural networks (CNNs), which have been shown to obtain cutting edge performance on a wide variety of prediction tasks. We adapted this approach to deal with genomic sequence inputs, and show it consistently outperforms already existing approaches, with relative improvements in prediction effectiveness of up to 80.9% when measured in terms of false discovery rate. However, a major criticism of CNNs concerns their ‘black box’ nature, as mechanisms to obtain insight into their reasoning processes are limited. To facilitate interpretability of the SpliceRover models, we introduce an approach to visualize the biologically relevant information learnt. We show that our visualization approach is able to recover features known to be important for splice site prediction (binding motifs around the splice site, presence of polypyrimidine tracts and branch points), as well as reveal new features (e.g. several types of exclusion patterns near splice sites).

Availability and implementation
SpliceRover is available as a web service. The prediction tool and instructions can be found at http://bioit2.irc.ugent.be/splicerover/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting miRNA–disease association based on inductive matrix completion
Authors: Chen Xing , Wang Lei , Qu Jia , Guan Na-Na , Li Jian-Qiang 
Published: June 2018

Abstract

Motivation
It has been shown that microRNAs (miRNAs) play key roles in variety of biological processes associated with human diseases. In Consideration of the cost and complexity of biological experiments, computational methods for predicting potential associations between miRNAs and diseases would be an effective complement.

Results
This paper presents a novel model of Inductive Matrix Completion for MiRNA–Disease Association prediction (IMCMDA). The integrated miRNA similarity and disease similarity are calculated based on miRNA functional similarity, disease semantic similarity and Gaussian interaction profile kernel similarity. The main idea is to complete the missing miRNA–disease association based on the known associations and the integrated miRNA similarity and disease similarity. IMCMDA achieves AUC of 0.8034 based on leave-one-out-cross-validation and improved previous models. In addition, IMCMDA was applied to five common human diseases in three types of case studies. In the first type, respectively, 42, 44, 45 out of top 50 predicted miRNAs of Colon Neoplasms, Kidney Neoplasms, Lymphoma were confirmed by experimental reports. In the second type of case study for new diseases without any known miRNAs, we chose Breast Neoplasms as the test example by hiding the association information between the miRNAs and Breast Neoplasms. As a result, 50 out of top 50 predicted Breast Neoplasms-related miRNAs are verified. In the third type of case study, IMCMDA was tested on HMDD V1.0 to assess the robustness of IMCMDA, 49 out of top 50 predicted Esophageal Neoplasms-related miRNAs are verified.

Availability and implementation
The code and dataset of IMCMDA are freely available at https://github.com/IMCMDAsourcecode/IMCMDA.

Supplementary information
Supplementary data are available at Bioinformatics online.
Reward-Driven Arousal Impacts Preparation to Perform a Task via Amygdala–Caudate Mechanisms
Authors: Watanabe Noriya , Bhanji Jamil P , Ohira Hideki , Delgado Mauricio R 
Published: June 2018

Abstract
Preparing for a challenging task can increase physiological arousal, in particular when potential incentives are large (e.g., a solo musical performance in front of an audience). Here, we examine how potential reward and its influence on arousal, measured by pupil dynamics, are represented in the brain while preparing for a challenging task. We further ask how neural representations during preparation relate to actual performance. Trials resulting in performance failure were characterized by increased pupil dilation as a function of increasing reward magnitude during preparation. Such failure trials were also associated with activation of the right amygdala representing pupil dilation, and the left caudate representing reward magnitude. Notably, increases in functional connectivity between amygdala and caudate preceded performance failure. These findings highlight increased connectivity between neural regions representing reward and arousal in circumstances where reward-driven arousal impairs performance.
Playing and Being in Georges Perec
Authors: Kemp Anna 
Published: June 2018

Abstract
In his brief account of his own psychoanalysis, Georges Perec describes the psychoanalytic encounter as a game. But what kind of a game is it, and how is it played? On the one hand Perec’s writing presents analysis as an often frustrating, puzzle-solving exercise in which the patient and analyst — like Perec’s notorious puzzle-fiends Percival Bartlebooth and Gaspard Winckler — are locked in intimate and exhausting combat. Such games express Perec’s ambivalent relationship to the psychoanalytic other who, while promising self-knowledge and healing, also threatens to reduce the specificity of his experience to the ‘quincaillerie anonyme’ of the Freudian handbook. However, Perec’s writing also articulates another kind of game — one that chimes with D. W. Winnicott’s understanding of psychoanalysis as a form of creative play. While the closed structures of many Perecquian games give expression to the fraught dynamics of a psychoanalytic encounter characterized by anxiety and suspicion, Perec’s work also elaborates more open and flexible literary games that foster the playful creativity that, in Winnicott’s account, is necessary to feeling alive and real. Such games produce an enabling framework that allows Perec’s autobiographical subject to better approach ‘ce qu[’il] cherche’ and cautiously to imagine connections with others.
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant
Authors: Dong Ai-Xiang , Xin Hai-Bo , Li Zi-Jing , Liu Hui , Sun Yan-Qiang , Nie Shuai , Zhao Zheng-Nan , Cui Rong-Feng , Zhang Ren-Gang , Yun Quan-Zheng , Wang Xin-Ning , Maghuly Fatemeh , Porth Ilga , Cong Ri-Chen , Mao Jian-Feng 
Published: June 2018

Abstract

Background
Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.

Findings
We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome.

Conclusions
We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.
Consistent decreased activity in the putamen in Parkinson's disease: a meta-analysis and an independent validation of resting-state fMRI
Authors: Wang Jue , Zhang Jia-Rong , Zang Yu-Feng , Wu Tao 
Published: June 2018

Abstract

Background
Resting-state functional magnetic resonance imaging (RS-fMRI) has frequently been used to investigate local spontaneous brain activity in Parkinson's disease (PD) in a whole-brain, voxel-wise manner. To quantitatively integrate these studies, we conducted a coordinate-based (CB) meta-analysis using the signed differential mapping method on 15 studies that used amplitude of low-frequency fluctuation (ALFF) and 11 studies that used regional homogeneity (ReHo). All ALFF and ReHo studies compared PD patients with healthy controls. We also performed a validation RS-fMRI study of ALFF and ReHo in a frequency-dependent manner for a novel dataset consisting of 49 PD and 49 healthy controls.

Findings
Decreased ALFF was found in the left putamen in PD by meta-analysis. This finding was replicated in our independent validation dataset in the 0.027–0.073 Hz band but not in the conventional frequency band of 0.01–0.08 Hz.

Conclusions
Findings from the current study suggested that decreased ALFF in the putamen of PD patients is the most consistent finding. RS-fMRI is a promising technique for the precise localization of abnormal spontaneous activity in PD. However, more frequency-dependent studies using the same analytical methods are needed to replicate these results.
Trial registration: NCT NCT03439163. Registered 20 February 2018, retrospectively registered.
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub
Authors: Gao Fei , Wang Xue , Li Xuming , Xu Mingyue , Li Huayun , Abla Merhaba , Sun Huigai , Wei Shanjun , Feng Jinchao , Zhou Yijun 
Published: June 2018

Abstract

Background
Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here, we report a draft genome assembly using the Pacific Biosciences (PacBio) platform and gene annotation for A. nanus.

Findings
A total of 64.72 Gb of raw PacBio sequel reads were generated from four 20-kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59× coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated using Benchmarking Universal Single-Copy Orthologs; 1,327 of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements and 53.44% is composed of long terminal repeat elements. We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated.

Conclusions
The genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift.
Equilibrated flux a posteriori error estimates in $L^2(H^1)$-norms for high-order discretizations of parabolic problems
Authors: Ern Alexandre , Smears Iain , Vohralík Martin 
Published: June 2018

Abstract
We consider the a posteriori error analysis of fully discrete approximations of parabolic problems based on conforming $hp$-finite element methods in space and an arbitrary order discontinuous Galerkin method in time. Using an equilibrated flux reconstruction we present a posteriori error estimates yielding guaranteed upper bounds on the $L^2(H^1)$-norm of the error, without unknown constants and without restrictions on the spatial and temporal meshes. It is known from the literature that the analysis of the efficiency of the estimators represents a significant challenge for $L^2(H^1)$-norm estimates. Here we show that the estimator is bounded by the $L^2(H^1)$-norm of the error plus the temporal jumps under the one-sided parabolic condition $h^2 \lesssim \tau $. This result improves on earlier works that required stronger two-sided hypotheses such as $h \simeq \tau $ or $h^2\simeq \tau $; instead, our result now encompasses practically relevant cases for computations and allows for locally refined spatial meshes. The constants in our bounds are robust with respect to the mesh and time-step sizes, the spatial polynomial degrees and the refinement and coarsening between time steps, thereby removing any transition condition.
Measures, drivers and effects of green employment: evidence from US local labor markets, 2006–2014
Authors: Vona Francesco , Marin Giovanni , Consoli Davide 
Published: June 2018

Abstract
This paper explores the nature and the key empirical regularities of green employment in US local labor markets in 2006–2014. The main methodological novelty consists of a new measure of green employment based on the task content of occupations. Descriptive analysis reveals that green employment is pro-cyclical, highly skilled, commands a 4% wage premium and is geographically concentrated. Green employment dynamics positively correlates with local green subsidies within the American Recovery and Reinvestment Act, local green knowledge, and resilience to the great recession. Finally, we find that one additional green job is associated with 4.2 (2.2 in the crisis period) new local jobs in non-tradable non-green activities.
Somatotopy and Organization of Spinothalamic Tracts in the Human Cervical Spinal Cord
Authors: Vedantam Aditya , Bruera Eduardo , Hess Kenneth R , Dougherty Patrick M , Viswanathan Ashwin 
Published: June 2018

Abstract

BACKGROUND
Understanding spinothalamic tract anatomy may improve lesioning and outcomes in patients undergoing percutaneous cordotomy.

OBJECTIVE
To investigate somatotopy and anatomical organization of spinothalamic tracts in the human cervical spinal cord.

METHODS
Patients with intractable cancer pain undergoing cordotomy underwent preoperative and postoperative quantitative sensory testing for sharp pain and heat pain on day 1 and 7 after cordotomy. Intraoperative sensory stimulation was performed with computed tomography (CT) imaging to confirm the location of the radiofrequency electrode during cordotomy. Postoperative magnetic resonance (MR) imaging was performed to define the location of the lesion.

RESULTS
Twelve patients were studied, and intraoperative sensory stimulation combined with CT imaging revealed a somatotopy where fibers from the legs were posterolateral to fibers from the hand. Sharpness detection thresholds were significantly elevated in the area of maximum pain on postoperative day 1 (P = .01). Heat pain thresholds for all areas were not elevated significantly on postoperative day 1, or postoperative day 7. MR imaging confirmed that the cordotomy lesion was in the anterolateral quadrant, and in this location the lesion had a sustained effect on sharp pain but a transient impact on heat pain.

CONCLUSION
In the high cervical spinal cord, spinothalamic fibers mediating sharp pain for the arms are located ventromedial to fibers for the legs, and these fibers are spatially distinct from fibers that mediate heat pain.